Date: 2021-07-22 17:49:07 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 375871 rows and 443 columns.
#> Performed in total 72800 partitions.
#> There are 35 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, 443 cols
#> |-- 01, 145 cols, 9343 signatures
#> | |-- 011, 104 cols, 1530 signatures
#> | | |-- 0111, 58 cols, 5908 signatures
#> | | | |-- 01111, 19 cols, 3038 signatures
#> | | | | |-- 011111, 9 cols (b)
#> | | | | `-- 011112, 10 cols (b)
#> | | | |-- 01112, 16 cols, 197 signatures (c)
#> | | | |-- 01113, 12 cols, 96 signatures (c)
#> | | | `-- 01114, 11 cols (b)
#> | | `-- 0112, 46 cols, 7485 signatures
#> | | |-- 01121, 16 cols, 74 signatures (c)
#> | | |-- 01122, 8 cols (b)
#> | | |-- 01123, 12 cols, 34 signatures (c)
#> | | `-- 01124, 10 cols (b)
#> | `-- 012, 41 cols, 3913 signatures
#> | |-- 0121, 16 cols, 1543 signatures
#> | | |-- 01211, 10 cols (b)
#> | | |-- 01212, 4 cols (b)
#> | | `-- 01213, 2 cols (b)
#> | `-- 0122, 25 cols, 5229 signatures
#> | |-- 01221, 12 cols, 271 signatures (c)
#> | |-- 01222, 8 cols (b)
#> | |-- 01223, 3 cols (b)
#> | `-- 01224, 2 cols (b)
#> |-- 02, 54 cols, 8434 signatures
#> | |-- 021, 36 cols, 3867 signatures
#> | | |-- 0211, 19 cols, 499 signatures (c)
#> | | `-- 0212, 17 cols, 1359 signatures
#> | | |-- 02121, 6 cols (b)
#> | | |-- 02122, 7 cols (b)
#> | | `-- 02123, 4 cols (b)
#> | |-- 022, 8 cols (b)
#> | `-- 023, 10 cols (b)
#> |-- 03, 162 cols, 504 signatures (c)
#> `-- 04, 82 cols, 17456 signatures
#> |-- 041, 31 cols, 7743 signatures
#> | |-- 0411, 7 cols (b)
#> | |-- 0412, 10 cols (b)
#> | |-- 0413, 9 cols (b)
#> | `-- 0414, 5 cols (b)
#> |-- 042, 34 cols, 4047 signatures
#> | |-- 0421, 11 cols (b)
#> | |-- 0422, 16 cols, 5533 signatures
#> | | |-- 04221, 6 cols (b)
#> | | |-- 04222, 7 cols (b)
#> | | `-- 04223, 3 cols (b)
#> | `-- 0423, 7 cols (b)
#> `-- 043, 17 cols, 10997 signatures
#> |-- 0431, 5 cols (b)
#> |-- 0432, 8 cols (b)
#> `-- 0433, 4 cols (b)
#> Stop reason:
#> b) Subgroup had too few columns.
#> c) There were too few signatures.
#>
#> Following methods can be applied to this 'HierarchicalPartition' object:
#> [1] "all_leaves" "all_nodes" "cola_report" "collect_classes"
#> [5] "colnames" "compare_signatures" "dimension_reduction" "functional_enrichment"
#> [9] "get_anno_col" "get_anno" "get_children_nodes" "get_classes"
#> [13] "get_matrix" "get_signatures" "is_leaf_node" "max_depth"
#> [17] "merge_node" "ncol" "node_info" "node_level"
#> [21] "nrow" "rownames" "show" "split_node"
#> [25] "suggest_best_k" "test_to_known_factors" "top_rows_heatmap" "top_rows_overlap"
#>
#> You can get result for a single node by e.g. object["01"]
The call of hierarchical_partition() was:
#> hierarchical_partition(data = mat, top_n = 1000, top_value_method = c("SD", "ATC"),
#> partition_method = c("kmeans", "skmeans"), subset = 500, group_diff = 0.25, min_n_signatures = 1000,
#> filter_fun = function(mat) {
#> s = rowSds(mat)
#> order(-s)[1:30000]
#> }, max_k = 8, scale_rows = FALSE, cores = 4)
Dimension of the input matrix:
mat = get_matrix(res_rh)
dim(mat)
#> [1] 375871 443
All the methods that were tried:
res_rh@param$combination_method
#> [[1]]
#> [1] "SD" "kmeans"
#>
#> [[2]]
#> [1] "ATC" "kmeans"
#>
#> [[3]]
#> [1] "SD" "skmeans"
#>
#> [[4]]
#> [1] "ATC" "skmeans"
The density distribution for each sample is visualized as one column in the following heatmap. The clustering is based on the distance which is the Kolmogorov-Smirnov statistic between two distributions.
library(ComplexHeatmap)
densityHeatmap(mat, ylab = "value", cluster_columns = TRUE, show_column_names = FALSE,
mc.cores = 1)
Some values about the hierarchy:
all_nodes(res_rh)
#> [1] "0" "01" "011" "0111" "01111" "011111" "011112" "01112" "01113" "01114"
#> [11] "0112" "01121" "01122" "01123" "01124" "012" "0121" "01211" "01212" "01213"
#> [21] "0122" "01221" "01222" "01223" "01224" "02" "021" "0211" "0212" "02121"
#> [31] "02122" "02123" "022" "023" "03" "04" "041" "0411" "0412" "0413"
#> [41] "0414" "042" "0421" "0422" "04221" "04222" "04223" "0423" "043" "0431"
#> [51] "0432" "0433"
all_leaves(res_rh)
#> [1] "011111" "011112" "01112" "01113" "01114" "01121" "01122" "01123" "01124" "01211"
#> [11] "01212" "01213" "01221" "01222" "01223" "01224" "0211" "02121" "02122" "02123"
#> [21] "022" "023" "03" "0411" "0412" "0413" "0414" "0421" "04221" "04222"
#> [31] "04223" "0423" "0431" "0432" "0433"
node_info(res_rh)
#> id best_method depth best_k n_columns n_signatures p_signatures is_leaf
#> 1 0 ATC:kmeans 1 4 443 34264 9.12e-02 FALSE
#> 2 01 ATC:kmeans 2 2 145 9343 2.49e-02 FALSE
#> 3 011 ATC:kmeans 3 2 104 1530 4.07e-03 FALSE
#> 4 0111 ATC:kmeans 4 4 58 5908 1.57e-02 FALSE
#> 5 01111 ATC:kmeans 5 2 19 3038 8.08e-03 FALSE
#> 6 011111 not applied 6 NA 9 NA NA TRUE
#> 7 011112 not applied 6 NA 10 NA NA TRUE
#> 8 01112 ATC:skmeans 5 2 16 197 5.24e-04 TRUE
#> 9 01113 ATC:kmeans 5 2 12 96 2.55e-04 TRUE
#> 10 01114 not applied 5 NA 11 NA NA TRUE
#> 11 0112 ATC:kmeans 4 4 46 7485 1.99e-02 FALSE
#> 12 01121 ATC:skmeans 5 2 16 74 1.97e-04 TRUE
#> 13 01122 not applied 5 NA 8 NA NA TRUE
#> 14 01123 ATC:skmeans 5 2 12 34 9.05e-05 TRUE
#> 15 01124 not applied 5 NA 10 NA NA TRUE
#> 16 012 ATC:kmeans 3 2 41 3913 1.04e-02 FALSE
#> 17 0121 ATC:skmeans 4 3 16 1543 4.11e-03 FALSE
#> 18 01211 not applied 5 NA 10 NA NA TRUE
#> 19 01212 not applied 5 NA 4 NA NA TRUE
#> 20 01213 not applied 5 NA 2 NA NA TRUE
#> 21 0122 ATC:skmeans 4 4 25 5229 1.39e-02 FALSE
#> 22 01221 SD:kmeans 5 2 12 271 7.21e-04 TRUE
#> 23 01222 not applied 5 NA 8 NA NA TRUE
#> 24 01223 not applied 5 NA 3 NA NA TRUE
#> 25 01224 not applied 5 NA 2 NA NA TRUE
#> 26 02 ATC:kmeans 2 3 54 8434 2.24e-02 FALSE
#> 27 021 SD:kmeans 3 2 36 3867 1.03e-02 FALSE
#> 28 0211 ATC:skmeans 4 4 19 499 1.33e-03 TRUE
#> 29 0212 ATC:kmeans 4 3 17 1359 3.62e-03 FALSE
#> 30 02121 not applied 5 NA 6 NA NA TRUE
#> 31 02122 not applied 5 NA 7 NA NA TRUE
#> 32 02123 not applied 5 NA 4 NA NA TRUE
#> 33 022 not applied 3 NA 8 NA NA TRUE
#> 34 023 not applied 3 NA 10 NA NA TRUE
#> 35 03 ATC:kmeans 2 2 162 504 1.34e-03 TRUE
#> 36 04 ATC:kmeans 2 3 82 17456 4.64e-02 FALSE
#> 37 041 ATC:skmeans 3 4 31 7743 2.06e-02 FALSE
#> 38 0411 not applied 4 NA 7 NA NA TRUE
#> 39 0412 not applied 4 NA 10 NA NA TRUE
#> 40 0413 not applied 4 NA 9 NA NA TRUE
#> 41 0414 not applied 4 NA 5 NA NA TRUE
#> 42 042 ATC:skmeans 3 3 34 4047 1.08e-02 FALSE
#> 43 0421 not applied 4 NA 11 NA NA TRUE
#> 44 0422 ATC:kmeans 4 3 16 5533 1.47e-02 FALSE
#> 45 04221 not applied 5 NA 6 NA NA TRUE
#> 46 04222 not applied 5 NA 7 NA NA TRUE
#> 47 04223 not applied 5 NA 3 NA NA TRUE
#> 48 0423 not applied 4 NA 7 NA NA TRUE
#> 49 043 ATC:kmeans 3 3 17 10997 2.93e-02 FALSE
#> 50 0431 not applied 4 NA 5 NA NA TRUE
#> 51 0432 not applied 4 NA 8 NA NA TRUE
#> 52 0433 not applied 4 NA 4 NA NA TRUE
In the output from node_info(), there are the following columns:
id: The node id.best_method: The best method selected.depth: Depth of the node in the hierarchy.best_k: Best number of groups of the partition on that node.n_columns: Number of columns in the submatrix.n_signatures: Number of signatures with the best_k.p_signatures: Proportion of hte signatures in total number of rows in the matrix.is_leaf: Whether the node is a leaf.Labels of nodes are encoded in a special way. The number of digits correspond to the depth of the node in the hierarchy and the value of the digits correspond to the index of the subgroup in the current node, E.g. a label of “012” means the node is the second subgroup of the partition which is the first subgroup of the root node.
Following table shows the best k (number of partitions) for each node in the
partition hierarchy. Clicking on the node name in the table goes to the
corresponding section for the partitioning on that node.
The cola vignette explains the definition of the metrics used for determining the best number of partitions.
suggest_best_k(res_rh)
| Node | Best method | Is leaf | Best k | 1-PAC | Mean silhouette | Concordance | #samples | |
|---|---|---|---|---|---|---|---|---|
| Node0 | ATC:kmeans | 4 | 1.00 | 0.98 | 0.99 | 443 | ** | |
| Node01 | ATC:kmeans | 6 | 0.93 | 0.86 | 0.93 | 145 | * | |
| Node011 | ATC:kmeans | 2 | 1.00 | 0.98 | 0.99 | 104 | ** | |
| Node0111 | ATC:kmeans | 4 | 0.90 | 0.95 | 0.96 | 58 | * | |
| Node01111 | ATC:kmeans | 2 | 1.00 | 1.00 | 1.00 | 19 | ** | |
| Node011111-leaf | not applied | ✓ (b) | 9 | |||||
| Node011112-leaf | not applied | ✓ (b) | 10 | |||||
| Node01112-leaf | ATC:skmeans | ✓ (c) | 2 | 1.00 | 1.00 | 1.00 | 16 | ** |
| Node01113-leaf | ATC:kmeans | ✓ (c) | 2 | 1.00 | 0.99 | 1.00 | 12 | ** |
| Node01114-leaf | not applied | ✓ (b) | 11 | |||||
| Node0112 | ATC:kmeans | 4 | 0.93 | 0.95 | 0.96 | 46 | * | |
| Node01121-leaf | ATC:skmeans | ✓ (c) | 2 | 1.00 | 1.00 | 1.00 | 16 | ** |
| Node01122-leaf | not applied | ✓ (b) | 8 | |||||
| Node01123-leaf | ATC:skmeans | ✓ (c) | 2 | 1.00 | 1.00 | 1.00 | 12 | ** |
| Node01124-leaf | not applied | ✓ (b) | 10 | |||||
| Node012 | ATC:kmeans | 4 | 0.98 | 0.90 | 0.95 | 41 | ** | |
| Node0121 | ATC:skmeans | 5 | 0.92 | 0.91 | 0.98 | 16 | * | |
| Node01211-leaf | not applied | ✓ (b) | 10 | |||||
| Node01212-leaf | not applied | ✓ (b) | 4 | |||||
| Node01213-leaf | not applied | ✓ (b) | 2 | |||||
| Node0122 | ATC:skmeans | 3 | 1.00 | 0.98 | 0.99 | 25 | ** | |
| Node01221-leaf | SD:kmeans | ✓ (c) | 2 | 1.00 | 0.98 | 0.99 | 12 | ** |
| Node01222-leaf | not applied | ✓ (b) | 8 | |||||
| Node01223-leaf | not applied | ✓ (b) | 3 | |||||
| Node01224-leaf | not applied | ✓ (b) | 2 | |||||
| Node02 | ATC:kmeans | 2 | 1.00 | 1.00 | 1.00 | 54 | ** | |
| Node021 | SD:kmeans | 2 | 1.00 | 1.00 | 1.00 | 36 | ** | |
| Node0211-leaf | ATC:skmeans | ✓ (c) | 4 | 1.00 | 1.00 | 1.00 | 19 | ** |
| Node0212 | ATC:kmeans | 2 | 1.00 | 1.00 | 1.00 | 17 | ** | |
| Node02121-leaf | not applied | ✓ (b) | 6 | |||||
| Node02122-leaf | not applied | ✓ (b) | 7 | |||||
| Node02123-leaf | not applied | ✓ (b) | 4 | |||||
| Node022-leaf | not applied | ✓ (b) | 8 | |||||
| Node023-leaf | not applied | ✓ (b) | 10 | |||||
| Node03-leaf | ATC:kmeans | ✓ (c) | 3 | 0.98 | 0.94 | 0.98 | 162 | ** |
| Node04 | ATC:kmeans | 3 | 1.00 | 0.96 | 0.98 | 82 | ** | |
| Node041 | ATC:skmeans | 4 | 1.00 | 1.00 | 1.00 | 31 | ** | |
| Node0411-leaf | not applied | ✓ (b) | 7 | |||||
| Node0412-leaf | not applied | ✓ (b) | 10 | |||||
| Node0413-leaf | not applied | ✓ (b) | 9 | |||||
| Node0414-leaf | not applied | ✓ (b) | 5 | |||||
| Node042 | ATC:skmeans | 4 | 1.00 | 1.00 | 1.00 | 34 | ** | |
| Node0421-leaf | not applied | ✓ (b) | 11 | |||||
| Node0422 | ATC:kmeans | 3 | 1.00 | 1.00 | 1.00 | 16 | ** | |
| Node04221-leaf | not applied | ✓ (b) | 6 | |||||
| Node04222-leaf | not applied | ✓ (b) | 7 | |||||
| Node04223-leaf | not applied | ✓ (b) | 3 | |||||
| Node0423-leaf | not applied | ✓ (b) | 7 | |||||
| Node043 | ATC:kmeans | 3 | 1.00 | 1.00 | 1.00 | 17 | ** | |
| Node0431-leaf | not applied | ✓ (b) | 5 | |||||
| Node0432-leaf | not applied | ✓ (b) | 8 | |||||
| Node0433-leaf | not applied | ✓ (b) | 4 |
Stop reason: b) Subgroup had too few columns. c) There were too few signatures.
**: 1-PAC > 0.95, *: 1-PAC > 0.9
The nodes of the hierarchy can be merged by setting the merge_node parameters. Here we
control the hierarchy with the min_n_signatures parameter. The value of min_n_signatures is
from node_info().
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 1359))
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 1530))
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 1543))
#> Error in lt[[hierarchy[i, 1]]]$AddChildNode({: attempt to apply non-function
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 3038))
#> Error in lt[[hierarchy[i, 1]]]$AddChildNode({: attempt to apply non-function
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 3867))
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 3913))
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 4047))
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 5229))
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 5533))
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 5908))
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 7485))
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 7743))
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 8434))
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 9343))
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 10997))
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 17456))
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 34264))
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 = 1359))
#> TCGA.AF.3911.01 TCGA.F4.6459.01 TCGA.AA.3494.11 TCGA.3L.AA1B.01 TCGA.D5.5538.01 TCGA.F4.6854.01
#> "03" "03" "023" "03" "03" "03"
#> TCGA.AG.A026.01 TCGA.G4.6303.01 TCGA.F5.6464.01 TCGA.T9.A92H.01 TCGA.AA.3712.11 TCGA.CM.5863.01
#> "01121" "011112" "0412" "011111" "0211" "03"
#> TCGA.AZ.4308.01 TCGA.AD.6965.01 TCGA.A6.2681.11 TCGA.AD.6548.01 TCGA.A6.5660.01 TCGA.AZ.6600.01
#> "0421" "01124" "02121" "03" "01121" "03"
#> TCGA.F4.6808.01 TCGA.D5.6540.01 TCGA.F5.6571.01 TCGA.D5.6926.01 TCGA.CM.4748.01 TCGA.A6.2675.11
#> "03" "01222" "011112" "03" "03" "0211"
#> TCGA.5M.AATE.01 TCGA.D5.5541.01 TCGA.CM.5862.01 TCGA.AA.3511.01 TCGA.AA.3663.11 TCGA.CI.6622.01
#> "03" "0421" "01121" "03" "0211" "011111"
#> TCGA.EI.6506.01 TCGA.AM.5821.01 TCGA.F5.6812.01 TCGA.G4.6588.01 TCGA.EI.6512.01 TCGA.A6.6648.01
#> "03" "03" "0414" "01221" "01112" "0421"
#> TCGA.A6.2671.11 TCGA.NH.A6GC.01 TCGA.F4.6805.01 TCGA.AA.3697.01 TCGA.QG.A5YX.01 TCGA.DM.A28C.01
#> "0211" "03" "0412" "03" "01123" "03"
#> TCGA.AG.A036.01 TCGA.AZ.6606.01 TCGA.F4.6570.01 TCGA.DC.4745.01 TCGA.AF.A56K.01 TCGA.G4.6627.01
#> "01121" "01223" "01221" "03" "0423" "0412"
#> TCGA.A6.5657.01 TCGA.A6.5662.01 TCGA.AA.3509.01 TCGA.D5.6929.01 TCGA.CM.6679.01 TCGA.A6.2680.11
#> "03" "03" "011112" "04222" "03" "02121"
#> TCGA.DC.6157.01 TCGA.AF.6655.01 TCGA.CM.6161.01 TCGA.EI.6883.01 TCGA.F5.6811.01 TCGA.D5.6930.01
#> "0432" "0421" "03" "01113" "03" "03"
#> TCGA.CM.6164.01 TCGA.AF.2687.01 TCGA.DY.A1H8.01 TCGA.G5.6641.01 TCGA.DC.6155.01 TCGA.RU.A8FL.01
#> "04222" "0423" "03" "03" "03" "01121"
#> TCGA.CK.4951.01 TCGA.F4.6704.01 TCGA.AZ.6599.01 TCGA.F5.6861.01 TCGA.CM.5860.01 TCGA.A6.6780.01
#> "03" "0423" "01122" "03" "01114" "01114"
#> TCGA.A6.2686.01 TCGA.CM.4750.01 TCGA.CM.6677.01 TCGA.A6.A567.01 TCGA.F5.6814.01 TCGA.D5.6898.01
#> "01212" "01121" "01123" "0433" "01123" "03"
#> TCGA.AG.A01W.01 TCGA.AZ.6598.11 TCGA.F5.6813.01 TCGA.AG.3732.01 TCGA.EI.6885.01 TCGA.G4.6299.01
#> "03" "02122" "03" "04223" "0433" "01222"
#> TCGA.A6.4105.01 TCGA.DM.A1D8.01 TCGA.DM.A285.01 TCGA.G4.6295.11 TCGA.DC.4749.01 TCGA.DT.5265.01
#> "01223" "01114" "03" "023" "0421" "01223"
#> TCGA.5M.AAT5.01 TCGA.DM.A0XD.01 TCGA.A6.6138.01 TCGA.D5.7000.01 TCGA.DM.A28F.01 TCGA.DY.A1DE.01
#> "0432" "01211" "01114" "01211" "01123" "03"
#> TCGA.A6.6142.01 TCGA.QL.A97D.01 TCGA.CK.6748.01 TCGA.DC.6160.01 TCGA.D5.6534.01 TCGA.AZ.4616.01
#> "022" "03" "03" "0421" "0413" "03"
#> TCGA.CK.6751.01 TCGA.CM.6171.01 TCGA.DM.A1DA.01 TCGA.AG.A020.11 TCGA.G4.6311.11 TCGA.G4.6625.11
#> "01211" "01221" "01211" "02123" "0211" "02122"
#> TCGA.F5.6863.01 TCGA.G4.6317.02 TCGA.G4.6317.01 TCGA.DM.A1D4.01 TCGA.AG.A01Y.11 TCGA.D5.6530.01
#> "04221" "0432" "03" "01114" "02123" "03"
#> TCGA.CK.4948.01 TCGA.AD.A5EJ.01 TCGA.A6.6651.01 TCGA.CA.5256.01 TCGA.DM.A0X9.01 TCGA.AY.A69D.01
#> "0431" "01221" "0412" "03" "01124" "01113"
#> TCGA.G4.6626.01 TCGA.CA.6716.01 TCGA.A6.2682.01 TCGA.A6.4107.11 TCGA.CA.6717.01 TCGA.G4.6293.01
#> "03" "01113" "03" "023" "03" "03"
#> TCGA.CK.5916.01 TCGA.G4.6309.01 TCGA.AA.3662.01 TCGA.AF.A56L.01 TCGA.NH.A6GB.01 TCGA.AD.5900.01
#> "01221" "04223" "03" "03" "01124" "03"
#> TCGA.NH.A50U.01 TCGA.AA.3712.01 TCGA.AZ.4614.01 TCGA.AH.6644.01 TCGA.AZ.6607.01 TCGA.AF.2693.01
#> "01124" "03" "01211" "011111" "03" "0411"
#> TCGA.D5.6924.01 TCGA.CM.5868.01 TCGA.AF.4110.01 TCGA.A6.3809.01 TCGA.AZ.4313.01 TCGA.A6.2675.01
#> "03" "04222" "0411" "01212" "04223" "0421"
#> TCGA.AZ.6608.01 TCGA.CM.5864.01 TCGA.AA.3494.01 TCGA.AD.6895.01 TCGA.CI.6620.01 TCGA.DC.6156.01
#> "03" "01123" "0432" "03" "03" "03"
#> TCGA.D5.6931.01 TCGA.CM.6165.01 TCGA.CM.5861.01 TCGA.A6.2671.01 TCGA.DC.6158.01 TCGA.AG.3742.01
#> "03" "03" "01221" "03" "03" "01123"
#> TCGA.AG.A02N.11 TCGA.G4.6307.01 TCGA.A6.5666.01 TCGA.EI.6511.01 TCGA.CI.6624.01 TCGA.AG.3591.01
#> "0211" "0432" "01121" "03" "04222" "01122"
#> TCGA.AY.A8YK.01 TCGA.F4.6856.01 TCGA.DM.A1D7.01 TCGA.A6.2685.01 TCGA.5M.AAT6.01 TCGA.AH.6643.01
#> "022" "03" "03" "022" "022" "011111"
#> TCGA.F4.6569.01 TCGA.G4.6298.01 TCGA.AY.6196.01 TCGA.EI.6510.01 TCGA.A6.5656.01 TCGA.A6.2684.11
#> "03" "03" "03" "01124" "011111" "02121"
#> TCGA.DY.A1DG.01 TCGA.AZ.4682.01 TCGA.EI.6884.01 TCGA.F4.6806.01 TCGA.G4.6320.11 TCGA.G4.6322.01
#> "01121" "03" "03" "01112" "0211" "01213"
#> TCGA.F5.6810.01 TCGA.5M.AAT4.01 TCGA.CL.4957.01 TCGA.DC.6681.01 TCGA.CM.6167.01 TCGA.AG.4022.01
#> "0431" "01112" "03" "03" "0412" "03"
#> TCGA.G4.6586.01 TCGA.EI.6514.01 TCGA.CK.4950.01 TCGA.DM.A282.01 TCGA.DY.A1DC.01 TCGA.D5.6535.01
#> "01221" "011112" "03" "011112" "03" "03"
#> TCGA.DM.A1HA.01 TCGA.DC.5869.01 TCGA.AZ.6599.11 TCGA.CM.4752.01 TCGA.AZ.4684.01 TCGA.EI.7004.01
#> "01114" "03" "0211" "0423" "03" "03"
#> TCGA.A6.A565.01 TCGA.D5.6531.01 TCGA.AZ.6598.01 TCGA.AD.6890.01 TCGA.AG.4021.01 TCGA.A6.6781.01
#> "023" "01211" "01222" "03" "01124" "0412"
#> TCGA.DM.A1D9.01 TCGA.CM.4744.01 TCGA.A6.2679.11 TCGA.A6.6652.01 TCGA.AD.6964.01 TCGA.SS.A7HO.01
#> "01124" "01124" "023" "011111" "022" "01121"
#> TCGA.A6.6650.01 TCGA.DM.A0XF.01 TCGA.G4.6295.01 TCGA.F4.6461.01 TCGA.AM.5820.01 TCGA.G4.6314.11
#> "011112" "04222" "0431" "01221" "03" "02121"
#> TCGA.AD.6889.01 TCGA.AZ.6605.01 TCGA.EI.6881.01 TCGA.NH.A50T.01 TCGA.AG.3725.11 TCGA.G4.6323.01
#> "01222" "0414" "03" "01121" "02122" "03"
#> TCGA.AA.3663.01 TCGA.AD.6899.01 TCGA.A6.5667.11 TCGA.A6.A56B.01 TCGA.G5.6572.01 TCGA.DM.A280.01
#> "01222" "01112" "02122" "01113" "0411" "0413"
#> TCGA.AG.A020.01 TCGA.AA.3713.01 TCGA.D5.5539.01 TCGA.AA.3655.11 TCGA.AA.3489.01 TCGA.AA.3495.01
#> "03" "03" "01122" "0211" "0412" "03"
#> TCGA.AG.A01Y.01 TCGA.AZ.6601.01 TCGA.AH.6903.01 TCGA.AZ.6603.01 TCGA.CA.5254.01 TCGA.A6.A5ZU.01
#> "0433" "03" "03" "0432" "01224" "03"
#> TCGA.G4.6302.01 TCGA.AZ.5403.01 TCGA.AY.A54L.01 TCGA.A6.4107.01 TCGA.NH.A5IV.01 TCGA.G4.6306.01
#> "0413" "022" "01124" "01224" "01112" "01112"
#> TCGA.AD.A5EK.01 TCGA.G5.6235.01 TCGA.DC.5337.01 TCGA.CM.6675.01 TCGA.AH.6544.01 TCGA.CK.6746.01
#> "01113" "0411" "01123" "01211" "03" "01212"
#> TCGA.CA.6718.01 TCGA.CI.6621.01 TCGA.CM.6676.01 TCGA.DM.A1DB.01 TCGA.A6.6654.01 TCGA.AA.3510.11
#> "03" "0411" "03" "03" "03" "023"
#> TCGA.CA.6715.01 TCGA.CM.5341.01 TCGA.CK.5912.01 TCGA.F4.6857.01 TCGA.QG.A5YW.01 TCGA.A6.5665.01
#> "03" "03" "03" "0413" "01123" "01221"
#> TCGA.CM.6168.01 TCGA.CL.5917.01 TCGA.AU.6004.01 TCGA.AY.5543.01 TCGA.AG.3731.01 TCGA.G4.6314.01
#> "03" "03" "03" "03" "03" "03"
#> TCGA.DC.6683.01 TCGA.CA.5796.01 TCGA.AG.A036.11 TCGA.AZ.4323.01 TCGA.EI.6882.01 TCGA.AZ.4315.01
#> "03" "03" "0211" "0413" "01122" "03"
#> TCGA.A6.2677.01 TCGA.DY.A1DF.01 TCGA.CM.6162.01 TCGA.F4.6703.01 TCGA.CM.5349.01 TCGA.AG.A02N.01
#> "01121" "03" "022" "022" "03" "03"
#> TCGA.AA.3506.01 TCGA.D5.6932.01 TCGA.D5.6538.01 TCGA.AA.3488.11 TCGA.AA.3502.01 TCGA.NH.A8F8.01
#> "03" "03" "01211" "0211" "01122" "03"
#> TCGA.AF.A56N.01 TCGA.AF.6672.01 TCGA.A6.2685.11 TCGA.A6.6141.01 TCGA.AD.6963.01 TCGA.G4.6298.11
#> "03" "0433" "02122" "03" "0423" "0211"
#> TCGA.EI.6917.01 TCGA.QG.A5Z2.01 TCGA.A6.2684.01 TCGA.CK.5915.01 TCGA.CM.6163.01 TCGA.G4.6322.11
#> "03" "01222" "03" "01113" "03" "0211"
#> TCGA.AY.6197.01 TCGA.D5.6928.01 TCGA.A6.3810.01 TCGA.G4.6294.01 TCGA.AA.3660.11 TCGA.A6.6137.01
#> "01114" "0413" "0421" "011111" "02122" "03"
#> TCGA.G4.6297.11 TCGA.AZ.4615.01 TCGA.CK.4952.01 TCGA.CM.6172.01 TCGA.AD.6901.01 TCGA.AA.3496.01
#> "02122" "03" "01213" "01113" "03" "01121"
#> TCGA.CK.5913.01 TCGA.DM.A28A.01 TCGA.EI.7002.01 TCGA.D5.6533.01 TCGA.QG.A5Z1.01 TCGA.D5.6923.01
#> "01212" "01113" "011111" "03" "01113" "0411"
#> TCGA.AF.2690.01 TCGA.DM.A28H.01 TCGA.G4.6320.01 TCGA.G4.6310.01 TCGA.DM.A28M.01 TCGA.DM.A288.01
#> "0414" "01114" "01211" "03" "01112" "01112"
#> TCGA.A6.2681.01 TCGA.A6.2679.01 TCGA.4N.A93T.01 TCGA.NH.A8F7.06 TCGA.NH.A8F7.01 TCGA.AZ.6600.11
#> "03" "03" "03" "03" "0432" "0211"
#> TCGA.G5.6572.02 TCGA.AY.6386.01 TCGA.G4.6628.01 TCGA.A6.6653.01 TCGA.CM.4746.01 TCGA.F4.6855.01
#> "0414" "03" "03" "01222" "03" "011112"
#> TCGA.EF.5830.01 TCGA.NH.A6GA.01 TCGA.NH.A50V.01 TCGA.DY.A0XA.01 TCGA.DM.A28E.01 TCGA.AG.3725.01
#> "03" "01112" "01114" "04221" "04221" "03"
#> TCGA.CK.6747.01 TCGA.CL.5918.01 TCGA.CI.6623.01 TCGA.A6.5667.01 TCGA.DM.A28K.01 TCGA.AA.3713.11
#> "01112" "01123" "0421" "03" "01112" "023"
#> TCGA.AA.3655.01 TCGA.AU.3779.01 TCGA.A6.5664.01 TCGA.AA.3697.11 TCGA.AZ.5407.01 TCGA.CM.6169.01
#> "011111" "04221" "03" "023" "01114" "03"
#> TCGA.AH.6547.01 TCGA.AZ.6601.11 TCGA.A6.5661.01 TCGA.F4.6807.01 TCGA.QG.A5YV.01 TCGA.AA.3509.11
#> "0412" "0211" "01221" "03" "011112" "02123"
#> TCGA.AY.A71X.01 TCGA.CA.5797.01 TCGA.F4.6460.01 TCGA.G4.6302.11 TCGA.F5.6702.01 TCGA.AH.6549.01
#> "01122" "0431" "04221" "023" "0423" "01121"
#> TCGA.D5.6927.01 TCGA.CM.6166.01 TCGA.AH.6897.01 TCGA.G4.6304.01 TCGA.CA.5255.01 TCGA.EI.6507.01
#> "0412" "011112" "01121" "0413" "03" "03"
#> TCGA.CK.4947.01 TCGA.D5.5540.01 TCGA.DC.6682.01 TCGA.G4.6321.01 TCGA.A6.6649.01 TCGA.CM.5348.01
#> "03" "01113" "03" "03" "03" "03"
#> TCGA.EI.6513.01 TCGA.A6.2672.01 TCGA.D5.6539.01 TCGA.AA.3510.01 TCGA.G5.6233.01 TCGA.BM.6198.01
#> "0431" "01221" "0411" "03" "01114" "0414"
#> TCGA.CA.6719.01 TCGA.DC.6154.01 TCGA.DM.A1D6.01 TCGA.AG.3731.11 TCGA.CM.6674.01 TCGA.CM.4743.01
#> "01112" "03" "03" "0211" "0412" "0413"
#> TCGA.F5.6465.01 TCGA.D5.5537.01 TCGA.F4.6463.01 TCGA.A6.2686.11 TCGA.4T.AA8H.01 TCGA.A6.6782.01
#> "04222" "01112" "03" "02121" "01122" "03"
#> TCGA.AG.3592.01 TCGA.AD.6888.01 TCGA.CM.6678.01 TCGA.CM.5344.01 TCGA.AA.3495.11 TCGA.AG.A01W.11
#> "01112" "03" "011112" "04222" "0211" "02123"
#> TCGA.F4.6809.01 TCGA.CK.5914.01 TCGA.AZ.4681.01 TCGA.AA.3492.01 TCGA.D5.6536.01 TCGA.AA.3506.11
#> "03" "01113" "0432" "01221" "03" "0211"
#> TCGA.AA.3488.01 TCGA.AA.3502.11 TCGA.A6.6140.01 TCGA.D5.6529.01 TCGA.DM.A1D0.01 TCGA.DM.A1HB.01
#> "03" "023" "0421" "03" "04221" "01222"
#> TCGA.D5.6920.01 TCGA.D5.6922.01 TCGA.EI.6508.01 TCGA.D5.6532.01 TCGA.5M.AATA.01 TCGA.EI.6509.01
#> "03" "03" "01123" "01123" "03" "0421"
#> TCGA.G4.6311.01 TCGA.A6.A566.01 TCGA.G4.6625.01 TCGA.CI.6619.01 TCGA.F5.6864.01 TCGA.AA.3492.11
#> "03" "03" "03" "0423" "03" "02121"
#> TCGA.A6.5659.01 TCGA.WS.AB45.01 TCGA.G4.6315.01 TCGA.D5.6541.01 TCGA.A6.2680.01 TCGA.CM.4751.01
#> "01211" "0413" "03" "03" "01123" "03"
#> TCGA.CM.6680.01 TCGA.AF.6136.01 TCGA.AA.3660.01 TCGA.CM.4747.01 TCGA.EF.5831.01 TCGA.DM.A28G.01
#> "01122" "03" "01112" "01112" "01113" "01124"
#> TCGA.G4.6297.01 TCGA.A6.2682.11 TCGA.D5.6537.01 TCGA.CM.6170.01 TCGA.DY.A1DD.01
#> "03" "0211" "01121" "03" "01121"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 1530))
#> TCGA.AF.3911.01 TCGA.F4.6459.01 TCGA.AA.3494.11 TCGA.3L.AA1B.01 TCGA.D5.5538.01 TCGA.F4.6854.01
#> "03" "03" "023" "03" "03" "03"
#> TCGA.AG.A026.01 TCGA.G4.6303.01 TCGA.F5.6464.01 TCGA.T9.A92H.01 TCGA.AA.3712.11 TCGA.CM.5863.01
#> "01121" "011112" "0412" "011111" "0211" "03"
#> TCGA.AZ.4308.01 TCGA.AD.6965.01 TCGA.A6.2681.11 TCGA.AD.6548.01 TCGA.A6.5660.01 TCGA.AZ.6600.01
#> "0421" "01124" "0212" "03" "01121" "03"
#> TCGA.F4.6808.01 TCGA.D5.6540.01 TCGA.F5.6571.01 TCGA.D5.6926.01 TCGA.CM.4748.01 TCGA.A6.2675.11
#> "03" "01222" "011112" "03" "03" "0211"
#> TCGA.5M.AATE.01 TCGA.D5.5541.01 TCGA.CM.5862.01 TCGA.AA.3511.01 TCGA.AA.3663.11 TCGA.CI.6622.01
#> "03" "0421" "01121" "03" "0211" "011111"
#> TCGA.EI.6506.01 TCGA.AM.5821.01 TCGA.F5.6812.01 TCGA.G4.6588.01 TCGA.EI.6512.01 TCGA.A6.6648.01
#> "03" "03" "0414" "01221" "01112" "0421"
#> TCGA.A6.2671.11 TCGA.NH.A6GC.01 TCGA.F4.6805.01 TCGA.AA.3697.01 TCGA.QG.A5YX.01 TCGA.DM.A28C.01
#> "0211" "03" "0412" "03" "01123" "03"
#> TCGA.AG.A036.01 TCGA.AZ.6606.01 TCGA.F4.6570.01 TCGA.DC.4745.01 TCGA.AF.A56K.01 TCGA.G4.6627.01
#> "01121" "01223" "01221" "03" "0423" "0412"
#> TCGA.A6.5657.01 TCGA.A6.5662.01 TCGA.AA.3509.01 TCGA.D5.6929.01 TCGA.CM.6679.01 TCGA.A6.2680.11
#> "03" "03" "011112" "04222" "03" "0212"
#> TCGA.DC.6157.01 TCGA.AF.6655.01 TCGA.CM.6161.01 TCGA.EI.6883.01 TCGA.F5.6811.01 TCGA.D5.6930.01
#> "0432" "0421" "03" "01113" "03" "03"
#> TCGA.CM.6164.01 TCGA.AF.2687.01 TCGA.DY.A1H8.01 TCGA.G5.6641.01 TCGA.DC.6155.01 TCGA.RU.A8FL.01
#> "04222" "0423" "03" "03" "03" "01121"
#> TCGA.CK.4951.01 TCGA.F4.6704.01 TCGA.AZ.6599.01 TCGA.F5.6861.01 TCGA.CM.5860.01 TCGA.A6.6780.01
#> "03" "0423" "01122" "03" "01114" "01114"
#> TCGA.A6.2686.01 TCGA.CM.4750.01 TCGA.CM.6677.01 TCGA.A6.A567.01 TCGA.F5.6814.01 TCGA.D5.6898.01
#> "01212" "01121" "01123" "0433" "01123" "03"
#> TCGA.AG.A01W.01 TCGA.AZ.6598.11 TCGA.F5.6813.01 TCGA.AG.3732.01 TCGA.EI.6885.01 TCGA.G4.6299.01
#> "03" "0212" "03" "04223" "0433" "01222"
#> TCGA.A6.4105.01 TCGA.DM.A1D8.01 TCGA.DM.A285.01 TCGA.G4.6295.11 TCGA.DC.4749.01 TCGA.DT.5265.01
#> "01223" "01114" "03" "023" "0421" "01223"
#> TCGA.5M.AAT5.01 TCGA.DM.A0XD.01 TCGA.A6.6138.01 TCGA.D5.7000.01 TCGA.DM.A28F.01 TCGA.DY.A1DE.01
#> "0432" "01211" "01114" "01211" "01123" "03"
#> TCGA.A6.6142.01 TCGA.QL.A97D.01 TCGA.CK.6748.01 TCGA.DC.6160.01 TCGA.D5.6534.01 TCGA.AZ.4616.01
#> "022" "03" "03" "0421" "0413" "03"
#> TCGA.CK.6751.01 TCGA.CM.6171.01 TCGA.DM.A1DA.01 TCGA.AG.A020.11 TCGA.G4.6311.11 TCGA.G4.6625.11
#> "01211" "01221" "01211" "0212" "0211" "0212"
#> TCGA.F5.6863.01 TCGA.G4.6317.02 TCGA.G4.6317.01 TCGA.DM.A1D4.01 TCGA.AG.A01Y.11 TCGA.D5.6530.01
#> "04221" "0432" "03" "01114" "0212" "03"
#> TCGA.CK.4948.01 TCGA.AD.A5EJ.01 TCGA.A6.6651.01 TCGA.CA.5256.01 TCGA.DM.A0X9.01 TCGA.AY.A69D.01
#> "0431" "01221" "0412" "03" "01124" "01113"
#> TCGA.G4.6626.01 TCGA.CA.6716.01 TCGA.A6.2682.01 TCGA.A6.4107.11 TCGA.CA.6717.01 TCGA.G4.6293.01
#> "03" "01113" "03" "023" "03" "03"
#> TCGA.CK.5916.01 TCGA.G4.6309.01 TCGA.AA.3662.01 TCGA.AF.A56L.01 TCGA.NH.A6GB.01 TCGA.AD.5900.01
#> "01221" "04223" "03" "03" "01124" "03"
#> TCGA.NH.A50U.01 TCGA.AA.3712.01 TCGA.AZ.4614.01 TCGA.AH.6644.01 TCGA.AZ.6607.01 TCGA.AF.2693.01
#> "01124" "03" "01211" "011111" "03" "0411"
#> TCGA.D5.6924.01 TCGA.CM.5868.01 TCGA.AF.4110.01 TCGA.A6.3809.01 TCGA.AZ.4313.01 TCGA.A6.2675.01
#> "03" "04222" "0411" "01212" "04223" "0421"
#> TCGA.AZ.6608.01 TCGA.CM.5864.01 TCGA.AA.3494.01 TCGA.AD.6895.01 TCGA.CI.6620.01 TCGA.DC.6156.01
#> "03" "01123" "0432" "03" "03" "03"
#> TCGA.D5.6931.01 TCGA.CM.6165.01 TCGA.CM.5861.01 TCGA.A6.2671.01 TCGA.DC.6158.01 TCGA.AG.3742.01
#> "03" "03" "01221" "03" "03" "01123"
#> TCGA.AG.A02N.11 TCGA.G4.6307.01 TCGA.A6.5666.01 TCGA.EI.6511.01 TCGA.CI.6624.01 TCGA.AG.3591.01
#> "0211" "0432" "01121" "03" "04222" "01122"
#> TCGA.AY.A8YK.01 TCGA.F4.6856.01 TCGA.DM.A1D7.01 TCGA.A6.2685.01 TCGA.5M.AAT6.01 TCGA.AH.6643.01
#> "022" "03" "03" "022" "022" "011111"
#> TCGA.F4.6569.01 TCGA.G4.6298.01 TCGA.AY.6196.01 TCGA.EI.6510.01 TCGA.A6.5656.01 TCGA.A6.2684.11
#> "03" "03" "03" "01124" "011111" "0212"
#> TCGA.DY.A1DG.01 TCGA.AZ.4682.01 TCGA.EI.6884.01 TCGA.F4.6806.01 TCGA.G4.6320.11 TCGA.G4.6322.01
#> "01121" "03" "03" "01112" "0211" "01213"
#> TCGA.F5.6810.01 TCGA.5M.AAT4.01 TCGA.CL.4957.01 TCGA.DC.6681.01 TCGA.CM.6167.01 TCGA.AG.4022.01
#> "0431" "01112" "03" "03" "0412" "03"
#> TCGA.G4.6586.01 TCGA.EI.6514.01 TCGA.CK.4950.01 TCGA.DM.A282.01 TCGA.DY.A1DC.01 TCGA.D5.6535.01
#> "01221" "011112" "03" "011112" "03" "03"
#> TCGA.DM.A1HA.01 TCGA.DC.5869.01 TCGA.AZ.6599.11 TCGA.CM.4752.01 TCGA.AZ.4684.01 TCGA.EI.7004.01
#> "01114" "03" "0211" "0423" "03" "03"
#> TCGA.A6.A565.01 TCGA.D5.6531.01 TCGA.AZ.6598.01 TCGA.AD.6890.01 TCGA.AG.4021.01 TCGA.A6.6781.01
#> "023" "01211" "01222" "03" "01124" "0412"
#> TCGA.DM.A1D9.01 TCGA.CM.4744.01 TCGA.A6.2679.11 TCGA.A6.6652.01 TCGA.AD.6964.01 TCGA.SS.A7HO.01
#> "01124" "01124" "023" "011111" "022" "01121"
#> TCGA.A6.6650.01 TCGA.DM.A0XF.01 TCGA.G4.6295.01 TCGA.F4.6461.01 TCGA.AM.5820.01 TCGA.G4.6314.11
#> "011112" "04222" "0431" "01221" "03" "0212"
#> TCGA.AD.6889.01 TCGA.AZ.6605.01 TCGA.EI.6881.01 TCGA.NH.A50T.01 TCGA.AG.3725.11 TCGA.G4.6323.01
#> "01222" "0414" "03" "01121" "0212" "03"
#> TCGA.AA.3663.01 TCGA.AD.6899.01 TCGA.A6.5667.11 TCGA.A6.A56B.01 TCGA.G5.6572.01 TCGA.DM.A280.01
#> "01222" "01112" "0212" "01113" "0411" "0413"
#> TCGA.AG.A020.01 TCGA.AA.3713.01 TCGA.D5.5539.01 TCGA.AA.3655.11 TCGA.AA.3489.01 TCGA.AA.3495.01
#> "03" "03" "01122" "0211" "0412" "03"
#> TCGA.AG.A01Y.01 TCGA.AZ.6601.01 TCGA.AH.6903.01 TCGA.AZ.6603.01 TCGA.CA.5254.01 TCGA.A6.A5ZU.01
#> "0433" "03" "03" "0432" "01224" "03"
#> TCGA.G4.6302.01 TCGA.AZ.5403.01 TCGA.AY.A54L.01 TCGA.A6.4107.01 TCGA.NH.A5IV.01 TCGA.G4.6306.01
#> "0413" "022" "01124" "01224" "01112" "01112"
#> TCGA.AD.A5EK.01 TCGA.G5.6235.01 TCGA.DC.5337.01 TCGA.CM.6675.01 TCGA.AH.6544.01 TCGA.CK.6746.01
#> "01113" "0411" "01123" "01211" "03" "01212"
#> TCGA.CA.6718.01 TCGA.CI.6621.01 TCGA.CM.6676.01 TCGA.DM.A1DB.01 TCGA.A6.6654.01 TCGA.AA.3510.11
#> "03" "0411" "03" "03" "03" "023"
#> TCGA.CA.6715.01 TCGA.CM.5341.01 TCGA.CK.5912.01 TCGA.F4.6857.01 TCGA.QG.A5YW.01 TCGA.A6.5665.01
#> "03" "03" "03" "0413" "01123" "01221"
#> TCGA.CM.6168.01 TCGA.CL.5917.01 TCGA.AU.6004.01 TCGA.AY.5543.01 TCGA.AG.3731.01 TCGA.G4.6314.01
#> "03" "03" "03" "03" "03" "03"
#> TCGA.DC.6683.01 TCGA.CA.5796.01 TCGA.AG.A036.11 TCGA.AZ.4323.01 TCGA.EI.6882.01 TCGA.AZ.4315.01
#> "03" "03" "0211" "0413" "01122" "03"
#> TCGA.A6.2677.01 TCGA.DY.A1DF.01 TCGA.CM.6162.01 TCGA.F4.6703.01 TCGA.CM.5349.01 TCGA.AG.A02N.01
#> "01121" "03" "022" "022" "03" "03"
#> TCGA.AA.3506.01 TCGA.D5.6932.01 TCGA.D5.6538.01 TCGA.AA.3488.11 TCGA.AA.3502.01 TCGA.NH.A8F8.01
#> "03" "03" "01211" "0211" "01122" "03"
#> TCGA.AF.A56N.01 TCGA.AF.6672.01 TCGA.A6.2685.11 TCGA.A6.6141.01 TCGA.AD.6963.01 TCGA.G4.6298.11
#> "03" "0433" "0212" "03" "0423" "0211"
#> TCGA.EI.6917.01 TCGA.QG.A5Z2.01 TCGA.A6.2684.01 TCGA.CK.5915.01 TCGA.CM.6163.01 TCGA.G4.6322.11
#> "03" "01222" "03" "01113" "03" "0211"
#> TCGA.AY.6197.01 TCGA.D5.6928.01 TCGA.A6.3810.01 TCGA.G4.6294.01 TCGA.AA.3660.11 TCGA.A6.6137.01
#> "01114" "0413" "0421" "011111" "0212" "03"
#> TCGA.G4.6297.11 TCGA.AZ.4615.01 TCGA.CK.4952.01 TCGA.CM.6172.01 TCGA.AD.6901.01 TCGA.AA.3496.01
#> "0212" "03" "01213" "01113" "03" "01121"
#> TCGA.CK.5913.01 TCGA.DM.A28A.01 TCGA.EI.7002.01 TCGA.D5.6533.01 TCGA.QG.A5Z1.01 TCGA.D5.6923.01
#> "01212" "01113" "011111" "03" "01113" "0411"
#> TCGA.AF.2690.01 TCGA.DM.A28H.01 TCGA.G4.6320.01 TCGA.G4.6310.01 TCGA.DM.A28M.01 TCGA.DM.A288.01
#> "0414" "01114" "01211" "03" "01112" "01112"
#> TCGA.A6.2681.01 TCGA.A6.2679.01 TCGA.4N.A93T.01 TCGA.NH.A8F7.06 TCGA.NH.A8F7.01 TCGA.AZ.6600.11
#> "03" "03" "03" "03" "0432" "0211"
#> TCGA.G5.6572.02 TCGA.AY.6386.01 TCGA.G4.6628.01 TCGA.A6.6653.01 TCGA.CM.4746.01 TCGA.F4.6855.01
#> "0414" "03" "03" "01222" "03" "011112"
#> TCGA.EF.5830.01 TCGA.NH.A6GA.01 TCGA.NH.A50V.01 TCGA.DY.A0XA.01 TCGA.DM.A28E.01 TCGA.AG.3725.01
#> "03" "01112" "01114" "04221" "04221" "03"
#> TCGA.CK.6747.01 TCGA.CL.5918.01 TCGA.CI.6623.01 TCGA.A6.5667.01 TCGA.DM.A28K.01 TCGA.AA.3713.11
#> "01112" "01123" "0421" "03" "01112" "023"
#> TCGA.AA.3655.01 TCGA.AU.3779.01 TCGA.A6.5664.01 TCGA.AA.3697.11 TCGA.AZ.5407.01 TCGA.CM.6169.01
#> "011111" "04221" "03" "023" "01114" "03"
#> TCGA.AH.6547.01 TCGA.AZ.6601.11 TCGA.A6.5661.01 TCGA.F4.6807.01 TCGA.QG.A5YV.01 TCGA.AA.3509.11
#> "0412" "0211" "01221" "03" "011112" "0212"
#> TCGA.AY.A71X.01 TCGA.CA.5797.01 TCGA.F4.6460.01 TCGA.G4.6302.11 TCGA.F5.6702.01 TCGA.AH.6549.01
#> "01122" "0431" "04221" "023" "0423" "01121"
#> TCGA.D5.6927.01 TCGA.CM.6166.01 TCGA.AH.6897.01 TCGA.G4.6304.01 TCGA.CA.5255.01 TCGA.EI.6507.01
#> "0412" "011112" "01121" "0413" "03" "03"
#> TCGA.CK.4947.01 TCGA.D5.5540.01 TCGA.DC.6682.01 TCGA.G4.6321.01 TCGA.A6.6649.01 TCGA.CM.5348.01
#> "03" "01113" "03" "03" "03" "03"
#> TCGA.EI.6513.01 TCGA.A6.2672.01 TCGA.D5.6539.01 TCGA.AA.3510.01 TCGA.G5.6233.01 TCGA.BM.6198.01
#> "0431" "01221" "0411" "03" "01114" "0414"
#> TCGA.CA.6719.01 TCGA.DC.6154.01 TCGA.DM.A1D6.01 TCGA.AG.3731.11 TCGA.CM.6674.01 TCGA.CM.4743.01
#> "01112" "03" "03" "0211" "0412" "0413"
#> TCGA.F5.6465.01 TCGA.D5.5537.01 TCGA.F4.6463.01 TCGA.A6.2686.11 TCGA.4T.AA8H.01 TCGA.A6.6782.01
#> "04222" "01112" "03" "0212" "01122" "03"
#> TCGA.AG.3592.01 TCGA.AD.6888.01 TCGA.CM.6678.01 TCGA.CM.5344.01 TCGA.AA.3495.11 TCGA.AG.A01W.11
#> "01112" "03" "011112" "04222" "0211" "0212"
#> TCGA.F4.6809.01 TCGA.CK.5914.01 TCGA.AZ.4681.01 TCGA.AA.3492.01 TCGA.D5.6536.01 TCGA.AA.3506.11
#> "03" "01113" "0432" "01221" "03" "0211"
#> TCGA.AA.3488.01 TCGA.AA.3502.11 TCGA.A6.6140.01 TCGA.D5.6529.01 TCGA.DM.A1D0.01 TCGA.DM.A1HB.01
#> "03" "023" "0421" "03" "04221" "01222"
#> TCGA.D5.6920.01 TCGA.D5.6922.01 TCGA.EI.6508.01 TCGA.D5.6532.01 TCGA.5M.AATA.01 TCGA.EI.6509.01
#> "03" "03" "01123" "01123" "03" "0421"
#> TCGA.G4.6311.01 TCGA.A6.A566.01 TCGA.G4.6625.01 TCGA.CI.6619.01 TCGA.F5.6864.01 TCGA.AA.3492.11
#> "03" "03" "03" "0423" "03" "0212"
#> TCGA.A6.5659.01 TCGA.WS.AB45.01 TCGA.G4.6315.01 TCGA.D5.6541.01 TCGA.A6.2680.01 TCGA.CM.4751.01
#> "01211" "0413" "03" "03" "01123" "03"
#> TCGA.CM.6680.01 TCGA.AF.6136.01 TCGA.AA.3660.01 TCGA.CM.4747.01 TCGA.EF.5831.01 TCGA.DM.A28G.01
#> "01122" "03" "01112" "01112" "01113" "01124"
#> TCGA.G4.6297.01 TCGA.A6.2682.11 TCGA.D5.6537.01 TCGA.CM.6170.01 TCGA.DY.A1DD.01
#> "03" "0211" "01121" "03" "01121"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 1543))
#> TCGA.AF.3911.01 TCGA.F4.6459.01 TCGA.AA.3494.11 TCGA.3L.AA1B.01 TCGA.D5.5538.01 TCGA.F4.6854.01
#> "03" "03" "023" "03" "03" "03"
#> TCGA.AG.A026.01 TCGA.G4.6303.01 TCGA.F5.6464.01 TCGA.T9.A92H.01 TCGA.AA.3712.11 TCGA.CM.5863.01
#> "011" "011112" "0412" "011111" "0211" "03"
#> TCGA.AZ.4308.01 TCGA.AD.6965.01 TCGA.A6.2681.11 TCGA.AD.6548.01 TCGA.A6.5660.01 TCGA.AZ.6600.01
#> "0421" "011" "0212" "03" "011" "03"
#> TCGA.F4.6808.01 TCGA.D5.6540.01 TCGA.F5.6571.01 TCGA.D5.6926.01 TCGA.CM.4748.01 TCGA.A6.2675.11
#> "03" "01222" "011112" "03" "03" "0211"
#> TCGA.5M.AATE.01 TCGA.D5.5541.01 TCGA.CM.5862.01 TCGA.AA.3511.01 TCGA.AA.3663.11 TCGA.CI.6622.01
#> "03" "0421" "011" "03" "0211" "011111"
#> TCGA.EI.6506.01 TCGA.AM.5821.01 TCGA.F5.6812.01 TCGA.G4.6588.01 TCGA.EI.6512.01 TCGA.A6.6648.01
#> "03" "03" "0414" "01221" "011" "0421"
#> TCGA.A6.2671.11 TCGA.NH.A6GC.01 TCGA.F4.6805.01 TCGA.AA.3697.01 TCGA.QG.A5YX.01 TCGA.DM.A28C.01
#> "0211" "03" "0412" "03" "011" "03"
#> TCGA.AG.A036.01 TCGA.AZ.6606.01 TCGA.F4.6570.01 TCGA.DC.4745.01 TCGA.AF.A56K.01 TCGA.G4.6627.01
#> "011" "01223" "01221" "03" "0423" "0412"
#> TCGA.A6.5657.01 TCGA.A6.5662.01 TCGA.AA.3509.01 TCGA.D5.6929.01 TCGA.CM.6679.01 TCGA.A6.2680.11
#> "03" "03" "011112" "04222" "03" "0212"
#> TCGA.DC.6157.01 TCGA.AF.6655.01 TCGA.CM.6161.01 TCGA.EI.6883.01 TCGA.F5.6811.01 TCGA.D5.6930.01
#> "0432" "0421" "03" "011" "03" "03"
#> TCGA.CM.6164.01 TCGA.AF.2687.01 TCGA.DY.A1H8.01 TCGA.G5.6641.01 TCGA.DC.6155.01 TCGA.RU.A8FL.01
#> "04222" "0423" "03" "03" "03" "011"
#> TCGA.CK.4951.01 TCGA.F4.6704.01 TCGA.AZ.6599.01 TCGA.F5.6861.01 TCGA.CM.5860.01 TCGA.A6.6780.01
#> "03" "0423" "011" "03" "011" "011"
#> TCGA.A6.2686.01 TCGA.CM.4750.01 TCGA.CM.6677.01 TCGA.A6.A567.01 TCGA.F5.6814.01 TCGA.D5.6898.01
#> "01212" "011" "011" "0433" "011" "03"
#> TCGA.AG.A01W.01 TCGA.AZ.6598.11 TCGA.F5.6813.01 TCGA.AG.3732.01 TCGA.EI.6885.01 TCGA.G4.6299.01
#> "03" "0212" "03" "04223" "0433" "01222"
#> TCGA.A6.4105.01 TCGA.DM.A1D8.01 TCGA.DM.A285.01 TCGA.G4.6295.11 TCGA.DC.4749.01 TCGA.DT.5265.01
#> "01223" "011" "03" "023" "0421" "01223"
#> TCGA.5M.AAT5.01 TCGA.DM.A0XD.01 TCGA.A6.6138.01 TCGA.D5.7000.01 TCGA.DM.A28F.01 TCGA.DY.A1DE.01
#> "0432" "01211" "011" "01211" "011" "03"
#> TCGA.A6.6142.01 TCGA.QL.A97D.01 TCGA.CK.6748.01 TCGA.DC.6160.01 TCGA.D5.6534.01 TCGA.AZ.4616.01
#> "022" "03" "03" "0421" "0413" "03"
#> TCGA.CK.6751.01 TCGA.CM.6171.01 TCGA.DM.A1DA.01 TCGA.AG.A020.11 TCGA.G4.6311.11 TCGA.G4.6625.11
#> "01211" "01221" "01211" "0212" "0211" "0212"
#> TCGA.F5.6863.01 TCGA.G4.6317.02 TCGA.G4.6317.01 TCGA.DM.A1D4.01 TCGA.AG.A01Y.11 TCGA.D5.6530.01
#> "04221" "0432" "03" "011" "0212" "03"
#> TCGA.CK.4948.01 TCGA.AD.A5EJ.01 TCGA.A6.6651.01 TCGA.CA.5256.01 TCGA.DM.A0X9.01 TCGA.AY.A69D.01
#> "0431" "01221" "0412" "03" "011" "011"
#> TCGA.G4.6626.01 TCGA.CA.6716.01 TCGA.A6.2682.01 TCGA.A6.4107.11 TCGA.CA.6717.01 TCGA.G4.6293.01
#> "03" "011" "03" "023" "03" "03"
#> TCGA.CK.5916.01 TCGA.G4.6309.01 TCGA.AA.3662.01 TCGA.AF.A56L.01 TCGA.NH.A6GB.01 TCGA.AD.5900.01
#> "01221" "04223" "03" "03" "011" "03"
#> TCGA.NH.A50U.01 TCGA.AA.3712.01 TCGA.AZ.4614.01 TCGA.AH.6644.01 TCGA.AZ.6607.01 TCGA.AF.2693.01
#> "011" "03" "01211" "011111" "03" "0411"
#> TCGA.D5.6924.01 TCGA.CM.5868.01 TCGA.AF.4110.01 TCGA.A6.3809.01 TCGA.AZ.4313.01 TCGA.A6.2675.01
#> "03" "04222" "0411" "01212" "04223" "0421"
#> TCGA.AZ.6608.01 TCGA.CM.5864.01 TCGA.AA.3494.01 TCGA.AD.6895.01 TCGA.CI.6620.01 TCGA.DC.6156.01
#> "03" "011" "0432" "03" "03" "03"
#> TCGA.D5.6931.01 TCGA.CM.6165.01 TCGA.CM.5861.01 TCGA.A6.2671.01 TCGA.DC.6158.01 TCGA.AG.3742.01
#> "03" "03" "01221" "03" "03" "011"
#> TCGA.AG.A02N.11 TCGA.G4.6307.01 TCGA.A6.5666.01 TCGA.EI.6511.01 TCGA.CI.6624.01 TCGA.AG.3591.01
#> "0211" "0432" "011" "03" "04222" "011"
#> TCGA.AY.A8YK.01 TCGA.F4.6856.01 TCGA.DM.A1D7.01 TCGA.A6.2685.01 TCGA.5M.AAT6.01 TCGA.AH.6643.01
#> "022" "03" "03" "022" "022" "011111"
#> TCGA.F4.6569.01 TCGA.G4.6298.01 TCGA.AY.6196.01 TCGA.EI.6510.01 TCGA.A6.5656.01 TCGA.A6.2684.11
#> "03" "03" "03" "011" "011111" "0212"
#> TCGA.DY.A1DG.01 TCGA.AZ.4682.01 TCGA.EI.6884.01 TCGA.F4.6806.01 TCGA.G4.6320.11 TCGA.G4.6322.01
#> "011" "03" "03" "011" "0211" "01213"
#> TCGA.F5.6810.01 TCGA.5M.AAT4.01 TCGA.CL.4957.01 TCGA.DC.6681.01 TCGA.CM.6167.01 TCGA.AG.4022.01
#> "0431" "011" "03" "03" "0412" "03"
#> TCGA.G4.6586.01 TCGA.EI.6514.01 TCGA.CK.4950.01 TCGA.DM.A282.01 TCGA.DY.A1DC.01 TCGA.D5.6535.01
#> "01221" "011112" "03" "011112" "03" "03"
#> TCGA.DM.A1HA.01 TCGA.DC.5869.01 TCGA.AZ.6599.11 TCGA.CM.4752.01 TCGA.AZ.4684.01 TCGA.EI.7004.01
#> "011" "03" "0211" "0423" "03" "03"
#> TCGA.A6.A565.01 TCGA.D5.6531.01 TCGA.AZ.6598.01 TCGA.AD.6890.01 TCGA.AG.4021.01 TCGA.A6.6781.01
#> "023" "01211" "01222" "03" "011" "0412"
#> TCGA.DM.A1D9.01 TCGA.CM.4744.01 TCGA.A6.2679.11 TCGA.A6.6652.01 TCGA.AD.6964.01 TCGA.SS.A7HO.01
#> "011" "011" "023" "011111" "022" "011"
#> TCGA.A6.6650.01 TCGA.DM.A0XF.01 TCGA.G4.6295.01 TCGA.F4.6461.01 TCGA.AM.5820.01 TCGA.G4.6314.11
#> "011112" "04222" "0431" "01221" "03" "0212"
#> TCGA.AD.6889.01 TCGA.AZ.6605.01 TCGA.EI.6881.01 TCGA.NH.A50T.01 TCGA.AG.3725.11 TCGA.G4.6323.01
#> "01222" "0414" "03" "011" "0212" "03"
#> TCGA.AA.3663.01 TCGA.AD.6899.01 TCGA.A6.5667.11 TCGA.A6.A56B.01 TCGA.G5.6572.01 TCGA.DM.A280.01
#> "01222" "011" "0212" "011" "0411" "0413"
#> TCGA.AG.A020.01 TCGA.AA.3713.01 TCGA.D5.5539.01 TCGA.AA.3655.11 TCGA.AA.3489.01 TCGA.AA.3495.01
#> "03" "03" "011" "0211" "0412" "03"
#> TCGA.AG.A01Y.01 TCGA.AZ.6601.01 TCGA.AH.6903.01 TCGA.AZ.6603.01 TCGA.CA.5254.01 TCGA.A6.A5ZU.01
#> "0433" "03" "03" "0432" "01224" "03"
#> TCGA.G4.6302.01 TCGA.AZ.5403.01 TCGA.AY.A54L.01 TCGA.A6.4107.01 TCGA.NH.A5IV.01 TCGA.G4.6306.01
#> "0413" "022" "011" "01224" "011" "011"
#> TCGA.AD.A5EK.01 TCGA.G5.6235.01 TCGA.DC.5337.01 TCGA.CM.6675.01 TCGA.AH.6544.01 TCGA.CK.6746.01
#> "011" "0411" "011" "01211" "03" "01212"
#> TCGA.CA.6718.01 TCGA.CI.6621.01 TCGA.CM.6676.01 TCGA.DM.A1DB.01 TCGA.A6.6654.01 TCGA.AA.3510.11
#> "03" "0411" "03" "03" "03" "023"
#> TCGA.CA.6715.01 TCGA.CM.5341.01 TCGA.CK.5912.01 TCGA.F4.6857.01 TCGA.QG.A5YW.01 TCGA.A6.5665.01
#> "03" "03" "03" "0413" "011" "01221"
#> TCGA.CM.6168.01 TCGA.CL.5917.01 TCGA.AU.6004.01 TCGA.AY.5543.01 TCGA.AG.3731.01 TCGA.G4.6314.01
#> "03" "03" "03" "03" "03" "03"
#> TCGA.DC.6683.01 TCGA.CA.5796.01 TCGA.AG.A036.11 TCGA.AZ.4323.01 TCGA.EI.6882.01 TCGA.AZ.4315.01
#> "03" "03" "0211" "0413" "011" "03"
#> TCGA.A6.2677.01 TCGA.DY.A1DF.01 TCGA.CM.6162.01 TCGA.F4.6703.01 TCGA.CM.5349.01 TCGA.AG.A02N.01
#> "011" "03" "022" "022" "03" "03"
#> TCGA.AA.3506.01 TCGA.D5.6932.01 TCGA.D5.6538.01 TCGA.AA.3488.11 TCGA.AA.3502.01 TCGA.NH.A8F8.01
#> "03" "03" "01211" "0211" "011" "03"
#> TCGA.AF.A56N.01 TCGA.AF.6672.01 TCGA.A6.2685.11 TCGA.A6.6141.01 TCGA.AD.6963.01 TCGA.G4.6298.11
#> "03" "0433" "0212" "03" "0423" "0211"
#> TCGA.EI.6917.01 TCGA.QG.A5Z2.01 TCGA.A6.2684.01 TCGA.CK.5915.01 TCGA.CM.6163.01 TCGA.G4.6322.11
#> "03" "01222" "03" "011" "03" "0211"
#> TCGA.AY.6197.01 TCGA.D5.6928.01 TCGA.A6.3810.01 TCGA.G4.6294.01 TCGA.AA.3660.11 TCGA.A6.6137.01
#> "011" "0413" "0421" "011111" "0212" "03"
#> TCGA.G4.6297.11 TCGA.AZ.4615.01 TCGA.CK.4952.01 TCGA.CM.6172.01 TCGA.AD.6901.01 TCGA.AA.3496.01
#> "0212" "03" "01213" "011" "03" "011"
#> TCGA.CK.5913.01 TCGA.DM.A28A.01 TCGA.EI.7002.01 TCGA.D5.6533.01 TCGA.QG.A5Z1.01 TCGA.D5.6923.01
#> "01212" "011" "011111" "03" "011" "0411"
#> TCGA.AF.2690.01 TCGA.DM.A28H.01 TCGA.G4.6320.01 TCGA.G4.6310.01 TCGA.DM.A28M.01 TCGA.DM.A288.01
#> "0414" "011" "01211" "03" "011" "011"
#> TCGA.A6.2681.01 TCGA.A6.2679.01 TCGA.4N.A93T.01 TCGA.NH.A8F7.06 TCGA.NH.A8F7.01 TCGA.AZ.6600.11
#> "03" "03" "03" "03" "0432" "0211"
#> TCGA.G5.6572.02 TCGA.AY.6386.01 TCGA.G4.6628.01 TCGA.A6.6653.01 TCGA.CM.4746.01 TCGA.F4.6855.01
#> "0414" "03" "03" "01222" "03" "011112"
#> TCGA.EF.5830.01 TCGA.NH.A6GA.01 TCGA.NH.A50V.01 TCGA.DY.A0XA.01 TCGA.DM.A28E.01 TCGA.AG.3725.01
#> "03" "011" "011" "04221" "04221" "03"
#> TCGA.CK.6747.01 TCGA.CL.5918.01 TCGA.CI.6623.01 TCGA.A6.5667.01 TCGA.DM.A28K.01 TCGA.AA.3713.11
#> "011" "011" "0421" "03" "011" "023"
#> TCGA.AA.3655.01 TCGA.AU.3779.01 TCGA.A6.5664.01 TCGA.AA.3697.11 TCGA.AZ.5407.01 TCGA.CM.6169.01
#> "011111" "04221" "03" "023" "011" "03"
#> TCGA.AH.6547.01 TCGA.AZ.6601.11 TCGA.A6.5661.01 TCGA.F4.6807.01 TCGA.QG.A5YV.01 TCGA.AA.3509.11
#> "0412" "0211" "01221" "03" "011112" "0212"
#> TCGA.AY.A71X.01 TCGA.CA.5797.01 TCGA.F4.6460.01 TCGA.G4.6302.11 TCGA.F5.6702.01 TCGA.AH.6549.01
#> "011" "0431" "04221" "023" "0423" "011"
#> TCGA.D5.6927.01 TCGA.CM.6166.01 TCGA.AH.6897.01 TCGA.G4.6304.01 TCGA.CA.5255.01 TCGA.EI.6507.01
#> "0412" "011112" "011" "0413" "03" "03"
#> TCGA.CK.4947.01 TCGA.D5.5540.01 TCGA.DC.6682.01 TCGA.G4.6321.01 TCGA.A6.6649.01 TCGA.CM.5348.01
#> "03" "011" "03" "03" "03" "03"
#> TCGA.EI.6513.01 TCGA.A6.2672.01 TCGA.D5.6539.01 TCGA.AA.3510.01 TCGA.G5.6233.01 TCGA.BM.6198.01
#> "0431" "01221" "0411" "03" "011" "0414"
#> TCGA.CA.6719.01 TCGA.DC.6154.01 TCGA.DM.A1D6.01 TCGA.AG.3731.11 TCGA.CM.6674.01 TCGA.CM.4743.01
#> "011" "03" "03" "0211" "0412" "0413"
#> TCGA.F5.6465.01 TCGA.D5.5537.01 TCGA.F4.6463.01 TCGA.A6.2686.11 TCGA.4T.AA8H.01 TCGA.A6.6782.01
#> "04222" "011" "03" "0212" "011" "03"
#> TCGA.AG.3592.01 TCGA.AD.6888.01 TCGA.CM.6678.01 TCGA.CM.5344.01 TCGA.AA.3495.11 TCGA.AG.A01W.11
#> "011" "03" "011112" "04222" "0211" "0212"
#> TCGA.F4.6809.01 TCGA.CK.5914.01 TCGA.AZ.4681.01 TCGA.AA.3492.01 TCGA.D5.6536.01 TCGA.AA.3506.11
#> "03" "011" "0432" "01221" "03" "0211"
#> TCGA.AA.3488.01 TCGA.AA.3502.11 TCGA.A6.6140.01 TCGA.D5.6529.01 TCGA.DM.A1D0.01 TCGA.DM.A1HB.01
#> "03" "023" "0421" "03" "04221" "01222"
#> TCGA.D5.6920.01 TCGA.D5.6922.01 TCGA.EI.6508.01 TCGA.D5.6532.01 TCGA.5M.AATA.01 TCGA.EI.6509.01
#> "03" "03" "011" "011" "03" "0421"
#> TCGA.G4.6311.01 TCGA.A6.A566.01 TCGA.G4.6625.01 TCGA.CI.6619.01 TCGA.F5.6864.01 TCGA.AA.3492.11
#> "03" "03" "03" "0423" "03" "0212"
#> TCGA.A6.5659.01 TCGA.WS.AB45.01 TCGA.G4.6315.01 TCGA.D5.6541.01 TCGA.A6.2680.01 TCGA.CM.4751.01
#> "01211" "0413" "03" "03" "011" "03"
#> TCGA.CM.6680.01 TCGA.AF.6136.01 TCGA.AA.3660.01 TCGA.CM.4747.01 TCGA.EF.5831.01 TCGA.DM.A28G.01
#> "011" "03" "011" "011" "011" "011"
#> TCGA.G4.6297.01 TCGA.A6.2682.11 TCGA.D5.6537.01 TCGA.CM.6170.01 TCGA.DY.A1DD.01
#> "03" "0211" "011" "03" "011"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 3038))
#> TCGA.AF.3911.01 TCGA.F4.6459.01 TCGA.AA.3494.11 TCGA.3L.AA1B.01 TCGA.D5.5538.01 TCGA.F4.6854.01
#> "03" "03" "023" "03" "03" "03"
#> TCGA.AG.A026.01 TCGA.G4.6303.01 TCGA.F5.6464.01 TCGA.T9.A92H.01 TCGA.AA.3712.11 TCGA.CM.5863.01
#> "011" "011112" "0412" "011111" "0211" "03"
#> TCGA.AZ.4308.01 TCGA.AD.6965.01 TCGA.A6.2681.11 TCGA.AD.6548.01 TCGA.A6.5660.01 TCGA.AZ.6600.01
#> "0421" "011" "0212" "03" "011" "03"
#> TCGA.F4.6808.01 TCGA.D5.6540.01 TCGA.F5.6571.01 TCGA.D5.6926.01 TCGA.CM.4748.01 TCGA.A6.2675.11
#> "03" "01222" "011112" "03" "03" "0211"
#> TCGA.5M.AATE.01 TCGA.D5.5541.01 TCGA.CM.5862.01 TCGA.AA.3511.01 TCGA.AA.3663.11 TCGA.CI.6622.01
#> "03" "0421" "011" "03" "0211" "011111"
#> TCGA.EI.6506.01 TCGA.AM.5821.01 TCGA.F5.6812.01 TCGA.G4.6588.01 TCGA.EI.6512.01 TCGA.A6.6648.01
#> "03" "03" "0414" "01221" "011" "0421"
#> TCGA.A6.2671.11 TCGA.NH.A6GC.01 TCGA.F4.6805.01 TCGA.AA.3697.01 TCGA.QG.A5YX.01 TCGA.DM.A28C.01
#> "0211" "03" "0412" "03" "011" "03"
#> TCGA.AG.A036.01 TCGA.AZ.6606.01 TCGA.F4.6570.01 TCGA.DC.4745.01 TCGA.AF.A56K.01 TCGA.G4.6627.01
#> "011" "01223" "01221" "03" "0423" "0412"
#> TCGA.A6.5657.01 TCGA.A6.5662.01 TCGA.AA.3509.01 TCGA.D5.6929.01 TCGA.CM.6679.01 TCGA.A6.2680.11
#> "03" "03" "011112" "04222" "03" "0212"
#> TCGA.DC.6157.01 TCGA.AF.6655.01 TCGA.CM.6161.01 TCGA.EI.6883.01 TCGA.F5.6811.01 TCGA.D5.6930.01
#> "0432" "0421" "03" "011" "03" "03"
#> TCGA.CM.6164.01 TCGA.AF.2687.01 TCGA.DY.A1H8.01 TCGA.G5.6641.01 TCGA.DC.6155.01 TCGA.RU.A8FL.01
#> "04222" "0423" "03" "03" "03" "011"
#> TCGA.CK.4951.01 TCGA.F4.6704.01 TCGA.AZ.6599.01 TCGA.F5.6861.01 TCGA.CM.5860.01 TCGA.A6.6780.01
#> "03" "0423" "011" "03" "011" "011"
#> TCGA.A6.2686.01 TCGA.CM.4750.01 TCGA.CM.6677.01 TCGA.A6.A567.01 TCGA.F5.6814.01 TCGA.D5.6898.01
#> "0121" "011" "011" "0433" "011" "03"
#> TCGA.AG.A01W.01 TCGA.AZ.6598.11 TCGA.F5.6813.01 TCGA.AG.3732.01 TCGA.EI.6885.01 TCGA.G4.6299.01
#> "03" "0212" "03" "04223" "0433" "01222"
#> TCGA.A6.4105.01 TCGA.DM.A1D8.01 TCGA.DM.A285.01 TCGA.G4.6295.11 TCGA.DC.4749.01 TCGA.DT.5265.01
#> "01223" "011" "03" "023" "0421" "01223"
#> TCGA.5M.AAT5.01 TCGA.DM.A0XD.01 TCGA.A6.6138.01 TCGA.D5.7000.01 TCGA.DM.A28F.01 TCGA.DY.A1DE.01
#> "0432" "0121" "011" "0121" "011" "03"
#> TCGA.A6.6142.01 TCGA.QL.A97D.01 TCGA.CK.6748.01 TCGA.DC.6160.01 TCGA.D5.6534.01 TCGA.AZ.4616.01
#> "022" "03" "03" "0421" "0413" "03"
#> TCGA.CK.6751.01 TCGA.CM.6171.01 TCGA.DM.A1DA.01 TCGA.AG.A020.11 TCGA.G4.6311.11 TCGA.G4.6625.11
#> "0121" "01221" "0121" "0212" "0211" "0212"
#> TCGA.F5.6863.01 TCGA.G4.6317.02 TCGA.G4.6317.01 TCGA.DM.A1D4.01 TCGA.AG.A01Y.11 TCGA.D5.6530.01
#> "04221" "0432" "03" "011" "0212" "03"
#> TCGA.CK.4948.01 TCGA.AD.A5EJ.01 TCGA.A6.6651.01 TCGA.CA.5256.01 TCGA.DM.A0X9.01 TCGA.AY.A69D.01
#> "0431" "01221" "0412" "03" "011" "011"
#> TCGA.G4.6626.01 TCGA.CA.6716.01 TCGA.A6.2682.01 TCGA.A6.4107.11 TCGA.CA.6717.01 TCGA.G4.6293.01
#> "03" "011" "03" "023" "03" "03"
#> TCGA.CK.5916.01 TCGA.G4.6309.01 TCGA.AA.3662.01 TCGA.AF.A56L.01 TCGA.NH.A6GB.01 TCGA.AD.5900.01
#> "01221" "04223" "03" "03" "011" "03"
#> TCGA.NH.A50U.01 TCGA.AA.3712.01 TCGA.AZ.4614.01 TCGA.AH.6644.01 TCGA.AZ.6607.01 TCGA.AF.2693.01
#> "011" "03" "0121" "011111" "03" "0411"
#> TCGA.D5.6924.01 TCGA.CM.5868.01 TCGA.AF.4110.01 TCGA.A6.3809.01 TCGA.AZ.4313.01 TCGA.A6.2675.01
#> "03" "04222" "0411" "0121" "04223" "0421"
#> TCGA.AZ.6608.01 TCGA.CM.5864.01 TCGA.AA.3494.01 TCGA.AD.6895.01 TCGA.CI.6620.01 TCGA.DC.6156.01
#> "03" "011" "0432" "03" "03" "03"
#> TCGA.D5.6931.01 TCGA.CM.6165.01 TCGA.CM.5861.01 TCGA.A6.2671.01 TCGA.DC.6158.01 TCGA.AG.3742.01
#> "03" "03" "01221" "03" "03" "011"
#> TCGA.AG.A02N.11 TCGA.G4.6307.01 TCGA.A6.5666.01 TCGA.EI.6511.01 TCGA.CI.6624.01 TCGA.AG.3591.01
#> "0211" "0432" "011" "03" "04222" "011"
#> TCGA.AY.A8YK.01 TCGA.F4.6856.01 TCGA.DM.A1D7.01 TCGA.A6.2685.01 TCGA.5M.AAT6.01 TCGA.AH.6643.01
#> "022" "03" "03" "022" "022" "011111"
#> TCGA.F4.6569.01 TCGA.G4.6298.01 TCGA.AY.6196.01 TCGA.EI.6510.01 TCGA.A6.5656.01 TCGA.A6.2684.11
#> "03" "03" "03" "011" "011111" "0212"
#> TCGA.DY.A1DG.01 TCGA.AZ.4682.01 TCGA.EI.6884.01 TCGA.F4.6806.01 TCGA.G4.6320.11 TCGA.G4.6322.01
#> "011" "03" "03" "011" "0211" "0121"
#> TCGA.F5.6810.01 TCGA.5M.AAT4.01 TCGA.CL.4957.01 TCGA.DC.6681.01 TCGA.CM.6167.01 TCGA.AG.4022.01
#> "0431" "011" "03" "03" "0412" "03"
#> TCGA.G4.6586.01 TCGA.EI.6514.01 TCGA.CK.4950.01 TCGA.DM.A282.01 TCGA.DY.A1DC.01 TCGA.D5.6535.01
#> "01221" "011112" "03" "011112" "03" "03"
#> TCGA.DM.A1HA.01 TCGA.DC.5869.01 TCGA.AZ.6599.11 TCGA.CM.4752.01 TCGA.AZ.4684.01 TCGA.EI.7004.01
#> "011" "03" "0211" "0423" "03" "03"
#> TCGA.A6.A565.01 TCGA.D5.6531.01 TCGA.AZ.6598.01 TCGA.AD.6890.01 TCGA.AG.4021.01 TCGA.A6.6781.01
#> "023" "0121" "01222" "03" "011" "0412"
#> TCGA.DM.A1D9.01 TCGA.CM.4744.01 TCGA.A6.2679.11 TCGA.A6.6652.01 TCGA.AD.6964.01 TCGA.SS.A7HO.01
#> "011" "011" "023" "011111" "022" "011"
#> TCGA.A6.6650.01 TCGA.DM.A0XF.01 TCGA.G4.6295.01 TCGA.F4.6461.01 TCGA.AM.5820.01 TCGA.G4.6314.11
#> "011112" "04222" "0431" "01221" "03" "0212"
#> TCGA.AD.6889.01 TCGA.AZ.6605.01 TCGA.EI.6881.01 TCGA.NH.A50T.01 TCGA.AG.3725.11 TCGA.G4.6323.01
#> "01222" "0414" "03" "011" "0212" "03"
#> TCGA.AA.3663.01 TCGA.AD.6899.01 TCGA.A6.5667.11 TCGA.A6.A56B.01 TCGA.G5.6572.01 TCGA.DM.A280.01
#> "01222" "011" "0212" "011" "0411" "0413"
#> TCGA.AG.A020.01 TCGA.AA.3713.01 TCGA.D5.5539.01 TCGA.AA.3655.11 TCGA.AA.3489.01 TCGA.AA.3495.01
#> "03" "03" "011" "0211" "0412" "03"
#> TCGA.AG.A01Y.01 TCGA.AZ.6601.01 TCGA.AH.6903.01 TCGA.AZ.6603.01 TCGA.CA.5254.01 TCGA.A6.A5ZU.01
#> "0433" "03" "03" "0432" "01224" "03"
#> TCGA.G4.6302.01 TCGA.AZ.5403.01 TCGA.AY.A54L.01 TCGA.A6.4107.01 TCGA.NH.A5IV.01 TCGA.G4.6306.01
#> "0413" "022" "011" "01224" "011" "011"
#> TCGA.AD.A5EK.01 TCGA.G5.6235.01 TCGA.DC.5337.01 TCGA.CM.6675.01 TCGA.AH.6544.01 TCGA.CK.6746.01
#> "011" "0411" "011" "0121" "03" "0121"
#> TCGA.CA.6718.01 TCGA.CI.6621.01 TCGA.CM.6676.01 TCGA.DM.A1DB.01 TCGA.A6.6654.01 TCGA.AA.3510.11
#> "03" "0411" "03" "03" "03" "023"
#> TCGA.CA.6715.01 TCGA.CM.5341.01 TCGA.CK.5912.01 TCGA.F4.6857.01 TCGA.QG.A5YW.01 TCGA.A6.5665.01
#> "03" "03" "03" "0413" "011" "01221"
#> TCGA.CM.6168.01 TCGA.CL.5917.01 TCGA.AU.6004.01 TCGA.AY.5543.01 TCGA.AG.3731.01 TCGA.G4.6314.01
#> "03" "03" "03" "03" "03" "03"
#> TCGA.DC.6683.01 TCGA.CA.5796.01 TCGA.AG.A036.11 TCGA.AZ.4323.01 TCGA.EI.6882.01 TCGA.AZ.4315.01
#> "03" "03" "0211" "0413" "011" "03"
#> TCGA.A6.2677.01 TCGA.DY.A1DF.01 TCGA.CM.6162.01 TCGA.F4.6703.01 TCGA.CM.5349.01 TCGA.AG.A02N.01
#> "011" "03" "022" "022" "03" "03"
#> TCGA.AA.3506.01 TCGA.D5.6932.01 TCGA.D5.6538.01 TCGA.AA.3488.11 TCGA.AA.3502.01 TCGA.NH.A8F8.01
#> "03" "03" "0121" "0211" "011" "03"
#> TCGA.AF.A56N.01 TCGA.AF.6672.01 TCGA.A6.2685.11 TCGA.A6.6141.01 TCGA.AD.6963.01 TCGA.G4.6298.11
#> "03" "0433" "0212" "03" "0423" "0211"
#> TCGA.EI.6917.01 TCGA.QG.A5Z2.01 TCGA.A6.2684.01 TCGA.CK.5915.01 TCGA.CM.6163.01 TCGA.G4.6322.11
#> "03" "01222" "03" "011" "03" "0211"
#> TCGA.AY.6197.01 TCGA.D5.6928.01 TCGA.A6.3810.01 TCGA.G4.6294.01 TCGA.AA.3660.11 TCGA.A6.6137.01
#> "011" "0413" "0421" "011111" "0212" "03"
#> TCGA.G4.6297.11 TCGA.AZ.4615.01 TCGA.CK.4952.01 TCGA.CM.6172.01 TCGA.AD.6901.01 TCGA.AA.3496.01
#> "0212" "03" "0121" "011" "03" "011"
#> TCGA.CK.5913.01 TCGA.DM.A28A.01 TCGA.EI.7002.01 TCGA.D5.6533.01 TCGA.QG.A5Z1.01 TCGA.D5.6923.01
#> "0121" "011" "011111" "03" "011" "0411"
#> TCGA.AF.2690.01 TCGA.DM.A28H.01 TCGA.G4.6320.01 TCGA.G4.6310.01 TCGA.DM.A28M.01 TCGA.DM.A288.01
#> "0414" "011" "0121" "03" "011" "011"
#> TCGA.A6.2681.01 TCGA.A6.2679.01 TCGA.4N.A93T.01 TCGA.NH.A8F7.06 TCGA.NH.A8F7.01 TCGA.AZ.6600.11
#> "03" "03" "03" "03" "0432" "0211"
#> TCGA.G5.6572.02 TCGA.AY.6386.01 TCGA.G4.6628.01 TCGA.A6.6653.01 TCGA.CM.4746.01 TCGA.F4.6855.01
#> "0414" "03" "03" "01222" "03" "011112"
#> TCGA.EF.5830.01 TCGA.NH.A6GA.01 TCGA.NH.A50V.01 TCGA.DY.A0XA.01 TCGA.DM.A28E.01 TCGA.AG.3725.01
#> "03" "011" "011" "04221" "04221" "03"
#> TCGA.CK.6747.01 TCGA.CL.5918.01 TCGA.CI.6623.01 TCGA.A6.5667.01 TCGA.DM.A28K.01 TCGA.AA.3713.11
#> "011" "011" "0421" "03" "011" "023"
#> TCGA.AA.3655.01 TCGA.AU.3779.01 TCGA.A6.5664.01 TCGA.AA.3697.11 TCGA.AZ.5407.01 TCGA.CM.6169.01
#> "011111" "04221" "03" "023" "011" "03"
#> TCGA.AH.6547.01 TCGA.AZ.6601.11 TCGA.A6.5661.01 TCGA.F4.6807.01 TCGA.QG.A5YV.01 TCGA.AA.3509.11
#> "0412" "0211" "01221" "03" "011112" "0212"
#> TCGA.AY.A71X.01 TCGA.CA.5797.01 TCGA.F4.6460.01 TCGA.G4.6302.11 TCGA.F5.6702.01 TCGA.AH.6549.01
#> "011" "0431" "04221" "023" "0423" "011"
#> TCGA.D5.6927.01 TCGA.CM.6166.01 TCGA.AH.6897.01 TCGA.G4.6304.01 TCGA.CA.5255.01 TCGA.EI.6507.01
#> "0412" "011112" "011" "0413" "03" "03"
#> TCGA.CK.4947.01 TCGA.D5.5540.01 TCGA.DC.6682.01 TCGA.G4.6321.01 TCGA.A6.6649.01 TCGA.CM.5348.01
#> "03" "011" "03" "03" "03" "03"
#> TCGA.EI.6513.01 TCGA.A6.2672.01 TCGA.D5.6539.01 TCGA.AA.3510.01 TCGA.G5.6233.01 TCGA.BM.6198.01
#> "0431" "01221" "0411" "03" "011" "0414"
#> TCGA.CA.6719.01 TCGA.DC.6154.01 TCGA.DM.A1D6.01 TCGA.AG.3731.11 TCGA.CM.6674.01 TCGA.CM.4743.01
#> "011" "03" "03" "0211" "0412" "0413"
#> TCGA.F5.6465.01 TCGA.D5.5537.01 TCGA.F4.6463.01 TCGA.A6.2686.11 TCGA.4T.AA8H.01 TCGA.A6.6782.01
#> "04222" "011" "03" "0212" "011" "03"
#> TCGA.AG.3592.01 TCGA.AD.6888.01 TCGA.CM.6678.01 TCGA.CM.5344.01 TCGA.AA.3495.11 TCGA.AG.A01W.11
#> "011" "03" "011112" "04222" "0211" "0212"
#> TCGA.F4.6809.01 TCGA.CK.5914.01 TCGA.AZ.4681.01 TCGA.AA.3492.01 TCGA.D5.6536.01 TCGA.AA.3506.11
#> "03" "011" "0432" "01221" "03" "0211"
#> TCGA.AA.3488.01 TCGA.AA.3502.11 TCGA.A6.6140.01 TCGA.D5.6529.01 TCGA.DM.A1D0.01 TCGA.DM.A1HB.01
#> "03" "023" "0421" "03" "04221" "01222"
#> TCGA.D5.6920.01 TCGA.D5.6922.01 TCGA.EI.6508.01 TCGA.D5.6532.01 TCGA.5M.AATA.01 TCGA.EI.6509.01
#> "03" "03" "011" "011" "03" "0421"
#> TCGA.G4.6311.01 TCGA.A6.A566.01 TCGA.G4.6625.01 TCGA.CI.6619.01 TCGA.F5.6864.01 TCGA.AA.3492.11
#> "03" "03" "03" "0423" "03" "0212"
#> TCGA.A6.5659.01 TCGA.WS.AB45.01 TCGA.G4.6315.01 TCGA.D5.6541.01 TCGA.A6.2680.01 TCGA.CM.4751.01
#> "0121" "0413" "03" "03" "011" "03"
#> TCGA.CM.6680.01 TCGA.AF.6136.01 TCGA.AA.3660.01 TCGA.CM.4747.01 TCGA.EF.5831.01 TCGA.DM.A28G.01
#> "011" "03" "011" "011" "011" "011"
#> TCGA.G4.6297.01 TCGA.A6.2682.11 TCGA.D5.6537.01 TCGA.CM.6170.01 TCGA.DY.A1DD.01
#> "03" "0211" "011" "03" "011"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 3867))
#> TCGA.AF.3911.01 TCGA.F4.6459.01 TCGA.AA.3494.11 TCGA.3L.AA1B.01 TCGA.D5.5538.01 TCGA.F4.6854.01
#> "03" "03" "023" "03" "03" "03"
#> TCGA.AG.A026.01 TCGA.G4.6303.01 TCGA.F5.6464.01 TCGA.T9.A92H.01 TCGA.AA.3712.11 TCGA.CM.5863.01
#> "011" "011" "0412" "011" "0211" "03"
#> TCGA.AZ.4308.01 TCGA.AD.6965.01 TCGA.A6.2681.11 TCGA.AD.6548.01 TCGA.A6.5660.01 TCGA.AZ.6600.01
#> "0421" "011" "0212" "03" "011" "03"
#> TCGA.F4.6808.01 TCGA.D5.6540.01 TCGA.F5.6571.01 TCGA.D5.6926.01 TCGA.CM.4748.01 TCGA.A6.2675.11
#> "03" "01222" "011" "03" "03" "0211"
#> TCGA.5M.AATE.01 TCGA.D5.5541.01 TCGA.CM.5862.01 TCGA.AA.3511.01 TCGA.AA.3663.11 TCGA.CI.6622.01
#> "03" "0421" "011" "03" "0211" "011"
#> TCGA.EI.6506.01 TCGA.AM.5821.01 TCGA.F5.6812.01 TCGA.G4.6588.01 TCGA.EI.6512.01 TCGA.A6.6648.01
#> "03" "03" "0414" "01221" "011" "0421"
#> TCGA.A6.2671.11 TCGA.NH.A6GC.01 TCGA.F4.6805.01 TCGA.AA.3697.01 TCGA.QG.A5YX.01 TCGA.DM.A28C.01
#> "0211" "03" "0412" "03" "011" "03"
#> TCGA.AG.A036.01 TCGA.AZ.6606.01 TCGA.F4.6570.01 TCGA.DC.4745.01 TCGA.AF.A56K.01 TCGA.G4.6627.01
#> "011" "01223" "01221" "03" "0423" "0412"
#> TCGA.A6.5657.01 TCGA.A6.5662.01 TCGA.AA.3509.01 TCGA.D5.6929.01 TCGA.CM.6679.01 TCGA.A6.2680.11
#> "03" "03" "011" "04222" "03" "0212"
#> TCGA.DC.6157.01 TCGA.AF.6655.01 TCGA.CM.6161.01 TCGA.EI.6883.01 TCGA.F5.6811.01 TCGA.D5.6930.01
#> "0432" "0421" "03" "011" "03" "03"
#> TCGA.CM.6164.01 TCGA.AF.2687.01 TCGA.DY.A1H8.01 TCGA.G5.6641.01 TCGA.DC.6155.01 TCGA.RU.A8FL.01
#> "04222" "0423" "03" "03" "03" "011"
#> TCGA.CK.4951.01 TCGA.F4.6704.01 TCGA.AZ.6599.01 TCGA.F5.6861.01 TCGA.CM.5860.01 TCGA.A6.6780.01
#> "03" "0423" "011" "03" "011" "011"
#> TCGA.A6.2686.01 TCGA.CM.4750.01 TCGA.CM.6677.01 TCGA.A6.A567.01 TCGA.F5.6814.01 TCGA.D5.6898.01
#> "0121" "011" "011" "0433" "011" "03"
#> TCGA.AG.A01W.01 TCGA.AZ.6598.11 TCGA.F5.6813.01 TCGA.AG.3732.01 TCGA.EI.6885.01 TCGA.G4.6299.01
#> "03" "0212" "03" "04223" "0433" "01222"
#> TCGA.A6.4105.01 TCGA.DM.A1D8.01 TCGA.DM.A285.01 TCGA.G4.6295.11 TCGA.DC.4749.01 TCGA.DT.5265.01
#> "01223" "011" "03" "023" "0421" "01223"
#> TCGA.5M.AAT5.01 TCGA.DM.A0XD.01 TCGA.A6.6138.01 TCGA.D5.7000.01 TCGA.DM.A28F.01 TCGA.DY.A1DE.01
#> "0432" "0121" "011" "0121" "011" "03"
#> TCGA.A6.6142.01 TCGA.QL.A97D.01 TCGA.CK.6748.01 TCGA.DC.6160.01 TCGA.D5.6534.01 TCGA.AZ.4616.01
#> "022" "03" "03" "0421" "0413" "03"
#> TCGA.CK.6751.01 TCGA.CM.6171.01 TCGA.DM.A1DA.01 TCGA.AG.A020.11 TCGA.G4.6311.11 TCGA.G4.6625.11
#> "0121" "01221" "0121" "0212" "0211" "0212"
#> TCGA.F5.6863.01 TCGA.G4.6317.02 TCGA.G4.6317.01 TCGA.DM.A1D4.01 TCGA.AG.A01Y.11 TCGA.D5.6530.01
#> "04221" "0432" "03" "011" "0212" "03"
#> TCGA.CK.4948.01 TCGA.AD.A5EJ.01 TCGA.A6.6651.01 TCGA.CA.5256.01 TCGA.DM.A0X9.01 TCGA.AY.A69D.01
#> "0431" "01221" "0412" "03" "011" "011"
#> TCGA.G4.6626.01 TCGA.CA.6716.01 TCGA.A6.2682.01 TCGA.A6.4107.11 TCGA.CA.6717.01 TCGA.G4.6293.01
#> "03" "011" "03" "023" "03" "03"
#> TCGA.CK.5916.01 TCGA.G4.6309.01 TCGA.AA.3662.01 TCGA.AF.A56L.01 TCGA.NH.A6GB.01 TCGA.AD.5900.01
#> "01221" "04223" "03" "03" "011" "03"
#> TCGA.NH.A50U.01 TCGA.AA.3712.01 TCGA.AZ.4614.01 TCGA.AH.6644.01 TCGA.AZ.6607.01 TCGA.AF.2693.01
#> "011" "03" "0121" "011" "03" "0411"
#> TCGA.D5.6924.01 TCGA.CM.5868.01 TCGA.AF.4110.01 TCGA.A6.3809.01 TCGA.AZ.4313.01 TCGA.A6.2675.01
#> "03" "04222" "0411" "0121" "04223" "0421"
#> TCGA.AZ.6608.01 TCGA.CM.5864.01 TCGA.AA.3494.01 TCGA.AD.6895.01 TCGA.CI.6620.01 TCGA.DC.6156.01
#> "03" "011" "0432" "03" "03" "03"
#> TCGA.D5.6931.01 TCGA.CM.6165.01 TCGA.CM.5861.01 TCGA.A6.2671.01 TCGA.DC.6158.01 TCGA.AG.3742.01
#> "03" "03" "01221" "03" "03" "011"
#> TCGA.AG.A02N.11 TCGA.G4.6307.01 TCGA.A6.5666.01 TCGA.EI.6511.01 TCGA.CI.6624.01 TCGA.AG.3591.01
#> "0211" "0432" "011" "03" "04222" "011"
#> TCGA.AY.A8YK.01 TCGA.F4.6856.01 TCGA.DM.A1D7.01 TCGA.A6.2685.01 TCGA.5M.AAT6.01 TCGA.AH.6643.01
#> "022" "03" "03" "022" "022" "011"
#> TCGA.F4.6569.01 TCGA.G4.6298.01 TCGA.AY.6196.01 TCGA.EI.6510.01 TCGA.A6.5656.01 TCGA.A6.2684.11
#> "03" "03" "03" "011" "011" "0212"
#> TCGA.DY.A1DG.01 TCGA.AZ.4682.01 TCGA.EI.6884.01 TCGA.F4.6806.01 TCGA.G4.6320.11 TCGA.G4.6322.01
#> "011" "03" "03" "011" "0211" "0121"
#> TCGA.F5.6810.01 TCGA.5M.AAT4.01 TCGA.CL.4957.01 TCGA.DC.6681.01 TCGA.CM.6167.01 TCGA.AG.4022.01
#> "0431" "011" "03" "03" "0412" "03"
#> TCGA.G4.6586.01 TCGA.EI.6514.01 TCGA.CK.4950.01 TCGA.DM.A282.01 TCGA.DY.A1DC.01 TCGA.D5.6535.01
#> "01221" "011" "03" "011" "03" "03"
#> TCGA.DM.A1HA.01 TCGA.DC.5869.01 TCGA.AZ.6599.11 TCGA.CM.4752.01 TCGA.AZ.4684.01 TCGA.EI.7004.01
#> "011" "03" "0211" "0423" "03" "03"
#> TCGA.A6.A565.01 TCGA.D5.6531.01 TCGA.AZ.6598.01 TCGA.AD.6890.01 TCGA.AG.4021.01 TCGA.A6.6781.01
#> "023" "0121" "01222" "03" "011" "0412"
#> TCGA.DM.A1D9.01 TCGA.CM.4744.01 TCGA.A6.2679.11 TCGA.A6.6652.01 TCGA.AD.6964.01 TCGA.SS.A7HO.01
#> "011" "011" "023" "011" "022" "011"
#> TCGA.A6.6650.01 TCGA.DM.A0XF.01 TCGA.G4.6295.01 TCGA.F4.6461.01 TCGA.AM.5820.01 TCGA.G4.6314.11
#> "011" "04222" "0431" "01221" "03" "0212"
#> TCGA.AD.6889.01 TCGA.AZ.6605.01 TCGA.EI.6881.01 TCGA.NH.A50T.01 TCGA.AG.3725.11 TCGA.G4.6323.01
#> "01222" "0414" "03" "011" "0212" "03"
#> TCGA.AA.3663.01 TCGA.AD.6899.01 TCGA.A6.5667.11 TCGA.A6.A56B.01 TCGA.G5.6572.01 TCGA.DM.A280.01
#> "01222" "011" "0212" "011" "0411" "0413"
#> TCGA.AG.A020.01 TCGA.AA.3713.01 TCGA.D5.5539.01 TCGA.AA.3655.11 TCGA.AA.3489.01 TCGA.AA.3495.01
#> "03" "03" "011" "0211" "0412" "03"
#> TCGA.AG.A01Y.01 TCGA.AZ.6601.01 TCGA.AH.6903.01 TCGA.AZ.6603.01 TCGA.CA.5254.01 TCGA.A6.A5ZU.01
#> "0433" "03" "03" "0432" "01224" "03"
#> TCGA.G4.6302.01 TCGA.AZ.5403.01 TCGA.AY.A54L.01 TCGA.A6.4107.01 TCGA.NH.A5IV.01 TCGA.G4.6306.01
#> "0413" "022" "011" "01224" "011" "011"
#> TCGA.AD.A5EK.01 TCGA.G5.6235.01 TCGA.DC.5337.01 TCGA.CM.6675.01 TCGA.AH.6544.01 TCGA.CK.6746.01
#> "011" "0411" "011" "0121" "03" "0121"
#> TCGA.CA.6718.01 TCGA.CI.6621.01 TCGA.CM.6676.01 TCGA.DM.A1DB.01 TCGA.A6.6654.01 TCGA.AA.3510.11
#> "03" "0411" "03" "03" "03" "023"
#> TCGA.CA.6715.01 TCGA.CM.5341.01 TCGA.CK.5912.01 TCGA.F4.6857.01 TCGA.QG.A5YW.01 TCGA.A6.5665.01
#> "03" "03" "03" "0413" "011" "01221"
#> TCGA.CM.6168.01 TCGA.CL.5917.01 TCGA.AU.6004.01 TCGA.AY.5543.01 TCGA.AG.3731.01 TCGA.G4.6314.01
#> "03" "03" "03" "03" "03" "03"
#> TCGA.DC.6683.01 TCGA.CA.5796.01 TCGA.AG.A036.11 TCGA.AZ.4323.01 TCGA.EI.6882.01 TCGA.AZ.4315.01
#> "03" "03" "0211" "0413" "011" "03"
#> TCGA.A6.2677.01 TCGA.DY.A1DF.01 TCGA.CM.6162.01 TCGA.F4.6703.01 TCGA.CM.5349.01 TCGA.AG.A02N.01
#> "011" "03" "022" "022" "03" "03"
#> TCGA.AA.3506.01 TCGA.D5.6932.01 TCGA.D5.6538.01 TCGA.AA.3488.11 TCGA.AA.3502.01 TCGA.NH.A8F8.01
#> "03" "03" "0121" "0211" "011" "03"
#> TCGA.AF.A56N.01 TCGA.AF.6672.01 TCGA.A6.2685.11 TCGA.A6.6141.01 TCGA.AD.6963.01 TCGA.G4.6298.11
#> "03" "0433" "0212" "03" "0423" "0211"
#> TCGA.EI.6917.01 TCGA.QG.A5Z2.01 TCGA.A6.2684.01 TCGA.CK.5915.01 TCGA.CM.6163.01 TCGA.G4.6322.11
#> "03" "01222" "03" "011" "03" "0211"
#> TCGA.AY.6197.01 TCGA.D5.6928.01 TCGA.A6.3810.01 TCGA.G4.6294.01 TCGA.AA.3660.11 TCGA.A6.6137.01
#> "011" "0413" "0421" "011" "0212" "03"
#> TCGA.G4.6297.11 TCGA.AZ.4615.01 TCGA.CK.4952.01 TCGA.CM.6172.01 TCGA.AD.6901.01 TCGA.AA.3496.01
#> "0212" "03" "0121" "011" "03" "011"
#> TCGA.CK.5913.01 TCGA.DM.A28A.01 TCGA.EI.7002.01 TCGA.D5.6533.01 TCGA.QG.A5Z1.01 TCGA.D5.6923.01
#> "0121" "011" "011" "03" "011" "0411"
#> TCGA.AF.2690.01 TCGA.DM.A28H.01 TCGA.G4.6320.01 TCGA.G4.6310.01 TCGA.DM.A28M.01 TCGA.DM.A288.01
#> "0414" "011" "0121" "03" "011" "011"
#> TCGA.A6.2681.01 TCGA.A6.2679.01 TCGA.4N.A93T.01 TCGA.NH.A8F7.06 TCGA.NH.A8F7.01 TCGA.AZ.6600.11
#> "03" "03" "03" "03" "0432" "0211"
#> TCGA.G5.6572.02 TCGA.AY.6386.01 TCGA.G4.6628.01 TCGA.A6.6653.01 TCGA.CM.4746.01 TCGA.F4.6855.01
#> "0414" "03" "03" "01222" "03" "011"
#> TCGA.EF.5830.01 TCGA.NH.A6GA.01 TCGA.NH.A50V.01 TCGA.DY.A0XA.01 TCGA.DM.A28E.01 TCGA.AG.3725.01
#> "03" "011" "011" "04221" "04221" "03"
#> TCGA.CK.6747.01 TCGA.CL.5918.01 TCGA.CI.6623.01 TCGA.A6.5667.01 TCGA.DM.A28K.01 TCGA.AA.3713.11
#> "011" "011" "0421" "03" "011" "023"
#> TCGA.AA.3655.01 TCGA.AU.3779.01 TCGA.A6.5664.01 TCGA.AA.3697.11 TCGA.AZ.5407.01 TCGA.CM.6169.01
#> "011" "04221" "03" "023" "011" "03"
#> TCGA.AH.6547.01 TCGA.AZ.6601.11 TCGA.A6.5661.01 TCGA.F4.6807.01 TCGA.QG.A5YV.01 TCGA.AA.3509.11
#> "0412" "0211" "01221" "03" "011" "0212"
#> TCGA.AY.A71X.01 TCGA.CA.5797.01 TCGA.F4.6460.01 TCGA.G4.6302.11 TCGA.F5.6702.01 TCGA.AH.6549.01
#> "011" "0431" "04221" "023" "0423" "011"
#> TCGA.D5.6927.01 TCGA.CM.6166.01 TCGA.AH.6897.01 TCGA.G4.6304.01 TCGA.CA.5255.01 TCGA.EI.6507.01
#> "0412" "011" "011" "0413" "03" "03"
#> TCGA.CK.4947.01 TCGA.D5.5540.01 TCGA.DC.6682.01 TCGA.G4.6321.01 TCGA.A6.6649.01 TCGA.CM.5348.01
#> "03" "011" "03" "03" "03" "03"
#> TCGA.EI.6513.01 TCGA.A6.2672.01 TCGA.D5.6539.01 TCGA.AA.3510.01 TCGA.G5.6233.01 TCGA.BM.6198.01
#> "0431" "01221" "0411" "03" "011" "0414"
#> TCGA.CA.6719.01 TCGA.DC.6154.01 TCGA.DM.A1D6.01 TCGA.AG.3731.11 TCGA.CM.6674.01 TCGA.CM.4743.01
#> "011" "03" "03" "0211" "0412" "0413"
#> TCGA.F5.6465.01 TCGA.D5.5537.01 TCGA.F4.6463.01 TCGA.A6.2686.11 TCGA.4T.AA8H.01 TCGA.A6.6782.01
#> "04222" "011" "03" "0212" "011" "03"
#> TCGA.AG.3592.01 TCGA.AD.6888.01 TCGA.CM.6678.01 TCGA.CM.5344.01 TCGA.AA.3495.11 TCGA.AG.A01W.11
#> "011" "03" "011" "04222" "0211" "0212"
#> TCGA.F4.6809.01 TCGA.CK.5914.01 TCGA.AZ.4681.01 TCGA.AA.3492.01 TCGA.D5.6536.01 TCGA.AA.3506.11
#> "03" "011" "0432" "01221" "03" "0211"
#> TCGA.AA.3488.01 TCGA.AA.3502.11 TCGA.A6.6140.01 TCGA.D5.6529.01 TCGA.DM.A1D0.01 TCGA.DM.A1HB.01
#> "03" "023" "0421" "03" "04221" "01222"
#> TCGA.D5.6920.01 TCGA.D5.6922.01 TCGA.EI.6508.01 TCGA.D5.6532.01 TCGA.5M.AATA.01 TCGA.EI.6509.01
#> "03" "03" "011" "011" "03" "0421"
#> TCGA.G4.6311.01 TCGA.A6.A566.01 TCGA.G4.6625.01 TCGA.CI.6619.01 TCGA.F5.6864.01 TCGA.AA.3492.11
#> "03" "03" "03" "0423" "03" "0212"
#> TCGA.A6.5659.01 TCGA.WS.AB45.01 TCGA.G4.6315.01 TCGA.D5.6541.01 TCGA.A6.2680.01 TCGA.CM.4751.01
#> "0121" "0413" "03" "03" "011" "03"
#> TCGA.CM.6680.01 TCGA.AF.6136.01 TCGA.AA.3660.01 TCGA.CM.4747.01 TCGA.EF.5831.01 TCGA.DM.A28G.01
#> "011" "03" "011" "011" "011" "011"
#> TCGA.G4.6297.01 TCGA.A6.2682.11 TCGA.D5.6537.01 TCGA.CM.6170.01 TCGA.DY.A1DD.01
#> "03" "0211" "011" "03" "011"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 3913))
#> TCGA.AF.3911.01 TCGA.F4.6459.01 TCGA.AA.3494.11 TCGA.3L.AA1B.01 TCGA.D5.5538.01 TCGA.F4.6854.01
#> "03" "03" "023" "03" "03" "03"
#> TCGA.AG.A026.01 TCGA.G4.6303.01 TCGA.F5.6464.01 TCGA.T9.A92H.01 TCGA.AA.3712.11 TCGA.CM.5863.01
#> "011" "011" "0412" "011" "021" "03"
#> TCGA.AZ.4308.01 TCGA.AD.6965.01 TCGA.A6.2681.11 TCGA.AD.6548.01 TCGA.A6.5660.01 TCGA.AZ.6600.01
#> "0421" "011" "021" "03" "011" "03"
#> TCGA.F4.6808.01 TCGA.D5.6540.01 TCGA.F5.6571.01 TCGA.D5.6926.01 TCGA.CM.4748.01 TCGA.A6.2675.11
#> "03" "01222" "011" "03" "03" "021"
#> TCGA.5M.AATE.01 TCGA.D5.5541.01 TCGA.CM.5862.01 TCGA.AA.3511.01 TCGA.AA.3663.11 TCGA.CI.6622.01
#> "03" "0421" "011" "03" "021" "011"
#> TCGA.EI.6506.01 TCGA.AM.5821.01 TCGA.F5.6812.01 TCGA.G4.6588.01 TCGA.EI.6512.01 TCGA.A6.6648.01
#> "03" "03" "0414" "01221" "011" "0421"
#> TCGA.A6.2671.11 TCGA.NH.A6GC.01 TCGA.F4.6805.01 TCGA.AA.3697.01 TCGA.QG.A5YX.01 TCGA.DM.A28C.01
#> "021" "03" "0412" "03" "011" "03"
#> TCGA.AG.A036.01 TCGA.AZ.6606.01 TCGA.F4.6570.01 TCGA.DC.4745.01 TCGA.AF.A56K.01 TCGA.G4.6627.01
#> "011" "01223" "01221" "03" "0423" "0412"
#> TCGA.A6.5657.01 TCGA.A6.5662.01 TCGA.AA.3509.01 TCGA.D5.6929.01 TCGA.CM.6679.01 TCGA.A6.2680.11
#> "03" "03" "011" "04222" "03" "021"
#> TCGA.DC.6157.01 TCGA.AF.6655.01 TCGA.CM.6161.01 TCGA.EI.6883.01 TCGA.F5.6811.01 TCGA.D5.6930.01
#> "0432" "0421" "03" "011" "03" "03"
#> TCGA.CM.6164.01 TCGA.AF.2687.01 TCGA.DY.A1H8.01 TCGA.G5.6641.01 TCGA.DC.6155.01 TCGA.RU.A8FL.01
#> "04222" "0423" "03" "03" "03" "011"
#> TCGA.CK.4951.01 TCGA.F4.6704.01 TCGA.AZ.6599.01 TCGA.F5.6861.01 TCGA.CM.5860.01 TCGA.A6.6780.01
#> "03" "0423" "011" "03" "011" "011"
#> TCGA.A6.2686.01 TCGA.CM.4750.01 TCGA.CM.6677.01 TCGA.A6.A567.01 TCGA.F5.6814.01 TCGA.D5.6898.01
#> "0121" "011" "011" "0433" "011" "03"
#> TCGA.AG.A01W.01 TCGA.AZ.6598.11 TCGA.F5.6813.01 TCGA.AG.3732.01 TCGA.EI.6885.01 TCGA.G4.6299.01
#> "03" "021" "03" "04223" "0433" "01222"
#> TCGA.A6.4105.01 TCGA.DM.A1D8.01 TCGA.DM.A285.01 TCGA.G4.6295.11 TCGA.DC.4749.01 TCGA.DT.5265.01
#> "01223" "011" "03" "023" "0421" "01223"
#> TCGA.5M.AAT5.01 TCGA.DM.A0XD.01 TCGA.A6.6138.01 TCGA.D5.7000.01 TCGA.DM.A28F.01 TCGA.DY.A1DE.01
#> "0432" "0121" "011" "0121" "011" "03"
#> TCGA.A6.6142.01 TCGA.QL.A97D.01 TCGA.CK.6748.01 TCGA.DC.6160.01 TCGA.D5.6534.01 TCGA.AZ.4616.01
#> "022" "03" "03" "0421" "0413" "03"
#> TCGA.CK.6751.01 TCGA.CM.6171.01 TCGA.DM.A1DA.01 TCGA.AG.A020.11 TCGA.G4.6311.11 TCGA.G4.6625.11
#> "0121" "01221" "0121" "021" "021" "021"
#> TCGA.F5.6863.01 TCGA.G4.6317.02 TCGA.G4.6317.01 TCGA.DM.A1D4.01 TCGA.AG.A01Y.11 TCGA.D5.6530.01
#> "04221" "0432" "03" "011" "021" "03"
#> TCGA.CK.4948.01 TCGA.AD.A5EJ.01 TCGA.A6.6651.01 TCGA.CA.5256.01 TCGA.DM.A0X9.01 TCGA.AY.A69D.01
#> "0431" "01221" "0412" "03" "011" "011"
#> TCGA.G4.6626.01 TCGA.CA.6716.01 TCGA.A6.2682.01 TCGA.A6.4107.11 TCGA.CA.6717.01 TCGA.G4.6293.01
#> "03" "011" "03" "023" "03" "03"
#> TCGA.CK.5916.01 TCGA.G4.6309.01 TCGA.AA.3662.01 TCGA.AF.A56L.01 TCGA.NH.A6GB.01 TCGA.AD.5900.01
#> "01221" "04223" "03" "03" "011" "03"
#> TCGA.NH.A50U.01 TCGA.AA.3712.01 TCGA.AZ.4614.01 TCGA.AH.6644.01 TCGA.AZ.6607.01 TCGA.AF.2693.01
#> "011" "03" "0121" "011" "03" "0411"
#> TCGA.D5.6924.01 TCGA.CM.5868.01 TCGA.AF.4110.01 TCGA.A6.3809.01 TCGA.AZ.4313.01 TCGA.A6.2675.01
#> "03" "04222" "0411" "0121" "04223" "0421"
#> TCGA.AZ.6608.01 TCGA.CM.5864.01 TCGA.AA.3494.01 TCGA.AD.6895.01 TCGA.CI.6620.01 TCGA.DC.6156.01
#> "03" "011" "0432" "03" "03" "03"
#> TCGA.D5.6931.01 TCGA.CM.6165.01 TCGA.CM.5861.01 TCGA.A6.2671.01 TCGA.DC.6158.01 TCGA.AG.3742.01
#> "03" "03" "01221" "03" "03" "011"
#> TCGA.AG.A02N.11 TCGA.G4.6307.01 TCGA.A6.5666.01 TCGA.EI.6511.01 TCGA.CI.6624.01 TCGA.AG.3591.01
#> "021" "0432" "011" "03" "04222" "011"
#> TCGA.AY.A8YK.01 TCGA.F4.6856.01 TCGA.DM.A1D7.01 TCGA.A6.2685.01 TCGA.5M.AAT6.01 TCGA.AH.6643.01
#> "022" "03" "03" "022" "022" "011"
#> TCGA.F4.6569.01 TCGA.G4.6298.01 TCGA.AY.6196.01 TCGA.EI.6510.01 TCGA.A6.5656.01 TCGA.A6.2684.11
#> "03" "03" "03" "011" "011" "021"
#> TCGA.DY.A1DG.01 TCGA.AZ.4682.01 TCGA.EI.6884.01 TCGA.F4.6806.01 TCGA.G4.6320.11 TCGA.G4.6322.01
#> "011" "03" "03" "011" "021" "0121"
#> TCGA.F5.6810.01 TCGA.5M.AAT4.01 TCGA.CL.4957.01 TCGA.DC.6681.01 TCGA.CM.6167.01 TCGA.AG.4022.01
#> "0431" "011" "03" "03" "0412" "03"
#> TCGA.G4.6586.01 TCGA.EI.6514.01 TCGA.CK.4950.01 TCGA.DM.A282.01 TCGA.DY.A1DC.01 TCGA.D5.6535.01
#> "01221" "011" "03" "011" "03" "03"
#> TCGA.DM.A1HA.01 TCGA.DC.5869.01 TCGA.AZ.6599.11 TCGA.CM.4752.01 TCGA.AZ.4684.01 TCGA.EI.7004.01
#> "011" "03" "021" "0423" "03" "03"
#> TCGA.A6.A565.01 TCGA.D5.6531.01 TCGA.AZ.6598.01 TCGA.AD.6890.01 TCGA.AG.4021.01 TCGA.A6.6781.01
#> "023" "0121" "01222" "03" "011" "0412"
#> TCGA.DM.A1D9.01 TCGA.CM.4744.01 TCGA.A6.2679.11 TCGA.A6.6652.01 TCGA.AD.6964.01 TCGA.SS.A7HO.01
#> "011" "011" "023" "011" "022" "011"
#> TCGA.A6.6650.01 TCGA.DM.A0XF.01 TCGA.G4.6295.01 TCGA.F4.6461.01 TCGA.AM.5820.01 TCGA.G4.6314.11
#> "011" "04222" "0431" "01221" "03" "021"
#> TCGA.AD.6889.01 TCGA.AZ.6605.01 TCGA.EI.6881.01 TCGA.NH.A50T.01 TCGA.AG.3725.11 TCGA.G4.6323.01
#> "01222" "0414" "03" "011" "021" "03"
#> TCGA.AA.3663.01 TCGA.AD.6899.01 TCGA.A6.5667.11 TCGA.A6.A56B.01 TCGA.G5.6572.01 TCGA.DM.A280.01
#> "01222" "011" "021" "011" "0411" "0413"
#> TCGA.AG.A020.01 TCGA.AA.3713.01 TCGA.D5.5539.01 TCGA.AA.3655.11 TCGA.AA.3489.01 TCGA.AA.3495.01
#> "03" "03" "011" "021" "0412" "03"
#> TCGA.AG.A01Y.01 TCGA.AZ.6601.01 TCGA.AH.6903.01 TCGA.AZ.6603.01 TCGA.CA.5254.01 TCGA.A6.A5ZU.01
#> "0433" "03" "03" "0432" "01224" "03"
#> TCGA.G4.6302.01 TCGA.AZ.5403.01 TCGA.AY.A54L.01 TCGA.A6.4107.01 TCGA.NH.A5IV.01 TCGA.G4.6306.01
#> "0413" "022" "011" "01224" "011" "011"
#> TCGA.AD.A5EK.01 TCGA.G5.6235.01 TCGA.DC.5337.01 TCGA.CM.6675.01 TCGA.AH.6544.01 TCGA.CK.6746.01
#> "011" "0411" "011" "0121" "03" "0121"
#> TCGA.CA.6718.01 TCGA.CI.6621.01 TCGA.CM.6676.01 TCGA.DM.A1DB.01 TCGA.A6.6654.01 TCGA.AA.3510.11
#> "03" "0411" "03" "03" "03" "023"
#> TCGA.CA.6715.01 TCGA.CM.5341.01 TCGA.CK.5912.01 TCGA.F4.6857.01 TCGA.QG.A5YW.01 TCGA.A6.5665.01
#> "03" "03" "03" "0413" "011" "01221"
#> TCGA.CM.6168.01 TCGA.CL.5917.01 TCGA.AU.6004.01 TCGA.AY.5543.01 TCGA.AG.3731.01 TCGA.G4.6314.01
#> "03" "03" "03" "03" "03" "03"
#> TCGA.DC.6683.01 TCGA.CA.5796.01 TCGA.AG.A036.11 TCGA.AZ.4323.01 TCGA.EI.6882.01 TCGA.AZ.4315.01
#> "03" "03" "021" "0413" "011" "03"
#> TCGA.A6.2677.01 TCGA.DY.A1DF.01 TCGA.CM.6162.01 TCGA.F4.6703.01 TCGA.CM.5349.01 TCGA.AG.A02N.01
#> "011" "03" "022" "022" "03" "03"
#> TCGA.AA.3506.01 TCGA.D5.6932.01 TCGA.D5.6538.01 TCGA.AA.3488.11 TCGA.AA.3502.01 TCGA.NH.A8F8.01
#> "03" "03" "0121" "021" "011" "03"
#> TCGA.AF.A56N.01 TCGA.AF.6672.01 TCGA.A6.2685.11 TCGA.A6.6141.01 TCGA.AD.6963.01 TCGA.G4.6298.11
#> "03" "0433" "021" "03" "0423" "021"
#> TCGA.EI.6917.01 TCGA.QG.A5Z2.01 TCGA.A6.2684.01 TCGA.CK.5915.01 TCGA.CM.6163.01 TCGA.G4.6322.11
#> "03" "01222" "03" "011" "03" "021"
#> TCGA.AY.6197.01 TCGA.D5.6928.01 TCGA.A6.3810.01 TCGA.G4.6294.01 TCGA.AA.3660.11 TCGA.A6.6137.01
#> "011" "0413" "0421" "011" "021" "03"
#> TCGA.G4.6297.11 TCGA.AZ.4615.01 TCGA.CK.4952.01 TCGA.CM.6172.01 TCGA.AD.6901.01 TCGA.AA.3496.01
#> "021" "03" "0121" "011" "03" "011"
#> TCGA.CK.5913.01 TCGA.DM.A28A.01 TCGA.EI.7002.01 TCGA.D5.6533.01 TCGA.QG.A5Z1.01 TCGA.D5.6923.01
#> "0121" "011" "011" "03" "011" "0411"
#> TCGA.AF.2690.01 TCGA.DM.A28H.01 TCGA.G4.6320.01 TCGA.G4.6310.01 TCGA.DM.A28M.01 TCGA.DM.A288.01
#> "0414" "011" "0121" "03" "011" "011"
#> TCGA.A6.2681.01 TCGA.A6.2679.01 TCGA.4N.A93T.01 TCGA.NH.A8F7.06 TCGA.NH.A8F7.01 TCGA.AZ.6600.11
#> "03" "03" "03" "03" "0432" "021"
#> TCGA.G5.6572.02 TCGA.AY.6386.01 TCGA.G4.6628.01 TCGA.A6.6653.01 TCGA.CM.4746.01 TCGA.F4.6855.01
#> "0414" "03" "03" "01222" "03" "011"
#> TCGA.EF.5830.01 TCGA.NH.A6GA.01 TCGA.NH.A50V.01 TCGA.DY.A0XA.01 TCGA.DM.A28E.01 TCGA.AG.3725.01
#> "03" "011" "011" "04221" "04221" "03"
#> TCGA.CK.6747.01 TCGA.CL.5918.01 TCGA.CI.6623.01 TCGA.A6.5667.01 TCGA.DM.A28K.01 TCGA.AA.3713.11
#> "011" "011" "0421" "03" "011" "023"
#> TCGA.AA.3655.01 TCGA.AU.3779.01 TCGA.A6.5664.01 TCGA.AA.3697.11 TCGA.AZ.5407.01 TCGA.CM.6169.01
#> "011" "04221" "03" "023" "011" "03"
#> TCGA.AH.6547.01 TCGA.AZ.6601.11 TCGA.A6.5661.01 TCGA.F4.6807.01 TCGA.QG.A5YV.01 TCGA.AA.3509.11
#> "0412" "021" "01221" "03" "011" "021"
#> TCGA.AY.A71X.01 TCGA.CA.5797.01 TCGA.F4.6460.01 TCGA.G4.6302.11 TCGA.F5.6702.01 TCGA.AH.6549.01
#> "011" "0431" "04221" "023" "0423" "011"
#> TCGA.D5.6927.01 TCGA.CM.6166.01 TCGA.AH.6897.01 TCGA.G4.6304.01 TCGA.CA.5255.01 TCGA.EI.6507.01
#> "0412" "011" "011" "0413" "03" "03"
#> TCGA.CK.4947.01 TCGA.D5.5540.01 TCGA.DC.6682.01 TCGA.G4.6321.01 TCGA.A6.6649.01 TCGA.CM.5348.01
#> "03" "011" "03" "03" "03" "03"
#> TCGA.EI.6513.01 TCGA.A6.2672.01 TCGA.D5.6539.01 TCGA.AA.3510.01 TCGA.G5.6233.01 TCGA.BM.6198.01
#> "0431" "01221" "0411" "03" "011" "0414"
#> TCGA.CA.6719.01 TCGA.DC.6154.01 TCGA.DM.A1D6.01 TCGA.AG.3731.11 TCGA.CM.6674.01 TCGA.CM.4743.01
#> "011" "03" "03" "021" "0412" "0413"
#> TCGA.F5.6465.01 TCGA.D5.5537.01 TCGA.F4.6463.01 TCGA.A6.2686.11 TCGA.4T.AA8H.01 TCGA.A6.6782.01
#> "04222" "011" "03" "021" "011" "03"
#> TCGA.AG.3592.01 TCGA.AD.6888.01 TCGA.CM.6678.01 TCGA.CM.5344.01 TCGA.AA.3495.11 TCGA.AG.A01W.11
#> "011" "03" "011" "04222" "021" "021"
#> TCGA.F4.6809.01 TCGA.CK.5914.01 TCGA.AZ.4681.01 TCGA.AA.3492.01 TCGA.D5.6536.01 TCGA.AA.3506.11
#> "03" "011" "0432" "01221" "03" "021"
#> TCGA.AA.3488.01 TCGA.AA.3502.11 TCGA.A6.6140.01 TCGA.D5.6529.01 TCGA.DM.A1D0.01 TCGA.DM.A1HB.01
#> "03" "023" "0421" "03" "04221" "01222"
#> TCGA.D5.6920.01 TCGA.D5.6922.01 TCGA.EI.6508.01 TCGA.D5.6532.01 TCGA.5M.AATA.01 TCGA.EI.6509.01
#> "03" "03" "011" "011" "03" "0421"
#> TCGA.G4.6311.01 TCGA.A6.A566.01 TCGA.G4.6625.01 TCGA.CI.6619.01 TCGA.F5.6864.01 TCGA.AA.3492.11
#> "03" "03" "03" "0423" "03" "021"
#> TCGA.A6.5659.01 TCGA.WS.AB45.01 TCGA.G4.6315.01 TCGA.D5.6541.01 TCGA.A6.2680.01 TCGA.CM.4751.01
#> "0121" "0413" "03" "03" "011" "03"
#> TCGA.CM.6680.01 TCGA.AF.6136.01 TCGA.AA.3660.01 TCGA.CM.4747.01 TCGA.EF.5831.01 TCGA.DM.A28G.01
#> "011" "03" "011" "011" "011" "011"
#> TCGA.G4.6297.01 TCGA.A6.2682.11 TCGA.D5.6537.01 TCGA.CM.6170.01 TCGA.DY.A1DD.01
#> "03" "021" "011" "03" "011"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 4047))
#> TCGA.AF.3911.01 TCGA.F4.6459.01 TCGA.AA.3494.11 TCGA.3L.AA1B.01 TCGA.D5.5538.01 TCGA.F4.6854.01
#> "03" "03" "023" "03" "03" "03"
#> TCGA.AG.A026.01 TCGA.G4.6303.01 TCGA.F5.6464.01 TCGA.T9.A92H.01 TCGA.AA.3712.11 TCGA.CM.5863.01
#> "011" "011" "0412" "011" "021" "03"
#> TCGA.AZ.4308.01 TCGA.AD.6965.01 TCGA.A6.2681.11 TCGA.AD.6548.01 TCGA.A6.5660.01 TCGA.AZ.6600.01
#> "0421" "011" "021" "03" "011" "03"
#> TCGA.F4.6808.01 TCGA.D5.6540.01 TCGA.F5.6571.01 TCGA.D5.6926.01 TCGA.CM.4748.01 TCGA.A6.2675.11
#> "03" "012" "011" "03" "03" "021"
#> TCGA.5M.AATE.01 TCGA.D5.5541.01 TCGA.CM.5862.01 TCGA.AA.3511.01 TCGA.AA.3663.11 TCGA.CI.6622.01
#> "03" "0421" "011" "03" "021" "011"
#> TCGA.EI.6506.01 TCGA.AM.5821.01 TCGA.F5.6812.01 TCGA.G4.6588.01 TCGA.EI.6512.01 TCGA.A6.6648.01
#> "03" "03" "0414" "012" "011" "0421"
#> TCGA.A6.2671.11 TCGA.NH.A6GC.01 TCGA.F4.6805.01 TCGA.AA.3697.01 TCGA.QG.A5YX.01 TCGA.DM.A28C.01
#> "021" "03" "0412" "03" "011" "03"
#> TCGA.AG.A036.01 TCGA.AZ.6606.01 TCGA.F4.6570.01 TCGA.DC.4745.01 TCGA.AF.A56K.01 TCGA.G4.6627.01
#> "011" "012" "012" "03" "0423" "0412"
#> TCGA.A6.5657.01 TCGA.A6.5662.01 TCGA.AA.3509.01 TCGA.D5.6929.01 TCGA.CM.6679.01 TCGA.A6.2680.11
#> "03" "03" "011" "04222" "03" "021"
#> TCGA.DC.6157.01 TCGA.AF.6655.01 TCGA.CM.6161.01 TCGA.EI.6883.01 TCGA.F5.6811.01 TCGA.D5.6930.01
#> "0432" "0421" "03" "011" "03" "03"
#> TCGA.CM.6164.01 TCGA.AF.2687.01 TCGA.DY.A1H8.01 TCGA.G5.6641.01 TCGA.DC.6155.01 TCGA.RU.A8FL.01
#> "04222" "0423" "03" "03" "03" "011"
#> TCGA.CK.4951.01 TCGA.F4.6704.01 TCGA.AZ.6599.01 TCGA.F5.6861.01 TCGA.CM.5860.01 TCGA.A6.6780.01
#> "03" "0423" "011" "03" "011" "011"
#> TCGA.A6.2686.01 TCGA.CM.4750.01 TCGA.CM.6677.01 TCGA.A6.A567.01 TCGA.F5.6814.01 TCGA.D5.6898.01
#> "012" "011" "011" "0433" "011" "03"
#> TCGA.AG.A01W.01 TCGA.AZ.6598.11 TCGA.F5.6813.01 TCGA.AG.3732.01 TCGA.EI.6885.01 TCGA.G4.6299.01
#> "03" "021" "03" "04223" "0433" "012"
#> TCGA.A6.4105.01 TCGA.DM.A1D8.01 TCGA.DM.A285.01 TCGA.G4.6295.11 TCGA.DC.4749.01 TCGA.DT.5265.01
#> "012" "011" "03" "023" "0421" "012"
#> TCGA.5M.AAT5.01 TCGA.DM.A0XD.01 TCGA.A6.6138.01 TCGA.D5.7000.01 TCGA.DM.A28F.01 TCGA.DY.A1DE.01
#> "0432" "012" "011" "012" "011" "03"
#> TCGA.A6.6142.01 TCGA.QL.A97D.01 TCGA.CK.6748.01 TCGA.DC.6160.01 TCGA.D5.6534.01 TCGA.AZ.4616.01
#> "022" "03" "03" "0421" "0413" "03"
#> TCGA.CK.6751.01 TCGA.CM.6171.01 TCGA.DM.A1DA.01 TCGA.AG.A020.11 TCGA.G4.6311.11 TCGA.G4.6625.11
#> "012" "012" "012" "021" "021" "021"
#> TCGA.F5.6863.01 TCGA.G4.6317.02 TCGA.G4.6317.01 TCGA.DM.A1D4.01 TCGA.AG.A01Y.11 TCGA.D5.6530.01
#> "04221" "0432" "03" "011" "021" "03"
#> TCGA.CK.4948.01 TCGA.AD.A5EJ.01 TCGA.A6.6651.01 TCGA.CA.5256.01 TCGA.DM.A0X9.01 TCGA.AY.A69D.01
#> "0431" "012" "0412" "03" "011" "011"
#> TCGA.G4.6626.01 TCGA.CA.6716.01 TCGA.A6.2682.01 TCGA.A6.4107.11 TCGA.CA.6717.01 TCGA.G4.6293.01
#> "03" "011" "03" "023" "03" "03"
#> TCGA.CK.5916.01 TCGA.G4.6309.01 TCGA.AA.3662.01 TCGA.AF.A56L.01 TCGA.NH.A6GB.01 TCGA.AD.5900.01
#> "012" "04223" "03" "03" "011" "03"
#> TCGA.NH.A50U.01 TCGA.AA.3712.01 TCGA.AZ.4614.01 TCGA.AH.6644.01 TCGA.AZ.6607.01 TCGA.AF.2693.01
#> "011" "03" "012" "011" "03" "0411"
#> TCGA.D5.6924.01 TCGA.CM.5868.01 TCGA.AF.4110.01 TCGA.A6.3809.01 TCGA.AZ.4313.01 TCGA.A6.2675.01
#> "03" "04222" "0411" "012" "04223" "0421"
#> TCGA.AZ.6608.01 TCGA.CM.5864.01 TCGA.AA.3494.01 TCGA.AD.6895.01 TCGA.CI.6620.01 TCGA.DC.6156.01
#> "03" "011" "0432" "03" "03" "03"
#> TCGA.D5.6931.01 TCGA.CM.6165.01 TCGA.CM.5861.01 TCGA.A6.2671.01 TCGA.DC.6158.01 TCGA.AG.3742.01
#> "03" "03" "012" "03" "03" "011"
#> TCGA.AG.A02N.11 TCGA.G4.6307.01 TCGA.A6.5666.01 TCGA.EI.6511.01 TCGA.CI.6624.01 TCGA.AG.3591.01
#> "021" "0432" "011" "03" "04222" "011"
#> TCGA.AY.A8YK.01 TCGA.F4.6856.01 TCGA.DM.A1D7.01 TCGA.A6.2685.01 TCGA.5M.AAT6.01 TCGA.AH.6643.01
#> "022" "03" "03" "022" "022" "011"
#> TCGA.F4.6569.01 TCGA.G4.6298.01 TCGA.AY.6196.01 TCGA.EI.6510.01 TCGA.A6.5656.01 TCGA.A6.2684.11
#> "03" "03" "03" "011" "011" "021"
#> TCGA.DY.A1DG.01 TCGA.AZ.4682.01 TCGA.EI.6884.01 TCGA.F4.6806.01 TCGA.G4.6320.11 TCGA.G4.6322.01
#> "011" "03" "03" "011" "021" "012"
#> TCGA.F5.6810.01 TCGA.5M.AAT4.01 TCGA.CL.4957.01 TCGA.DC.6681.01 TCGA.CM.6167.01 TCGA.AG.4022.01
#> "0431" "011" "03" "03" "0412" "03"
#> TCGA.G4.6586.01 TCGA.EI.6514.01 TCGA.CK.4950.01 TCGA.DM.A282.01 TCGA.DY.A1DC.01 TCGA.D5.6535.01
#> "012" "011" "03" "011" "03" "03"
#> TCGA.DM.A1HA.01 TCGA.DC.5869.01 TCGA.AZ.6599.11 TCGA.CM.4752.01 TCGA.AZ.4684.01 TCGA.EI.7004.01
#> "011" "03" "021" "0423" "03" "03"
#> TCGA.A6.A565.01 TCGA.D5.6531.01 TCGA.AZ.6598.01 TCGA.AD.6890.01 TCGA.AG.4021.01 TCGA.A6.6781.01
#> "023" "012" "012" "03" "011" "0412"
#> TCGA.DM.A1D9.01 TCGA.CM.4744.01 TCGA.A6.2679.11 TCGA.A6.6652.01 TCGA.AD.6964.01 TCGA.SS.A7HO.01
#> "011" "011" "023" "011" "022" "011"
#> TCGA.A6.6650.01 TCGA.DM.A0XF.01 TCGA.G4.6295.01 TCGA.F4.6461.01 TCGA.AM.5820.01 TCGA.G4.6314.11
#> "011" "04222" "0431" "012" "03" "021"
#> TCGA.AD.6889.01 TCGA.AZ.6605.01 TCGA.EI.6881.01 TCGA.NH.A50T.01 TCGA.AG.3725.11 TCGA.G4.6323.01
#> "012" "0414" "03" "011" "021" "03"
#> TCGA.AA.3663.01 TCGA.AD.6899.01 TCGA.A6.5667.11 TCGA.A6.A56B.01 TCGA.G5.6572.01 TCGA.DM.A280.01
#> "012" "011" "021" "011" "0411" "0413"
#> TCGA.AG.A020.01 TCGA.AA.3713.01 TCGA.D5.5539.01 TCGA.AA.3655.11 TCGA.AA.3489.01 TCGA.AA.3495.01
#> "03" "03" "011" "021" "0412" "03"
#> TCGA.AG.A01Y.01 TCGA.AZ.6601.01 TCGA.AH.6903.01 TCGA.AZ.6603.01 TCGA.CA.5254.01 TCGA.A6.A5ZU.01
#> "0433" "03" "03" "0432" "012" "03"
#> TCGA.G4.6302.01 TCGA.AZ.5403.01 TCGA.AY.A54L.01 TCGA.A6.4107.01 TCGA.NH.A5IV.01 TCGA.G4.6306.01
#> "0413" "022" "011" "012" "011" "011"
#> TCGA.AD.A5EK.01 TCGA.G5.6235.01 TCGA.DC.5337.01 TCGA.CM.6675.01 TCGA.AH.6544.01 TCGA.CK.6746.01
#> "011" "0411" "011" "012" "03" "012"
#> TCGA.CA.6718.01 TCGA.CI.6621.01 TCGA.CM.6676.01 TCGA.DM.A1DB.01 TCGA.A6.6654.01 TCGA.AA.3510.11
#> "03" "0411" "03" "03" "03" "023"
#> TCGA.CA.6715.01 TCGA.CM.5341.01 TCGA.CK.5912.01 TCGA.F4.6857.01 TCGA.QG.A5YW.01 TCGA.A6.5665.01
#> "03" "03" "03" "0413" "011" "012"
#> TCGA.CM.6168.01 TCGA.CL.5917.01 TCGA.AU.6004.01 TCGA.AY.5543.01 TCGA.AG.3731.01 TCGA.G4.6314.01
#> "03" "03" "03" "03" "03" "03"
#> TCGA.DC.6683.01 TCGA.CA.5796.01 TCGA.AG.A036.11 TCGA.AZ.4323.01 TCGA.EI.6882.01 TCGA.AZ.4315.01
#> "03" "03" "021" "0413" "011" "03"
#> TCGA.A6.2677.01 TCGA.DY.A1DF.01 TCGA.CM.6162.01 TCGA.F4.6703.01 TCGA.CM.5349.01 TCGA.AG.A02N.01
#> "011" "03" "022" "022" "03" "03"
#> TCGA.AA.3506.01 TCGA.D5.6932.01 TCGA.D5.6538.01 TCGA.AA.3488.11 TCGA.AA.3502.01 TCGA.NH.A8F8.01
#> "03" "03" "012" "021" "011" "03"
#> TCGA.AF.A56N.01 TCGA.AF.6672.01 TCGA.A6.2685.11 TCGA.A6.6141.01 TCGA.AD.6963.01 TCGA.G4.6298.11
#> "03" "0433" "021" "03" "0423" "021"
#> TCGA.EI.6917.01 TCGA.QG.A5Z2.01 TCGA.A6.2684.01 TCGA.CK.5915.01 TCGA.CM.6163.01 TCGA.G4.6322.11
#> "03" "012" "03" "011" "03" "021"
#> TCGA.AY.6197.01 TCGA.D5.6928.01 TCGA.A6.3810.01 TCGA.G4.6294.01 TCGA.AA.3660.11 TCGA.A6.6137.01
#> "011" "0413" "0421" "011" "021" "03"
#> TCGA.G4.6297.11 TCGA.AZ.4615.01 TCGA.CK.4952.01 TCGA.CM.6172.01 TCGA.AD.6901.01 TCGA.AA.3496.01
#> "021" "03" "012" "011" "03" "011"
#> TCGA.CK.5913.01 TCGA.DM.A28A.01 TCGA.EI.7002.01 TCGA.D5.6533.01 TCGA.QG.A5Z1.01 TCGA.D5.6923.01
#> "012" "011" "011" "03" "011" "0411"
#> TCGA.AF.2690.01 TCGA.DM.A28H.01 TCGA.G4.6320.01 TCGA.G4.6310.01 TCGA.DM.A28M.01 TCGA.DM.A288.01
#> "0414" "011" "012" "03" "011" "011"
#> TCGA.A6.2681.01 TCGA.A6.2679.01 TCGA.4N.A93T.01 TCGA.NH.A8F7.06 TCGA.NH.A8F7.01 TCGA.AZ.6600.11
#> "03" "03" "03" "03" "0432" "021"
#> TCGA.G5.6572.02 TCGA.AY.6386.01 TCGA.G4.6628.01 TCGA.A6.6653.01 TCGA.CM.4746.01 TCGA.F4.6855.01
#> "0414" "03" "03" "012" "03" "011"
#> TCGA.EF.5830.01 TCGA.NH.A6GA.01 TCGA.NH.A50V.01 TCGA.DY.A0XA.01 TCGA.DM.A28E.01 TCGA.AG.3725.01
#> "03" "011" "011" "04221" "04221" "03"
#> TCGA.CK.6747.01 TCGA.CL.5918.01 TCGA.CI.6623.01 TCGA.A6.5667.01 TCGA.DM.A28K.01 TCGA.AA.3713.11
#> "011" "011" "0421" "03" "011" "023"
#> TCGA.AA.3655.01 TCGA.AU.3779.01 TCGA.A6.5664.01 TCGA.AA.3697.11 TCGA.AZ.5407.01 TCGA.CM.6169.01
#> "011" "04221" "03" "023" "011" "03"
#> TCGA.AH.6547.01 TCGA.AZ.6601.11 TCGA.A6.5661.01 TCGA.F4.6807.01 TCGA.QG.A5YV.01 TCGA.AA.3509.11
#> "0412" "021" "012" "03" "011" "021"
#> TCGA.AY.A71X.01 TCGA.CA.5797.01 TCGA.F4.6460.01 TCGA.G4.6302.11 TCGA.F5.6702.01 TCGA.AH.6549.01
#> "011" "0431" "04221" "023" "0423" "011"
#> TCGA.D5.6927.01 TCGA.CM.6166.01 TCGA.AH.6897.01 TCGA.G4.6304.01 TCGA.CA.5255.01 TCGA.EI.6507.01
#> "0412" "011" "011" "0413" "03" "03"
#> TCGA.CK.4947.01 TCGA.D5.5540.01 TCGA.DC.6682.01 TCGA.G4.6321.01 TCGA.A6.6649.01 TCGA.CM.5348.01
#> "03" "011" "03" "03" "03" "03"
#> TCGA.EI.6513.01 TCGA.A6.2672.01 TCGA.D5.6539.01 TCGA.AA.3510.01 TCGA.G5.6233.01 TCGA.BM.6198.01
#> "0431" "012" "0411" "03" "011" "0414"
#> TCGA.CA.6719.01 TCGA.DC.6154.01 TCGA.DM.A1D6.01 TCGA.AG.3731.11 TCGA.CM.6674.01 TCGA.CM.4743.01
#> "011" "03" "03" "021" "0412" "0413"
#> TCGA.F5.6465.01 TCGA.D5.5537.01 TCGA.F4.6463.01 TCGA.A6.2686.11 TCGA.4T.AA8H.01 TCGA.A6.6782.01
#> "04222" "011" "03" "021" "011" "03"
#> TCGA.AG.3592.01 TCGA.AD.6888.01 TCGA.CM.6678.01 TCGA.CM.5344.01 TCGA.AA.3495.11 TCGA.AG.A01W.11
#> "011" "03" "011" "04222" "021" "021"
#> TCGA.F4.6809.01 TCGA.CK.5914.01 TCGA.AZ.4681.01 TCGA.AA.3492.01 TCGA.D5.6536.01 TCGA.AA.3506.11
#> "03" "011" "0432" "012" "03" "021"
#> TCGA.AA.3488.01 TCGA.AA.3502.11 TCGA.A6.6140.01 TCGA.D5.6529.01 TCGA.DM.A1D0.01 TCGA.DM.A1HB.01
#> "03" "023" "0421" "03" "04221" "012"
#> TCGA.D5.6920.01 TCGA.D5.6922.01 TCGA.EI.6508.01 TCGA.D5.6532.01 TCGA.5M.AATA.01 TCGA.EI.6509.01
#> "03" "03" "011" "011" "03" "0421"
#> TCGA.G4.6311.01 TCGA.A6.A566.01 TCGA.G4.6625.01 TCGA.CI.6619.01 TCGA.F5.6864.01 TCGA.AA.3492.11
#> "03" "03" "03" "0423" "03" "021"
#> TCGA.A6.5659.01 TCGA.WS.AB45.01 TCGA.G4.6315.01 TCGA.D5.6541.01 TCGA.A6.2680.01 TCGA.CM.4751.01
#> "012" "0413" "03" "03" "011" "03"
#> TCGA.CM.6680.01 TCGA.AF.6136.01 TCGA.AA.3660.01 TCGA.CM.4747.01 TCGA.EF.5831.01 TCGA.DM.A28G.01
#> "011" "03" "011" "011" "011" "011"
#> TCGA.G4.6297.01 TCGA.A6.2682.11 TCGA.D5.6537.01 TCGA.CM.6170.01 TCGA.DY.A1DD.01
#> "03" "021" "011" "03" "011"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 5229))
#> TCGA.AF.3911.01 TCGA.F4.6459.01 TCGA.AA.3494.11 TCGA.3L.AA1B.01 TCGA.D5.5538.01 TCGA.F4.6854.01
#> "03" "03" "023" "03" "03" "03"
#> TCGA.AG.A026.01 TCGA.G4.6303.01 TCGA.F5.6464.01 TCGA.T9.A92H.01 TCGA.AA.3712.11 TCGA.CM.5863.01
#> "011" "011" "0412" "011" "021" "03"
#> TCGA.AZ.4308.01 TCGA.AD.6965.01 TCGA.A6.2681.11 TCGA.AD.6548.01 TCGA.A6.5660.01 TCGA.AZ.6600.01
#> "042" "011" "021" "03" "011" "03"
#> TCGA.F4.6808.01 TCGA.D5.6540.01 TCGA.F5.6571.01 TCGA.D5.6926.01 TCGA.CM.4748.01 TCGA.A6.2675.11
#> "03" "012" "011" "03" "03" "021"
#> TCGA.5M.AATE.01 TCGA.D5.5541.01 TCGA.CM.5862.01 TCGA.AA.3511.01 TCGA.AA.3663.11 TCGA.CI.6622.01
#> "03" "042" "011" "03" "021" "011"
#> TCGA.EI.6506.01 TCGA.AM.5821.01 TCGA.F5.6812.01 TCGA.G4.6588.01 TCGA.EI.6512.01 TCGA.A6.6648.01
#> "03" "03" "0414" "012" "011" "042"
#> TCGA.A6.2671.11 TCGA.NH.A6GC.01 TCGA.F4.6805.01 TCGA.AA.3697.01 TCGA.QG.A5YX.01 TCGA.DM.A28C.01
#> "021" "03" "0412" "03" "011" "03"
#> TCGA.AG.A036.01 TCGA.AZ.6606.01 TCGA.F4.6570.01 TCGA.DC.4745.01 TCGA.AF.A56K.01 TCGA.G4.6627.01
#> "011" "012" "012" "03" "042" "0412"
#> TCGA.A6.5657.01 TCGA.A6.5662.01 TCGA.AA.3509.01 TCGA.D5.6929.01 TCGA.CM.6679.01 TCGA.A6.2680.11
#> "03" "03" "011" "042" "03" "021"
#> TCGA.DC.6157.01 TCGA.AF.6655.01 TCGA.CM.6161.01 TCGA.EI.6883.01 TCGA.F5.6811.01 TCGA.D5.6930.01
#> "0432" "042" "03" "011" "03" "03"
#> TCGA.CM.6164.01 TCGA.AF.2687.01 TCGA.DY.A1H8.01 TCGA.G5.6641.01 TCGA.DC.6155.01 TCGA.RU.A8FL.01
#> "042" "042" "03" "03" "03" "011"
#> TCGA.CK.4951.01 TCGA.F4.6704.01 TCGA.AZ.6599.01 TCGA.F5.6861.01 TCGA.CM.5860.01 TCGA.A6.6780.01
#> "03" "042" "011" "03" "011" "011"
#> TCGA.A6.2686.01 TCGA.CM.4750.01 TCGA.CM.6677.01 TCGA.A6.A567.01 TCGA.F5.6814.01 TCGA.D5.6898.01
#> "012" "011" "011" "0433" "011" "03"
#> TCGA.AG.A01W.01 TCGA.AZ.6598.11 TCGA.F5.6813.01 TCGA.AG.3732.01 TCGA.EI.6885.01 TCGA.G4.6299.01
#> "03" "021" "03" "042" "0433" "012"
#> TCGA.A6.4105.01 TCGA.DM.A1D8.01 TCGA.DM.A285.01 TCGA.G4.6295.11 TCGA.DC.4749.01 TCGA.DT.5265.01
#> "012" "011" "03" "023" "042" "012"
#> TCGA.5M.AAT5.01 TCGA.DM.A0XD.01 TCGA.A6.6138.01 TCGA.D5.7000.01 TCGA.DM.A28F.01 TCGA.DY.A1DE.01
#> "0432" "012" "011" "012" "011" "03"
#> TCGA.A6.6142.01 TCGA.QL.A97D.01 TCGA.CK.6748.01 TCGA.DC.6160.01 TCGA.D5.6534.01 TCGA.AZ.4616.01
#> "022" "03" "03" "042" "0413" "03"
#> TCGA.CK.6751.01 TCGA.CM.6171.01 TCGA.DM.A1DA.01 TCGA.AG.A020.11 TCGA.G4.6311.11 TCGA.G4.6625.11
#> "012" "012" "012" "021" "021" "021"
#> TCGA.F5.6863.01 TCGA.G4.6317.02 TCGA.G4.6317.01 TCGA.DM.A1D4.01 TCGA.AG.A01Y.11 TCGA.D5.6530.01
#> "042" "0432" "03" "011" "021" "03"
#> TCGA.CK.4948.01 TCGA.AD.A5EJ.01 TCGA.A6.6651.01 TCGA.CA.5256.01 TCGA.DM.A0X9.01 TCGA.AY.A69D.01
#> "0431" "012" "0412" "03" "011" "011"
#> TCGA.G4.6626.01 TCGA.CA.6716.01 TCGA.A6.2682.01 TCGA.A6.4107.11 TCGA.CA.6717.01 TCGA.G4.6293.01
#> "03" "011" "03" "023" "03" "03"
#> TCGA.CK.5916.01 TCGA.G4.6309.01 TCGA.AA.3662.01 TCGA.AF.A56L.01 TCGA.NH.A6GB.01 TCGA.AD.5900.01
#> "012" "042" "03" "03" "011" "03"
#> TCGA.NH.A50U.01 TCGA.AA.3712.01 TCGA.AZ.4614.01 TCGA.AH.6644.01 TCGA.AZ.6607.01 TCGA.AF.2693.01
#> "011" "03" "012" "011" "03" "0411"
#> TCGA.D5.6924.01 TCGA.CM.5868.01 TCGA.AF.4110.01 TCGA.A6.3809.01 TCGA.AZ.4313.01 TCGA.A6.2675.01
#> "03" "042" "0411" "012" "042" "042"
#> TCGA.AZ.6608.01 TCGA.CM.5864.01 TCGA.AA.3494.01 TCGA.AD.6895.01 TCGA.CI.6620.01 TCGA.DC.6156.01
#> "03" "011" "0432" "03" "03" "03"
#> TCGA.D5.6931.01 TCGA.CM.6165.01 TCGA.CM.5861.01 TCGA.A6.2671.01 TCGA.DC.6158.01 TCGA.AG.3742.01
#> "03" "03" "012" "03" "03" "011"
#> TCGA.AG.A02N.11 TCGA.G4.6307.01 TCGA.A6.5666.01 TCGA.EI.6511.01 TCGA.CI.6624.01 TCGA.AG.3591.01
#> "021" "0432" "011" "03" "042" "011"
#> TCGA.AY.A8YK.01 TCGA.F4.6856.01 TCGA.DM.A1D7.01 TCGA.A6.2685.01 TCGA.5M.AAT6.01 TCGA.AH.6643.01
#> "022" "03" "03" "022" "022" "011"
#> TCGA.F4.6569.01 TCGA.G4.6298.01 TCGA.AY.6196.01 TCGA.EI.6510.01 TCGA.A6.5656.01 TCGA.A6.2684.11
#> "03" "03" "03" "011" "011" "021"
#> TCGA.DY.A1DG.01 TCGA.AZ.4682.01 TCGA.EI.6884.01 TCGA.F4.6806.01 TCGA.G4.6320.11 TCGA.G4.6322.01
#> "011" "03" "03" "011" "021" "012"
#> TCGA.F5.6810.01 TCGA.5M.AAT4.01 TCGA.CL.4957.01 TCGA.DC.6681.01 TCGA.CM.6167.01 TCGA.AG.4022.01
#> "0431" "011" "03" "03" "0412" "03"
#> TCGA.G4.6586.01 TCGA.EI.6514.01 TCGA.CK.4950.01 TCGA.DM.A282.01 TCGA.DY.A1DC.01 TCGA.D5.6535.01
#> "012" "011" "03" "011" "03" "03"
#> TCGA.DM.A1HA.01 TCGA.DC.5869.01 TCGA.AZ.6599.11 TCGA.CM.4752.01 TCGA.AZ.4684.01 TCGA.EI.7004.01
#> "011" "03" "021" "042" "03" "03"
#> TCGA.A6.A565.01 TCGA.D5.6531.01 TCGA.AZ.6598.01 TCGA.AD.6890.01 TCGA.AG.4021.01 TCGA.A6.6781.01
#> "023" "012" "012" "03" "011" "0412"
#> TCGA.DM.A1D9.01 TCGA.CM.4744.01 TCGA.A6.2679.11 TCGA.A6.6652.01 TCGA.AD.6964.01 TCGA.SS.A7HO.01
#> "011" "011" "023" "011" "022" "011"
#> TCGA.A6.6650.01 TCGA.DM.A0XF.01 TCGA.G4.6295.01 TCGA.F4.6461.01 TCGA.AM.5820.01 TCGA.G4.6314.11
#> "011" "042" "0431" "012" "03" "021"
#> TCGA.AD.6889.01 TCGA.AZ.6605.01 TCGA.EI.6881.01 TCGA.NH.A50T.01 TCGA.AG.3725.11 TCGA.G4.6323.01
#> "012" "0414" "03" "011" "021" "03"
#> TCGA.AA.3663.01 TCGA.AD.6899.01 TCGA.A6.5667.11 TCGA.A6.A56B.01 TCGA.G5.6572.01 TCGA.DM.A280.01
#> "012" "011" "021" "011" "0411" "0413"
#> TCGA.AG.A020.01 TCGA.AA.3713.01 TCGA.D5.5539.01 TCGA.AA.3655.11 TCGA.AA.3489.01 TCGA.AA.3495.01
#> "03" "03" "011" "021" "0412" "03"
#> TCGA.AG.A01Y.01 TCGA.AZ.6601.01 TCGA.AH.6903.01 TCGA.AZ.6603.01 TCGA.CA.5254.01 TCGA.A6.A5ZU.01
#> "0433" "03" "03" "0432" "012" "03"
#> TCGA.G4.6302.01 TCGA.AZ.5403.01 TCGA.AY.A54L.01 TCGA.A6.4107.01 TCGA.NH.A5IV.01 TCGA.G4.6306.01
#> "0413" "022" "011" "012" "011" "011"
#> TCGA.AD.A5EK.01 TCGA.G5.6235.01 TCGA.DC.5337.01 TCGA.CM.6675.01 TCGA.AH.6544.01 TCGA.CK.6746.01
#> "011" "0411" "011" "012" "03" "012"
#> TCGA.CA.6718.01 TCGA.CI.6621.01 TCGA.CM.6676.01 TCGA.DM.A1DB.01 TCGA.A6.6654.01 TCGA.AA.3510.11
#> "03" "0411" "03" "03" "03" "023"
#> TCGA.CA.6715.01 TCGA.CM.5341.01 TCGA.CK.5912.01 TCGA.F4.6857.01 TCGA.QG.A5YW.01 TCGA.A6.5665.01
#> "03" "03" "03" "0413" "011" "012"
#> TCGA.CM.6168.01 TCGA.CL.5917.01 TCGA.AU.6004.01 TCGA.AY.5543.01 TCGA.AG.3731.01 TCGA.G4.6314.01
#> "03" "03" "03" "03" "03" "03"
#> TCGA.DC.6683.01 TCGA.CA.5796.01 TCGA.AG.A036.11 TCGA.AZ.4323.01 TCGA.EI.6882.01 TCGA.AZ.4315.01
#> "03" "03" "021" "0413" "011" "03"
#> TCGA.A6.2677.01 TCGA.DY.A1DF.01 TCGA.CM.6162.01 TCGA.F4.6703.01 TCGA.CM.5349.01 TCGA.AG.A02N.01
#> "011" "03" "022" "022" "03" "03"
#> TCGA.AA.3506.01 TCGA.D5.6932.01 TCGA.D5.6538.01 TCGA.AA.3488.11 TCGA.AA.3502.01 TCGA.NH.A8F8.01
#> "03" "03" "012" "021" "011" "03"
#> TCGA.AF.A56N.01 TCGA.AF.6672.01 TCGA.A6.2685.11 TCGA.A6.6141.01 TCGA.AD.6963.01 TCGA.G4.6298.11
#> "03" "0433" "021" "03" "042" "021"
#> TCGA.EI.6917.01 TCGA.QG.A5Z2.01 TCGA.A6.2684.01 TCGA.CK.5915.01 TCGA.CM.6163.01 TCGA.G4.6322.11
#> "03" "012" "03" "011" "03" "021"
#> TCGA.AY.6197.01 TCGA.D5.6928.01 TCGA.A6.3810.01 TCGA.G4.6294.01 TCGA.AA.3660.11 TCGA.A6.6137.01
#> "011" "0413" "042" "011" "021" "03"
#> TCGA.G4.6297.11 TCGA.AZ.4615.01 TCGA.CK.4952.01 TCGA.CM.6172.01 TCGA.AD.6901.01 TCGA.AA.3496.01
#> "021" "03" "012" "011" "03" "011"
#> TCGA.CK.5913.01 TCGA.DM.A28A.01 TCGA.EI.7002.01 TCGA.D5.6533.01 TCGA.QG.A5Z1.01 TCGA.D5.6923.01
#> "012" "011" "011" "03" "011" "0411"
#> TCGA.AF.2690.01 TCGA.DM.A28H.01 TCGA.G4.6320.01 TCGA.G4.6310.01 TCGA.DM.A28M.01 TCGA.DM.A288.01
#> "0414" "011" "012" "03" "011" "011"
#> TCGA.A6.2681.01 TCGA.A6.2679.01 TCGA.4N.A93T.01 TCGA.NH.A8F7.06 TCGA.NH.A8F7.01 TCGA.AZ.6600.11
#> "03" "03" "03" "03" "0432" "021"
#> TCGA.G5.6572.02 TCGA.AY.6386.01 TCGA.G4.6628.01 TCGA.A6.6653.01 TCGA.CM.4746.01 TCGA.F4.6855.01
#> "0414" "03" "03" "012" "03" "011"
#> TCGA.EF.5830.01 TCGA.NH.A6GA.01 TCGA.NH.A50V.01 TCGA.DY.A0XA.01 TCGA.DM.A28E.01 TCGA.AG.3725.01
#> "03" "011" "011" "042" "042" "03"
#> TCGA.CK.6747.01 TCGA.CL.5918.01 TCGA.CI.6623.01 TCGA.A6.5667.01 TCGA.DM.A28K.01 TCGA.AA.3713.11
#> "011" "011" "042" "03" "011" "023"
#> TCGA.AA.3655.01 TCGA.AU.3779.01 TCGA.A6.5664.01 TCGA.AA.3697.11 TCGA.AZ.5407.01 TCGA.CM.6169.01
#> "011" "042" "03" "023" "011" "03"
#> TCGA.AH.6547.01 TCGA.AZ.6601.11 TCGA.A6.5661.01 TCGA.F4.6807.01 TCGA.QG.A5YV.01 TCGA.AA.3509.11
#> "0412" "021" "012" "03" "011" "021"
#> TCGA.AY.A71X.01 TCGA.CA.5797.01 TCGA.F4.6460.01 TCGA.G4.6302.11 TCGA.F5.6702.01 TCGA.AH.6549.01
#> "011" "0431" "042" "023" "042" "011"
#> TCGA.D5.6927.01 TCGA.CM.6166.01 TCGA.AH.6897.01 TCGA.G4.6304.01 TCGA.CA.5255.01 TCGA.EI.6507.01
#> "0412" "011" "011" "0413" "03" "03"
#> TCGA.CK.4947.01 TCGA.D5.5540.01 TCGA.DC.6682.01 TCGA.G4.6321.01 TCGA.A6.6649.01 TCGA.CM.5348.01
#> "03" "011" "03" "03" "03" "03"
#> TCGA.EI.6513.01 TCGA.A6.2672.01 TCGA.D5.6539.01 TCGA.AA.3510.01 TCGA.G5.6233.01 TCGA.BM.6198.01
#> "0431" "012" "0411" "03" "011" "0414"
#> TCGA.CA.6719.01 TCGA.DC.6154.01 TCGA.DM.A1D6.01 TCGA.AG.3731.11 TCGA.CM.6674.01 TCGA.CM.4743.01
#> "011" "03" "03" "021" "0412" "0413"
#> TCGA.F5.6465.01 TCGA.D5.5537.01 TCGA.F4.6463.01 TCGA.A6.2686.11 TCGA.4T.AA8H.01 TCGA.A6.6782.01
#> "042" "011" "03" "021" "011" "03"
#> TCGA.AG.3592.01 TCGA.AD.6888.01 TCGA.CM.6678.01 TCGA.CM.5344.01 TCGA.AA.3495.11 TCGA.AG.A01W.11
#> "011" "03" "011" "042" "021" "021"
#> TCGA.F4.6809.01 TCGA.CK.5914.01 TCGA.AZ.4681.01 TCGA.AA.3492.01 TCGA.D5.6536.01 TCGA.AA.3506.11
#> "03" "011" "0432" "012" "03" "021"
#> TCGA.AA.3488.01 TCGA.AA.3502.11 TCGA.A6.6140.01 TCGA.D5.6529.01 TCGA.DM.A1D0.01 TCGA.DM.A1HB.01
#> "03" "023" "042" "03" "042" "012"
#> TCGA.D5.6920.01 TCGA.D5.6922.01 TCGA.EI.6508.01 TCGA.D5.6532.01 TCGA.5M.AATA.01 TCGA.EI.6509.01
#> "03" "03" "011" "011" "03" "042"
#> TCGA.G4.6311.01 TCGA.A6.A566.01 TCGA.G4.6625.01 TCGA.CI.6619.01 TCGA.F5.6864.01 TCGA.AA.3492.11
#> "03" "03" "03" "042" "03" "021"
#> TCGA.A6.5659.01 TCGA.WS.AB45.01 TCGA.G4.6315.01 TCGA.D5.6541.01 TCGA.A6.2680.01 TCGA.CM.4751.01
#> "012" "0413" "03" "03" "011" "03"
#> TCGA.CM.6680.01 TCGA.AF.6136.01 TCGA.AA.3660.01 TCGA.CM.4747.01 TCGA.EF.5831.01 TCGA.DM.A28G.01
#> "011" "03" "011" "011" "011" "011"
#> TCGA.G4.6297.01 TCGA.A6.2682.11 TCGA.D5.6537.01 TCGA.CM.6170.01 TCGA.DY.A1DD.01
#> "03" "021" "011" "03" "011"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 5533))
#> TCGA.AF.3911.01 TCGA.F4.6459.01 TCGA.AA.3494.11 TCGA.3L.AA1B.01 TCGA.D5.5538.01 TCGA.F4.6854.01
#> "03" "03" "023" "03" "03" "03"
#> TCGA.AG.A026.01 TCGA.G4.6303.01 TCGA.F5.6464.01 TCGA.T9.A92H.01 TCGA.AA.3712.11 TCGA.CM.5863.01
#> "011" "011" "0412" "011" "021" "03"
#> TCGA.AZ.4308.01 TCGA.AD.6965.01 TCGA.A6.2681.11 TCGA.AD.6548.01 TCGA.A6.5660.01 TCGA.AZ.6600.01
#> "042" "011" "021" "03" "011" "03"
#> TCGA.F4.6808.01 TCGA.D5.6540.01 TCGA.F5.6571.01 TCGA.D5.6926.01 TCGA.CM.4748.01 TCGA.A6.2675.11
#> "03" "012" "011" "03" "03" "021"
#> TCGA.5M.AATE.01 TCGA.D5.5541.01 TCGA.CM.5862.01 TCGA.AA.3511.01 TCGA.AA.3663.11 TCGA.CI.6622.01
#> "03" "042" "011" "03" "021" "011"
#> TCGA.EI.6506.01 TCGA.AM.5821.01 TCGA.F5.6812.01 TCGA.G4.6588.01 TCGA.EI.6512.01 TCGA.A6.6648.01
#> "03" "03" "0414" "012" "011" "042"
#> TCGA.A6.2671.11 TCGA.NH.A6GC.01 TCGA.F4.6805.01 TCGA.AA.3697.01 TCGA.QG.A5YX.01 TCGA.DM.A28C.01
#> "021" "03" "0412" "03" "011" "03"
#> TCGA.AG.A036.01 TCGA.AZ.6606.01 TCGA.F4.6570.01 TCGA.DC.4745.01 TCGA.AF.A56K.01 TCGA.G4.6627.01
#> "011" "012" "012" "03" "042" "0412"
#> TCGA.A6.5657.01 TCGA.A6.5662.01 TCGA.AA.3509.01 TCGA.D5.6929.01 TCGA.CM.6679.01 TCGA.A6.2680.11
#> "03" "03" "011" "042" "03" "021"
#> TCGA.DC.6157.01 TCGA.AF.6655.01 TCGA.CM.6161.01 TCGA.EI.6883.01 TCGA.F5.6811.01 TCGA.D5.6930.01
#> "0432" "042" "03" "011" "03" "03"
#> TCGA.CM.6164.01 TCGA.AF.2687.01 TCGA.DY.A1H8.01 TCGA.G5.6641.01 TCGA.DC.6155.01 TCGA.RU.A8FL.01
#> "042" "042" "03" "03" "03" "011"
#> TCGA.CK.4951.01 TCGA.F4.6704.01 TCGA.AZ.6599.01 TCGA.F5.6861.01 TCGA.CM.5860.01 TCGA.A6.6780.01
#> "03" "042" "011" "03" "011" "011"
#> TCGA.A6.2686.01 TCGA.CM.4750.01 TCGA.CM.6677.01 TCGA.A6.A567.01 TCGA.F5.6814.01 TCGA.D5.6898.01
#> "012" "011" "011" "0433" "011" "03"
#> TCGA.AG.A01W.01 TCGA.AZ.6598.11 TCGA.F5.6813.01 TCGA.AG.3732.01 TCGA.EI.6885.01 TCGA.G4.6299.01
#> "03" "021" "03" "042" "0433" "012"
#> TCGA.A6.4105.01 TCGA.DM.A1D8.01 TCGA.DM.A285.01 TCGA.G4.6295.11 TCGA.DC.4749.01 TCGA.DT.5265.01
#> "012" "011" "03" "023" "042" "012"
#> TCGA.5M.AAT5.01 TCGA.DM.A0XD.01 TCGA.A6.6138.01 TCGA.D5.7000.01 TCGA.DM.A28F.01 TCGA.DY.A1DE.01
#> "0432" "012" "011" "012" "011" "03"
#> TCGA.A6.6142.01 TCGA.QL.A97D.01 TCGA.CK.6748.01 TCGA.DC.6160.01 TCGA.D5.6534.01 TCGA.AZ.4616.01
#> "022" "03" "03" "042" "0413" "03"
#> TCGA.CK.6751.01 TCGA.CM.6171.01 TCGA.DM.A1DA.01 TCGA.AG.A020.11 TCGA.G4.6311.11 TCGA.G4.6625.11
#> "012" "012" "012" "021" "021" "021"
#> TCGA.F5.6863.01 TCGA.G4.6317.02 TCGA.G4.6317.01 TCGA.DM.A1D4.01 TCGA.AG.A01Y.11 TCGA.D5.6530.01
#> "042" "0432" "03" "011" "021" "03"
#> TCGA.CK.4948.01 TCGA.AD.A5EJ.01 TCGA.A6.6651.01 TCGA.CA.5256.01 TCGA.DM.A0X9.01 TCGA.AY.A69D.01
#> "0431" "012" "0412" "03" "011" "011"
#> TCGA.G4.6626.01 TCGA.CA.6716.01 TCGA.A6.2682.01 TCGA.A6.4107.11 TCGA.CA.6717.01 TCGA.G4.6293.01
#> "03" "011" "03" "023" "03" "03"
#> TCGA.CK.5916.01 TCGA.G4.6309.01 TCGA.AA.3662.01 TCGA.AF.A56L.01 TCGA.NH.A6GB.01 TCGA.AD.5900.01
#> "012" "042" "03" "03" "011" "03"
#> TCGA.NH.A50U.01 TCGA.AA.3712.01 TCGA.AZ.4614.01 TCGA.AH.6644.01 TCGA.AZ.6607.01 TCGA.AF.2693.01
#> "011" "03" "012" "011" "03" "0411"
#> TCGA.D5.6924.01 TCGA.CM.5868.01 TCGA.AF.4110.01 TCGA.A6.3809.01 TCGA.AZ.4313.01 TCGA.A6.2675.01
#> "03" "042" "0411" "012" "042" "042"
#> TCGA.AZ.6608.01 TCGA.CM.5864.01 TCGA.AA.3494.01 TCGA.AD.6895.01 TCGA.CI.6620.01 TCGA.DC.6156.01
#> "03" "011" "0432" "03" "03" "03"
#> TCGA.D5.6931.01 TCGA.CM.6165.01 TCGA.CM.5861.01 TCGA.A6.2671.01 TCGA.DC.6158.01 TCGA.AG.3742.01
#> "03" "03" "012" "03" "03" "011"
#> TCGA.AG.A02N.11 TCGA.G4.6307.01 TCGA.A6.5666.01 TCGA.EI.6511.01 TCGA.CI.6624.01 TCGA.AG.3591.01
#> "021" "0432" "011" "03" "042" "011"
#> TCGA.AY.A8YK.01 TCGA.F4.6856.01 TCGA.DM.A1D7.01 TCGA.A6.2685.01 TCGA.5M.AAT6.01 TCGA.AH.6643.01
#> "022" "03" "03" "022" "022" "011"
#> TCGA.F4.6569.01 TCGA.G4.6298.01 TCGA.AY.6196.01 TCGA.EI.6510.01 TCGA.A6.5656.01 TCGA.A6.2684.11
#> "03" "03" "03" "011" "011" "021"
#> TCGA.DY.A1DG.01 TCGA.AZ.4682.01 TCGA.EI.6884.01 TCGA.F4.6806.01 TCGA.G4.6320.11 TCGA.G4.6322.01
#> "011" "03" "03" "011" "021" "012"
#> TCGA.F5.6810.01 TCGA.5M.AAT4.01 TCGA.CL.4957.01 TCGA.DC.6681.01 TCGA.CM.6167.01 TCGA.AG.4022.01
#> "0431" "011" "03" "03" "0412" "03"
#> TCGA.G4.6586.01 TCGA.EI.6514.01 TCGA.CK.4950.01 TCGA.DM.A282.01 TCGA.DY.A1DC.01 TCGA.D5.6535.01
#> "012" "011" "03" "011" "03" "03"
#> TCGA.DM.A1HA.01 TCGA.DC.5869.01 TCGA.AZ.6599.11 TCGA.CM.4752.01 TCGA.AZ.4684.01 TCGA.EI.7004.01
#> "011" "03" "021" "042" "03" "03"
#> TCGA.A6.A565.01 TCGA.D5.6531.01 TCGA.AZ.6598.01 TCGA.AD.6890.01 TCGA.AG.4021.01 TCGA.A6.6781.01
#> "023" "012" "012" "03" "011" "0412"
#> TCGA.DM.A1D9.01 TCGA.CM.4744.01 TCGA.A6.2679.11 TCGA.A6.6652.01 TCGA.AD.6964.01 TCGA.SS.A7HO.01
#> "011" "011" "023" "011" "022" "011"
#> TCGA.A6.6650.01 TCGA.DM.A0XF.01 TCGA.G4.6295.01 TCGA.F4.6461.01 TCGA.AM.5820.01 TCGA.G4.6314.11
#> "011" "042" "0431" "012" "03" "021"
#> TCGA.AD.6889.01 TCGA.AZ.6605.01 TCGA.EI.6881.01 TCGA.NH.A50T.01 TCGA.AG.3725.11 TCGA.G4.6323.01
#> "012" "0414" "03" "011" "021" "03"
#> TCGA.AA.3663.01 TCGA.AD.6899.01 TCGA.A6.5667.11 TCGA.A6.A56B.01 TCGA.G5.6572.01 TCGA.DM.A280.01
#> "012" "011" "021" "011" "0411" "0413"
#> TCGA.AG.A020.01 TCGA.AA.3713.01 TCGA.D5.5539.01 TCGA.AA.3655.11 TCGA.AA.3489.01 TCGA.AA.3495.01
#> "03" "03" "011" "021" "0412" "03"
#> TCGA.AG.A01Y.01 TCGA.AZ.6601.01 TCGA.AH.6903.01 TCGA.AZ.6603.01 TCGA.CA.5254.01 TCGA.A6.A5ZU.01
#> "0433" "03" "03" "0432" "012" "03"
#> TCGA.G4.6302.01 TCGA.AZ.5403.01 TCGA.AY.A54L.01 TCGA.A6.4107.01 TCGA.NH.A5IV.01 TCGA.G4.6306.01
#> "0413" "022" "011" "012" "011" "011"
#> TCGA.AD.A5EK.01 TCGA.G5.6235.01 TCGA.DC.5337.01 TCGA.CM.6675.01 TCGA.AH.6544.01 TCGA.CK.6746.01
#> "011" "0411" "011" "012" "03" "012"
#> TCGA.CA.6718.01 TCGA.CI.6621.01 TCGA.CM.6676.01 TCGA.DM.A1DB.01 TCGA.A6.6654.01 TCGA.AA.3510.11
#> "03" "0411" "03" "03" "03" "023"
#> TCGA.CA.6715.01 TCGA.CM.5341.01 TCGA.CK.5912.01 TCGA.F4.6857.01 TCGA.QG.A5YW.01 TCGA.A6.5665.01
#> "03" "03" "03" "0413" "011" "012"
#> TCGA.CM.6168.01 TCGA.CL.5917.01 TCGA.AU.6004.01 TCGA.AY.5543.01 TCGA.AG.3731.01 TCGA.G4.6314.01
#> "03" "03" "03" "03" "03" "03"
#> TCGA.DC.6683.01 TCGA.CA.5796.01 TCGA.AG.A036.11 TCGA.AZ.4323.01 TCGA.EI.6882.01 TCGA.AZ.4315.01
#> "03" "03" "021" "0413" "011" "03"
#> TCGA.A6.2677.01 TCGA.DY.A1DF.01 TCGA.CM.6162.01 TCGA.F4.6703.01 TCGA.CM.5349.01 TCGA.AG.A02N.01
#> "011" "03" "022" "022" "03" "03"
#> TCGA.AA.3506.01 TCGA.D5.6932.01 TCGA.D5.6538.01 TCGA.AA.3488.11 TCGA.AA.3502.01 TCGA.NH.A8F8.01
#> "03" "03" "012" "021" "011" "03"
#> TCGA.AF.A56N.01 TCGA.AF.6672.01 TCGA.A6.2685.11 TCGA.A6.6141.01 TCGA.AD.6963.01 TCGA.G4.6298.11
#> "03" "0433" "021" "03" "042" "021"
#> TCGA.EI.6917.01 TCGA.QG.A5Z2.01 TCGA.A6.2684.01 TCGA.CK.5915.01 TCGA.CM.6163.01 TCGA.G4.6322.11
#> "03" "012" "03" "011" "03" "021"
#> TCGA.AY.6197.01 TCGA.D5.6928.01 TCGA.A6.3810.01 TCGA.G4.6294.01 TCGA.AA.3660.11 TCGA.A6.6137.01
#> "011" "0413" "042" "011" "021" "03"
#> TCGA.G4.6297.11 TCGA.AZ.4615.01 TCGA.CK.4952.01 TCGA.CM.6172.01 TCGA.AD.6901.01 TCGA.AA.3496.01
#> "021" "03" "012" "011" "03" "011"
#> TCGA.CK.5913.01 TCGA.DM.A28A.01 TCGA.EI.7002.01 TCGA.D5.6533.01 TCGA.QG.A5Z1.01 TCGA.D5.6923.01
#> "012" "011" "011" "03" "011" "0411"
#> TCGA.AF.2690.01 TCGA.DM.A28H.01 TCGA.G4.6320.01 TCGA.G4.6310.01 TCGA.DM.A28M.01 TCGA.DM.A288.01
#> "0414" "011" "012" "03" "011" "011"
#> TCGA.A6.2681.01 TCGA.A6.2679.01 TCGA.4N.A93T.01 TCGA.NH.A8F7.06 TCGA.NH.A8F7.01 TCGA.AZ.6600.11
#> "03" "03" "03" "03" "0432" "021"
#> TCGA.G5.6572.02 TCGA.AY.6386.01 TCGA.G4.6628.01 TCGA.A6.6653.01 TCGA.CM.4746.01 TCGA.F4.6855.01
#> "0414" "03" "03" "012" "03" "011"
#> TCGA.EF.5830.01 TCGA.NH.A6GA.01 TCGA.NH.A50V.01 TCGA.DY.A0XA.01 TCGA.DM.A28E.01 TCGA.AG.3725.01
#> "03" "011" "011" "042" "042" "03"
#> TCGA.CK.6747.01 TCGA.CL.5918.01 TCGA.CI.6623.01 TCGA.A6.5667.01 TCGA.DM.A28K.01 TCGA.AA.3713.11
#> "011" "011" "042" "03" "011" "023"
#> TCGA.AA.3655.01 TCGA.AU.3779.01 TCGA.A6.5664.01 TCGA.AA.3697.11 TCGA.AZ.5407.01 TCGA.CM.6169.01
#> "011" "042" "03" "023" "011" "03"
#> TCGA.AH.6547.01 TCGA.AZ.6601.11 TCGA.A6.5661.01 TCGA.F4.6807.01 TCGA.QG.A5YV.01 TCGA.AA.3509.11
#> "0412" "021" "012" "03" "011" "021"
#> TCGA.AY.A71X.01 TCGA.CA.5797.01 TCGA.F4.6460.01 TCGA.G4.6302.11 TCGA.F5.6702.01 TCGA.AH.6549.01
#> "011" "0431" "042" "023" "042" "011"
#> TCGA.D5.6927.01 TCGA.CM.6166.01 TCGA.AH.6897.01 TCGA.G4.6304.01 TCGA.CA.5255.01 TCGA.EI.6507.01
#> "0412" "011" "011" "0413" "03" "03"
#> TCGA.CK.4947.01 TCGA.D5.5540.01 TCGA.DC.6682.01 TCGA.G4.6321.01 TCGA.A6.6649.01 TCGA.CM.5348.01
#> "03" "011" "03" "03" "03" "03"
#> TCGA.EI.6513.01 TCGA.A6.2672.01 TCGA.D5.6539.01 TCGA.AA.3510.01 TCGA.G5.6233.01 TCGA.BM.6198.01
#> "0431" "012" "0411" "03" "011" "0414"
#> TCGA.CA.6719.01 TCGA.DC.6154.01 TCGA.DM.A1D6.01 TCGA.AG.3731.11 TCGA.CM.6674.01 TCGA.CM.4743.01
#> "011" "03" "03" "021" "0412" "0413"
#> TCGA.F5.6465.01 TCGA.D5.5537.01 TCGA.F4.6463.01 TCGA.A6.2686.11 TCGA.4T.AA8H.01 TCGA.A6.6782.01
#> "042" "011" "03" "021" "011" "03"
#> TCGA.AG.3592.01 TCGA.AD.6888.01 TCGA.CM.6678.01 TCGA.CM.5344.01 TCGA.AA.3495.11 TCGA.AG.A01W.11
#> "011" "03" "011" "042" "021" "021"
#> TCGA.F4.6809.01 TCGA.CK.5914.01 TCGA.AZ.4681.01 TCGA.AA.3492.01 TCGA.D5.6536.01 TCGA.AA.3506.11
#> "03" "011" "0432" "012" "03" "021"
#> TCGA.AA.3488.01 TCGA.AA.3502.11 TCGA.A6.6140.01 TCGA.D5.6529.01 TCGA.DM.A1D0.01 TCGA.DM.A1HB.01
#> "03" "023" "042" "03" "042" "012"
#> TCGA.D5.6920.01 TCGA.D5.6922.01 TCGA.EI.6508.01 TCGA.D5.6532.01 TCGA.5M.AATA.01 TCGA.EI.6509.01
#> "03" "03" "011" "011" "03" "042"
#> TCGA.G4.6311.01 TCGA.A6.A566.01 TCGA.G4.6625.01 TCGA.CI.6619.01 TCGA.F5.6864.01 TCGA.AA.3492.11
#> "03" "03" "03" "042" "03" "021"
#> TCGA.A6.5659.01 TCGA.WS.AB45.01 TCGA.G4.6315.01 TCGA.D5.6541.01 TCGA.A6.2680.01 TCGA.CM.4751.01
#> "012" "0413" "03" "03" "011" "03"
#> TCGA.CM.6680.01 TCGA.AF.6136.01 TCGA.AA.3660.01 TCGA.CM.4747.01 TCGA.EF.5831.01 TCGA.DM.A28G.01
#> "011" "03" "011" "011" "011" "011"
#> TCGA.G4.6297.01 TCGA.A6.2682.11 TCGA.D5.6537.01 TCGA.CM.6170.01 TCGA.DY.A1DD.01
#> "03" "021" "011" "03" "011"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 5908))
#> TCGA.AF.3911.01 TCGA.F4.6459.01 TCGA.AA.3494.11 TCGA.3L.AA1B.01 TCGA.D5.5538.01 TCGA.F4.6854.01
#> "03" "03" "023" "03" "03" "03"
#> TCGA.AG.A026.01 TCGA.G4.6303.01 TCGA.F5.6464.01 TCGA.T9.A92H.01 TCGA.AA.3712.11 TCGA.CM.5863.01
#> "011" "011" "0412" "011" "021" "03"
#> TCGA.AZ.4308.01 TCGA.AD.6965.01 TCGA.A6.2681.11 TCGA.AD.6548.01 TCGA.A6.5660.01 TCGA.AZ.6600.01
#> "042" "011" "021" "03" "011" "03"
#> TCGA.F4.6808.01 TCGA.D5.6540.01 TCGA.F5.6571.01 TCGA.D5.6926.01 TCGA.CM.4748.01 TCGA.A6.2675.11
#> "03" "012" "011" "03" "03" "021"
#> TCGA.5M.AATE.01 TCGA.D5.5541.01 TCGA.CM.5862.01 TCGA.AA.3511.01 TCGA.AA.3663.11 TCGA.CI.6622.01
#> "03" "042" "011" "03" "021" "011"
#> TCGA.EI.6506.01 TCGA.AM.5821.01 TCGA.F5.6812.01 TCGA.G4.6588.01 TCGA.EI.6512.01 TCGA.A6.6648.01
#> "03" "03" "0414" "012" "011" "042"
#> TCGA.A6.2671.11 TCGA.NH.A6GC.01 TCGA.F4.6805.01 TCGA.AA.3697.01 TCGA.QG.A5YX.01 TCGA.DM.A28C.01
#> "021" "03" "0412" "03" "011" "03"
#> TCGA.AG.A036.01 TCGA.AZ.6606.01 TCGA.F4.6570.01 TCGA.DC.4745.01 TCGA.AF.A56K.01 TCGA.G4.6627.01
#> "011" "012" "012" "03" "042" "0412"
#> TCGA.A6.5657.01 TCGA.A6.5662.01 TCGA.AA.3509.01 TCGA.D5.6929.01 TCGA.CM.6679.01 TCGA.A6.2680.11
#> "03" "03" "011" "042" "03" "021"
#> TCGA.DC.6157.01 TCGA.AF.6655.01 TCGA.CM.6161.01 TCGA.EI.6883.01 TCGA.F5.6811.01 TCGA.D5.6930.01
#> "0432" "042" "03" "011" "03" "03"
#> TCGA.CM.6164.01 TCGA.AF.2687.01 TCGA.DY.A1H8.01 TCGA.G5.6641.01 TCGA.DC.6155.01 TCGA.RU.A8FL.01
#> "042" "042" "03" "03" "03" "011"
#> TCGA.CK.4951.01 TCGA.F4.6704.01 TCGA.AZ.6599.01 TCGA.F5.6861.01 TCGA.CM.5860.01 TCGA.A6.6780.01
#> "03" "042" "011" "03" "011" "011"
#> TCGA.A6.2686.01 TCGA.CM.4750.01 TCGA.CM.6677.01 TCGA.A6.A567.01 TCGA.F5.6814.01 TCGA.D5.6898.01
#> "012" "011" "011" "0433" "011" "03"
#> TCGA.AG.A01W.01 TCGA.AZ.6598.11 TCGA.F5.6813.01 TCGA.AG.3732.01 TCGA.EI.6885.01 TCGA.G4.6299.01
#> "03" "021" "03" "042" "0433" "012"
#> TCGA.A6.4105.01 TCGA.DM.A1D8.01 TCGA.DM.A285.01 TCGA.G4.6295.11 TCGA.DC.4749.01 TCGA.DT.5265.01
#> "012" "011" "03" "023" "042" "012"
#> TCGA.5M.AAT5.01 TCGA.DM.A0XD.01 TCGA.A6.6138.01 TCGA.D5.7000.01 TCGA.DM.A28F.01 TCGA.DY.A1DE.01
#> "0432" "012" "011" "012" "011" "03"
#> TCGA.A6.6142.01 TCGA.QL.A97D.01 TCGA.CK.6748.01 TCGA.DC.6160.01 TCGA.D5.6534.01 TCGA.AZ.4616.01
#> "022" "03" "03" "042" "0413" "03"
#> TCGA.CK.6751.01 TCGA.CM.6171.01 TCGA.DM.A1DA.01 TCGA.AG.A020.11 TCGA.G4.6311.11 TCGA.G4.6625.11
#> "012" "012" "012" "021" "021" "021"
#> TCGA.F5.6863.01 TCGA.G4.6317.02 TCGA.G4.6317.01 TCGA.DM.A1D4.01 TCGA.AG.A01Y.11 TCGA.D5.6530.01
#> "042" "0432" "03" "011" "021" "03"
#> TCGA.CK.4948.01 TCGA.AD.A5EJ.01 TCGA.A6.6651.01 TCGA.CA.5256.01 TCGA.DM.A0X9.01 TCGA.AY.A69D.01
#> "0431" "012" "0412" "03" "011" "011"
#> TCGA.G4.6626.01 TCGA.CA.6716.01 TCGA.A6.2682.01 TCGA.A6.4107.11 TCGA.CA.6717.01 TCGA.G4.6293.01
#> "03" "011" "03" "023" "03" "03"
#> TCGA.CK.5916.01 TCGA.G4.6309.01 TCGA.AA.3662.01 TCGA.AF.A56L.01 TCGA.NH.A6GB.01 TCGA.AD.5900.01
#> "012" "042" "03" "03" "011" "03"
#> TCGA.NH.A50U.01 TCGA.AA.3712.01 TCGA.AZ.4614.01 TCGA.AH.6644.01 TCGA.AZ.6607.01 TCGA.AF.2693.01
#> "011" "03" "012" "011" "03" "0411"
#> TCGA.D5.6924.01 TCGA.CM.5868.01 TCGA.AF.4110.01 TCGA.A6.3809.01 TCGA.AZ.4313.01 TCGA.A6.2675.01
#> "03" "042" "0411" "012" "042" "042"
#> TCGA.AZ.6608.01 TCGA.CM.5864.01 TCGA.AA.3494.01 TCGA.AD.6895.01 TCGA.CI.6620.01 TCGA.DC.6156.01
#> "03" "011" "0432" "03" "03" "03"
#> TCGA.D5.6931.01 TCGA.CM.6165.01 TCGA.CM.5861.01 TCGA.A6.2671.01 TCGA.DC.6158.01 TCGA.AG.3742.01
#> "03" "03" "012" "03" "03" "011"
#> TCGA.AG.A02N.11 TCGA.G4.6307.01 TCGA.A6.5666.01 TCGA.EI.6511.01 TCGA.CI.6624.01 TCGA.AG.3591.01
#> "021" "0432" "011" "03" "042" "011"
#> TCGA.AY.A8YK.01 TCGA.F4.6856.01 TCGA.DM.A1D7.01 TCGA.A6.2685.01 TCGA.5M.AAT6.01 TCGA.AH.6643.01
#> "022" "03" "03" "022" "022" "011"
#> TCGA.F4.6569.01 TCGA.G4.6298.01 TCGA.AY.6196.01 TCGA.EI.6510.01 TCGA.A6.5656.01 TCGA.A6.2684.11
#> "03" "03" "03" "011" "011" "021"
#> TCGA.DY.A1DG.01 TCGA.AZ.4682.01 TCGA.EI.6884.01 TCGA.F4.6806.01 TCGA.G4.6320.11 TCGA.G4.6322.01
#> "011" "03" "03" "011" "021" "012"
#> TCGA.F5.6810.01 TCGA.5M.AAT4.01 TCGA.CL.4957.01 TCGA.DC.6681.01 TCGA.CM.6167.01 TCGA.AG.4022.01
#> "0431" "011" "03" "03" "0412" "03"
#> TCGA.G4.6586.01 TCGA.EI.6514.01 TCGA.CK.4950.01 TCGA.DM.A282.01 TCGA.DY.A1DC.01 TCGA.D5.6535.01
#> "012" "011" "03" "011" "03" "03"
#> TCGA.DM.A1HA.01 TCGA.DC.5869.01 TCGA.AZ.6599.11 TCGA.CM.4752.01 TCGA.AZ.4684.01 TCGA.EI.7004.01
#> "011" "03" "021" "042" "03" "03"
#> TCGA.A6.A565.01 TCGA.D5.6531.01 TCGA.AZ.6598.01 TCGA.AD.6890.01 TCGA.AG.4021.01 TCGA.A6.6781.01
#> "023" "012" "012" "03" "011" "0412"
#> TCGA.DM.A1D9.01 TCGA.CM.4744.01 TCGA.A6.2679.11 TCGA.A6.6652.01 TCGA.AD.6964.01 TCGA.SS.A7HO.01
#> "011" "011" "023" "011" "022" "011"
#> TCGA.A6.6650.01 TCGA.DM.A0XF.01 TCGA.G4.6295.01 TCGA.F4.6461.01 TCGA.AM.5820.01 TCGA.G4.6314.11
#> "011" "042" "0431" "012" "03" "021"
#> TCGA.AD.6889.01 TCGA.AZ.6605.01 TCGA.EI.6881.01 TCGA.NH.A50T.01 TCGA.AG.3725.11 TCGA.G4.6323.01
#> "012" "0414" "03" "011" "021" "03"
#> TCGA.AA.3663.01 TCGA.AD.6899.01 TCGA.A6.5667.11 TCGA.A6.A56B.01 TCGA.G5.6572.01 TCGA.DM.A280.01
#> "012" "011" "021" "011" "0411" "0413"
#> TCGA.AG.A020.01 TCGA.AA.3713.01 TCGA.D5.5539.01 TCGA.AA.3655.11 TCGA.AA.3489.01 TCGA.AA.3495.01
#> "03" "03" "011" "021" "0412" "03"
#> TCGA.AG.A01Y.01 TCGA.AZ.6601.01 TCGA.AH.6903.01 TCGA.AZ.6603.01 TCGA.CA.5254.01 TCGA.A6.A5ZU.01
#> "0433" "03" "03" "0432" "012" "03"
#> TCGA.G4.6302.01 TCGA.AZ.5403.01 TCGA.AY.A54L.01 TCGA.A6.4107.01 TCGA.NH.A5IV.01 TCGA.G4.6306.01
#> "0413" "022" "011" "012" "011" "011"
#> TCGA.AD.A5EK.01 TCGA.G5.6235.01 TCGA.DC.5337.01 TCGA.CM.6675.01 TCGA.AH.6544.01 TCGA.CK.6746.01
#> "011" "0411" "011" "012" "03" "012"
#> TCGA.CA.6718.01 TCGA.CI.6621.01 TCGA.CM.6676.01 TCGA.DM.A1DB.01 TCGA.A6.6654.01 TCGA.AA.3510.11
#> "03" "0411" "03" "03" "03" "023"
#> TCGA.CA.6715.01 TCGA.CM.5341.01 TCGA.CK.5912.01 TCGA.F4.6857.01 TCGA.QG.A5YW.01 TCGA.A6.5665.01
#> "03" "03" "03" "0413" "011" "012"
#> TCGA.CM.6168.01 TCGA.CL.5917.01 TCGA.AU.6004.01 TCGA.AY.5543.01 TCGA.AG.3731.01 TCGA.G4.6314.01
#> "03" "03" "03" "03" "03" "03"
#> TCGA.DC.6683.01 TCGA.CA.5796.01 TCGA.AG.A036.11 TCGA.AZ.4323.01 TCGA.EI.6882.01 TCGA.AZ.4315.01
#> "03" "03" "021" "0413" "011" "03"
#> TCGA.A6.2677.01 TCGA.DY.A1DF.01 TCGA.CM.6162.01 TCGA.F4.6703.01 TCGA.CM.5349.01 TCGA.AG.A02N.01
#> "011" "03" "022" "022" "03" "03"
#> TCGA.AA.3506.01 TCGA.D5.6932.01 TCGA.D5.6538.01 TCGA.AA.3488.11 TCGA.AA.3502.01 TCGA.NH.A8F8.01
#> "03" "03" "012" "021" "011" "03"
#> TCGA.AF.A56N.01 TCGA.AF.6672.01 TCGA.A6.2685.11 TCGA.A6.6141.01 TCGA.AD.6963.01 TCGA.G4.6298.11
#> "03" "0433" "021" "03" "042" "021"
#> TCGA.EI.6917.01 TCGA.QG.A5Z2.01 TCGA.A6.2684.01 TCGA.CK.5915.01 TCGA.CM.6163.01 TCGA.G4.6322.11
#> "03" "012" "03" "011" "03" "021"
#> TCGA.AY.6197.01 TCGA.D5.6928.01 TCGA.A6.3810.01 TCGA.G4.6294.01 TCGA.AA.3660.11 TCGA.A6.6137.01
#> "011" "0413" "042" "011" "021" "03"
#> TCGA.G4.6297.11 TCGA.AZ.4615.01 TCGA.CK.4952.01 TCGA.CM.6172.01 TCGA.AD.6901.01 TCGA.AA.3496.01
#> "021" "03" "012" "011" "03" "011"
#> TCGA.CK.5913.01 TCGA.DM.A28A.01 TCGA.EI.7002.01 TCGA.D5.6533.01 TCGA.QG.A5Z1.01 TCGA.D5.6923.01
#> "012" "011" "011" "03" "011" "0411"
#> TCGA.AF.2690.01 TCGA.DM.A28H.01 TCGA.G4.6320.01 TCGA.G4.6310.01 TCGA.DM.A28M.01 TCGA.DM.A288.01
#> "0414" "011" "012" "03" "011" "011"
#> TCGA.A6.2681.01 TCGA.A6.2679.01 TCGA.4N.A93T.01 TCGA.NH.A8F7.06 TCGA.NH.A8F7.01 TCGA.AZ.6600.11
#> "03" "03" "03" "03" "0432" "021"
#> TCGA.G5.6572.02 TCGA.AY.6386.01 TCGA.G4.6628.01 TCGA.A6.6653.01 TCGA.CM.4746.01 TCGA.F4.6855.01
#> "0414" "03" "03" "012" "03" "011"
#> TCGA.EF.5830.01 TCGA.NH.A6GA.01 TCGA.NH.A50V.01 TCGA.DY.A0XA.01 TCGA.DM.A28E.01 TCGA.AG.3725.01
#> "03" "011" "011" "042" "042" "03"
#> TCGA.CK.6747.01 TCGA.CL.5918.01 TCGA.CI.6623.01 TCGA.A6.5667.01 TCGA.DM.A28K.01 TCGA.AA.3713.11
#> "011" "011" "042" "03" "011" "023"
#> TCGA.AA.3655.01 TCGA.AU.3779.01 TCGA.A6.5664.01 TCGA.AA.3697.11 TCGA.AZ.5407.01 TCGA.CM.6169.01
#> "011" "042" "03" "023" "011" "03"
#> TCGA.AH.6547.01 TCGA.AZ.6601.11 TCGA.A6.5661.01 TCGA.F4.6807.01 TCGA.QG.A5YV.01 TCGA.AA.3509.11
#> "0412" "021" "012" "03" "011" "021"
#> TCGA.AY.A71X.01 TCGA.CA.5797.01 TCGA.F4.6460.01 TCGA.G4.6302.11 TCGA.F5.6702.01 TCGA.AH.6549.01
#> "011" "0431" "042" "023" "042" "011"
#> TCGA.D5.6927.01 TCGA.CM.6166.01 TCGA.AH.6897.01 TCGA.G4.6304.01 TCGA.CA.5255.01 TCGA.EI.6507.01
#> "0412" "011" "011" "0413" "03" "03"
#> TCGA.CK.4947.01 TCGA.D5.5540.01 TCGA.DC.6682.01 TCGA.G4.6321.01 TCGA.A6.6649.01 TCGA.CM.5348.01
#> "03" "011" "03" "03" "03" "03"
#> TCGA.EI.6513.01 TCGA.A6.2672.01 TCGA.D5.6539.01 TCGA.AA.3510.01 TCGA.G5.6233.01 TCGA.BM.6198.01
#> "0431" "012" "0411" "03" "011" "0414"
#> TCGA.CA.6719.01 TCGA.DC.6154.01 TCGA.DM.A1D6.01 TCGA.AG.3731.11 TCGA.CM.6674.01 TCGA.CM.4743.01
#> "011" "03" "03" "021" "0412" "0413"
#> TCGA.F5.6465.01 TCGA.D5.5537.01 TCGA.F4.6463.01 TCGA.A6.2686.11 TCGA.4T.AA8H.01 TCGA.A6.6782.01
#> "042" "011" "03" "021" "011" "03"
#> TCGA.AG.3592.01 TCGA.AD.6888.01 TCGA.CM.6678.01 TCGA.CM.5344.01 TCGA.AA.3495.11 TCGA.AG.A01W.11
#> "011" "03" "011" "042" "021" "021"
#> TCGA.F4.6809.01 TCGA.CK.5914.01 TCGA.AZ.4681.01 TCGA.AA.3492.01 TCGA.D5.6536.01 TCGA.AA.3506.11
#> "03" "011" "0432" "012" "03" "021"
#> TCGA.AA.3488.01 TCGA.AA.3502.11 TCGA.A6.6140.01 TCGA.D5.6529.01 TCGA.DM.A1D0.01 TCGA.DM.A1HB.01
#> "03" "023" "042" "03" "042" "012"
#> TCGA.D5.6920.01 TCGA.D5.6922.01 TCGA.EI.6508.01 TCGA.D5.6532.01 TCGA.5M.AATA.01 TCGA.EI.6509.01
#> "03" "03" "011" "011" "03" "042"
#> TCGA.G4.6311.01 TCGA.A6.A566.01 TCGA.G4.6625.01 TCGA.CI.6619.01 TCGA.F5.6864.01 TCGA.AA.3492.11
#> "03" "03" "03" "042" "03" "021"
#> TCGA.A6.5659.01 TCGA.WS.AB45.01 TCGA.G4.6315.01 TCGA.D5.6541.01 TCGA.A6.2680.01 TCGA.CM.4751.01
#> "012" "0413" "03" "03" "011" "03"
#> TCGA.CM.6680.01 TCGA.AF.6136.01 TCGA.AA.3660.01 TCGA.CM.4747.01 TCGA.EF.5831.01 TCGA.DM.A28G.01
#> "011" "03" "011" "011" "011" "011"
#> TCGA.G4.6297.01 TCGA.A6.2682.11 TCGA.D5.6537.01 TCGA.CM.6170.01 TCGA.DY.A1DD.01
#> "03" "021" "011" "03" "011"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 7485))
#> TCGA.AF.3911.01 TCGA.F4.6459.01 TCGA.AA.3494.11 TCGA.3L.AA1B.01 TCGA.D5.5538.01 TCGA.F4.6854.01
#> "03" "03" "023" "03" "03" "03"
#> TCGA.AG.A026.01 TCGA.G4.6303.01 TCGA.F5.6464.01 TCGA.T9.A92H.01 TCGA.AA.3712.11 TCGA.CM.5863.01
#> "011" "011" "0412" "011" "021" "03"
#> TCGA.AZ.4308.01 TCGA.AD.6965.01 TCGA.A6.2681.11 TCGA.AD.6548.01 TCGA.A6.5660.01 TCGA.AZ.6600.01
#> "042" "011" "021" "03" "011" "03"
#> TCGA.F4.6808.01 TCGA.D5.6540.01 TCGA.F5.6571.01 TCGA.D5.6926.01 TCGA.CM.4748.01 TCGA.A6.2675.11
#> "03" "012" "011" "03" "03" "021"
#> TCGA.5M.AATE.01 TCGA.D5.5541.01 TCGA.CM.5862.01 TCGA.AA.3511.01 TCGA.AA.3663.11 TCGA.CI.6622.01
#> "03" "042" "011" "03" "021" "011"
#> TCGA.EI.6506.01 TCGA.AM.5821.01 TCGA.F5.6812.01 TCGA.G4.6588.01 TCGA.EI.6512.01 TCGA.A6.6648.01
#> "03" "03" "0414" "012" "011" "042"
#> TCGA.A6.2671.11 TCGA.NH.A6GC.01 TCGA.F4.6805.01 TCGA.AA.3697.01 TCGA.QG.A5YX.01 TCGA.DM.A28C.01
#> "021" "03" "0412" "03" "011" "03"
#> TCGA.AG.A036.01 TCGA.AZ.6606.01 TCGA.F4.6570.01 TCGA.DC.4745.01 TCGA.AF.A56K.01 TCGA.G4.6627.01
#> "011" "012" "012" "03" "042" "0412"
#> TCGA.A6.5657.01 TCGA.A6.5662.01 TCGA.AA.3509.01 TCGA.D5.6929.01 TCGA.CM.6679.01 TCGA.A6.2680.11
#> "03" "03" "011" "042" "03" "021"
#> TCGA.DC.6157.01 TCGA.AF.6655.01 TCGA.CM.6161.01 TCGA.EI.6883.01 TCGA.F5.6811.01 TCGA.D5.6930.01
#> "0432" "042" "03" "011" "03" "03"
#> TCGA.CM.6164.01 TCGA.AF.2687.01 TCGA.DY.A1H8.01 TCGA.G5.6641.01 TCGA.DC.6155.01 TCGA.RU.A8FL.01
#> "042" "042" "03" "03" "03" "011"
#> TCGA.CK.4951.01 TCGA.F4.6704.01 TCGA.AZ.6599.01 TCGA.F5.6861.01 TCGA.CM.5860.01 TCGA.A6.6780.01
#> "03" "042" "011" "03" "011" "011"
#> TCGA.A6.2686.01 TCGA.CM.4750.01 TCGA.CM.6677.01 TCGA.A6.A567.01 TCGA.F5.6814.01 TCGA.D5.6898.01
#> "012" "011" "011" "0433" "011" "03"
#> TCGA.AG.A01W.01 TCGA.AZ.6598.11 TCGA.F5.6813.01 TCGA.AG.3732.01 TCGA.EI.6885.01 TCGA.G4.6299.01
#> "03" "021" "03" "042" "0433" "012"
#> TCGA.A6.4105.01 TCGA.DM.A1D8.01 TCGA.DM.A285.01 TCGA.G4.6295.11 TCGA.DC.4749.01 TCGA.DT.5265.01
#> "012" "011" "03" "023" "042" "012"
#> TCGA.5M.AAT5.01 TCGA.DM.A0XD.01 TCGA.A6.6138.01 TCGA.D5.7000.01 TCGA.DM.A28F.01 TCGA.DY.A1DE.01
#> "0432" "012" "011" "012" "011" "03"
#> TCGA.A6.6142.01 TCGA.QL.A97D.01 TCGA.CK.6748.01 TCGA.DC.6160.01 TCGA.D5.6534.01 TCGA.AZ.4616.01
#> "022" "03" "03" "042" "0413" "03"
#> TCGA.CK.6751.01 TCGA.CM.6171.01 TCGA.DM.A1DA.01 TCGA.AG.A020.11 TCGA.G4.6311.11 TCGA.G4.6625.11
#> "012" "012" "012" "021" "021" "021"
#> TCGA.F5.6863.01 TCGA.G4.6317.02 TCGA.G4.6317.01 TCGA.DM.A1D4.01 TCGA.AG.A01Y.11 TCGA.D5.6530.01
#> "042" "0432" "03" "011" "021" "03"
#> TCGA.CK.4948.01 TCGA.AD.A5EJ.01 TCGA.A6.6651.01 TCGA.CA.5256.01 TCGA.DM.A0X9.01 TCGA.AY.A69D.01
#> "0431" "012" "0412" "03" "011" "011"
#> TCGA.G4.6626.01 TCGA.CA.6716.01 TCGA.A6.2682.01 TCGA.A6.4107.11 TCGA.CA.6717.01 TCGA.G4.6293.01
#> "03" "011" "03" "023" "03" "03"
#> TCGA.CK.5916.01 TCGA.G4.6309.01 TCGA.AA.3662.01 TCGA.AF.A56L.01 TCGA.NH.A6GB.01 TCGA.AD.5900.01
#> "012" "042" "03" "03" "011" "03"
#> TCGA.NH.A50U.01 TCGA.AA.3712.01 TCGA.AZ.4614.01 TCGA.AH.6644.01 TCGA.AZ.6607.01 TCGA.AF.2693.01
#> "011" "03" "012" "011" "03" "0411"
#> TCGA.D5.6924.01 TCGA.CM.5868.01 TCGA.AF.4110.01 TCGA.A6.3809.01 TCGA.AZ.4313.01 TCGA.A6.2675.01
#> "03" "042" "0411" "012" "042" "042"
#> TCGA.AZ.6608.01 TCGA.CM.5864.01 TCGA.AA.3494.01 TCGA.AD.6895.01 TCGA.CI.6620.01 TCGA.DC.6156.01
#> "03" "011" "0432" "03" "03" "03"
#> TCGA.D5.6931.01 TCGA.CM.6165.01 TCGA.CM.5861.01 TCGA.A6.2671.01 TCGA.DC.6158.01 TCGA.AG.3742.01
#> "03" "03" "012" "03" "03" "011"
#> TCGA.AG.A02N.11 TCGA.G4.6307.01 TCGA.A6.5666.01 TCGA.EI.6511.01 TCGA.CI.6624.01 TCGA.AG.3591.01
#> "021" "0432" "011" "03" "042" "011"
#> TCGA.AY.A8YK.01 TCGA.F4.6856.01 TCGA.DM.A1D7.01 TCGA.A6.2685.01 TCGA.5M.AAT6.01 TCGA.AH.6643.01
#> "022" "03" "03" "022" "022" "011"
#> TCGA.F4.6569.01 TCGA.G4.6298.01 TCGA.AY.6196.01 TCGA.EI.6510.01 TCGA.A6.5656.01 TCGA.A6.2684.11
#> "03" "03" "03" "011" "011" "021"
#> TCGA.DY.A1DG.01 TCGA.AZ.4682.01 TCGA.EI.6884.01 TCGA.F4.6806.01 TCGA.G4.6320.11 TCGA.G4.6322.01
#> "011" "03" "03" "011" "021" "012"
#> TCGA.F5.6810.01 TCGA.5M.AAT4.01 TCGA.CL.4957.01 TCGA.DC.6681.01 TCGA.CM.6167.01 TCGA.AG.4022.01
#> "0431" "011" "03" "03" "0412" "03"
#> TCGA.G4.6586.01 TCGA.EI.6514.01 TCGA.CK.4950.01 TCGA.DM.A282.01 TCGA.DY.A1DC.01 TCGA.D5.6535.01
#> "012" "011" "03" "011" "03" "03"
#> TCGA.DM.A1HA.01 TCGA.DC.5869.01 TCGA.AZ.6599.11 TCGA.CM.4752.01 TCGA.AZ.4684.01 TCGA.EI.7004.01
#> "011" "03" "021" "042" "03" "03"
#> TCGA.A6.A565.01 TCGA.D5.6531.01 TCGA.AZ.6598.01 TCGA.AD.6890.01 TCGA.AG.4021.01 TCGA.A6.6781.01
#> "023" "012" "012" "03" "011" "0412"
#> TCGA.DM.A1D9.01 TCGA.CM.4744.01 TCGA.A6.2679.11 TCGA.A6.6652.01 TCGA.AD.6964.01 TCGA.SS.A7HO.01
#> "011" "011" "023" "011" "022" "011"
#> TCGA.A6.6650.01 TCGA.DM.A0XF.01 TCGA.G4.6295.01 TCGA.F4.6461.01 TCGA.AM.5820.01 TCGA.G4.6314.11
#> "011" "042" "0431" "012" "03" "021"
#> TCGA.AD.6889.01 TCGA.AZ.6605.01 TCGA.EI.6881.01 TCGA.NH.A50T.01 TCGA.AG.3725.11 TCGA.G4.6323.01
#> "012" "0414" "03" "011" "021" "03"
#> TCGA.AA.3663.01 TCGA.AD.6899.01 TCGA.A6.5667.11 TCGA.A6.A56B.01 TCGA.G5.6572.01 TCGA.DM.A280.01
#> "012" "011" "021" "011" "0411" "0413"
#> TCGA.AG.A020.01 TCGA.AA.3713.01 TCGA.D5.5539.01 TCGA.AA.3655.11 TCGA.AA.3489.01 TCGA.AA.3495.01
#> "03" "03" "011" "021" "0412" "03"
#> TCGA.AG.A01Y.01 TCGA.AZ.6601.01 TCGA.AH.6903.01 TCGA.AZ.6603.01 TCGA.CA.5254.01 TCGA.A6.A5ZU.01
#> "0433" "03" "03" "0432" "012" "03"
#> TCGA.G4.6302.01 TCGA.AZ.5403.01 TCGA.AY.A54L.01 TCGA.A6.4107.01 TCGA.NH.A5IV.01 TCGA.G4.6306.01
#> "0413" "022" "011" "012" "011" "011"
#> TCGA.AD.A5EK.01 TCGA.G5.6235.01 TCGA.DC.5337.01 TCGA.CM.6675.01 TCGA.AH.6544.01 TCGA.CK.6746.01
#> "011" "0411" "011" "012" "03" "012"
#> TCGA.CA.6718.01 TCGA.CI.6621.01 TCGA.CM.6676.01 TCGA.DM.A1DB.01 TCGA.A6.6654.01 TCGA.AA.3510.11
#> "03" "0411" "03" "03" "03" "023"
#> TCGA.CA.6715.01 TCGA.CM.5341.01 TCGA.CK.5912.01 TCGA.F4.6857.01 TCGA.QG.A5YW.01 TCGA.A6.5665.01
#> "03" "03" "03" "0413" "011" "012"
#> TCGA.CM.6168.01 TCGA.CL.5917.01 TCGA.AU.6004.01 TCGA.AY.5543.01 TCGA.AG.3731.01 TCGA.G4.6314.01
#> "03" "03" "03" "03" "03" "03"
#> TCGA.DC.6683.01 TCGA.CA.5796.01 TCGA.AG.A036.11 TCGA.AZ.4323.01 TCGA.EI.6882.01 TCGA.AZ.4315.01
#> "03" "03" "021" "0413" "011" "03"
#> TCGA.A6.2677.01 TCGA.DY.A1DF.01 TCGA.CM.6162.01 TCGA.F4.6703.01 TCGA.CM.5349.01 TCGA.AG.A02N.01
#> "011" "03" "022" "022" "03" "03"
#> TCGA.AA.3506.01 TCGA.D5.6932.01 TCGA.D5.6538.01 TCGA.AA.3488.11 TCGA.AA.3502.01 TCGA.NH.A8F8.01
#> "03" "03" "012" "021" "011" "03"
#> TCGA.AF.A56N.01 TCGA.AF.6672.01 TCGA.A6.2685.11 TCGA.A6.6141.01 TCGA.AD.6963.01 TCGA.G4.6298.11
#> "03" "0433" "021" "03" "042" "021"
#> TCGA.EI.6917.01 TCGA.QG.A5Z2.01 TCGA.A6.2684.01 TCGA.CK.5915.01 TCGA.CM.6163.01 TCGA.G4.6322.11
#> "03" "012" "03" "011" "03" "021"
#> TCGA.AY.6197.01 TCGA.D5.6928.01 TCGA.A6.3810.01 TCGA.G4.6294.01 TCGA.AA.3660.11 TCGA.A6.6137.01
#> "011" "0413" "042" "011" "021" "03"
#> TCGA.G4.6297.11 TCGA.AZ.4615.01 TCGA.CK.4952.01 TCGA.CM.6172.01 TCGA.AD.6901.01 TCGA.AA.3496.01
#> "021" "03" "012" "011" "03" "011"
#> TCGA.CK.5913.01 TCGA.DM.A28A.01 TCGA.EI.7002.01 TCGA.D5.6533.01 TCGA.QG.A5Z1.01 TCGA.D5.6923.01
#> "012" "011" "011" "03" "011" "0411"
#> TCGA.AF.2690.01 TCGA.DM.A28H.01 TCGA.G4.6320.01 TCGA.G4.6310.01 TCGA.DM.A28M.01 TCGA.DM.A288.01
#> "0414" "011" "012" "03" "011" "011"
#> TCGA.A6.2681.01 TCGA.A6.2679.01 TCGA.4N.A93T.01 TCGA.NH.A8F7.06 TCGA.NH.A8F7.01 TCGA.AZ.6600.11
#> "03" "03" "03" "03" "0432" "021"
#> TCGA.G5.6572.02 TCGA.AY.6386.01 TCGA.G4.6628.01 TCGA.A6.6653.01 TCGA.CM.4746.01 TCGA.F4.6855.01
#> "0414" "03" "03" "012" "03" "011"
#> TCGA.EF.5830.01 TCGA.NH.A6GA.01 TCGA.NH.A50V.01 TCGA.DY.A0XA.01 TCGA.DM.A28E.01 TCGA.AG.3725.01
#> "03" "011" "011" "042" "042" "03"
#> TCGA.CK.6747.01 TCGA.CL.5918.01 TCGA.CI.6623.01 TCGA.A6.5667.01 TCGA.DM.A28K.01 TCGA.AA.3713.11
#> "011" "011" "042" "03" "011" "023"
#> TCGA.AA.3655.01 TCGA.AU.3779.01 TCGA.A6.5664.01 TCGA.AA.3697.11 TCGA.AZ.5407.01 TCGA.CM.6169.01
#> "011" "042" "03" "023" "011" "03"
#> TCGA.AH.6547.01 TCGA.AZ.6601.11 TCGA.A6.5661.01 TCGA.F4.6807.01 TCGA.QG.A5YV.01 TCGA.AA.3509.11
#> "0412" "021" "012" "03" "011" "021"
#> TCGA.AY.A71X.01 TCGA.CA.5797.01 TCGA.F4.6460.01 TCGA.G4.6302.11 TCGA.F5.6702.01 TCGA.AH.6549.01
#> "011" "0431" "042" "023" "042" "011"
#> TCGA.D5.6927.01 TCGA.CM.6166.01 TCGA.AH.6897.01 TCGA.G4.6304.01 TCGA.CA.5255.01 TCGA.EI.6507.01
#> "0412" "011" "011" "0413" "03" "03"
#> TCGA.CK.4947.01 TCGA.D5.5540.01 TCGA.DC.6682.01 TCGA.G4.6321.01 TCGA.A6.6649.01 TCGA.CM.5348.01
#> "03" "011" "03" "03" "03" "03"
#> TCGA.EI.6513.01 TCGA.A6.2672.01 TCGA.D5.6539.01 TCGA.AA.3510.01 TCGA.G5.6233.01 TCGA.BM.6198.01
#> "0431" "012" "0411" "03" "011" "0414"
#> TCGA.CA.6719.01 TCGA.DC.6154.01 TCGA.DM.A1D6.01 TCGA.AG.3731.11 TCGA.CM.6674.01 TCGA.CM.4743.01
#> "011" "03" "03" "021" "0412" "0413"
#> TCGA.F5.6465.01 TCGA.D5.5537.01 TCGA.F4.6463.01 TCGA.A6.2686.11 TCGA.4T.AA8H.01 TCGA.A6.6782.01
#> "042" "011" "03" "021" "011" "03"
#> TCGA.AG.3592.01 TCGA.AD.6888.01 TCGA.CM.6678.01 TCGA.CM.5344.01 TCGA.AA.3495.11 TCGA.AG.A01W.11
#> "011" "03" "011" "042" "021" "021"
#> TCGA.F4.6809.01 TCGA.CK.5914.01 TCGA.AZ.4681.01 TCGA.AA.3492.01 TCGA.D5.6536.01 TCGA.AA.3506.11
#> "03" "011" "0432" "012" "03" "021"
#> TCGA.AA.3488.01 TCGA.AA.3502.11 TCGA.A6.6140.01 TCGA.D5.6529.01 TCGA.DM.A1D0.01 TCGA.DM.A1HB.01
#> "03" "023" "042" "03" "042" "012"
#> TCGA.D5.6920.01 TCGA.D5.6922.01 TCGA.EI.6508.01 TCGA.D5.6532.01 TCGA.5M.AATA.01 TCGA.EI.6509.01
#> "03" "03" "011" "011" "03" "042"
#> TCGA.G4.6311.01 TCGA.A6.A566.01 TCGA.G4.6625.01 TCGA.CI.6619.01 TCGA.F5.6864.01 TCGA.AA.3492.11
#> "03" "03" "03" "042" "03" "021"
#> TCGA.A6.5659.01 TCGA.WS.AB45.01 TCGA.G4.6315.01 TCGA.D5.6541.01 TCGA.A6.2680.01 TCGA.CM.4751.01
#> "012" "0413" "03" "03" "011" "03"
#> TCGA.CM.6680.01 TCGA.AF.6136.01 TCGA.AA.3660.01 TCGA.CM.4747.01 TCGA.EF.5831.01 TCGA.DM.A28G.01
#> "011" "03" "011" "011" "011" "011"
#> TCGA.G4.6297.01 TCGA.A6.2682.11 TCGA.D5.6537.01 TCGA.CM.6170.01 TCGA.DY.A1DD.01
#> "03" "021" "011" "03" "011"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 7743))
#> TCGA.AF.3911.01 TCGA.F4.6459.01 TCGA.AA.3494.11 TCGA.3L.AA1B.01 TCGA.D5.5538.01 TCGA.F4.6854.01
#> "03" "03" "023" "03" "03" "03"
#> TCGA.AG.A026.01 TCGA.G4.6303.01 TCGA.F5.6464.01 TCGA.T9.A92H.01 TCGA.AA.3712.11 TCGA.CM.5863.01
#> "011" "011" "0412" "011" "021" "03"
#> TCGA.AZ.4308.01 TCGA.AD.6965.01 TCGA.A6.2681.11 TCGA.AD.6548.01 TCGA.A6.5660.01 TCGA.AZ.6600.01
#> "042" "011" "021" "03" "011" "03"
#> TCGA.F4.6808.01 TCGA.D5.6540.01 TCGA.F5.6571.01 TCGA.D5.6926.01 TCGA.CM.4748.01 TCGA.A6.2675.11
#> "03" "012" "011" "03" "03" "021"
#> TCGA.5M.AATE.01 TCGA.D5.5541.01 TCGA.CM.5862.01 TCGA.AA.3511.01 TCGA.AA.3663.11 TCGA.CI.6622.01
#> "03" "042" "011" "03" "021" "011"
#> TCGA.EI.6506.01 TCGA.AM.5821.01 TCGA.F5.6812.01 TCGA.G4.6588.01 TCGA.EI.6512.01 TCGA.A6.6648.01
#> "03" "03" "0414" "012" "011" "042"
#> TCGA.A6.2671.11 TCGA.NH.A6GC.01 TCGA.F4.6805.01 TCGA.AA.3697.01 TCGA.QG.A5YX.01 TCGA.DM.A28C.01
#> "021" "03" "0412" "03" "011" "03"
#> TCGA.AG.A036.01 TCGA.AZ.6606.01 TCGA.F4.6570.01 TCGA.DC.4745.01 TCGA.AF.A56K.01 TCGA.G4.6627.01
#> "011" "012" "012" "03" "042" "0412"
#> TCGA.A6.5657.01 TCGA.A6.5662.01 TCGA.AA.3509.01 TCGA.D5.6929.01 TCGA.CM.6679.01 TCGA.A6.2680.11
#> "03" "03" "011" "042" "03" "021"
#> TCGA.DC.6157.01 TCGA.AF.6655.01 TCGA.CM.6161.01 TCGA.EI.6883.01 TCGA.F5.6811.01 TCGA.D5.6930.01
#> "0432" "042" "03" "011" "03" "03"
#> TCGA.CM.6164.01 TCGA.AF.2687.01 TCGA.DY.A1H8.01 TCGA.G5.6641.01 TCGA.DC.6155.01 TCGA.RU.A8FL.01
#> "042" "042" "03" "03" "03" "011"
#> TCGA.CK.4951.01 TCGA.F4.6704.01 TCGA.AZ.6599.01 TCGA.F5.6861.01 TCGA.CM.5860.01 TCGA.A6.6780.01
#> "03" "042" "011" "03" "011" "011"
#> TCGA.A6.2686.01 TCGA.CM.4750.01 TCGA.CM.6677.01 TCGA.A6.A567.01 TCGA.F5.6814.01 TCGA.D5.6898.01
#> "012" "011" "011" "0433" "011" "03"
#> TCGA.AG.A01W.01 TCGA.AZ.6598.11 TCGA.F5.6813.01 TCGA.AG.3732.01 TCGA.EI.6885.01 TCGA.G4.6299.01
#> "03" "021" "03" "042" "0433" "012"
#> TCGA.A6.4105.01 TCGA.DM.A1D8.01 TCGA.DM.A285.01 TCGA.G4.6295.11 TCGA.DC.4749.01 TCGA.DT.5265.01
#> "012" "011" "03" "023" "042" "012"
#> TCGA.5M.AAT5.01 TCGA.DM.A0XD.01 TCGA.A6.6138.01 TCGA.D5.7000.01 TCGA.DM.A28F.01 TCGA.DY.A1DE.01
#> "0432" "012" "011" "012" "011" "03"
#> TCGA.A6.6142.01 TCGA.QL.A97D.01 TCGA.CK.6748.01 TCGA.DC.6160.01 TCGA.D5.6534.01 TCGA.AZ.4616.01
#> "022" "03" "03" "042" "0413" "03"
#> TCGA.CK.6751.01 TCGA.CM.6171.01 TCGA.DM.A1DA.01 TCGA.AG.A020.11 TCGA.G4.6311.11 TCGA.G4.6625.11
#> "012" "012" "012" "021" "021" "021"
#> TCGA.F5.6863.01 TCGA.G4.6317.02 TCGA.G4.6317.01 TCGA.DM.A1D4.01 TCGA.AG.A01Y.11 TCGA.D5.6530.01
#> "042" "0432" "03" "011" "021" "03"
#> TCGA.CK.4948.01 TCGA.AD.A5EJ.01 TCGA.A6.6651.01 TCGA.CA.5256.01 TCGA.DM.A0X9.01 TCGA.AY.A69D.01
#> "0431" "012" "0412" "03" "011" "011"
#> TCGA.G4.6626.01 TCGA.CA.6716.01 TCGA.A6.2682.01 TCGA.A6.4107.11 TCGA.CA.6717.01 TCGA.G4.6293.01
#> "03" "011" "03" "023" "03" "03"
#> TCGA.CK.5916.01 TCGA.G4.6309.01 TCGA.AA.3662.01 TCGA.AF.A56L.01 TCGA.NH.A6GB.01 TCGA.AD.5900.01
#> "012" "042" "03" "03" "011" "03"
#> TCGA.NH.A50U.01 TCGA.AA.3712.01 TCGA.AZ.4614.01 TCGA.AH.6644.01 TCGA.AZ.6607.01 TCGA.AF.2693.01
#> "011" "03" "012" "011" "03" "0411"
#> TCGA.D5.6924.01 TCGA.CM.5868.01 TCGA.AF.4110.01 TCGA.A6.3809.01 TCGA.AZ.4313.01 TCGA.A6.2675.01
#> "03" "042" "0411" "012" "042" "042"
#> TCGA.AZ.6608.01 TCGA.CM.5864.01 TCGA.AA.3494.01 TCGA.AD.6895.01 TCGA.CI.6620.01 TCGA.DC.6156.01
#> "03" "011" "0432" "03" "03" "03"
#> TCGA.D5.6931.01 TCGA.CM.6165.01 TCGA.CM.5861.01 TCGA.A6.2671.01 TCGA.DC.6158.01 TCGA.AG.3742.01
#> "03" "03" "012" "03" "03" "011"
#> TCGA.AG.A02N.11 TCGA.G4.6307.01 TCGA.A6.5666.01 TCGA.EI.6511.01 TCGA.CI.6624.01 TCGA.AG.3591.01
#> "021" "0432" "011" "03" "042" "011"
#> TCGA.AY.A8YK.01 TCGA.F4.6856.01 TCGA.DM.A1D7.01 TCGA.A6.2685.01 TCGA.5M.AAT6.01 TCGA.AH.6643.01
#> "022" "03" "03" "022" "022" "011"
#> TCGA.F4.6569.01 TCGA.G4.6298.01 TCGA.AY.6196.01 TCGA.EI.6510.01 TCGA.A6.5656.01 TCGA.A6.2684.11
#> "03" "03" "03" "011" "011" "021"
#> TCGA.DY.A1DG.01 TCGA.AZ.4682.01 TCGA.EI.6884.01 TCGA.F4.6806.01 TCGA.G4.6320.11 TCGA.G4.6322.01
#> "011" "03" "03" "011" "021" "012"
#> TCGA.F5.6810.01 TCGA.5M.AAT4.01 TCGA.CL.4957.01 TCGA.DC.6681.01 TCGA.CM.6167.01 TCGA.AG.4022.01
#> "0431" "011" "03" "03" "0412" "03"
#> TCGA.G4.6586.01 TCGA.EI.6514.01 TCGA.CK.4950.01 TCGA.DM.A282.01 TCGA.DY.A1DC.01 TCGA.D5.6535.01
#> "012" "011" "03" "011" "03" "03"
#> TCGA.DM.A1HA.01 TCGA.DC.5869.01 TCGA.AZ.6599.11 TCGA.CM.4752.01 TCGA.AZ.4684.01 TCGA.EI.7004.01
#> "011" "03" "021" "042" "03" "03"
#> TCGA.A6.A565.01 TCGA.D5.6531.01 TCGA.AZ.6598.01 TCGA.AD.6890.01 TCGA.AG.4021.01 TCGA.A6.6781.01
#> "023" "012" "012" "03" "011" "0412"
#> TCGA.DM.A1D9.01 TCGA.CM.4744.01 TCGA.A6.2679.11 TCGA.A6.6652.01 TCGA.AD.6964.01 TCGA.SS.A7HO.01
#> "011" "011" "023" "011" "022" "011"
#> TCGA.A6.6650.01 TCGA.DM.A0XF.01 TCGA.G4.6295.01 TCGA.F4.6461.01 TCGA.AM.5820.01 TCGA.G4.6314.11
#> "011" "042" "0431" "012" "03" "021"
#> TCGA.AD.6889.01 TCGA.AZ.6605.01 TCGA.EI.6881.01 TCGA.NH.A50T.01 TCGA.AG.3725.11 TCGA.G4.6323.01
#> "012" "0414" "03" "011" "021" "03"
#> TCGA.AA.3663.01 TCGA.AD.6899.01 TCGA.A6.5667.11 TCGA.A6.A56B.01 TCGA.G5.6572.01 TCGA.DM.A280.01
#> "012" "011" "021" "011" "0411" "0413"
#> TCGA.AG.A020.01 TCGA.AA.3713.01 TCGA.D5.5539.01 TCGA.AA.3655.11 TCGA.AA.3489.01 TCGA.AA.3495.01
#> "03" "03" "011" "021" "0412" "03"
#> TCGA.AG.A01Y.01 TCGA.AZ.6601.01 TCGA.AH.6903.01 TCGA.AZ.6603.01 TCGA.CA.5254.01 TCGA.A6.A5ZU.01
#> "0433" "03" "03" "0432" "012" "03"
#> TCGA.G4.6302.01 TCGA.AZ.5403.01 TCGA.AY.A54L.01 TCGA.A6.4107.01 TCGA.NH.A5IV.01 TCGA.G4.6306.01
#> "0413" "022" "011" "012" "011" "011"
#> TCGA.AD.A5EK.01 TCGA.G5.6235.01 TCGA.DC.5337.01 TCGA.CM.6675.01 TCGA.AH.6544.01 TCGA.CK.6746.01
#> "011" "0411" "011" "012" "03" "012"
#> TCGA.CA.6718.01 TCGA.CI.6621.01 TCGA.CM.6676.01 TCGA.DM.A1DB.01 TCGA.A6.6654.01 TCGA.AA.3510.11
#> "03" "0411" "03" "03" "03" "023"
#> TCGA.CA.6715.01 TCGA.CM.5341.01 TCGA.CK.5912.01 TCGA.F4.6857.01 TCGA.QG.A5YW.01 TCGA.A6.5665.01
#> "03" "03" "03" "0413" "011" "012"
#> TCGA.CM.6168.01 TCGA.CL.5917.01 TCGA.AU.6004.01 TCGA.AY.5543.01 TCGA.AG.3731.01 TCGA.G4.6314.01
#> "03" "03" "03" "03" "03" "03"
#> TCGA.DC.6683.01 TCGA.CA.5796.01 TCGA.AG.A036.11 TCGA.AZ.4323.01 TCGA.EI.6882.01 TCGA.AZ.4315.01
#> "03" "03" "021" "0413" "011" "03"
#> TCGA.A6.2677.01 TCGA.DY.A1DF.01 TCGA.CM.6162.01 TCGA.F4.6703.01 TCGA.CM.5349.01 TCGA.AG.A02N.01
#> "011" "03" "022" "022" "03" "03"
#> TCGA.AA.3506.01 TCGA.D5.6932.01 TCGA.D5.6538.01 TCGA.AA.3488.11 TCGA.AA.3502.01 TCGA.NH.A8F8.01
#> "03" "03" "012" "021" "011" "03"
#> TCGA.AF.A56N.01 TCGA.AF.6672.01 TCGA.A6.2685.11 TCGA.A6.6141.01 TCGA.AD.6963.01 TCGA.G4.6298.11
#> "03" "0433" "021" "03" "042" "021"
#> TCGA.EI.6917.01 TCGA.QG.A5Z2.01 TCGA.A6.2684.01 TCGA.CK.5915.01 TCGA.CM.6163.01 TCGA.G4.6322.11
#> "03" "012" "03" "011" "03" "021"
#> TCGA.AY.6197.01 TCGA.D5.6928.01 TCGA.A6.3810.01 TCGA.G4.6294.01 TCGA.AA.3660.11 TCGA.A6.6137.01
#> "011" "0413" "042" "011" "021" "03"
#> TCGA.G4.6297.11 TCGA.AZ.4615.01 TCGA.CK.4952.01 TCGA.CM.6172.01 TCGA.AD.6901.01 TCGA.AA.3496.01
#> "021" "03" "012" "011" "03" "011"
#> TCGA.CK.5913.01 TCGA.DM.A28A.01 TCGA.EI.7002.01 TCGA.D5.6533.01 TCGA.QG.A5Z1.01 TCGA.D5.6923.01
#> "012" "011" "011" "03" "011" "0411"
#> TCGA.AF.2690.01 TCGA.DM.A28H.01 TCGA.G4.6320.01 TCGA.G4.6310.01 TCGA.DM.A28M.01 TCGA.DM.A288.01
#> "0414" "011" "012" "03" "011" "011"
#> TCGA.A6.2681.01 TCGA.A6.2679.01 TCGA.4N.A93T.01 TCGA.NH.A8F7.06 TCGA.NH.A8F7.01 TCGA.AZ.6600.11
#> "03" "03" "03" "03" "0432" "021"
#> TCGA.G5.6572.02 TCGA.AY.6386.01 TCGA.G4.6628.01 TCGA.A6.6653.01 TCGA.CM.4746.01 TCGA.F4.6855.01
#> "0414" "03" "03" "012" "03" "011"
#> TCGA.EF.5830.01 TCGA.NH.A6GA.01 TCGA.NH.A50V.01 TCGA.DY.A0XA.01 TCGA.DM.A28E.01 TCGA.AG.3725.01
#> "03" "011" "011" "042" "042" "03"
#> TCGA.CK.6747.01 TCGA.CL.5918.01 TCGA.CI.6623.01 TCGA.A6.5667.01 TCGA.DM.A28K.01 TCGA.AA.3713.11
#> "011" "011" "042" "03" "011" "023"
#> TCGA.AA.3655.01 TCGA.AU.3779.01 TCGA.A6.5664.01 TCGA.AA.3697.11 TCGA.AZ.5407.01 TCGA.CM.6169.01
#> "011" "042" "03" "023" "011" "03"
#> TCGA.AH.6547.01 TCGA.AZ.6601.11 TCGA.A6.5661.01 TCGA.F4.6807.01 TCGA.QG.A5YV.01 TCGA.AA.3509.11
#> "0412" "021" "012" "03" "011" "021"
#> TCGA.AY.A71X.01 TCGA.CA.5797.01 TCGA.F4.6460.01 TCGA.G4.6302.11 TCGA.F5.6702.01 TCGA.AH.6549.01
#> "011" "0431" "042" "023" "042" "011"
#> TCGA.D5.6927.01 TCGA.CM.6166.01 TCGA.AH.6897.01 TCGA.G4.6304.01 TCGA.CA.5255.01 TCGA.EI.6507.01
#> "0412" "011" "011" "0413" "03" "03"
#> TCGA.CK.4947.01 TCGA.D5.5540.01 TCGA.DC.6682.01 TCGA.G4.6321.01 TCGA.A6.6649.01 TCGA.CM.5348.01
#> "03" "011" "03" "03" "03" "03"
#> TCGA.EI.6513.01 TCGA.A6.2672.01 TCGA.D5.6539.01 TCGA.AA.3510.01 TCGA.G5.6233.01 TCGA.BM.6198.01
#> "0431" "012" "0411" "03" "011" "0414"
#> TCGA.CA.6719.01 TCGA.DC.6154.01 TCGA.DM.A1D6.01 TCGA.AG.3731.11 TCGA.CM.6674.01 TCGA.CM.4743.01
#> "011" "03" "03" "021" "0412" "0413"
#> TCGA.F5.6465.01 TCGA.D5.5537.01 TCGA.F4.6463.01 TCGA.A6.2686.11 TCGA.4T.AA8H.01 TCGA.A6.6782.01
#> "042" "011" "03" "021" "011" "03"
#> TCGA.AG.3592.01 TCGA.AD.6888.01 TCGA.CM.6678.01 TCGA.CM.5344.01 TCGA.AA.3495.11 TCGA.AG.A01W.11
#> "011" "03" "011" "042" "021" "021"
#> TCGA.F4.6809.01 TCGA.CK.5914.01 TCGA.AZ.4681.01 TCGA.AA.3492.01 TCGA.D5.6536.01 TCGA.AA.3506.11
#> "03" "011" "0432" "012" "03" "021"
#> TCGA.AA.3488.01 TCGA.AA.3502.11 TCGA.A6.6140.01 TCGA.D5.6529.01 TCGA.DM.A1D0.01 TCGA.DM.A1HB.01
#> "03" "023" "042" "03" "042" "012"
#> TCGA.D5.6920.01 TCGA.D5.6922.01 TCGA.EI.6508.01 TCGA.D5.6532.01 TCGA.5M.AATA.01 TCGA.EI.6509.01
#> "03" "03" "011" "011" "03" "042"
#> TCGA.G4.6311.01 TCGA.A6.A566.01 TCGA.G4.6625.01 TCGA.CI.6619.01 TCGA.F5.6864.01 TCGA.AA.3492.11
#> "03" "03" "03" "042" "03" "021"
#> TCGA.A6.5659.01 TCGA.WS.AB45.01 TCGA.G4.6315.01 TCGA.D5.6541.01 TCGA.A6.2680.01 TCGA.CM.4751.01
#> "012" "0413" "03" "03" "011" "03"
#> TCGA.CM.6680.01 TCGA.AF.6136.01 TCGA.AA.3660.01 TCGA.CM.4747.01 TCGA.EF.5831.01 TCGA.DM.A28G.01
#> "011" "03" "011" "011" "011" "011"
#> TCGA.G4.6297.01 TCGA.A6.2682.11 TCGA.D5.6537.01 TCGA.CM.6170.01 TCGA.DY.A1DD.01
#> "03" "021" "011" "03" "011"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 8434))
#> TCGA.AF.3911.01 TCGA.F4.6459.01 TCGA.AA.3494.11 TCGA.3L.AA1B.01 TCGA.D5.5538.01 TCGA.F4.6854.01
#> "03" "03" "023" "03" "03" "03"
#> TCGA.AG.A026.01 TCGA.G4.6303.01 TCGA.F5.6464.01 TCGA.T9.A92H.01 TCGA.AA.3712.11 TCGA.CM.5863.01
#> "011" "011" "041" "011" "021" "03"
#> TCGA.AZ.4308.01 TCGA.AD.6965.01 TCGA.A6.2681.11 TCGA.AD.6548.01 TCGA.A6.5660.01 TCGA.AZ.6600.01
#> "042" "011" "021" "03" "011" "03"
#> TCGA.F4.6808.01 TCGA.D5.6540.01 TCGA.F5.6571.01 TCGA.D5.6926.01 TCGA.CM.4748.01 TCGA.A6.2675.11
#> "03" "012" "011" "03" "03" "021"
#> TCGA.5M.AATE.01 TCGA.D5.5541.01 TCGA.CM.5862.01 TCGA.AA.3511.01 TCGA.AA.3663.11 TCGA.CI.6622.01
#> "03" "042" "011" "03" "021" "011"
#> TCGA.EI.6506.01 TCGA.AM.5821.01 TCGA.F5.6812.01 TCGA.G4.6588.01 TCGA.EI.6512.01 TCGA.A6.6648.01
#> "03" "03" "041" "012" "011" "042"
#> TCGA.A6.2671.11 TCGA.NH.A6GC.01 TCGA.F4.6805.01 TCGA.AA.3697.01 TCGA.QG.A5YX.01 TCGA.DM.A28C.01
#> "021" "03" "041" "03" "011" "03"
#> TCGA.AG.A036.01 TCGA.AZ.6606.01 TCGA.F4.6570.01 TCGA.DC.4745.01 TCGA.AF.A56K.01 TCGA.G4.6627.01
#> "011" "012" "012" "03" "042" "041"
#> TCGA.A6.5657.01 TCGA.A6.5662.01 TCGA.AA.3509.01 TCGA.D5.6929.01 TCGA.CM.6679.01 TCGA.A6.2680.11
#> "03" "03" "011" "042" "03" "021"
#> TCGA.DC.6157.01 TCGA.AF.6655.01 TCGA.CM.6161.01 TCGA.EI.6883.01 TCGA.F5.6811.01 TCGA.D5.6930.01
#> "0432" "042" "03" "011" "03" "03"
#> TCGA.CM.6164.01 TCGA.AF.2687.01 TCGA.DY.A1H8.01 TCGA.G5.6641.01 TCGA.DC.6155.01 TCGA.RU.A8FL.01
#> "042" "042" "03" "03" "03" "011"
#> TCGA.CK.4951.01 TCGA.F4.6704.01 TCGA.AZ.6599.01 TCGA.F5.6861.01 TCGA.CM.5860.01 TCGA.A6.6780.01
#> "03" "042" "011" "03" "011" "011"
#> TCGA.A6.2686.01 TCGA.CM.4750.01 TCGA.CM.6677.01 TCGA.A6.A567.01 TCGA.F5.6814.01 TCGA.D5.6898.01
#> "012" "011" "011" "0433" "011" "03"
#> TCGA.AG.A01W.01 TCGA.AZ.6598.11 TCGA.F5.6813.01 TCGA.AG.3732.01 TCGA.EI.6885.01 TCGA.G4.6299.01
#> "03" "021" "03" "042" "0433" "012"
#> TCGA.A6.4105.01 TCGA.DM.A1D8.01 TCGA.DM.A285.01 TCGA.G4.6295.11 TCGA.DC.4749.01 TCGA.DT.5265.01
#> "012" "011" "03" "023" "042" "012"
#> TCGA.5M.AAT5.01 TCGA.DM.A0XD.01 TCGA.A6.6138.01 TCGA.D5.7000.01 TCGA.DM.A28F.01 TCGA.DY.A1DE.01
#> "0432" "012" "011" "012" "011" "03"
#> TCGA.A6.6142.01 TCGA.QL.A97D.01 TCGA.CK.6748.01 TCGA.DC.6160.01 TCGA.D5.6534.01 TCGA.AZ.4616.01
#> "022" "03" "03" "042" "041" "03"
#> TCGA.CK.6751.01 TCGA.CM.6171.01 TCGA.DM.A1DA.01 TCGA.AG.A020.11 TCGA.G4.6311.11 TCGA.G4.6625.11
#> "012" "012" "012" "021" "021" "021"
#> TCGA.F5.6863.01 TCGA.G4.6317.02 TCGA.G4.6317.01 TCGA.DM.A1D4.01 TCGA.AG.A01Y.11 TCGA.D5.6530.01
#> "042" "0432" "03" "011" "021" "03"
#> TCGA.CK.4948.01 TCGA.AD.A5EJ.01 TCGA.A6.6651.01 TCGA.CA.5256.01 TCGA.DM.A0X9.01 TCGA.AY.A69D.01
#> "0431" "012" "041" "03" "011" "011"
#> TCGA.G4.6626.01 TCGA.CA.6716.01 TCGA.A6.2682.01 TCGA.A6.4107.11 TCGA.CA.6717.01 TCGA.G4.6293.01
#> "03" "011" "03" "023" "03" "03"
#> TCGA.CK.5916.01 TCGA.G4.6309.01 TCGA.AA.3662.01 TCGA.AF.A56L.01 TCGA.NH.A6GB.01 TCGA.AD.5900.01
#> "012" "042" "03" "03" "011" "03"
#> TCGA.NH.A50U.01 TCGA.AA.3712.01 TCGA.AZ.4614.01 TCGA.AH.6644.01 TCGA.AZ.6607.01 TCGA.AF.2693.01
#> "011" "03" "012" "011" "03" "041"
#> TCGA.D5.6924.01 TCGA.CM.5868.01 TCGA.AF.4110.01 TCGA.A6.3809.01 TCGA.AZ.4313.01 TCGA.A6.2675.01
#> "03" "042" "041" "012" "042" "042"
#> TCGA.AZ.6608.01 TCGA.CM.5864.01 TCGA.AA.3494.01 TCGA.AD.6895.01 TCGA.CI.6620.01 TCGA.DC.6156.01
#> "03" "011" "0432" "03" "03" "03"
#> TCGA.D5.6931.01 TCGA.CM.6165.01 TCGA.CM.5861.01 TCGA.A6.2671.01 TCGA.DC.6158.01 TCGA.AG.3742.01
#> "03" "03" "012" "03" "03" "011"
#> TCGA.AG.A02N.11 TCGA.G4.6307.01 TCGA.A6.5666.01 TCGA.EI.6511.01 TCGA.CI.6624.01 TCGA.AG.3591.01
#> "021" "0432" "011" "03" "042" "011"
#> TCGA.AY.A8YK.01 TCGA.F4.6856.01 TCGA.DM.A1D7.01 TCGA.A6.2685.01 TCGA.5M.AAT6.01 TCGA.AH.6643.01
#> "022" "03" "03" "022" "022" "011"
#> TCGA.F4.6569.01 TCGA.G4.6298.01 TCGA.AY.6196.01 TCGA.EI.6510.01 TCGA.A6.5656.01 TCGA.A6.2684.11
#> "03" "03" "03" "011" "011" "021"
#> TCGA.DY.A1DG.01 TCGA.AZ.4682.01 TCGA.EI.6884.01 TCGA.F4.6806.01 TCGA.G4.6320.11 TCGA.G4.6322.01
#> "011" "03" "03" "011" "021" "012"
#> TCGA.F5.6810.01 TCGA.5M.AAT4.01 TCGA.CL.4957.01 TCGA.DC.6681.01 TCGA.CM.6167.01 TCGA.AG.4022.01
#> "0431" "011" "03" "03" "041" "03"
#> TCGA.G4.6586.01 TCGA.EI.6514.01 TCGA.CK.4950.01 TCGA.DM.A282.01 TCGA.DY.A1DC.01 TCGA.D5.6535.01
#> "012" "011" "03" "011" "03" "03"
#> TCGA.DM.A1HA.01 TCGA.DC.5869.01 TCGA.AZ.6599.11 TCGA.CM.4752.01 TCGA.AZ.4684.01 TCGA.EI.7004.01
#> "011" "03" "021" "042" "03" "03"
#> TCGA.A6.A565.01 TCGA.D5.6531.01 TCGA.AZ.6598.01 TCGA.AD.6890.01 TCGA.AG.4021.01 TCGA.A6.6781.01
#> "023" "012" "012" "03" "011" "041"
#> TCGA.DM.A1D9.01 TCGA.CM.4744.01 TCGA.A6.2679.11 TCGA.A6.6652.01 TCGA.AD.6964.01 TCGA.SS.A7HO.01
#> "011" "011" "023" "011" "022" "011"
#> TCGA.A6.6650.01 TCGA.DM.A0XF.01 TCGA.G4.6295.01 TCGA.F4.6461.01 TCGA.AM.5820.01 TCGA.G4.6314.11
#> "011" "042" "0431" "012" "03" "021"
#> TCGA.AD.6889.01 TCGA.AZ.6605.01 TCGA.EI.6881.01 TCGA.NH.A50T.01 TCGA.AG.3725.11 TCGA.G4.6323.01
#> "012" "041" "03" "011" "021" "03"
#> TCGA.AA.3663.01 TCGA.AD.6899.01 TCGA.A6.5667.11 TCGA.A6.A56B.01 TCGA.G5.6572.01 TCGA.DM.A280.01
#> "012" "011" "021" "011" "041" "041"
#> TCGA.AG.A020.01 TCGA.AA.3713.01 TCGA.D5.5539.01 TCGA.AA.3655.11 TCGA.AA.3489.01 TCGA.AA.3495.01
#> "03" "03" "011" "021" "041" "03"
#> TCGA.AG.A01Y.01 TCGA.AZ.6601.01 TCGA.AH.6903.01 TCGA.AZ.6603.01 TCGA.CA.5254.01 TCGA.A6.A5ZU.01
#> "0433" "03" "03" "0432" "012" "03"
#> TCGA.G4.6302.01 TCGA.AZ.5403.01 TCGA.AY.A54L.01 TCGA.A6.4107.01 TCGA.NH.A5IV.01 TCGA.G4.6306.01
#> "041" "022" "011" "012" "011" "011"
#> TCGA.AD.A5EK.01 TCGA.G5.6235.01 TCGA.DC.5337.01 TCGA.CM.6675.01 TCGA.AH.6544.01 TCGA.CK.6746.01
#> "011" "041" "011" "012" "03" "012"
#> TCGA.CA.6718.01 TCGA.CI.6621.01 TCGA.CM.6676.01 TCGA.DM.A1DB.01 TCGA.A6.6654.01 TCGA.AA.3510.11
#> "03" "041" "03" "03" "03" "023"
#> TCGA.CA.6715.01 TCGA.CM.5341.01 TCGA.CK.5912.01 TCGA.F4.6857.01 TCGA.QG.A5YW.01 TCGA.A6.5665.01
#> "03" "03" "03" "041" "011" "012"
#> TCGA.CM.6168.01 TCGA.CL.5917.01 TCGA.AU.6004.01 TCGA.AY.5543.01 TCGA.AG.3731.01 TCGA.G4.6314.01
#> "03" "03" "03" "03" "03" "03"
#> TCGA.DC.6683.01 TCGA.CA.5796.01 TCGA.AG.A036.11 TCGA.AZ.4323.01 TCGA.EI.6882.01 TCGA.AZ.4315.01
#> "03" "03" "021" "041" "011" "03"
#> TCGA.A6.2677.01 TCGA.DY.A1DF.01 TCGA.CM.6162.01 TCGA.F4.6703.01 TCGA.CM.5349.01 TCGA.AG.A02N.01
#> "011" "03" "022" "022" "03" "03"
#> TCGA.AA.3506.01 TCGA.D5.6932.01 TCGA.D5.6538.01 TCGA.AA.3488.11 TCGA.AA.3502.01 TCGA.NH.A8F8.01
#> "03" "03" "012" "021" "011" "03"
#> TCGA.AF.A56N.01 TCGA.AF.6672.01 TCGA.A6.2685.11 TCGA.A6.6141.01 TCGA.AD.6963.01 TCGA.G4.6298.11
#> "03" "0433" "021" "03" "042" "021"
#> TCGA.EI.6917.01 TCGA.QG.A5Z2.01 TCGA.A6.2684.01 TCGA.CK.5915.01 TCGA.CM.6163.01 TCGA.G4.6322.11
#> "03" "012" "03" "011" "03" "021"
#> TCGA.AY.6197.01 TCGA.D5.6928.01 TCGA.A6.3810.01 TCGA.G4.6294.01 TCGA.AA.3660.11 TCGA.A6.6137.01
#> "011" "041" "042" "011" "021" "03"
#> TCGA.G4.6297.11 TCGA.AZ.4615.01 TCGA.CK.4952.01 TCGA.CM.6172.01 TCGA.AD.6901.01 TCGA.AA.3496.01
#> "021" "03" "012" "011" "03" "011"
#> TCGA.CK.5913.01 TCGA.DM.A28A.01 TCGA.EI.7002.01 TCGA.D5.6533.01 TCGA.QG.A5Z1.01 TCGA.D5.6923.01
#> "012" "011" "011" "03" "011" "041"
#> TCGA.AF.2690.01 TCGA.DM.A28H.01 TCGA.G4.6320.01 TCGA.G4.6310.01 TCGA.DM.A28M.01 TCGA.DM.A288.01
#> "041" "011" "012" "03" "011" "011"
#> TCGA.A6.2681.01 TCGA.A6.2679.01 TCGA.4N.A93T.01 TCGA.NH.A8F7.06 TCGA.NH.A8F7.01 TCGA.AZ.6600.11
#> "03" "03" "03" "03" "0432" "021"
#> TCGA.G5.6572.02 TCGA.AY.6386.01 TCGA.G4.6628.01 TCGA.A6.6653.01 TCGA.CM.4746.01 TCGA.F4.6855.01
#> "041" "03" "03" "012" "03" "011"
#> TCGA.EF.5830.01 TCGA.NH.A6GA.01 TCGA.NH.A50V.01 TCGA.DY.A0XA.01 TCGA.DM.A28E.01 TCGA.AG.3725.01
#> "03" "011" "011" "042" "042" "03"
#> TCGA.CK.6747.01 TCGA.CL.5918.01 TCGA.CI.6623.01 TCGA.A6.5667.01 TCGA.DM.A28K.01 TCGA.AA.3713.11
#> "011" "011" "042" "03" "011" "023"
#> TCGA.AA.3655.01 TCGA.AU.3779.01 TCGA.A6.5664.01 TCGA.AA.3697.11 TCGA.AZ.5407.01 TCGA.CM.6169.01
#> "011" "042" "03" "023" "011" "03"
#> TCGA.AH.6547.01 TCGA.AZ.6601.11 TCGA.A6.5661.01 TCGA.F4.6807.01 TCGA.QG.A5YV.01 TCGA.AA.3509.11
#> "041" "021" "012" "03" "011" "021"
#> TCGA.AY.A71X.01 TCGA.CA.5797.01 TCGA.F4.6460.01 TCGA.G4.6302.11 TCGA.F5.6702.01 TCGA.AH.6549.01
#> "011" "0431" "042" "023" "042" "011"
#> TCGA.D5.6927.01 TCGA.CM.6166.01 TCGA.AH.6897.01 TCGA.G4.6304.01 TCGA.CA.5255.01 TCGA.EI.6507.01
#> "041" "011" "011" "041" "03" "03"
#> TCGA.CK.4947.01 TCGA.D5.5540.01 TCGA.DC.6682.01 TCGA.G4.6321.01 TCGA.A6.6649.01 TCGA.CM.5348.01
#> "03" "011" "03" "03" "03" "03"
#> TCGA.EI.6513.01 TCGA.A6.2672.01 TCGA.D5.6539.01 TCGA.AA.3510.01 TCGA.G5.6233.01 TCGA.BM.6198.01
#> "0431" "012" "041" "03" "011" "041"
#> TCGA.CA.6719.01 TCGA.DC.6154.01 TCGA.DM.A1D6.01 TCGA.AG.3731.11 TCGA.CM.6674.01 TCGA.CM.4743.01
#> "011" "03" "03" "021" "041" "041"
#> TCGA.F5.6465.01 TCGA.D5.5537.01 TCGA.F4.6463.01 TCGA.A6.2686.11 TCGA.4T.AA8H.01 TCGA.A6.6782.01
#> "042" "011" "03" "021" "011" "03"
#> TCGA.AG.3592.01 TCGA.AD.6888.01 TCGA.CM.6678.01 TCGA.CM.5344.01 TCGA.AA.3495.11 TCGA.AG.A01W.11
#> "011" "03" "011" "042" "021" "021"
#> TCGA.F4.6809.01 TCGA.CK.5914.01 TCGA.AZ.4681.01 TCGA.AA.3492.01 TCGA.D5.6536.01 TCGA.AA.3506.11
#> "03" "011" "0432" "012" "03" "021"
#> TCGA.AA.3488.01 TCGA.AA.3502.11 TCGA.A6.6140.01 TCGA.D5.6529.01 TCGA.DM.A1D0.01 TCGA.DM.A1HB.01
#> "03" "023" "042" "03" "042" "012"
#> TCGA.D5.6920.01 TCGA.D5.6922.01 TCGA.EI.6508.01 TCGA.D5.6532.01 TCGA.5M.AATA.01 TCGA.EI.6509.01
#> "03" "03" "011" "011" "03" "042"
#> TCGA.G4.6311.01 TCGA.A6.A566.01 TCGA.G4.6625.01 TCGA.CI.6619.01 TCGA.F5.6864.01 TCGA.AA.3492.11
#> "03" "03" "03" "042" "03" "021"
#> TCGA.A6.5659.01 TCGA.WS.AB45.01 TCGA.G4.6315.01 TCGA.D5.6541.01 TCGA.A6.2680.01 TCGA.CM.4751.01
#> "012" "041" "03" "03" "011" "03"
#> TCGA.CM.6680.01 TCGA.AF.6136.01 TCGA.AA.3660.01 TCGA.CM.4747.01 TCGA.EF.5831.01 TCGA.DM.A28G.01
#> "011" "03" "011" "011" "011" "011"
#> TCGA.G4.6297.01 TCGA.A6.2682.11 TCGA.D5.6537.01 TCGA.CM.6170.01 TCGA.DY.A1DD.01
#> "03" "021" "011" "03" "011"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 9343))
#> TCGA.AF.3911.01 TCGA.F4.6459.01 TCGA.AA.3494.11 TCGA.3L.AA1B.01 TCGA.D5.5538.01 TCGA.F4.6854.01
#> "03" "03" "02" "03" "03" "03"
#> TCGA.AG.A026.01 TCGA.G4.6303.01 TCGA.F5.6464.01 TCGA.T9.A92H.01 TCGA.AA.3712.11 TCGA.CM.5863.01
#> "011" "011" "041" "011" "02" "03"
#> TCGA.AZ.4308.01 TCGA.AD.6965.01 TCGA.A6.2681.11 TCGA.AD.6548.01 TCGA.A6.5660.01 TCGA.AZ.6600.01
#> "042" "011" "02" "03" "011" "03"
#> TCGA.F4.6808.01 TCGA.D5.6540.01 TCGA.F5.6571.01 TCGA.D5.6926.01 TCGA.CM.4748.01 TCGA.A6.2675.11
#> "03" "012" "011" "03" "03" "02"
#> TCGA.5M.AATE.01 TCGA.D5.5541.01 TCGA.CM.5862.01 TCGA.AA.3511.01 TCGA.AA.3663.11 TCGA.CI.6622.01
#> "03" "042" "011" "03" "02" "011"
#> TCGA.EI.6506.01 TCGA.AM.5821.01 TCGA.F5.6812.01 TCGA.G4.6588.01 TCGA.EI.6512.01 TCGA.A6.6648.01
#> "03" "03" "041" "012" "011" "042"
#> TCGA.A6.2671.11 TCGA.NH.A6GC.01 TCGA.F4.6805.01 TCGA.AA.3697.01 TCGA.QG.A5YX.01 TCGA.DM.A28C.01
#> "02" "03" "041" "03" "011" "03"
#> TCGA.AG.A036.01 TCGA.AZ.6606.01 TCGA.F4.6570.01 TCGA.DC.4745.01 TCGA.AF.A56K.01 TCGA.G4.6627.01
#> "011" "012" "012" "03" "042" "041"
#> TCGA.A6.5657.01 TCGA.A6.5662.01 TCGA.AA.3509.01 TCGA.D5.6929.01 TCGA.CM.6679.01 TCGA.A6.2680.11
#> "03" "03" "011" "042" "03" "02"
#> TCGA.DC.6157.01 TCGA.AF.6655.01 TCGA.CM.6161.01 TCGA.EI.6883.01 TCGA.F5.6811.01 TCGA.D5.6930.01
#> "0432" "042" "03" "011" "03" "03"
#> TCGA.CM.6164.01 TCGA.AF.2687.01 TCGA.DY.A1H8.01 TCGA.G5.6641.01 TCGA.DC.6155.01 TCGA.RU.A8FL.01
#> "042" "042" "03" "03" "03" "011"
#> TCGA.CK.4951.01 TCGA.F4.6704.01 TCGA.AZ.6599.01 TCGA.F5.6861.01 TCGA.CM.5860.01 TCGA.A6.6780.01
#> "03" "042" "011" "03" "011" "011"
#> TCGA.A6.2686.01 TCGA.CM.4750.01 TCGA.CM.6677.01 TCGA.A6.A567.01 TCGA.F5.6814.01 TCGA.D5.6898.01
#> "012" "011" "011" "0433" "011" "03"
#> TCGA.AG.A01W.01 TCGA.AZ.6598.11 TCGA.F5.6813.01 TCGA.AG.3732.01 TCGA.EI.6885.01 TCGA.G4.6299.01
#> "03" "02" "03" "042" "0433" "012"
#> TCGA.A6.4105.01 TCGA.DM.A1D8.01 TCGA.DM.A285.01 TCGA.G4.6295.11 TCGA.DC.4749.01 TCGA.DT.5265.01
#> "012" "011" "03" "02" "042" "012"
#> TCGA.5M.AAT5.01 TCGA.DM.A0XD.01 TCGA.A6.6138.01 TCGA.D5.7000.01 TCGA.DM.A28F.01 TCGA.DY.A1DE.01
#> "0432" "012" "011" "012" "011" "03"
#> TCGA.A6.6142.01 TCGA.QL.A97D.01 TCGA.CK.6748.01 TCGA.DC.6160.01 TCGA.D5.6534.01 TCGA.AZ.4616.01
#> "02" "03" "03" "042" "041" "03"
#> TCGA.CK.6751.01 TCGA.CM.6171.01 TCGA.DM.A1DA.01 TCGA.AG.A020.11 TCGA.G4.6311.11 TCGA.G4.6625.11
#> "012" "012" "012" "02" "02" "02"
#> TCGA.F5.6863.01 TCGA.G4.6317.02 TCGA.G4.6317.01 TCGA.DM.A1D4.01 TCGA.AG.A01Y.11 TCGA.D5.6530.01
#> "042" "0432" "03" "011" "02" "03"
#> TCGA.CK.4948.01 TCGA.AD.A5EJ.01 TCGA.A6.6651.01 TCGA.CA.5256.01 TCGA.DM.A0X9.01 TCGA.AY.A69D.01
#> "0431" "012" "041" "03" "011" "011"
#> TCGA.G4.6626.01 TCGA.CA.6716.01 TCGA.A6.2682.01 TCGA.A6.4107.11 TCGA.CA.6717.01 TCGA.G4.6293.01
#> "03" "011" "03" "02" "03" "03"
#> TCGA.CK.5916.01 TCGA.G4.6309.01 TCGA.AA.3662.01 TCGA.AF.A56L.01 TCGA.NH.A6GB.01 TCGA.AD.5900.01
#> "012" "042" "03" "03" "011" "03"
#> TCGA.NH.A50U.01 TCGA.AA.3712.01 TCGA.AZ.4614.01 TCGA.AH.6644.01 TCGA.AZ.6607.01 TCGA.AF.2693.01
#> "011" "03" "012" "011" "03" "041"
#> TCGA.D5.6924.01 TCGA.CM.5868.01 TCGA.AF.4110.01 TCGA.A6.3809.01 TCGA.AZ.4313.01 TCGA.A6.2675.01
#> "03" "042" "041" "012" "042" "042"
#> TCGA.AZ.6608.01 TCGA.CM.5864.01 TCGA.AA.3494.01 TCGA.AD.6895.01 TCGA.CI.6620.01 TCGA.DC.6156.01
#> "03" "011" "0432" "03" "03" "03"
#> TCGA.D5.6931.01 TCGA.CM.6165.01 TCGA.CM.5861.01 TCGA.A6.2671.01 TCGA.DC.6158.01 TCGA.AG.3742.01
#> "03" "03" "012" "03" "03" "011"
#> TCGA.AG.A02N.11 TCGA.G4.6307.01 TCGA.A6.5666.01 TCGA.EI.6511.01 TCGA.CI.6624.01 TCGA.AG.3591.01
#> "02" "0432" "011" "03" "042" "011"
#> TCGA.AY.A8YK.01 TCGA.F4.6856.01 TCGA.DM.A1D7.01 TCGA.A6.2685.01 TCGA.5M.AAT6.01 TCGA.AH.6643.01
#> "02" "03" "03" "02" "02" "011"
#> TCGA.F4.6569.01 TCGA.G4.6298.01 TCGA.AY.6196.01 TCGA.EI.6510.01 TCGA.A6.5656.01 TCGA.A6.2684.11
#> "03" "03" "03" "011" "011" "02"
#> TCGA.DY.A1DG.01 TCGA.AZ.4682.01 TCGA.EI.6884.01 TCGA.F4.6806.01 TCGA.G4.6320.11 TCGA.G4.6322.01
#> "011" "03" "03" "011" "02" "012"
#> TCGA.F5.6810.01 TCGA.5M.AAT4.01 TCGA.CL.4957.01 TCGA.DC.6681.01 TCGA.CM.6167.01 TCGA.AG.4022.01
#> "0431" "011" "03" "03" "041" "03"
#> TCGA.G4.6586.01 TCGA.EI.6514.01 TCGA.CK.4950.01 TCGA.DM.A282.01 TCGA.DY.A1DC.01 TCGA.D5.6535.01
#> "012" "011" "03" "011" "03" "03"
#> TCGA.DM.A1HA.01 TCGA.DC.5869.01 TCGA.AZ.6599.11 TCGA.CM.4752.01 TCGA.AZ.4684.01 TCGA.EI.7004.01
#> "011" "03" "02" "042" "03" "03"
#> TCGA.A6.A565.01 TCGA.D5.6531.01 TCGA.AZ.6598.01 TCGA.AD.6890.01 TCGA.AG.4021.01 TCGA.A6.6781.01
#> "02" "012" "012" "03" "011" "041"
#> TCGA.DM.A1D9.01 TCGA.CM.4744.01 TCGA.A6.2679.11 TCGA.A6.6652.01 TCGA.AD.6964.01 TCGA.SS.A7HO.01
#> "011" "011" "02" "011" "02" "011"
#> TCGA.A6.6650.01 TCGA.DM.A0XF.01 TCGA.G4.6295.01 TCGA.F4.6461.01 TCGA.AM.5820.01 TCGA.G4.6314.11
#> "011" "042" "0431" "012" "03" "02"
#> TCGA.AD.6889.01 TCGA.AZ.6605.01 TCGA.EI.6881.01 TCGA.NH.A50T.01 TCGA.AG.3725.11 TCGA.G4.6323.01
#> "012" "041" "03" "011" "02" "03"
#> TCGA.AA.3663.01 TCGA.AD.6899.01 TCGA.A6.5667.11 TCGA.A6.A56B.01 TCGA.G5.6572.01 TCGA.DM.A280.01
#> "012" "011" "02" "011" "041" "041"
#> TCGA.AG.A020.01 TCGA.AA.3713.01 TCGA.D5.5539.01 TCGA.AA.3655.11 TCGA.AA.3489.01 TCGA.AA.3495.01
#> "03" "03" "011" "02" "041" "03"
#> TCGA.AG.A01Y.01 TCGA.AZ.6601.01 TCGA.AH.6903.01 TCGA.AZ.6603.01 TCGA.CA.5254.01 TCGA.A6.A5ZU.01
#> "0433" "03" "03" "0432" "012" "03"
#> TCGA.G4.6302.01 TCGA.AZ.5403.01 TCGA.AY.A54L.01 TCGA.A6.4107.01 TCGA.NH.A5IV.01 TCGA.G4.6306.01
#> "041" "02" "011" "012" "011" "011"
#> TCGA.AD.A5EK.01 TCGA.G5.6235.01 TCGA.DC.5337.01 TCGA.CM.6675.01 TCGA.AH.6544.01 TCGA.CK.6746.01
#> "011" "041" "011" "012" "03" "012"
#> TCGA.CA.6718.01 TCGA.CI.6621.01 TCGA.CM.6676.01 TCGA.DM.A1DB.01 TCGA.A6.6654.01 TCGA.AA.3510.11
#> "03" "041" "03" "03" "03" "02"
#> TCGA.CA.6715.01 TCGA.CM.5341.01 TCGA.CK.5912.01 TCGA.F4.6857.01 TCGA.QG.A5YW.01 TCGA.A6.5665.01
#> "03" "03" "03" "041" "011" "012"
#> TCGA.CM.6168.01 TCGA.CL.5917.01 TCGA.AU.6004.01 TCGA.AY.5543.01 TCGA.AG.3731.01 TCGA.G4.6314.01
#> "03" "03" "03" "03" "03" "03"
#> TCGA.DC.6683.01 TCGA.CA.5796.01 TCGA.AG.A036.11 TCGA.AZ.4323.01 TCGA.EI.6882.01 TCGA.AZ.4315.01
#> "03" "03" "02" "041" "011" "03"
#> TCGA.A6.2677.01 TCGA.DY.A1DF.01 TCGA.CM.6162.01 TCGA.F4.6703.01 TCGA.CM.5349.01 TCGA.AG.A02N.01
#> "011" "03" "02" "02" "03" "03"
#> TCGA.AA.3506.01 TCGA.D5.6932.01 TCGA.D5.6538.01 TCGA.AA.3488.11 TCGA.AA.3502.01 TCGA.NH.A8F8.01
#> "03" "03" "012" "02" "011" "03"
#> TCGA.AF.A56N.01 TCGA.AF.6672.01 TCGA.A6.2685.11 TCGA.A6.6141.01 TCGA.AD.6963.01 TCGA.G4.6298.11
#> "03" "0433" "02" "03" "042" "02"
#> TCGA.EI.6917.01 TCGA.QG.A5Z2.01 TCGA.A6.2684.01 TCGA.CK.5915.01 TCGA.CM.6163.01 TCGA.G4.6322.11
#> "03" "012" "03" "011" "03" "02"
#> TCGA.AY.6197.01 TCGA.D5.6928.01 TCGA.A6.3810.01 TCGA.G4.6294.01 TCGA.AA.3660.11 TCGA.A6.6137.01
#> "011" "041" "042" "011" "02" "03"
#> TCGA.G4.6297.11 TCGA.AZ.4615.01 TCGA.CK.4952.01 TCGA.CM.6172.01 TCGA.AD.6901.01 TCGA.AA.3496.01
#> "02" "03" "012" "011" "03" "011"
#> TCGA.CK.5913.01 TCGA.DM.A28A.01 TCGA.EI.7002.01 TCGA.D5.6533.01 TCGA.QG.A5Z1.01 TCGA.D5.6923.01
#> "012" "011" "011" "03" "011" "041"
#> TCGA.AF.2690.01 TCGA.DM.A28H.01 TCGA.G4.6320.01 TCGA.G4.6310.01 TCGA.DM.A28M.01 TCGA.DM.A288.01
#> "041" "011" "012" "03" "011" "011"
#> TCGA.A6.2681.01 TCGA.A6.2679.01 TCGA.4N.A93T.01 TCGA.NH.A8F7.06 TCGA.NH.A8F7.01 TCGA.AZ.6600.11
#> "03" "03" "03" "03" "0432" "02"
#> TCGA.G5.6572.02 TCGA.AY.6386.01 TCGA.G4.6628.01 TCGA.A6.6653.01 TCGA.CM.4746.01 TCGA.F4.6855.01
#> "041" "03" "03" "012" "03" "011"
#> TCGA.EF.5830.01 TCGA.NH.A6GA.01 TCGA.NH.A50V.01 TCGA.DY.A0XA.01 TCGA.DM.A28E.01 TCGA.AG.3725.01
#> "03" "011" "011" "042" "042" "03"
#> TCGA.CK.6747.01 TCGA.CL.5918.01 TCGA.CI.6623.01 TCGA.A6.5667.01 TCGA.DM.A28K.01 TCGA.AA.3713.11
#> "011" "011" "042" "03" "011" "02"
#> TCGA.AA.3655.01 TCGA.AU.3779.01 TCGA.A6.5664.01 TCGA.AA.3697.11 TCGA.AZ.5407.01 TCGA.CM.6169.01
#> "011" "042" "03" "02" "011" "03"
#> TCGA.AH.6547.01 TCGA.AZ.6601.11 TCGA.A6.5661.01 TCGA.F4.6807.01 TCGA.QG.A5YV.01 TCGA.AA.3509.11
#> "041" "02" "012" "03" "011" "02"
#> TCGA.AY.A71X.01 TCGA.CA.5797.01 TCGA.F4.6460.01 TCGA.G4.6302.11 TCGA.F5.6702.01 TCGA.AH.6549.01
#> "011" "0431" "042" "02" "042" "011"
#> TCGA.D5.6927.01 TCGA.CM.6166.01 TCGA.AH.6897.01 TCGA.G4.6304.01 TCGA.CA.5255.01 TCGA.EI.6507.01
#> "041" "011" "011" "041" "03" "03"
#> TCGA.CK.4947.01 TCGA.D5.5540.01 TCGA.DC.6682.01 TCGA.G4.6321.01 TCGA.A6.6649.01 TCGA.CM.5348.01
#> "03" "011" "03" "03" "03" "03"
#> TCGA.EI.6513.01 TCGA.A6.2672.01 TCGA.D5.6539.01 TCGA.AA.3510.01 TCGA.G5.6233.01 TCGA.BM.6198.01
#> "0431" "012" "041" "03" "011" "041"
#> TCGA.CA.6719.01 TCGA.DC.6154.01 TCGA.DM.A1D6.01 TCGA.AG.3731.11 TCGA.CM.6674.01 TCGA.CM.4743.01
#> "011" "03" "03" "02" "041" "041"
#> TCGA.F5.6465.01 TCGA.D5.5537.01 TCGA.F4.6463.01 TCGA.A6.2686.11 TCGA.4T.AA8H.01 TCGA.A6.6782.01
#> "042" "011" "03" "02" "011" "03"
#> TCGA.AG.3592.01 TCGA.AD.6888.01 TCGA.CM.6678.01 TCGA.CM.5344.01 TCGA.AA.3495.11 TCGA.AG.A01W.11
#> "011" "03" "011" "042" "02" "02"
#> TCGA.F4.6809.01 TCGA.CK.5914.01 TCGA.AZ.4681.01 TCGA.AA.3492.01 TCGA.D5.6536.01 TCGA.AA.3506.11
#> "03" "011" "0432" "012" "03" "02"
#> TCGA.AA.3488.01 TCGA.AA.3502.11 TCGA.A6.6140.01 TCGA.D5.6529.01 TCGA.DM.A1D0.01 TCGA.DM.A1HB.01
#> "03" "02" "042" "03" "042" "012"
#> TCGA.D5.6920.01 TCGA.D5.6922.01 TCGA.EI.6508.01 TCGA.D5.6532.01 TCGA.5M.AATA.01 TCGA.EI.6509.01
#> "03" "03" "011" "011" "03" "042"
#> TCGA.G4.6311.01 TCGA.A6.A566.01 TCGA.G4.6625.01 TCGA.CI.6619.01 TCGA.F5.6864.01 TCGA.AA.3492.11
#> "03" "03" "03" "042" "03" "02"
#> TCGA.A6.5659.01 TCGA.WS.AB45.01 TCGA.G4.6315.01 TCGA.D5.6541.01 TCGA.A6.2680.01 TCGA.CM.4751.01
#> "012" "041" "03" "03" "011" "03"
#> TCGA.CM.6680.01 TCGA.AF.6136.01 TCGA.AA.3660.01 TCGA.CM.4747.01 TCGA.EF.5831.01 TCGA.DM.A28G.01
#> "011" "03" "011" "011" "011" "011"
#> TCGA.G4.6297.01 TCGA.A6.2682.11 TCGA.D5.6537.01 TCGA.CM.6170.01 TCGA.DY.A1DD.01
#> "03" "02" "011" "03" "011"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 10997))
#> TCGA.AF.3911.01 TCGA.F4.6459.01 TCGA.AA.3494.11 TCGA.3L.AA1B.01 TCGA.D5.5538.01 TCGA.F4.6854.01
#> "03" "03" "02" "03" "03" "03"
#> TCGA.AG.A026.01 TCGA.G4.6303.01 TCGA.F5.6464.01 TCGA.T9.A92H.01 TCGA.AA.3712.11 TCGA.CM.5863.01
#> "01" "01" "041" "01" "02" "03"
#> TCGA.AZ.4308.01 TCGA.AD.6965.01 TCGA.A6.2681.11 TCGA.AD.6548.01 TCGA.A6.5660.01 TCGA.AZ.6600.01
#> "042" "01" "02" "03" "01" "03"
#> TCGA.F4.6808.01 TCGA.D5.6540.01 TCGA.F5.6571.01 TCGA.D5.6926.01 TCGA.CM.4748.01 TCGA.A6.2675.11
#> "03" "01" "01" "03" "03" "02"
#> TCGA.5M.AATE.01 TCGA.D5.5541.01 TCGA.CM.5862.01 TCGA.AA.3511.01 TCGA.AA.3663.11 TCGA.CI.6622.01
#> "03" "042" "01" "03" "02" "01"
#> TCGA.EI.6506.01 TCGA.AM.5821.01 TCGA.F5.6812.01 TCGA.G4.6588.01 TCGA.EI.6512.01 TCGA.A6.6648.01
#> "03" "03" "041" "01" "01" "042"
#> TCGA.A6.2671.11 TCGA.NH.A6GC.01 TCGA.F4.6805.01 TCGA.AA.3697.01 TCGA.QG.A5YX.01 TCGA.DM.A28C.01
#> "02" "03" "041" "03" "01" "03"
#> TCGA.AG.A036.01 TCGA.AZ.6606.01 TCGA.F4.6570.01 TCGA.DC.4745.01 TCGA.AF.A56K.01 TCGA.G4.6627.01
#> "01" "01" "01" "03" "042" "041"
#> TCGA.A6.5657.01 TCGA.A6.5662.01 TCGA.AA.3509.01 TCGA.D5.6929.01 TCGA.CM.6679.01 TCGA.A6.2680.11
#> "03" "03" "01" "042" "03" "02"
#> TCGA.DC.6157.01 TCGA.AF.6655.01 TCGA.CM.6161.01 TCGA.EI.6883.01 TCGA.F5.6811.01 TCGA.D5.6930.01
#> "0432" "042" "03" "01" "03" "03"
#> TCGA.CM.6164.01 TCGA.AF.2687.01 TCGA.DY.A1H8.01 TCGA.G5.6641.01 TCGA.DC.6155.01 TCGA.RU.A8FL.01
#> "042" "042" "03" "03" "03" "01"
#> TCGA.CK.4951.01 TCGA.F4.6704.01 TCGA.AZ.6599.01 TCGA.F5.6861.01 TCGA.CM.5860.01 TCGA.A6.6780.01
#> "03" "042" "01" "03" "01" "01"
#> TCGA.A6.2686.01 TCGA.CM.4750.01 TCGA.CM.6677.01 TCGA.A6.A567.01 TCGA.F5.6814.01 TCGA.D5.6898.01
#> "01" "01" "01" "0433" "01" "03"
#> TCGA.AG.A01W.01 TCGA.AZ.6598.11 TCGA.F5.6813.01 TCGA.AG.3732.01 TCGA.EI.6885.01 TCGA.G4.6299.01
#> "03" "02" "03" "042" "0433" "01"
#> TCGA.A6.4105.01 TCGA.DM.A1D8.01 TCGA.DM.A285.01 TCGA.G4.6295.11 TCGA.DC.4749.01 TCGA.DT.5265.01
#> "01" "01" "03" "02" "042" "01"
#> TCGA.5M.AAT5.01 TCGA.DM.A0XD.01 TCGA.A6.6138.01 TCGA.D5.7000.01 TCGA.DM.A28F.01 TCGA.DY.A1DE.01
#> "0432" "01" "01" "01" "01" "03"
#> TCGA.A6.6142.01 TCGA.QL.A97D.01 TCGA.CK.6748.01 TCGA.DC.6160.01 TCGA.D5.6534.01 TCGA.AZ.4616.01
#> "02" "03" "03" "042" "041" "03"
#> TCGA.CK.6751.01 TCGA.CM.6171.01 TCGA.DM.A1DA.01 TCGA.AG.A020.11 TCGA.G4.6311.11 TCGA.G4.6625.11
#> "01" "01" "01" "02" "02" "02"
#> TCGA.F5.6863.01 TCGA.G4.6317.02 TCGA.G4.6317.01 TCGA.DM.A1D4.01 TCGA.AG.A01Y.11 TCGA.D5.6530.01
#> "042" "0432" "03" "01" "02" "03"
#> TCGA.CK.4948.01 TCGA.AD.A5EJ.01 TCGA.A6.6651.01 TCGA.CA.5256.01 TCGA.DM.A0X9.01 TCGA.AY.A69D.01
#> "0431" "01" "041" "03" "01" "01"
#> TCGA.G4.6626.01 TCGA.CA.6716.01 TCGA.A6.2682.01 TCGA.A6.4107.11 TCGA.CA.6717.01 TCGA.G4.6293.01
#> "03" "01" "03" "02" "03" "03"
#> TCGA.CK.5916.01 TCGA.G4.6309.01 TCGA.AA.3662.01 TCGA.AF.A56L.01 TCGA.NH.A6GB.01 TCGA.AD.5900.01
#> "01" "042" "03" "03" "01" "03"
#> TCGA.NH.A50U.01 TCGA.AA.3712.01 TCGA.AZ.4614.01 TCGA.AH.6644.01 TCGA.AZ.6607.01 TCGA.AF.2693.01
#> "01" "03" "01" "01" "03" "041"
#> TCGA.D5.6924.01 TCGA.CM.5868.01 TCGA.AF.4110.01 TCGA.A6.3809.01 TCGA.AZ.4313.01 TCGA.A6.2675.01
#> "03" "042" "041" "01" "042" "042"
#> TCGA.AZ.6608.01 TCGA.CM.5864.01 TCGA.AA.3494.01 TCGA.AD.6895.01 TCGA.CI.6620.01 TCGA.DC.6156.01
#> "03" "01" "0432" "03" "03" "03"
#> TCGA.D5.6931.01 TCGA.CM.6165.01 TCGA.CM.5861.01 TCGA.A6.2671.01 TCGA.DC.6158.01 TCGA.AG.3742.01
#> "03" "03" "01" "03" "03" "01"
#> TCGA.AG.A02N.11 TCGA.G4.6307.01 TCGA.A6.5666.01 TCGA.EI.6511.01 TCGA.CI.6624.01 TCGA.AG.3591.01
#> "02" "0432" "01" "03" "042" "01"
#> TCGA.AY.A8YK.01 TCGA.F4.6856.01 TCGA.DM.A1D7.01 TCGA.A6.2685.01 TCGA.5M.AAT6.01 TCGA.AH.6643.01
#> "02" "03" "03" "02" "02" "01"
#> TCGA.F4.6569.01 TCGA.G4.6298.01 TCGA.AY.6196.01 TCGA.EI.6510.01 TCGA.A6.5656.01 TCGA.A6.2684.11
#> "03" "03" "03" "01" "01" "02"
#> TCGA.DY.A1DG.01 TCGA.AZ.4682.01 TCGA.EI.6884.01 TCGA.F4.6806.01 TCGA.G4.6320.11 TCGA.G4.6322.01
#> "01" "03" "03" "01" "02" "01"
#> TCGA.F5.6810.01 TCGA.5M.AAT4.01 TCGA.CL.4957.01 TCGA.DC.6681.01 TCGA.CM.6167.01 TCGA.AG.4022.01
#> "0431" "01" "03" "03" "041" "03"
#> TCGA.G4.6586.01 TCGA.EI.6514.01 TCGA.CK.4950.01 TCGA.DM.A282.01 TCGA.DY.A1DC.01 TCGA.D5.6535.01
#> "01" "01" "03" "01" "03" "03"
#> TCGA.DM.A1HA.01 TCGA.DC.5869.01 TCGA.AZ.6599.11 TCGA.CM.4752.01 TCGA.AZ.4684.01 TCGA.EI.7004.01
#> "01" "03" "02" "042" "03" "03"
#> TCGA.A6.A565.01 TCGA.D5.6531.01 TCGA.AZ.6598.01 TCGA.AD.6890.01 TCGA.AG.4021.01 TCGA.A6.6781.01
#> "02" "01" "01" "03" "01" "041"
#> TCGA.DM.A1D9.01 TCGA.CM.4744.01 TCGA.A6.2679.11 TCGA.A6.6652.01 TCGA.AD.6964.01 TCGA.SS.A7HO.01
#> "01" "01" "02" "01" "02" "01"
#> TCGA.A6.6650.01 TCGA.DM.A0XF.01 TCGA.G4.6295.01 TCGA.F4.6461.01 TCGA.AM.5820.01 TCGA.G4.6314.11
#> "01" "042" "0431" "01" "03" "02"
#> TCGA.AD.6889.01 TCGA.AZ.6605.01 TCGA.EI.6881.01 TCGA.NH.A50T.01 TCGA.AG.3725.11 TCGA.G4.6323.01
#> "01" "041" "03" "01" "02" "03"
#> TCGA.AA.3663.01 TCGA.AD.6899.01 TCGA.A6.5667.11 TCGA.A6.A56B.01 TCGA.G5.6572.01 TCGA.DM.A280.01
#> "01" "01" "02" "01" "041" "041"
#> TCGA.AG.A020.01 TCGA.AA.3713.01 TCGA.D5.5539.01 TCGA.AA.3655.11 TCGA.AA.3489.01 TCGA.AA.3495.01
#> "03" "03" "01" "02" "041" "03"
#> TCGA.AG.A01Y.01 TCGA.AZ.6601.01 TCGA.AH.6903.01 TCGA.AZ.6603.01 TCGA.CA.5254.01 TCGA.A6.A5ZU.01
#> "0433" "03" "03" "0432" "01" "03"
#> TCGA.G4.6302.01 TCGA.AZ.5403.01 TCGA.AY.A54L.01 TCGA.A6.4107.01 TCGA.NH.A5IV.01 TCGA.G4.6306.01
#> "041" "02" "01" "01" "01" "01"
#> TCGA.AD.A5EK.01 TCGA.G5.6235.01 TCGA.DC.5337.01 TCGA.CM.6675.01 TCGA.AH.6544.01 TCGA.CK.6746.01
#> "01" "041" "01" "01" "03" "01"
#> TCGA.CA.6718.01 TCGA.CI.6621.01 TCGA.CM.6676.01 TCGA.DM.A1DB.01 TCGA.A6.6654.01 TCGA.AA.3510.11
#> "03" "041" "03" "03" "03" "02"
#> TCGA.CA.6715.01 TCGA.CM.5341.01 TCGA.CK.5912.01 TCGA.F4.6857.01 TCGA.QG.A5YW.01 TCGA.A6.5665.01
#> "03" "03" "03" "041" "01" "01"
#> TCGA.CM.6168.01 TCGA.CL.5917.01 TCGA.AU.6004.01 TCGA.AY.5543.01 TCGA.AG.3731.01 TCGA.G4.6314.01
#> "03" "03" "03" "03" "03" "03"
#> TCGA.DC.6683.01 TCGA.CA.5796.01 TCGA.AG.A036.11 TCGA.AZ.4323.01 TCGA.EI.6882.01 TCGA.AZ.4315.01
#> "03" "03" "02" "041" "01" "03"
#> TCGA.A6.2677.01 TCGA.DY.A1DF.01 TCGA.CM.6162.01 TCGA.F4.6703.01 TCGA.CM.5349.01 TCGA.AG.A02N.01
#> "01" "03" "02" "02" "03" "03"
#> TCGA.AA.3506.01 TCGA.D5.6932.01 TCGA.D5.6538.01 TCGA.AA.3488.11 TCGA.AA.3502.01 TCGA.NH.A8F8.01
#> "03" "03" "01" "02" "01" "03"
#> TCGA.AF.A56N.01 TCGA.AF.6672.01 TCGA.A6.2685.11 TCGA.A6.6141.01 TCGA.AD.6963.01 TCGA.G4.6298.11
#> "03" "0433" "02" "03" "042" "02"
#> TCGA.EI.6917.01 TCGA.QG.A5Z2.01 TCGA.A6.2684.01 TCGA.CK.5915.01 TCGA.CM.6163.01 TCGA.G4.6322.11
#> "03" "01" "03" "01" "03" "02"
#> TCGA.AY.6197.01 TCGA.D5.6928.01 TCGA.A6.3810.01 TCGA.G4.6294.01 TCGA.AA.3660.11 TCGA.A6.6137.01
#> "01" "041" "042" "01" "02" "03"
#> TCGA.G4.6297.11 TCGA.AZ.4615.01 TCGA.CK.4952.01 TCGA.CM.6172.01 TCGA.AD.6901.01 TCGA.AA.3496.01
#> "02" "03" "01" "01" "03" "01"
#> TCGA.CK.5913.01 TCGA.DM.A28A.01 TCGA.EI.7002.01 TCGA.D5.6533.01 TCGA.QG.A5Z1.01 TCGA.D5.6923.01
#> "01" "01" "01" "03" "01" "041"
#> TCGA.AF.2690.01 TCGA.DM.A28H.01 TCGA.G4.6320.01 TCGA.G4.6310.01 TCGA.DM.A28M.01 TCGA.DM.A288.01
#> "041" "01" "01" "03" "01" "01"
#> TCGA.A6.2681.01 TCGA.A6.2679.01 TCGA.4N.A93T.01 TCGA.NH.A8F7.06 TCGA.NH.A8F7.01 TCGA.AZ.6600.11
#> "03" "03" "03" "03" "0432" "02"
#> TCGA.G5.6572.02 TCGA.AY.6386.01 TCGA.G4.6628.01 TCGA.A6.6653.01 TCGA.CM.4746.01 TCGA.F4.6855.01
#> "041" "03" "03" "01" "03" "01"
#> TCGA.EF.5830.01 TCGA.NH.A6GA.01 TCGA.NH.A50V.01 TCGA.DY.A0XA.01 TCGA.DM.A28E.01 TCGA.AG.3725.01
#> "03" "01" "01" "042" "042" "03"
#> TCGA.CK.6747.01 TCGA.CL.5918.01 TCGA.CI.6623.01 TCGA.A6.5667.01 TCGA.DM.A28K.01 TCGA.AA.3713.11
#> "01" "01" "042" "03" "01" "02"
#> TCGA.AA.3655.01 TCGA.AU.3779.01 TCGA.A6.5664.01 TCGA.AA.3697.11 TCGA.AZ.5407.01 TCGA.CM.6169.01
#> "01" "042" "03" "02" "01" "03"
#> TCGA.AH.6547.01 TCGA.AZ.6601.11 TCGA.A6.5661.01 TCGA.F4.6807.01 TCGA.QG.A5YV.01 TCGA.AA.3509.11
#> "041" "02" "01" "03" "01" "02"
#> TCGA.AY.A71X.01 TCGA.CA.5797.01 TCGA.F4.6460.01 TCGA.G4.6302.11 TCGA.F5.6702.01 TCGA.AH.6549.01
#> "01" "0431" "042" "02" "042" "01"
#> TCGA.D5.6927.01 TCGA.CM.6166.01 TCGA.AH.6897.01 TCGA.G4.6304.01 TCGA.CA.5255.01 TCGA.EI.6507.01
#> "041" "01" "01" "041" "03" "03"
#> TCGA.CK.4947.01 TCGA.D5.5540.01 TCGA.DC.6682.01 TCGA.G4.6321.01 TCGA.A6.6649.01 TCGA.CM.5348.01
#> "03" "01" "03" "03" "03" "03"
#> TCGA.EI.6513.01 TCGA.A6.2672.01 TCGA.D5.6539.01 TCGA.AA.3510.01 TCGA.G5.6233.01 TCGA.BM.6198.01
#> "0431" "01" "041" "03" "01" "041"
#> TCGA.CA.6719.01 TCGA.DC.6154.01 TCGA.DM.A1D6.01 TCGA.AG.3731.11 TCGA.CM.6674.01 TCGA.CM.4743.01
#> "01" "03" "03" "02" "041" "041"
#> TCGA.F5.6465.01 TCGA.D5.5537.01 TCGA.F4.6463.01 TCGA.A6.2686.11 TCGA.4T.AA8H.01 TCGA.A6.6782.01
#> "042" "01" "03" "02" "01" "03"
#> TCGA.AG.3592.01 TCGA.AD.6888.01 TCGA.CM.6678.01 TCGA.CM.5344.01 TCGA.AA.3495.11 TCGA.AG.A01W.11
#> "01" "03" "01" "042" "02" "02"
#> TCGA.F4.6809.01 TCGA.CK.5914.01 TCGA.AZ.4681.01 TCGA.AA.3492.01 TCGA.D5.6536.01 TCGA.AA.3506.11
#> "03" "01" "0432" "01" "03" "02"
#> TCGA.AA.3488.01 TCGA.AA.3502.11 TCGA.A6.6140.01 TCGA.D5.6529.01 TCGA.DM.A1D0.01 TCGA.DM.A1HB.01
#> "03" "02" "042" "03" "042" "01"
#> TCGA.D5.6920.01 TCGA.D5.6922.01 TCGA.EI.6508.01 TCGA.D5.6532.01 TCGA.5M.AATA.01 TCGA.EI.6509.01
#> "03" "03" "01" "01" "03" "042"
#> TCGA.G4.6311.01 TCGA.A6.A566.01 TCGA.G4.6625.01 TCGA.CI.6619.01 TCGA.F5.6864.01 TCGA.AA.3492.11
#> "03" "03" "03" "042" "03" "02"
#> TCGA.A6.5659.01 TCGA.WS.AB45.01 TCGA.G4.6315.01 TCGA.D5.6541.01 TCGA.A6.2680.01 TCGA.CM.4751.01
#> "01" "041" "03" "03" "01" "03"
#> TCGA.CM.6680.01 TCGA.AF.6136.01 TCGA.AA.3660.01 TCGA.CM.4747.01 TCGA.EF.5831.01 TCGA.DM.A28G.01
#> "01" "03" "01" "01" "01" "01"
#> TCGA.G4.6297.01 TCGA.A6.2682.11 TCGA.D5.6537.01 TCGA.CM.6170.01 TCGA.DY.A1DD.01
#> "03" "02" "01" "03" "01"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 17456))
#> TCGA.AF.3911.01 TCGA.F4.6459.01 TCGA.AA.3494.11 TCGA.3L.AA1B.01 TCGA.D5.5538.01 TCGA.F4.6854.01
#> "03" "03" "02" "03" "03" "03"
#> TCGA.AG.A026.01 TCGA.G4.6303.01 TCGA.F5.6464.01 TCGA.T9.A92H.01 TCGA.AA.3712.11 TCGA.CM.5863.01
#> "01" "01" "041" "01" "02" "03"
#> TCGA.AZ.4308.01 TCGA.AD.6965.01 TCGA.A6.2681.11 TCGA.AD.6548.01 TCGA.A6.5660.01 TCGA.AZ.6600.01
#> "042" "01" "02" "03" "01" "03"
#> TCGA.F4.6808.01 TCGA.D5.6540.01 TCGA.F5.6571.01 TCGA.D5.6926.01 TCGA.CM.4748.01 TCGA.A6.2675.11
#> "03" "01" "01" "03" "03" "02"
#> TCGA.5M.AATE.01 TCGA.D5.5541.01 TCGA.CM.5862.01 TCGA.AA.3511.01 TCGA.AA.3663.11 TCGA.CI.6622.01
#> "03" "042" "01" "03" "02" "01"
#> TCGA.EI.6506.01 TCGA.AM.5821.01 TCGA.F5.6812.01 TCGA.G4.6588.01 TCGA.EI.6512.01 TCGA.A6.6648.01
#> "03" "03" "041" "01" "01" "042"
#> TCGA.A6.2671.11 TCGA.NH.A6GC.01 TCGA.F4.6805.01 TCGA.AA.3697.01 TCGA.QG.A5YX.01 TCGA.DM.A28C.01
#> "02" "03" "041" "03" "01" "03"
#> TCGA.AG.A036.01 TCGA.AZ.6606.01 TCGA.F4.6570.01 TCGA.DC.4745.01 TCGA.AF.A56K.01 TCGA.G4.6627.01
#> "01" "01" "01" "03" "042" "041"
#> TCGA.A6.5657.01 TCGA.A6.5662.01 TCGA.AA.3509.01 TCGA.D5.6929.01 TCGA.CM.6679.01 TCGA.A6.2680.11
#> "03" "03" "01" "042" "03" "02"
#> TCGA.DC.6157.01 TCGA.AF.6655.01 TCGA.CM.6161.01 TCGA.EI.6883.01 TCGA.F5.6811.01 TCGA.D5.6930.01
#> "043" "042" "03" "01" "03" "03"
#> TCGA.CM.6164.01 TCGA.AF.2687.01 TCGA.DY.A1H8.01 TCGA.G5.6641.01 TCGA.DC.6155.01 TCGA.RU.A8FL.01
#> "042" "042" "03" "03" "03" "01"
#> TCGA.CK.4951.01 TCGA.F4.6704.01 TCGA.AZ.6599.01 TCGA.F5.6861.01 TCGA.CM.5860.01 TCGA.A6.6780.01
#> "03" "042" "01" "03" "01" "01"
#> TCGA.A6.2686.01 TCGA.CM.4750.01 TCGA.CM.6677.01 TCGA.A6.A567.01 TCGA.F5.6814.01 TCGA.D5.6898.01
#> "01" "01" "01" "043" "01" "03"
#> TCGA.AG.A01W.01 TCGA.AZ.6598.11 TCGA.F5.6813.01 TCGA.AG.3732.01 TCGA.EI.6885.01 TCGA.G4.6299.01
#> "03" "02" "03" "042" "043" "01"
#> TCGA.A6.4105.01 TCGA.DM.A1D8.01 TCGA.DM.A285.01 TCGA.G4.6295.11 TCGA.DC.4749.01 TCGA.DT.5265.01
#> "01" "01" "03" "02" "042" "01"
#> TCGA.5M.AAT5.01 TCGA.DM.A0XD.01 TCGA.A6.6138.01 TCGA.D5.7000.01 TCGA.DM.A28F.01 TCGA.DY.A1DE.01
#> "043" "01" "01" "01" "01" "03"
#> TCGA.A6.6142.01 TCGA.QL.A97D.01 TCGA.CK.6748.01 TCGA.DC.6160.01 TCGA.D5.6534.01 TCGA.AZ.4616.01
#> "02" "03" "03" "042" "041" "03"
#> TCGA.CK.6751.01 TCGA.CM.6171.01 TCGA.DM.A1DA.01 TCGA.AG.A020.11 TCGA.G4.6311.11 TCGA.G4.6625.11
#> "01" "01" "01" "02" "02" "02"
#> TCGA.F5.6863.01 TCGA.G4.6317.02 TCGA.G4.6317.01 TCGA.DM.A1D4.01 TCGA.AG.A01Y.11 TCGA.D5.6530.01
#> "042" "043" "03" "01" "02" "03"
#> TCGA.CK.4948.01 TCGA.AD.A5EJ.01 TCGA.A6.6651.01 TCGA.CA.5256.01 TCGA.DM.A0X9.01 TCGA.AY.A69D.01
#> "043" "01" "041" "03" "01" "01"
#> TCGA.G4.6626.01 TCGA.CA.6716.01 TCGA.A6.2682.01 TCGA.A6.4107.11 TCGA.CA.6717.01 TCGA.G4.6293.01
#> "03" "01" "03" "02" "03" "03"
#> TCGA.CK.5916.01 TCGA.G4.6309.01 TCGA.AA.3662.01 TCGA.AF.A56L.01 TCGA.NH.A6GB.01 TCGA.AD.5900.01
#> "01" "042" "03" "03" "01" "03"
#> TCGA.NH.A50U.01 TCGA.AA.3712.01 TCGA.AZ.4614.01 TCGA.AH.6644.01 TCGA.AZ.6607.01 TCGA.AF.2693.01
#> "01" "03" "01" "01" "03" "041"
#> TCGA.D5.6924.01 TCGA.CM.5868.01 TCGA.AF.4110.01 TCGA.A6.3809.01 TCGA.AZ.4313.01 TCGA.A6.2675.01
#> "03" "042" "041" "01" "042" "042"
#> TCGA.AZ.6608.01 TCGA.CM.5864.01 TCGA.AA.3494.01 TCGA.AD.6895.01 TCGA.CI.6620.01 TCGA.DC.6156.01
#> "03" "01" "043" "03" "03" "03"
#> TCGA.D5.6931.01 TCGA.CM.6165.01 TCGA.CM.5861.01 TCGA.A6.2671.01 TCGA.DC.6158.01 TCGA.AG.3742.01
#> "03" "03" "01" "03" "03" "01"
#> TCGA.AG.A02N.11 TCGA.G4.6307.01 TCGA.A6.5666.01 TCGA.EI.6511.01 TCGA.CI.6624.01 TCGA.AG.3591.01
#> "02" "043" "01" "03" "042" "01"
#> TCGA.AY.A8YK.01 TCGA.F4.6856.01 TCGA.DM.A1D7.01 TCGA.A6.2685.01 TCGA.5M.AAT6.01 TCGA.AH.6643.01
#> "02" "03" "03" "02" "02" "01"
#> TCGA.F4.6569.01 TCGA.G4.6298.01 TCGA.AY.6196.01 TCGA.EI.6510.01 TCGA.A6.5656.01 TCGA.A6.2684.11
#> "03" "03" "03" "01" "01" "02"
#> TCGA.DY.A1DG.01 TCGA.AZ.4682.01 TCGA.EI.6884.01 TCGA.F4.6806.01 TCGA.G4.6320.11 TCGA.G4.6322.01
#> "01" "03" "03" "01" "02" "01"
#> TCGA.F5.6810.01 TCGA.5M.AAT4.01 TCGA.CL.4957.01 TCGA.DC.6681.01 TCGA.CM.6167.01 TCGA.AG.4022.01
#> "043" "01" "03" "03" "041" "03"
#> TCGA.G4.6586.01 TCGA.EI.6514.01 TCGA.CK.4950.01 TCGA.DM.A282.01 TCGA.DY.A1DC.01 TCGA.D5.6535.01
#> "01" "01" "03" "01" "03" "03"
#> TCGA.DM.A1HA.01 TCGA.DC.5869.01 TCGA.AZ.6599.11 TCGA.CM.4752.01 TCGA.AZ.4684.01 TCGA.EI.7004.01
#> "01" "03" "02" "042" "03" "03"
#> TCGA.A6.A565.01 TCGA.D5.6531.01 TCGA.AZ.6598.01 TCGA.AD.6890.01 TCGA.AG.4021.01 TCGA.A6.6781.01
#> "02" "01" "01" "03" "01" "041"
#> TCGA.DM.A1D9.01 TCGA.CM.4744.01 TCGA.A6.2679.11 TCGA.A6.6652.01 TCGA.AD.6964.01 TCGA.SS.A7HO.01
#> "01" "01" "02" "01" "02" "01"
#> TCGA.A6.6650.01 TCGA.DM.A0XF.01 TCGA.G4.6295.01 TCGA.F4.6461.01 TCGA.AM.5820.01 TCGA.G4.6314.11
#> "01" "042" "043" "01" "03" "02"
#> TCGA.AD.6889.01 TCGA.AZ.6605.01 TCGA.EI.6881.01 TCGA.NH.A50T.01 TCGA.AG.3725.11 TCGA.G4.6323.01
#> "01" "041" "03" "01" "02" "03"
#> TCGA.AA.3663.01 TCGA.AD.6899.01 TCGA.A6.5667.11 TCGA.A6.A56B.01 TCGA.G5.6572.01 TCGA.DM.A280.01
#> "01" "01" "02" "01" "041" "041"
#> TCGA.AG.A020.01 TCGA.AA.3713.01 TCGA.D5.5539.01 TCGA.AA.3655.11 TCGA.AA.3489.01 TCGA.AA.3495.01
#> "03" "03" "01" "02" "041" "03"
#> TCGA.AG.A01Y.01 TCGA.AZ.6601.01 TCGA.AH.6903.01 TCGA.AZ.6603.01 TCGA.CA.5254.01 TCGA.A6.A5ZU.01
#> "043" "03" "03" "043" "01" "03"
#> TCGA.G4.6302.01 TCGA.AZ.5403.01 TCGA.AY.A54L.01 TCGA.A6.4107.01 TCGA.NH.A5IV.01 TCGA.G4.6306.01
#> "041" "02" "01" "01" "01" "01"
#> TCGA.AD.A5EK.01 TCGA.G5.6235.01 TCGA.DC.5337.01 TCGA.CM.6675.01 TCGA.AH.6544.01 TCGA.CK.6746.01
#> "01" "041" "01" "01" "03" "01"
#> TCGA.CA.6718.01 TCGA.CI.6621.01 TCGA.CM.6676.01 TCGA.DM.A1DB.01 TCGA.A6.6654.01 TCGA.AA.3510.11
#> "03" "041" "03" "03" "03" "02"
#> TCGA.CA.6715.01 TCGA.CM.5341.01 TCGA.CK.5912.01 TCGA.F4.6857.01 TCGA.QG.A5YW.01 TCGA.A6.5665.01
#> "03" "03" "03" "041" "01" "01"
#> TCGA.CM.6168.01 TCGA.CL.5917.01 TCGA.AU.6004.01 TCGA.AY.5543.01 TCGA.AG.3731.01 TCGA.G4.6314.01
#> "03" "03" "03" "03" "03" "03"
#> TCGA.DC.6683.01 TCGA.CA.5796.01 TCGA.AG.A036.11 TCGA.AZ.4323.01 TCGA.EI.6882.01 TCGA.AZ.4315.01
#> "03" "03" "02" "041" "01" "03"
#> TCGA.A6.2677.01 TCGA.DY.A1DF.01 TCGA.CM.6162.01 TCGA.F4.6703.01 TCGA.CM.5349.01 TCGA.AG.A02N.01
#> "01" "03" "02" "02" "03" "03"
#> TCGA.AA.3506.01 TCGA.D5.6932.01 TCGA.D5.6538.01 TCGA.AA.3488.11 TCGA.AA.3502.01 TCGA.NH.A8F8.01
#> "03" "03" "01" "02" "01" "03"
#> TCGA.AF.A56N.01 TCGA.AF.6672.01 TCGA.A6.2685.11 TCGA.A6.6141.01 TCGA.AD.6963.01 TCGA.G4.6298.11
#> "03" "043" "02" "03" "042" "02"
#> TCGA.EI.6917.01 TCGA.QG.A5Z2.01 TCGA.A6.2684.01 TCGA.CK.5915.01 TCGA.CM.6163.01 TCGA.G4.6322.11
#> "03" "01" "03" "01" "03" "02"
#> TCGA.AY.6197.01 TCGA.D5.6928.01 TCGA.A6.3810.01 TCGA.G4.6294.01 TCGA.AA.3660.11 TCGA.A6.6137.01
#> "01" "041" "042" "01" "02" "03"
#> TCGA.G4.6297.11 TCGA.AZ.4615.01 TCGA.CK.4952.01 TCGA.CM.6172.01 TCGA.AD.6901.01 TCGA.AA.3496.01
#> "02" "03" "01" "01" "03" "01"
#> TCGA.CK.5913.01 TCGA.DM.A28A.01 TCGA.EI.7002.01 TCGA.D5.6533.01 TCGA.QG.A5Z1.01 TCGA.D5.6923.01
#> "01" "01" "01" "03" "01" "041"
#> TCGA.AF.2690.01 TCGA.DM.A28H.01 TCGA.G4.6320.01 TCGA.G4.6310.01 TCGA.DM.A28M.01 TCGA.DM.A288.01
#> "041" "01" "01" "03" "01" "01"
#> TCGA.A6.2681.01 TCGA.A6.2679.01 TCGA.4N.A93T.01 TCGA.NH.A8F7.06 TCGA.NH.A8F7.01 TCGA.AZ.6600.11
#> "03" "03" "03" "03" "043" "02"
#> TCGA.G5.6572.02 TCGA.AY.6386.01 TCGA.G4.6628.01 TCGA.A6.6653.01 TCGA.CM.4746.01 TCGA.F4.6855.01
#> "041" "03" "03" "01" "03" "01"
#> TCGA.EF.5830.01 TCGA.NH.A6GA.01 TCGA.NH.A50V.01 TCGA.DY.A0XA.01 TCGA.DM.A28E.01 TCGA.AG.3725.01
#> "03" "01" "01" "042" "042" "03"
#> TCGA.CK.6747.01 TCGA.CL.5918.01 TCGA.CI.6623.01 TCGA.A6.5667.01 TCGA.DM.A28K.01 TCGA.AA.3713.11
#> "01" "01" "042" "03" "01" "02"
#> TCGA.AA.3655.01 TCGA.AU.3779.01 TCGA.A6.5664.01 TCGA.AA.3697.11 TCGA.AZ.5407.01 TCGA.CM.6169.01
#> "01" "042" "03" "02" "01" "03"
#> TCGA.AH.6547.01 TCGA.AZ.6601.11 TCGA.A6.5661.01 TCGA.F4.6807.01 TCGA.QG.A5YV.01 TCGA.AA.3509.11
#> "041" "02" "01" "03" "01" "02"
#> TCGA.AY.A71X.01 TCGA.CA.5797.01 TCGA.F4.6460.01 TCGA.G4.6302.11 TCGA.F5.6702.01 TCGA.AH.6549.01
#> "01" "043" "042" "02" "042" "01"
#> TCGA.D5.6927.01 TCGA.CM.6166.01 TCGA.AH.6897.01 TCGA.G4.6304.01 TCGA.CA.5255.01 TCGA.EI.6507.01
#> "041" "01" "01" "041" "03" "03"
#> TCGA.CK.4947.01 TCGA.D5.5540.01 TCGA.DC.6682.01 TCGA.G4.6321.01 TCGA.A6.6649.01 TCGA.CM.5348.01
#> "03" "01" "03" "03" "03" "03"
#> TCGA.EI.6513.01 TCGA.A6.2672.01 TCGA.D5.6539.01 TCGA.AA.3510.01 TCGA.G5.6233.01 TCGA.BM.6198.01
#> "043" "01" "041" "03" "01" "041"
#> TCGA.CA.6719.01 TCGA.DC.6154.01 TCGA.DM.A1D6.01 TCGA.AG.3731.11 TCGA.CM.6674.01 TCGA.CM.4743.01
#> "01" "03" "03" "02" "041" "041"
#> TCGA.F5.6465.01 TCGA.D5.5537.01 TCGA.F4.6463.01 TCGA.A6.2686.11 TCGA.4T.AA8H.01 TCGA.A6.6782.01
#> "042" "01" "03" "02" "01" "03"
#> TCGA.AG.3592.01 TCGA.AD.6888.01 TCGA.CM.6678.01 TCGA.CM.5344.01 TCGA.AA.3495.11 TCGA.AG.A01W.11
#> "01" "03" "01" "042" "02" "02"
#> TCGA.F4.6809.01 TCGA.CK.5914.01 TCGA.AZ.4681.01 TCGA.AA.3492.01 TCGA.D5.6536.01 TCGA.AA.3506.11
#> "03" "01" "043" "01" "03" "02"
#> TCGA.AA.3488.01 TCGA.AA.3502.11 TCGA.A6.6140.01 TCGA.D5.6529.01 TCGA.DM.A1D0.01 TCGA.DM.A1HB.01
#> "03" "02" "042" "03" "042" "01"
#> TCGA.D5.6920.01 TCGA.D5.6922.01 TCGA.EI.6508.01 TCGA.D5.6532.01 TCGA.5M.AATA.01 TCGA.EI.6509.01
#> "03" "03" "01" "01" "03" "042"
#> TCGA.G4.6311.01 TCGA.A6.A566.01 TCGA.G4.6625.01 TCGA.CI.6619.01 TCGA.F5.6864.01 TCGA.AA.3492.11
#> "03" "03" "03" "042" "03" "02"
#> TCGA.A6.5659.01 TCGA.WS.AB45.01 TCGA.G4.6315.01 TCGA.D5.6541.01 TCGA.A6.2680.01 TCGA.CM.4751.01
#> "01" "041" "03" "03" "01" "03"
#> TCGA.CM.6680.01 TCGA.AF.6136.01 TCGA.AA.3660.01 TCGA.CM.4747.01 TCGA.EF.5831.01 TCGA.DM.A28G.01
#> "01" "03" "01" "01" "01" "01"
#> TCGA.G4.6297.01 TCGA.A6.2682.11 TCGA.D5.6537.01 TCGA.CM.6170.01 TCGA.DY.A1DD.01
#> "03" "02" "01" "03" "01"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 34264))
#> TCGA.AF.3911.01 TCGA.F4.6459.01 TCGA.AA.3494.11 TCGA.3L.AA1B.01 TCGA.D5.5538.01 TCGA.F4.6854.01
#> "03" "03" "02" "03" "03" "03"
#> TCGA.AG.A026.01 TCGA.G4.6303.01 TCGA.F5.6464.01 TCGA.T9.A92H.01 TCGA.AA.3712.11 TCGA.CM.5863.01
#> "01" "01" "04" "01" "02" "03"
#> TCGA.AZ.4308.01 TCGA.AD.6965.01 TCGA.A6.2681.11 TCGA.AD.6548.01 TCGA.A6.5660.01 TCGA.AZ.6600.01
#> "04" "01" "02" "03" "01" "03"
#> TCGA.F4.6808.01 TCGA.D5.6540.01 TCGA.F5.6571.01 TCGA.D5.6926.01 TCGA.CM.4748.01 TCGA.A6.2675.11
#> "03" "01" "01" "03" "03" "02"
#> TCGA.5M.AATE.01 TCGA.D5.5541.01 TCGA.CM.5862.01 TCGA.AA.3511.01 TCGA.AA.3663.11 TCGA.CI.6622.01
#> "03" "04" "01" "03" "02" "01"
#> TCGA.EI.6506.01 TCGA.AM.5821.01 TCGA.F5.6812.01 TCGA.G4.6588.01 TCGA.EI.6512.01 TCGA.A6.6648.01
#> "03" "03" "04" "01" "01" "04"
#> TCGA.A6.2671.11 TCGA.NH.A6GC.01 TCGA.F4.6805.01 TCGA.AA.3697.01 TCGA.QG.A5YX.01 TCGA.DM.A28C.01
#> "02" "03" "04" "03" "01" "03"
#> TCGA.AG.A036.01 TCGA.AZ.6606.01 TCGA.F4.6570.01 TCGA.DC.4745.01 TCGA.AF.A56K.01 TCGA.G4.6627.01
#> "01" "01" "01" "03" "04" "04"
#> TCGA.A6.5657.01 TCGA.A6.5662.01 TCGA.AA.3509.01 TCGA.D5.6929.01 TCGA.CM.6679.01 TCGA.A6.2680.11
#> "03" "03" "01" "04" "03" "02"
#> TCGA.DC.6157.01 TCGA.AF.6655.01 TCGA.CM.6161.01 TCGA.EI.6883.01 TCGA.F5.6811.01 TCGA.D5.6930.01
#> "04" "04" "03" "01" "03" "03"
#> TCGA.CM.6164.01 TCGA.AF.2687.01 TCGA.DY.A1H8.01 TCGA.G5.6641.01 TCGA.DC.6155.01 TCGA.RU.A8FL.01
#> "04" "04" "03" "03" "03" "01"
#> TCGA.CK.4951.01 TCGA.F4.6704.01 TCGA.AZ.6599.01 TCGA.F5.6861.01 TCGA.CM.5860.01 TCGA.A6.6780.01
#> "03" "04" "01" "03" "01" "01"
#> TCGA.A6.2686.01 TCGA.CM.4750.01 TCGA.CM.6677.01 TCGA.A6.A567.01 TCGA.F5.6814.01 TCGA.D5.6898.01
#> "01" "01" "01" "04" "01" "03"
#> TCGA.AG.A01W.01 TCGA.AZ.6598.11 TCGA.F5.6813.01 TCGA.AG.3732.01 TCGA.EI.6885.01 TCGA.G4.6299.01
#> "03" "02" "03" "04" "04" "01"
#> TCGA.A6.4105.01 TCGA.DM.A1D8.01 TCGA.DM.A285.01 TCGA.G4.6295.11 TCGA.DC.4749.01 TCGA.DT.5265.01
#> "01" "01" "03" "02" "04" "01"
#> TCGA.5M.AAT5.01 TCGA.DM.A0XD.01 TCGA.A6.6138.01 TCGA.D5.7000.01 TCGA.DM.A28F.01 TCGA.DY.A1DE.01
#> "04" "01" "01" "01" "01" "03"
#> TCGA.A6.6142.01 TCGA.QL.A97D.01 TCGA.CK.6748.01 TCGA.DC.6160.01 TCGA.D5.6534.01 TCGA.AZ.4616.01
#> "02" "03" "03" "04" "04" "03"
#> TCGA.CK.6751.01 TCGA.CM.6171.01 TCGA.DM.A1DA.01 TCGA.AG.A020.11 TCGA.G4.6311.11 TCGA.G4.6625.11
#> "01" "01" "01" "02" "02" "02"
#> TCGA.F5.6863.01 TCGA.G4.6317.02 TCGA.G4.6317.01 TCGA.DM.A1D4.01 TCGA.AG.A01Y.11 TCGA.D5.6530.01
#> "04" "04" "03" "01" "02" "03"
#> TCGA.CK.4948.01 TCGA.AD.A5EJ.01 TCGA.A6.6651.01 TCGA.CA.5256.01 TCGA.DM.A0X9.01 TCGA.AY.A69D.01
#> "04" "01" "04" "03" "01" "01"
#> TCGA.G4.6626.01 TCGA.CA.6716.01 TCGA.A6.2682.01 TCGA.A6.4107.11 TCGA.CA.6717.01 TCGA.G4.6293.01
#> "03" "01" "03" "02" "03" "03"
#> TCGA.CK.5916.01 TCGA.G4.6309.01 TCGA.AA.3662.01 TCGA.AF.A56L.01 TCGA.NH.A6GB.01 TCGA.AD.5900.01
#> "01" "04" "03" "03" "01" "03"
#> TCGA.NH.A50U.01 TCGA.AA.3712.01 TCGA.AZ.4614.01 TCGA.AH.6644.01 TCGA.AZ.6607.01 TCGA.AF.2693.01
#> "01" "03" "01" "01" "03" "04"
#> TCGA.D5.6924.01 TCGA.CM.5868.01 TCGA.AF.4110.01 TCGA.A6.3809.01 TCGA.AZ.4313.01 TCGA.A6.2675.01
#> "03" "04" "04" "01" "04" "04"
#> TCGA.AZ.6608.01 TCGA.CM.5864.01 TCGA.AA.3494.01 TCGA.AD.6895.01 TCGA.CI.6620.01 TCGA.DC.6156.01
#> "03" "01" "04" "03" "03" "03"
#> TCGA.D5.6931.01 TCGA.CM.6165.01 TCGA.CM.5861.01 TCGA.A6.2671.01 TCGA.DC.6158.01 TCGA.AG.3742.01
#> "03" "03" "01" "03" "03" "01"
#> TCGA.AG.A02N.11 TCGA.G4.6307.01 TCGA.A6.5666.01 TCGA.EI.6511.01 TCGA.CI.6624.01 TCGA.AG.3591.01
#> "02" "04" "01" "03" "04" "01"
#> TCGA.AY.A8YK.01 TCGA.F4.6856.01 TCGA.DM.A1D7.01 TCGA.A6.2685.01 TCGA.5M.AAT6.01 TCGA.AH.6643.01
#> "02" "03" "03" "02" "02" "01"
#> TCGA.F4.6569.01 TCGA.G4.6298.01 TCGA.AY.6196.01 TCGA.EI.6510.01 TCGA.A6.5656.01 TCGA.A6.2684.11
#> "03" "03" "03" "01" "01" "02"
#> TCGA.DY.A1DG.01 TCGA.AZ.4682.01 TCGA.EI.6884.01 TCGA.F4.6806.01 TCGA.G4.6320.11 TCGA.G4.6322.01
#> "01" "03" "03" "01" "02" "01"
#> TCGA.F5.6810.01 TCGA.5M.AAT4.01 TCGA.CL.4957.01 TCGA.DC.6681.01 TCGA.CM.6167.01 TCGA.AG.4022.01
#> "04" "01" "03" "03" "04" "03"
#> TCGA.G4.6586.01 TCGA.EI.6514.01 TCGA.CK.4950.01 TCGA.DM.A282.01 TCGA.DY.A1DC.01 TCGA.D5.6535.01
#> "01" "01" "03" "01" "03" "03"
#> TCGA.DM.A1HA.01 TCGA.DC.5869.01 TCGA.AZ.6599.11 TCGA.CM.4752.01 TCGA.AZ.4684.01 TCGA.EI.7004.01
#> "01" "03" "02" "04" "03" "03"
#> TCGA.A6.A565.01 TCGA.D5.6531.01 TCGA.AZ.6598.01 TCGA.AD.6890.01 TCGA.AG.4021.01 TCGA.A6.6781.01
#> "02" "01" "01" "03" "01" "04"
#> TCGA.DM.A1D9.01 TCGA.CM.4744.01 TCGA.A6.2679.11 TCGA.A6.6652.01 TCGA.AD.6964.01 TCGA.SS.A7HO.01
#> "01" "01" "02" "01" "02" "01"
#> TCGA.A6.6650.01 TCGA.DM.A0XF.01 TCGA.G4.6295.01 TCGA.F4.6461.01 TCGA.AM.5820.01 TCGA.G4.6314.11
#> "01" "04" "04" "01" "03" "02"
#> TCGA.AD.6889.01 TCGA.AZ.6605.01 TCGA.EI.6881.01 TCGA.NH.A50T.01 TCGA.AG.3725.11 TCGA.G4.6323.01
#> "01" "04" "03" "01" "02" "03"
#> TCGA.AA.3663.01 TCGA.AD.6899.01 TCGA.A6.5667.11 TCGA.A6.A56B.01 TCGA.G5.6572.01 TCGA.DM.A280.01
#> "01" "01" "02" "01" "04" "04"
#> TCGA.AG.A020.01 TCGA.AA.3713.01 TCGA.D5.5539.01 TCGA.AA.3655.11 TCGA.AA.3489.01 TCGA.AA.3495.01
#> "03" "03" "01" "02" "04" "03"
#> TCGA.AG.A01Y.01 TCGA.AZ.6601.01 TCGA.AH.6903.01 TCGA.AZ.6603.01 TCGA.CA.5254.01 TCGA.A6.A5ZU.01
#> "04" "03" "03" "04" "01" "03"
#> TCGA.G4.6302.01 TCGA.AZ.5403.01 TCGA.AY.A54L.01 TCGA.A6.4107.01 TCGA.NH.A5IV.01 TCGA.G4.6306.01
#> "04" "02" "01" "01" "01" "01"
#> TCGA.AD.A5EK.01 TCGA.G5.6235.01 TCGA.DC.5337.01 TCGA.CM.6675.01 TCGA.AH.6544.01 TCGA.CK.6746.01
#> "01" "04" "01" "01" "03" "01"
#> TCGA.CA.6718.01 TCGA.CI.6621.01 TCGA.CM.6676.01 TCGA.DM.A1DB.01 TCGA.A6.6654.01 TCGA.AA.3510.11
#> "03" "04" "03" "03" "03" "02"
#> TCGA.CA.6715.01 TCGA.CM.5341.01 TCGA.CK.5912.01 TCGA.F4.6857.01 TCGA.QG.A5YW.01 TCGA.A6.5665.01
#> "03" "03" "03" "04" "01" "01"
#> TCGA.CM.6168.01 TCGA.CL.5917.01 TCGA.AU.6004.01 TCGA.AY.5543.01 TCGA.AG.3731.01 TCGA.G4.6314.01
#> "03" "03" "03" "03" "03" "03"
#> TCGA.DC.6683.01 TCGA.CA.5796.01 TCGA.AG.A036.11 TCGA.AZ.4323.01 TCGA.EI.6882.01 TCGA.AZ.4315.01
#> "03" "03" "02" "04" "01" "03"
#> TCGA.A6.2677.01 TCGA.DY.A1DF.01 TCGA.CM.6162.01 TCGA.F4.6703.01 TCGA.CM.5349.01 TCGA.AG.A02N.01
#> "01" "03" "02" "02" "03" "03"
#> TCGA.AA.3506.01 TCGA.D5.6932.01 TCGA.D5.6538.01 TCGA.AA.3488.11 TCGA.AA.3502.01 TCGA.NH.A8F8.01
#> "03" "03" "01" "02" "01" "03"
#> TCGA.AF.A56N.01 TCGA.AF.6672.01 TCGA.A6.2685.11 TCGA.A6.6141.01 TCGA.AD.6963.01 TCGA.G4.6298.11
#> "03" "04" "02" "03" "04" "02"
#> TCGA.EI.6917.01 TCGA.QG.A5Z2.01 TCGA.A6.2684.01 TCGA.CK.5915.01 TCGA.CM.6163.01 TCGA.G4.6322.11
#> "03" "01" "03" "01" "03" "02"
#> TCGA.AY.6197.01 TCGA.D5.6928.01 TCGA.A6.3810.01 TCGA.G4.6294.01 TCGA.AA.3660.11 TCGA.A6.6137.01
#> "01" "04" "04" "01" "02" "03"
#> TCGA.G4.6297.11 TCGA.AZ.4615.01 TCGA.CK.4952.01 TCGA.CM.6172.01 TCGA.AD.6901.01 TCGA.AA.3496.01
#> "02" "03" "01" "01" "03" "01"
#> TCGA.CK.5913.01 TCGA.DM.A28A.01 TCGA.EI.7002.01 TCGA.D5.6533.01 TCGA.QG.A5Z1.01 TCGA.D5.6923.01
#> "01" "01" "01" "03" "01" "04"
#> TCGA.AF.2690.01 TCGA.DM.A28H.01 TCGA.G4.6320.01 TCGA.G4.6310.01 TCGA.DM.A28M.01 TCGA.DM.A288.01
#> "04" "01" "01" "03" "01" "01"
#> TCGA.A6.2681.01 TCGA.A6.2679.01 TCGA.4N.A93T.01 TCGA.NH.A8F7.06 TCGA.NH.A8F7.01 TCGA.AZ.6600.11
#> "03" "03" "03" "03" "04" "02"
#> TCGA.G5.6572.02 TCGA.AY.6386.01 TCGA.G4.6628.01 TCGA.A6.6653.01 TCGA.CM.4746.01 TCGA.F4.6855.01
#> "04" "03" "03" "01" "03" "01"
#> TCGA.EF.5830.01 TCGA.NH.A6GA.01 TCGA.NH.A50V.01 TCGA.DY.A0XA.01 TCGA.DM.A28E.01 TCGA.AG.3725.01
#> "03" "01" "01" "04" "04" "03"
#> TCGA.CK.6747.01 TCGA.CL.5918.01 TCGA.CI.6623.01 TCGA.A6.5667.01 TCGA.DM.A28K.01 TCGA.AA.3713.11
#> "01" "01" "04" "03" "01" "02"
#> TCGA.AA.3655.01 TCGA.AU.3779.01 TCGA.A6.5664.01 TCGA.AA.3697.11 TCGA.AZ.5407.01 TCGA.CM.6169.01
#> "01" "04" "03" "02" "01" "03"
#> TCGA.AH.6547.01 TCGA.AZ.6601.11 TCGA.A6.5661.01 TCGA.F4.6807.01 TCGA.QG.A5YV.01 TCGA.AA.3509.11
#> "04" "02" "01" "03" "01" "02"
#> TCGA.AY.A71X.01 TCGA.CA.5797.01 TCGA.F4.6460.01 TCGA.G4.6302.11 TCGA.F5.6702.01 TCGA.AH.6549.01
#> "01" "04" "04" "02" "04" "01"
#> TCGA.D5.6927.01 TCGA.CM.6166.01 TCGA.AH.6897.01 TCGA.G4.6304.01 TCGA.CA.5255.01 TCGA.EI.6507.01
#> "04" "01" "01" "04" "03" "03"
#> TCGA.CK.4947.01 TCGA.D5.5540.01 TCGA.DC.6682.01 TCGA.G4.6321.01 TCGA.A6.6649.01 TCGA.CM.5348.01
#> "03" "01" "03" "03" "03" "03"
#> TCGA.EI.6513.01 TCGA.A6.2672.01 TCGA.D5.6539.01 TCGA.AA.3510.01 TCGA.G5.6233.01 TCGA.BM.6198.01
#> "04" "01" "04" "03" "01" "04"
#> TCGA.CA.6719.01 TCGA.DC.6154.01 TCGA.DM.A1D6.01 TCGA.AG.3731.11 TCGA.CM.6674.01 TCGA.CM.4743.01
#> "01" "03" "03" "02" "04" "04"
#> TCGA.F5.6465.01 TCGA.D5.5537.01 TCGA.F4.6463.01 TCGA.A6.2686.11 TCGA.4T.AA8H.01 TCGA.A6.6782.01
#> "04" "01" "03" "02" "01" "03"
#> TCGA.AG.3592.01 TCGA.AD.6888.01 TCGA.CM.6678.01 TCGA.CM.5344.01 TCGA.AA.3495.11 TCGA.AG.A01W.11
#> "01" "03" "01" "04" "02" "02"
#> TCGA.F4.6809.01 TCGA.CK.5914.01 TCGA.AZ.4681.01 TCGA.AA.3492.01 TCGA.D5.6536.01 TCGA.AA.3506.11
#> "03" "01" "04" "01" "03" "02"
#> TCGA.AA.3488.01 TCGA.AA.3502.11 TCGA.A6.6140.01 TCGA.D5.6529.01 TCGA.DM.A1D0.01 TCGA.DM.A1HB.01
#> "03" "02" "04" "03" "04" "01"
#> TCGA.D5.6920.01 TCGA.D5.6922.01 TCGA.EI.6508.01 TCGA.D5.6532.01 TCGA.5M.AATA.01 TCGA.EI.6509.01
#> "03" "03" "01" "01" "03" "04"
#> TCGA.G4.6311.01 TCGA.A6.A566.01 TCGA.G4.6625.01 TCGA.CI.6619.01 TCGA.F5.6864.01 TCGA.AA.3492.11
#> "03" "03" "03" "04" "03" "02"
#> TCGA.A6.5659.01 TCGA.WS.AB45.01 TCGA.G4.6315.01 TCGA.D5.6541.01 TCGA.A6.2680.01 TCGA.CM.4751.01
#> "01" "04" "03" "03" "01" "03"
#> TCGA.CM.6680.01 TCGA.AF.6136.01 TCGA.AA.3660.01 TCGA.CM.4747.01 TCGA.EF.5831.01 TCGA.DM.A28G.01
#> "01" "03" "01" "01" "01" "01"
#> TCGA.G4.6297.01 TCGA.A6.2682.11 TCGA.D5.6537.01 TCGA.CM.6170.01 TCGA.DY.A1DD.01
#> "03" "02" "01" "03" "01"
Heatmaps of the top rows:
top_rows_heatmap(res_rh)
#> Error in h(simpleError(msg, call)) :
#> error in evaluating the argument 'object' in selecting a method for function 'draw': no applicable method for 'height' applied to an object of class "list"
Top rows on each node:
top_rows_overlap(res_rh, method = "upset")
UMAP plot which shows how samples are separated.
par(mfrow = c(1, 2))
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 1359),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 1359),
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 = 1530),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 1530),
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 = 1543),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 1543),
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 = 3038),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 3038),
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 = 3867),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 3867),
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 = 3913),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 3913),
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 = 4047),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 4047),
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 = 5229),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 5229),
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 = 5533),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 5533),
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 = 5908),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 5908),
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 = 7485),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 7485),
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 = 7743),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 7743),
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 = 8434),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 8434),
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 = 9343),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 9343),
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 = 10997),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 10997),
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 = 17456),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 17456),
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 = 34264),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 34264),
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 = 1359))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 1530))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 1543))
#> Error in lt[[hierarchy[i, 1]]]$AddChildNode({: attempt to apply non-function
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 3038))
#> Error in lt[[hierarchy[i, 1]]]$AddChildNode({: attempt to apply non-function
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 3867))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 3913))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 4047))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 5229))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 5533))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 5908))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 7485))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 7743))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 8434))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 9343))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 10997))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 17456))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 34264))
Compare signatures from different nodes:
compare_signatures(res_rh, verbose = FALSE)
If there are too many signatures, top_signatures = ... can be set to only show the
signatures with the highest FDRs. Note it only works on every node and the final signatures
are the union of all signatures of all nodes.
# code only for demonstration
# e.g. to show the top 500 most significant rows on each node.
tb = get_signature(res_rh, top_signatures = 500)
Child nodes: Node01 , Node02 , Node03-leaf , Node04 .
The object with results only for a single top-value method and a single partitioning method can be extracted as:
res = res_rh["0"]
A summary of res and all the functions that can be applied to it:
res
#> A 'ConsensusPartition' object with k = 2, 3, 4, 5, 6, 7, 8.
#> On a matrix with 30000 rows and 443 columns.
#> Top rows (1000) are extracted by 'ATC' method.
#> Subgroups are detected by 'kmeans' method.
#> Performed in total 350 partitions by row resampling.
#> Best k for subgroups seems to be 4.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_partitions"
#> [7] "compare_signatures" "consensus_heatmap" "dimension_reduction"
#> [10] "functional_enrichment" "get_anno_col" "get_anno"
#> [13] "get_classes" "get_consensus" "get_matrix"
#> [16] "get_membership" "get_param" "get_signatures"
#> [19] "get_stats" "is_best_k" "is_stable_k"
#> [22] "membership_heatmap" "ncol" "nrow"
#> [25] "plot_ecdf" "predict_classes" "rownames"
#> [28] "select_partition_number" "show" "suggest_best_k"
#> [31] "test_to_known_factors" "top_rows_heatmap"
collect_plots() function collects all the plots made from res for all k (number of subgroups)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
The plots are:
k and the heatmap of
predicted classes for each k.k.k.k.All the plots in panels can be made by individual functions and they are plotted later in this section.
select_partition_number() produces several plots showing different
statistics for choosing “optimized” k. There are following statistics:
k;k, the area increased is defined as \(A_k - A_{k-1}\).The detailed explanations of these statistics can be found in the cola vignette.
Generally speaking, higher 1-PAC score, higher mean silhouette score or higher
concordance corresponds to better partition. Rand index and Jaccard index
measure how similar the current partition is compared to partition with k-1.
If they are too similar, we won't accept k is better than k-1.
select_partition_number(res)
The numeric values for all these statistics can be obtained by get_stats().
get_stats(res)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> 2 2 1.000 0.990 0.996 0.4118 0.586 0.586
#> 3 3 1.000 0.981 0.993 0.5182 0.660 0.478
#> 4 4 1.000 0.983 0.993 0.1385 0.768 0.483
#> 5 5 0.783 0.798 0.898 0.0988 0.835 0.504
#> 6 6 0.728 0.613 0.801 0.0457 0.887 0.551
#> 7 7 0.771 0.653 0.806 0.0323 0.897 0.534
#> 8 8 0.818 0.795 0.859 0.0218 0.919 0.571
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.AF.3911.01 1 0.000 0.999 1.00 0.00
#> TCGA.F4.6459.01 1 0.000 0.999 1.00 0.00
#> TCGA.AA.3494.11 2 0.000 0.988 0.00 1.00
#> TCGA.3L.AA1B.01 1 0.000 0.999 1.00 0.00
#> TCGA.D5.5538.01 1 0.000 0.999 1.00 0.00
#> TCGA.F4.6854.01 1 0.000 0.999 1.00 0.00
#> TCGA.AG.A026.01 1 0.000 0.999 1.00 0.00
#> TCGA.G4.6303.01 1 0.000 0.999 1.00 0.00
#> TCGA.F5.6464.01 1 0.000 0.999 1.00 0.00
#> TCGA.T9.A92H.01 1 0.000 0.999 1.00 0.00
#> TCGA.AA.3712.11 2 0.000 0.988 0.00 1.00
#> TCGA.CM.5863.01 1 0.000 0.999 1.00 0.00
#> TCGA.AZ.4308.01 2 0.000 0.988 0.00 1.00
#> TCGA.AD.6965.01 1 0.000 0.999 1.00 0.00
#> TCGA.A6.2681.11 2 0.000 0.988 0.00 1.00
#> TCGA.AD.6548.01 1 0.000 0.999 1.00 0.00
#> TCGA.A6.5660.01 1 0.000 0.999 1.00 0.00
#> TCGA.AZ.6600.01 1 0.000 0.999 1.00 0.00
#> TCGA.F4.6808.01 1 0.000 0.999 1.00 0.00
#> TCGA.D5.6540.01 1 0.000 0.999 1.00 0.00
#> TCGA.F5.6571.01 1 0.000 0.999 1.00 0.00
#> TCGA.D5.6926.01 1 0.000 0.999 1.00 0.00
#> TCGA.CM.4748.01 1 0.000 0.999 1.00 0.00
#> TCGA.A6.2675.11 2 0.000 0.988 0.00 1.00
#> TCGA.5M.AATE.01 1 0.000 0.999 1.00 0.00
#> TCGA.D5.5541.01 2 0.000 0.988 0.00 1.00
#> TCGA.CM.5862.01 1 0.000 0.999 1.00 0.00
#> TCGA.AA.3511.01 1 0.000 0.999 1.00 0.00
#> TCGA.AA.3663.11 2 0.000 0.988 0.00 1.00
#> TCGA.CI.6622.01 1 0.000 0.999 1.00 0.00
#> TCGA.EI.6506.01 1 0.000 0.999 1.00 0.00
#> TCGA.AM.5821.01 1 0.000 0.999 1.00 0.00
#> TCGA.F5.6812.01 2 0.000 0.988 0.00 1.00
#> TCGA.G4.6588.01 1 0.000 0.999 1.00 0.00
#> TCGA.EI.6512.01 1 0.000 0.999 1.00 0.00
#> TCGA.A6.6648.01 2 0.000 0.988 0.00 1.00
#> TCGA.A6.2671.11 2 0.000 0.988 0.00 1.00
#> TCGA.NH.A6GC.01 1 0.000 0.999 1.00 0.00
#> TCGA.F4.6805.01 2 0.000 0.988 0.00 1.00
#> TCGA.AA.3697.01 1 0.000 0.999 1.00 0.00
#> TCGA.QG.A5YX.01 1 0.000 0.999 1.00 0.00
#> TCGA.DM.A28C.01 1 0.000 0.999 1.00 0.00
#> TCGA.AG.A036.01 1 0.000 0.999 1.00 0.00
#> TCGA.AZ.6606.01 1 0.000 0.999 1.00 0.00
#> TCGA.F4.6570.01 1 0.000 0.999 1.00 0.00
#> TCGA.DC.4745.01 1 0.000 0.999 1.00 0.00
#> TCGA.AF.A56K.01 2 0.000 0.988 0.00 1.00
#> TCGA.G4.6627.01 2 0.000 0.988 0.00 1.00
#> TCGA.A6.5657.01 1 0.000 0.999 1.00 0.00
#> TCGA.A6.5662.01 1 0.000 0.999 1.00 0.00
#> TCGA.AA.3509.01 1 0.000 0.999 1.00 0.00
#> TCGA.D5.6929.01 2 0.000 0.988 0.00 1.00
#> TCGA.CM.6679.01 1 0.000 0.999 1.00 0.00
#> TCGA.A6.2680.11 2 0.000 0.988 0.00 1.00
#> TCGA.DC.6157.01 2 0.000 0.988 0.00 1.00
#> TCGA.AF.6655.01 2 0.000 0.988 0.00 1.00
#> TCGA.CM.6161.01 1 0.000 0.999 1.00 0.00
#> TCGA.EI.6883.01 1 0.000 0.999 1.00 0.00
#> TCGA.F5.6811.01 1 0.000 0.999 1.00 0.00
#> TCGA.D5.6930.01 1 0.000 0.999 1.00 0.00
#> TCGA.CM.6164.01 2 0.000 0.988 0.00 1.00
#> TCGA.AF.2687.01 2 0.000 0.988 0.00 1.00
#> TCGA.DY.A1H8.01 1 0.000 0.999 1.00 0.00
#> TCGA.G5.6641.01 1 0.000 0.999 1.00 0.00
#> TCGA.DC.6155.01 1 0.000 0.999 1.00 0.00
#> TCGA.RU.A8FL.01 1 0.000 0.999 1.00 0.00
#> TCGA.CK.4951.01 1 0.000 0.999 1.00 0.00
#> TCGA.F4.6704.01 2 0.000 0.988 0.00 1.00
#> TCGA.AZ.6599.01 1 0.000 0.999 1.00 0.00
#> TCGA.F5.6861.01 1 0.000 0.999 1.00 0.00
#> TCGA.CM.5860.01 1 0.000 0.999 1.00 0.00
#> TCGA.A6.6780.01 1 0.000 0.999 1.00 0.00
#> TCGA.A6.2686.01 1 0.000 0.999 1.00 0.00
#> TCGA.CM.4750.01 1 0.000 0.999 1.00 0.00
#> TCGA.CM.6677.01 1 0.000 0.999 1.00 0.00
#> TCGA.A6.A567.01 2 0.000 0.988 0.00 1.00
#> TCGA.F5.6814.01 1 0.000 0.999 1.00 0.00
#> TCGA.D5.6898.01 1 0.000 0.999 1.00 0.00
#> TCGA.AG.A01W.01 1 0.000 0.999 1.00 0.00
#> TCGA.AZ.6598.11 2 0.000 0.988 0.00 1.00
#> TCGA.F5.6813.01 1 0.000 0.999 1.00 0.00
#> TCGA.AG.3732.01 2 0.000 0.988 0.00 1.00
#> TCGA.EI.6885.01 2 0.000 0.988 0.00 1.00
#> TCGA.G4.6299.01 1 0.000 0.999 1.00 0.00
#> TCGA.A6.4105.01 1 0.000 0.999 1.00 0.00
#> TCGA.DM.A1D8.01 1 0.000 0.999 1.00 0.00
#> TCGA.DM.A285.01 1 0.000 0.999 1.00 0.00
#> TCGA.G4.6295.11 2 0.000 0.988 0.00 1.00
#> TCGA.DC.4749.01 1 0.000 0.999 1.00 0.00
#> TCGA.DT.5265.01 1 0.000 0.999 1.00 0.00
#> TCGA.5M.AAT5.01 2 0.000 0.988 0.00 1.00
#> TCGA.DM.A0XD.01 1 0.000 0.999 1.00 0.00
#> TCGA.A6.6138.01 1 0.000 0.999 1.00 0.00
#> TCGA.D5.7000.01 1 0.000 0.999 1.00 0.00
#> TCGA.DM.A28F.01 1 0.000 0.999 1.00 0.00
#> TCGA.DY.A1DE.01 1 0.000 0.999 1.00 0.00
#> TCGA.A6.6142.01 2 0.000 0.988 0.00 1.00
#> TCGA.QL.A97D.01 1 0.000 0.999 1.00 0.00
#> TCGA.CK.6748.01 1 0.000 0.999 1.00 0.00
#> TCGA.DC.6160.01 2 0.000 0.988 0.00 1.00
#> TCGA.D5.6534.01 2 0.000 0.988 0.00 1.00
#> TCGA.AZ.4616.01 1 0.000 0.999 1.00 0.00
#> TCGA.CK.6751.01 1 0.000 0.999 1.00 0.00
#> TCGA.CM.6171.01 1 0.000 0.999 1.00 0.00
#> TCGA.DM.A1DA.01 1 0.000 0.999 1.00 0.00
#> TCGA.AG.A020.11 2 0.000 0.988 0.00 1.00
#> TCGA.G4.6311.11 2 0.000 0.988 0.00 1.00
#> TCGA.G4.6625.11 2 0.000 0.988 0.00 1.00
#> TCGA.F5.6863.01 2 0.000 0.988 0.00 1.00
#> TCGA.G4.6317.02 1 0.000 0.999 1.00 0.00
#> TCGA.G4.6317.01 1 0.000 0.999 1.00 0.00
#> TCGA.DM.A1D4.01 1 0.000 0.999 1.00 0.00
#> TCGA.AG.A01Y.11 2 0.000 0.988 0.00 1.00
#> TCGA.D5.6530.01 1 0.000 0.999 1.00 0.00
#> TCGA.CK.4948.01 2 0.000 0.988 0.00 1.00
#> TCGA.AD.A5EJ.01 1 0.000 0.999 1.00 0.00
#> TCGA.A6.6651.01 2 0.000 0.988 0.00 1.00
#> TCGA.CA.5256.01 1 0.000 0.999 1.00 0.00
#> TCGA.DM.A0X9.01 1 0.000 0.999 1.00 0.00
#> TCGA.AY.A69D.01 1 0.000 0.999 1.00 0.00
#> TCGA.G4.6626.01 1 0.000 0.999 1.00 0.00
#> TCGA.CA.6716.01 1 0.000 0.999 1.00 0.00
#> TCGA.A6.2682.01 1 0.000 0.999 1.00 0.00
#> TCGA.A6.4107.11 2 0.000 0.988 0.00 1.00
#> TCGA.CA.6717.01 1 0.000 0.999 1.00 0.00
#> TCGA.G4.6293.01 1 0.000 0.999 1.00 0.00
#> TCGA.CK.5916.01 1 0.000 0.999 1.00 0.00
#> TCGA.G4.6309.01 2 0.000 0.988 0.00 1.00
#> TCGA.AA.3662.01 1 0.000 0.999 1.00 0.00
#> TCGA.AF.A56L.01 1 0.000 0.999 1.00 0.00
#> TCGA.NH.A6GB.01 1 0.000 0.999 1.00 0.00
#> TCGA.AD.5900.01 1 0.000 0.999 1.00 0.00
#> TCGA.NH.A50U.01 1 0.000 0.999 1.00 0.00
#> TCGA.AA.3712.01 1 0.000 0.999 1.00 0.00
#> TCGA.AZ.4614.01 1 0.000 0.999 1.00 0.00
#> TCGA.AH.6644.01 1 0.000 0.999 1.00 0.00
#> TCGA.AZ.6607.01 1 0.000 0.999 1.00 0.00
#> TCGA.AF.2693.01 2 0.904 0.542 0.32 0.68
#> TCGA.D5.6924.01 1 0.000 0.999 1.00 0.00
#> TCGA.CM.5868.01 2 0.000 0.988 0.00 1.00
#> TCGA.AF.4110.01 2 0.000 0.988 0.00 1.00
#> TCGA.A6.3809.01 1 0.000 0.999 1.00 0.00
#> TCGA.AZ.4313.01 2 0.000 0.988 0.00 1.00
#> TCGA.A6.2675.01 2 0.000 0.988 0.00 1.00
#> TCGA.AZ.6608.01 1 0.000 0.999 1.00 0.00
#> TCGA.CM.5864.01 1 0.000 0.999 1.00 0.00
#> TCGA.AA.3494.01 2 0.000 0.988 0.00 1.00
#> TCGA.AD.6895.01 1 0.000 0.999 1.00 0.00
#> TCGA.CI.6620.01 1 0.000 0.999 1.00 0.00
#> TCGA.DC.6156.01 1 0.000 0.999 1.00 0.00
#> TCGA.D5.6931.01 1 0.000 0.999 1.00 0.00
#> TCGA.CM.6165.01 1 0.000 0.999 1.00 0.00
#> TCGA.CM.5861.01 1 0.000 0.999 1.00 0.00
#> TCGA.A6.2671.01 1 0.000 0.999 1.00 0.00
#> TCGA.DC.6158.01 1 0.000 0.999 1.00 0.00
#> TCGA.AG.3742.01 1 0.000 0.999 1.00 0.00
#> TCGA.AG.A02N.11 2 0.000 0.988 0.00 1.00
#> TCGA.G4.6307.01 2 0.000 0.988 0.00 1.00
#> TCGA.A6.5666.01 1 0.000 0.999 1.00 0.00
#> TCGA.EI.6511.01 1 0.000 0.999 1.00 0.00
#> TCGA.CI.6624.01 2 0.000 0.988 0.00 1.00
#> TCGA.AG.3591.01 1 0.000 0.999 1.00 0.00
#> TCGA.AY.A8YK.01 2 0.000 0.988 0.00 1.00
#> TCGA.F4.6856.01 1 0.000 0.999 1.00 0.00
#> TCGA.DM.A1D7.01 1 0.000 0.999 1.00 0.00
#> TCGA.A6.2685.01 2 0.000 0.988 0.00 1.00
#> TCGA.5M.AAT6.01 2 0.000 0.988 0.00 1.00
#> TCGA.AH.6643.01 1 0.000 0.999 1.00 0.00
#> TCGA.F4.6569.01 1 0.000 0.999 1.00 0.00
#> TCGA.G4.6298.01 1 0.000 0.999 1.00 0.00
#> TCGA.AY.6196.01 1 0.000 0.999 1.00 0.00
#> TCGA.EI.6510.01 1 0.000 0.999 1.00 0.00
#> TCGA.A6.5656.01 1 0.000 0.999 1.00 0.00
#> TCGA.A6.2684.11 2 0.000 0.988 0.00 1.00
#> TCGA.DY.A1DG.01 1 0.000 0.999 1.00 0.00
#> TCGA.AZ.4682.01 1 0.000 0.999 1.00 0.00
#> TCGA.EI.6884.01 1 0.000 0.999 1.00 0.00
#> TCGA.F4.6806.01 1 0.000 0.999 1.00 0.00
#> TCGA.G4.6320.11 2 0.000 0.988 0.00 1.00
#> TCGA.G4.6322.01 1 0.000 0.999 1.00 0.00
#> TCGA.F5.6810.01 2 0.000 0.988 0.00 1.00
#> TCGA.5M.AAT4.01 1 0.000 0.999 1.00 0.00
#> TCGA.CL.4957.01 1 0.000 0.999 1.00 0.00
#> TCGA.DC.6681.01 1 0.000 0.999 1.00 0.00
#> TCGA.CM.6167.01 2 0.000 0.988 0.00 1.00
#> TCGA.AG.4022.01 1 0.000 0.999 1.00 0.00
#> TCGA.G4.6586.01 1 0.000 0.999 1.00 0.00
#> TCGA.EI.6514.01 1 0.000 0.999 1.00 0.00
#> TCGA.CK.4950.01 1 0.000 0.999 1.00 0.00
#> TCGA.DM.A282.01 1 0.000 0.999 1.00 0.00
#> TCGA.DY.A1DC.01 1 0.000 0.999 1.00 0.00
#> TCGA.D5.6535.01 1 0.000 0.999 1.00 0.00
#> TCGA.DM.A1HA.01 1 0.000 0.999 1.00 0.00
#> TCGA.DC.5869.01 1 0.000 0.999 1.00 0.00
#> TCGA.AZ.6599.11 2 0.000 0.988 0.00 1.00
#> TCGA.CM.4752.01 2 0.000 0.988 0.00 1.00
#> TCGA.AZ.4684.01 1 0.000 0.999 1.00 0.00
#> TCGA.EI.7004.01 1 0.000 0.999 1.00 0.00
#> TCGA.A6.A565.01 2 0.000 0.988 0.00 1.00
#> TCGA.D5.6531.01 1 0.000 0.999 1.00 0.00
#> TCGA.AZ.6598.01 1 0.000 0.999 1.00 0.00
#> TCGA.AD.6890.01 1 0.000 0.999 1.00 0.00
#> TCGA.AG.4021.01 1 0.000 0.999 1.00 0.00
#> TCGA.A6.6781.01 2 0.000 0.988 0.00 1.00
#> TCGA.DM.A1D9.01 1 0.000 0.999 1.00 0.00
#> TCGA.CM.4744.01 1 0.000 0.999 1.00 0.00
#> TCGA.A6.2679.11 2 0.000 0.988 0.00 1.00
#> TCGA.A6.6652.01 1 0.000 0.999 1.00 0.00
#> TCGA.AD.6964.01 2 0.000 0.988 0.00 1.00
#> TCGA.SS.A7HO.01 1 0.000 0.999 1.00 0.00
#> TCGA.A6.6650.01 1 0.000 0.999 1.00 0.00
#> TCGA.DM.A0XF.01 2 0.881 0.582 0.30 0.70
#> TCGA.G4.6295.01 2 0.000 0.988 0.00 1.00
#> TCGA.F4.6461.01 1 0.000 0.999 1.00 0.00
#> TCGA.AM.5820.01 1 0.000 0.999 1.00 0.00
#> TCGA.G4.6314.11 2 0.000 0.988 0.00 1.00
#> TCGA.AD.6889.01 1 0.000 0.999 1.00 0.00
#> TCGA.AZ.6605.01 1 0.000 0.999 1.00 0.00
#> TCGA.EI.6881.01 1 0.000 0.999 1.00 0.00
#> TCGA.NH.A50T.01 1 0.000 0.999 1.00 0.00
#> TCGA.AG.3725.11 2 0.000 0.988 0.00 1.00
#> TCGA.G4.6323.01 1 0.000 0.999 1.00 0.00
#> TCGA.AA.3663.01 1 0.000 0.999 1.00 0.00
#> TCGA.AD.6899.01 1 0.000 0.999 1.00 0.00
#> TCGA.A6.5667.11 2 0.000 0.988 0.00 1.00
#> TCGA.A6.A56B.01 1 0.000 0.999 1.00 0.00
#> TCGA.G5.6572.01 2 0.958 0.402 0.38 0.62
#> TCGA.DM.A280.01 2 0.760 0.722 0.22 0.78
#> TCGA.AG.A020.01 1 0.000 0.999 1.00 0.00
#> TCGA.AA.3713.01 1 0.000 0.999 1.00 0.00
#> TCGA.D5.5539.01 1 0.000 0.999 1.00 0.00
#> TCGA.AA.3655.11 2 0.000 0.988 0.00 1.00
#> TCGA.AA.3489.01 2 0.000 0.988 0.00 1.00
#> TCGA.AA.3495.01 1 0.000 0.999 1.00 0.00
#> TCGA.AG.A01Y.01 2 0.000 0.988 0.00 1.00
#> TCGA.AZ.6601.01 1 0.000 0.999 1.00 0.00
#> TCGA.AH.6903.01 1 0.000 0.999 1.00 0.00
#> TCGA.AZ.6603.01 2 0.000 0.988 0.00 1.00
#> TCGA.CA.5254.01 1 0.000 0.999 1.00 0.00
#> TCGA.A6.A5ZU.01 1 0.000 0.999 1.00 0.00
#> TCGA.G4.6302.01 2 0.000 0.988 0.00 1.00
#> TCGA.AZ.5403.01 2 0.000 0.988 0.00 1.00
#> TCGA.AY.A54L.01 1 0.000 0.999 1.00 0.00
#> TCGA.A6.4107.01 1 0.000 0.999 1.00 0.00
#> TCGA.NH.A5IV.01 1 0.000 0.999 1.00 0.00
#> TCGA.G4.6306.01 1 0.000 0.999 1.00 0.00
#> TCGA.AD.A5EK.01 1 0.000 0.999 1.00 0.00
#> TCGA.G5.6235.01 2 0.000 0.988 0.00 1.00
#> TCGA.DC.5337.01 1 0.000 0.999 1.00 0.00
#> TCGA.CM.6675.01 1 0.000 0.999 1.00 0.00
#> TCGA.AH.6544.01 1 0.000 0.999 1.00 0.00
#> TCGA.CK.6746.01 1 0.000 0.999 1.00 0.00
#> TCGA.CA.6718.01 1 0.000 0.999 1.00 0.00
#> TCGA.CI.6621.01 2 0.000 0.988 0.00 1.00
#> TCGA.CM.6676.01 1 0.000 0.999 1.00 0.00
#> TCGA.DM.A1DB.01 1 0.000 0.999 1.00 0.00
#> TCGA.A6.6654.01 1 0.000 0.999 1.00 0.00
#> TCGA.AA.3510.11 2 0.000 0.988 0.00 1.00
#> TCGA.CA.6715.01 1 0.000 0.999 1.00 0.00
#> TCGA.CM.5341.01 1 0.000 0.999 1.00 0.00
#> TCGA.CK.5912.01 1 0.000 0.999 1.00 0.00
#> TCGA.F4.6857.01 2 0.000 0.988 0.00 1.00
#> TCGA.QG.A5YW.01 1 0.000 0.999 1.00 0.00
#> TCGA.A6.5665.01 1 0.000 0.999 1.00 0.00
#> TCGA.CM.6168.01 1 0.000 0.999 1.00 0.00
#> TCGA.CL.5917.01 1 0.000 0.999 1.00 0.00
#> TCGA.AU.6004.01 1 0.000 0.999 1.00 0.00
#> TCGA.AY.5543.01 1 0.000 0.999 1.00 0.00
#> TCGA.AG.3731.01 1 0.000 0.999 1.00 0.00
#> TCGA.G4.6314.01 1 0.000 0.999 1.00 0.00
#> TCGA.DC.6683.01 1 0.000 0.999 1.00 0.00
#> TCGA.CA.5796.01 1 0.000 0.999 1.00 0.00
#> TCGA.AG.A036.11 2 0.000 0.988 0.00 1.00
#> TCGA.AZ.4323.01 2 0.000 0.988 0.00 1.00
#> TCGA.EI.6882.01 1 0.000 0.999 1.00 0.00
#> TCGA.AZ.4315.01 1 0.000 0.999 1.00 0.00
#> TCGA.A6.2677.01 1 0.000 0.999 1.00 0.00
#> TCGA.DY.A1DF.01 1 0.000 0.999 1.00 0.00
#> TCGA.CM.6162.01 2 0.000 0.988 0.00 1.00
#> TCGA.F4.6703.01 2 0.000 0.988 0.00 1.00
#> TCGA.CM.5349.01 1 0.000 0.999 1.00 0.00
#> TCGA.AG.A02N.01 1 0.000 0.999 1.00 0.00
#> TCGA.AA.3506.01 1 0.000 0.999 1.00 0.00
#> TCGA.D5.6932.01 1 0.000 0.999 1.00 0.00
#> TCGA.D5.6538.01 1 0.000 0.999 1.00 0.00
#> TCGA.AA.3488.11 2 0.000 0.988 0.00 1.00
#> TCGA.AA.3502.01 1 0.000 0.999 1.00 0.00
#> TCGA.NH.A8F8.01 1 0.000 0.999 1.00 0.00
#> TCGA.AF.A56N.01 1 0.000 0.999 1.00 0.00
#> TCGA.AF.6672.01 2 0.000 0.988 0.00 1.00
#> TCGA.A6.2685.11 2 0.000 0.988 0.00 1.00
#> TCGA.A6.6141.01 1 0.000 0.999 1.00 0.00
#> TCGA.AD.6963.01 2 0.000 0.988 0.00 1.00
#> TCGA.G4.6298.11 2 0.000 0.988 0.00 1.00
#> TCGA.EI.6917.01 1 0.000 0.999 1.00 0.00
#> TCGA.QG.A5Z2.01 1 0.000 0.999 1.00 0.00
#> TCGA.A6.2684.01 1 0.000 0.999 1.00 0.00
#> TCGA.CK.5915.01 1 0.000 0.999 1.00 0.00
#> TCGA.CM.6163.01 1 0.000 0.999 1.00 0.00
#> TCGA.G4.6322.11 2 0.000 0.988 0.00 1.00
#> TCGA.AY.6197.01 1 0.000 0.999 1.00 0.00
#> TCGA.D5.6928.01 2 0.000 0.988 0.00 1.00
#> TCGA.A6.3810.01 2 0.000 0.988 0.00 1.00
#> TCGA.G4.6294.01 1 0.000 0.999 1.00 0.00
#> TCGA.AA.3660.11 2 0.000 0.988 0.00 1.00
#> TCGA.A6.6137.01 1 0.000 0.999 1.00 0.00
#> TCGA.G4.6297.11 2 0.000 0.988 0.00 1.00
#> TCGA.AZ.4615.01 1 0.000 0.999 1.00 0.00
#> TCGA.CK.4952.01 1 0.000 0.999 1.00 0.00
#> TCGA.CM.6172.01 1 0.000 0.999 1.00 0.00
#> TCGA.AD.6901.01 1 0.000 0.999 1.00 0.00
#> TCGA.AA.3496.01 1 0.000 0.999 1.00 0.00
#> TCGA.CK.5913.01 1 0.000 0.999 1.00 0.00
#> TCGA.DM.A28A.01 1 0.000 0.999 1.00 0.00
#> TCGA.EI.7002.01 1 0.000 0.999 1.00 0.00
#> TCGA.D5.6533.01 1 0.000 0.999 1.00 0.00
#> TCGA.QG.A5Z1.01 1 0.000 0.999 1.00 0.00
#> TCGA.D5.6923.01 2 0.000 0.988 0.00 1.00
#> TCGA.AF.2690.01 2 0.000 0.988 0.00 1.00
#> TCGA.DM.A28H.01 1 0.000 0.999 1.00 0.00
#> TCGA.G4.6320.01 1 0.000 0.999 1.00 0.00
#> TCGA.G4.6310.01 1 0.000 0.999 1.00 0.00
#> TCGA.DM.A28M.01 1 0.000 0.999 1.00 0.00
#> TCGA.DM.A288.01 1 0.000 0.999 1.00 0.00
#> TCGA.A6.2681.01 1 0.000 0.999 1.00 0.00
#> TCGA.A6.2679.01 1 0.000 0.999 1.00 0.00
#> TCGA.4N.A93T.01 1 0.000 0.999 1.00 0.00
#> TCGA.NH.A8F7.06 1 0.000 0.999 1.00 0.00
#> TCGA.NH.A8F7.01 1 0.000 0.999 1.00 0.00
#> TCGA.AZ.6600.11 2 0.000 0.988 0.00 1.00
#> TCGA.G5.6572.02 2 0.000 0.988 0.00 1.00
#> TCGA.AY.6386.01 1 0.000 0.999 1.00 0.00
#> TCGA.G4.6628.01 1 0.000 0.999 1.00 0.00
#> TCGA.A6.6653.01 1 0.000 0.999 1.00 0.00
#> TCGA.CM.4746.01 1 0.000 0.999 1.00 0.00
#> TCGA.F4.6855.01 1 0.000 0.999 1.00 0.00
#> TCGA.EF.5830.01 1 0.000 0.999 1.00 0.00
#> TCGA.NH.A6GA.01 1 0.000 0.999 1.00 0.00
#> TCGA.NH.A50V.01 1 0.000 0.999 1.00 0.00
#> TCGA.DY.A0XA.01 2 0.000 0.988 0.00 1.00
#> TCGA.DM.A28E.01 1 0.000 0.999 1.00 0.00
#> TCGA.AG.3725.01 1 0.000 0.999 1.00 0.00
#> TCGA.CK.6747.01 1 0.000 0.999 1.00 0.00
#> TCGA.CL.5918.01 1 0.000 0.999 1.00 0.00
#> TCGA.CI.6623.01 2 0.000 0.988 0.00 1.00
#> TCGA.A6.5667.01 1 0.000 0.999 1.00 0.00
#> TCGA.DM.A28K.01 1 0.000 0.999 1.00 0.00
#> TCGA.AA.3713.11 2 0.000 0.988 0.00 1.00
#> TCGA.AA.3655.01 1 0.000 0.999 1.00 0.00
#> TCGA.AU.3779.01 2 0.904 0.542 0.32 0.68
#> TCGA.A6.5664.01 1 0.000 0.999 1.00 0.00
#> TCGA.AA.3697.11 2 0.000 0.988 0.00 1.00
#> TCGA.AZ.5407.01 1 0.000 0.999 1.00 0.00
#> TCGA.CM.6169.01 1 0.000 0.999 1.00 0.00
#> TCGA.AH.6547.01 2 0.000 0.988 0.00 1.00
#> TCGA.AZ.6601.11 2 0.000 0.988 0.00 1.00
#> TCGA.A6.5661.01 1 0.000 0.999 1.00 0.00
#> TCGA.F4.6807.01 1 0.000 0.999 1.00 0.00
#> TCGA.QG.A5YV.01 1 0.000 0.999 1.00 0.00
#> TCGA.AA.3509.11 2 0.000 0.988 0.00 1.00
#> TCGA.AY.A71X.01 1 0.000 0.999 1.00 0.00
#> TCGA.CA.5797.01 2 0.000 0.988 0.00 1.00
#> TCGA.F4.6460.01 2 0.000 0.988 0.00 1.00
#> TCGA.G4.6302.11 2 0.000 0.988 0.00 1.00
#> TCGA.F5.6702.01 2 0.000 0.988 0.00 1.00
#> TCGA.AH.6549.01 1 0.000 0.999 1.00 0.00
#> TCGA.D5.6927.01 2 0.000 0.988 0.00 1.00
#> TCGA.CM.6166.01 1 0.000 0.999 1.00 0.00
#> TCGA.AH.6897.01 1 0.000 0.999 1.00 0.00
#> TCGA.G4.6304.01 2 0.000 0.988 0.00 1.00
#> TCGA.CA.5255.01 1 0.000 0.999 1.00 0.00
#> TCGA.EI.6507.01 1 0.000 0.999 1.00 0.00
#> TCGA.CK.4947.01 1 0.000 0.999 1.00 0.00
#> TCGA.D5.5540.01 1 0.000 0.999 1.00 0.00
#> TCGA.DC.6682.01 1 0.000 0.999 1.00 0.00
#> TCGA.G4.6321.01 1 0.000 0.999 1.00 0.00
#> TCGA.A6.6649.01 1 0.000 0.999 1.00 0.00
#> TCGA.CM.5348.01 1 0.000 0.999 1.00 0.00
#> TCGA.EI.6513.01 2 0.000 0.988 0.00 1.00
#> TCGA.A6.2672.01 1 0.000 0.999 1.00 0.00
#> TCGA.D5.6539.01 2 0.000 0.988 0.00 1.00
#> TCGA.AA.3510.01 1 0.000 0.999 1.00 0.00
#> TCGA.G5.6233.01 1 0.000 0.999 1.00 0.00
#> TCGA.BM.6198.01 2 0.000 0.988 0.00 1.00
#> TCGA.CA.6719.01 1 0.000 0.999 1.00 0.00
#> TCGA.DC.6154.01 1 0.000 0.999 1.00 0.00
#> TCGA.DM.A1D6.01 1 0.000 0.999 1.00 0.00
#> TCGA.AG.3731.11 2 0.000 0.988 0.00 1.00
#> TCGA.CM.6674.01 2 0.000 0.988 0.00 1.00
#> TCGA.CM.4743.01 1 0.760 0.713 0.78 0.22
#> TCGA.F5.6465.01 2 0.000 0.988 0.00 1.00
#> TCGA.D5.5537.01 1 0.000 0.999 1.00 0.00
#> TCGA.F4.6463.01 1 0.000 0.999 1.00 0.00
#> TCGA.A6.2686.11 2 0.000 0.988 0.00 1.00
#> TCGA.4T.AA8H.01 1 0.000 0.999 1.00 0.00
#> TCGA.A6.6782.01 1 0.000 0.999 1.00 0.00
#> TCGA.AG.3592.01 1 0.000 0.999 1.00 0.00
#> TCGA.AD.6888.01 1 0.000 0.999 1.00 0.00
#> TCGA.CM.6678.01 1 0.000 0.999 1.00 0.00
#> TCGA.CM.5344.01 2 0.000 0.988 0.00 1.00
#> TCGA.AA.3495.11 2 0.000 0.988 0.00 1.00
#> TCGA.AG.A01W.11 2 0.000 0.988 0.00 1.00
#> TCGA.F4.6809.01 1 0.000 0.999 1.00 0.00
#> TCGA.CK.5914.01 1 0.000 0.999 1.00 0.00
#> TCGA.AZ.4681.01 2 0.000 0.988 0.00 1.00
#> TCGA.AA.3492.01 1 0.000 0.999 1.00 0.00
#> TCGA.D5.6536.01 1 0.000 0.999 1.00 0.00
#> TCGA.AA.3506.11 2 0.000 0.988 0.00 1.00
#> TCGA.AA.3488.01 1 0.000 0.999 1.00 0.00
#> TCGA.AA.3502.11 2 0.000 0.988 0.00 1.00
#> TCGA.A6.6140.01 2 0.000 0.988 0.00 1.00
#> TCGA.D5.6529.01 1 0.000 0.999 1.00 0.00
#> TCGA.DM.A1D0.01 2 0.000 0.988 0.00 1.00
#> TCGA.DM.A1HB.01 1 0.000 0.999 1.00 0.00
#> TCGA.D5.6920.01 1 0.000 0.999 1.00 0.00
#> TCGA.D5.6922.01 1 0.000 0.999 1.00 0.00
#> TCGA.EI.6508.01 1 0.000 0.999 1.00 0.00
#> TCGA.D5.6532.01 1 0.000 0.999 1.00 0.00
#> TCGA.5M.AATA.01 1 0.000 0.999 1.00 0.00
#> TCGA.EI.6509.01 2 0.000 0.988 0.00 1.00
#> TCGA.G4.6311.01 1 0.000 0.999 1.00 0.00
#> TCGA.A6.A566.01 1 0.000 0.999 1.00 0.00
#> TCGA.G4.6625.01 1 0.000 0.999 1.00 0.00
#> TCGA.CI.6619.01 2 0.000 0.988 0.00 1.00
#> TCGA.F5.6864.01 1 0.000 0.999 1.00 0.00
#> TCGA.AA.3492.11 2 0.000 0.988 0.00 1.00
#> TCGA.A6.5659.01 1 0.000 0.999 1.00 0.00
#> TCGA.WS.AB45.01 2 0.000 0.988 0.00 1.00
#> TCGA.G4.6315.01 1 0.000 0.999 1.00 0.00
#> TCGA.D5.6541.01 1 0.000 0.999 1.00 0.00
#> TCGA.A6.2680.01 1 0.000 0.999 1.00 0.00
#> TCGA.CM.4751.01 1 0.000 0.999 1.00 0.00
#> TCGA.CM.6680.01 1 0.000 0.999 1.00 0.00
#> TCGA.AF.6136.01 1 0.000 0.999 1.00 0.00
#> TCGA.AA.3660.01 1 0.000 0.999 1.00 0.00
#> TCGA.CM.4747.01 1 0.000 0.999 1.00 0.00
#> TCGA.EF.5831.01 1 0.000 0.999 1.00 0.00
#> TCGA.DM.A28G.01 1 0.000 0.999 1.00 0.00
#> TCGA.G4.6297.01 1 0.000 0.999 1.00 0.00
#> TCGA.A6.2682.11 2 0.000 0.988 0.00 1.00
#> TCGA.D5.6537.01 1 0.000 0.999 1.00 0.00
#> TCGA.CM.6170.01 1 0.000 0.999 1.00 0.00
#> TCGA.DY.A1DD.01 1 0.000 0.999 1.00 0.00
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.AF.3911.01 3 0.0000 0.997 0.00 0.00 1.00
#> TCGA.F4.6459.01 3 0.0000 0.997 0.00 0.00 1.00
#> TCGA.AA.3494.11 2 0.0000 0.993 0.00 1.00 0.00
#> TCGA.3L.AA1B.01 3 0.0000 0.997 0.00 0.00 1.00
#> TCGA.D5.5538.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.F4.6854.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.AG.A026.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.G4.6303.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.F5.6464.01 3 0.0000 0.997 0.00 0.00 1.00
#> TCGA.T9.A92H.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.AA.3712.11 2 0.0000 0.993 0.00 1.00 0.00
#> TCGA.CM.5863.01 3 0.0000 0.997 0.00 0.00 1.00
#> TCGA.AZ.4308.01 3 0.0000 0.997 0.00 0.00 1.00
#> TCGA.AD.6965.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.A6.2681.11 2 0.0000 0.993 0.00 1.00 0.00
#> TCGA.AD.6548.01 3 0.0000 0.997 0.00 0.00 1.00
#> TCGA.A6.5660.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.AZ.6600.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.F4.6808.01 3 0.0000 0.997 0.00 0.00 1.00
#> TCGA.D5.6540.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.F5.6571.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.D5.6926.01 3 0.0000 0.997 0.00 0.00 1.00
#> TCGA.CM.4748.01 3 0.0000 0.997 0.00 0.00 1.00
#> TCGA.A6.2675.11 2 0.0000 0.993 0.00 1.00 0.00
#> TCGA.5M.AATE.01 3 0.0000 0.997 0.00 0.00 1.00
#> TCGA.D5.5541.01 3 0.0000 0.997 0.00 0.00 1.00
#> TCGA.CM.5862.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.AA.3511.01 3 0.0000 0.997 0.00 0.00 1.00
#> TCGA.AA.3663.11 2 0.0000 0.993 0.00 1.00 0.00
#> TCGA.CI.6622.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.EI.6506.01 3 0.0000 0.997 0.00 0.00 1.00
#> TCGA.AM.5821.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.F5.6812.01 3 0.0000 0.997 0.00 0.00 1.00
#> TCGA.G4.6588.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.EI.6512.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.A6.6648.01 2 0.0000 0.993 0.00 1.00 0.00
#> TCGA.A6.2671.11 2 0.0000 0.993 0.00 1.00 0.00
#> TCGA.NH.A6GC.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.F4.6805.01 3 0.0000 0.997 0.00 0.00 1.00
#> TCGA.AA.3697.01 3 0.0000 0.997 0.00 0.00 1.00
#> TCGA.QG.A5YX.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.DM.A28C.01 1 0.2537 0.899 0.92 0.00 0.08
#> TCGA.AG.A036.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.AZ.6606.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.F4.6570.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.DC.4745.01 3 0.0000 0.997 0.00 0.00 1.00
#> TCGA.AF.A56K.01 2 0.0000 0.993 0.00 1.00 0.00
#> TCGA.G4.6627.01 3 0.0000 0.997 0.00 0.00 1.00
#> TCGA.A6.5657.01 3 0.0000 0.997 0.00 0.00 1.00
#> TCGA.A6.5662.01 3 0.0000 0.997 0.00 0.00 1.00
#> TCGA.AA.3509.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.D5.6929.01 3 0.0000 0.997 0.00 0.00 1.00
#> TCGA.CM.6679.01 3 0.0000 0.997 0.00 0.00 1.00
#> TCGA.A6.2680.11 2 0.0000 0.993 0.00 1.00 0.00
#> TCGA.DC.6157.01 3 0.0000 0.997 0.00 0.00 1.00
#> TCGA.AF.6655.01 3 0.0000 0.997 0.00 0.00 1.00
#> TCGA.CM.6161.01 1 0.5016 0.687 0.76 0.00 0.24
#> TCGA.EI.6883.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.F5.6811.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.D5.6930.01 3 0.0000 0.997 0.00 0.00 1.00
#> TCGA.CM.6164.01 3 0.0000 0.997 0.00 0.00 1.00
#> TCGA.AF.2687.01 3 0.0000 0.997 0.00 0.00 1.00
#> TCGA.DY.A1H8.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.G5.6641.01 3 0.0000 0.997 0.00 0.00 1.00
#> TCGA.DC.6155.01 3 0.0000 0.997 0.00 0.00 1.00
#> TCGA.RU.A8FL.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.CK.4951.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.F4.6704.01 3 0.0000 0.997 0.00 0.00 1.00
#> TCGA.AZ.6599.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.F5.6861.01 3 0.0000 0.997 0.00 0.00 1.00
#> TCGA.CM.5860.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.A6.6780.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.A6.2686.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.CM.4750.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.CM.6677.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.A6.A567.01 3 0.0000 0.997 0.00 0.00 1.00
#> TCGA.F5.6814.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.D5.6898.01 3 0.0000 0.997 0.00 0.00 1.00
#> TCGA.AG.A01W.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.AZ.6598.11 2 0.0000 0.993 0.00 1.00 0.00
#> TCGA.F5.6813.01 3 0.0000 0.997 0.00 0.00 1.00
#> TCGA.AG.3732.01 3 0.0000 0.997 0.00 0.00 1.00
#> TCGA.EI.6885.01 3 0.0000 0.997 0.00 0.00 1.00
#> TCGA.G4.6299.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.A6.4105.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.DM.A1D8.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.DM.A285.01 3 0.0000 0.997 0.00 0.00 1.00
#> TCGA.G4.6295.11 2 0.0000 0.993 0.00 1.00 0.00
#> TCGA.DC.4749.01 3 0.0000 0.997 0.00 0.00 1.00
#> TCGA.DT.5265.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.5M.AAT5.01 3 0.0000 0.997 0.00 0.00 1.00
#> TCGA.DM.A0XD.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.A6.6138.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.D5.7000.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.DM.A28F.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.DY.A1DE.01 3 0.0000 0.997 0.00 0.00 1.00
#> TCGA.A6.6142.01 2 0.0000 0.993 0.00 1.00 0.00
#> TCGA.QL.A97D.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.CK.6748.01 3 0.0000 0.997 0.00 0.00 1.00
#> TCGA.DC.6160.01 3 0.0000 0.997 0.00 0.00 1.00
#> TCGA.D5.6534.01 3 0.0000 0.997 0.00 0.00 1.00
#> TCGA.AZ.4616.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.CK.6751.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.CM.6171.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.DM.A1DA.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.AG.A020.11 2 0.0000 0.993 0.00 1.00 0.00
#> TCGA.G4.6311.11 2 0.0000 0.993 0.00 1.00 0.00
#> TCGA.G4.6625.11 2 0.0000 0.993 0.00 1.00 0.00
#> TCGA.F5.6863.01 3 0.0000 0.997 0.00 0.00 1.00
#> TCGA.G4.6317.02 3 0.0000 0.997 0.00 0.00 1.00
#> TCGA.G4.6317.01 3 0.0000 0.997 0.00 0.00 1.00
#> TCGA.DM.A1D4.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.AG.A01Y.11 2 0.0000 0.993 0.00 1.00 0.00
#> TCGA.D5.6530.01 3 0.0000 0.997 0.00 0.00 1.00
#> TCGA.CK.4948.01 3 0.0000 0.997 0.00 0.00 1.00
#> TCGA.AD.A5EJ.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.A6.6651.01 2 0.0000 0.993 0.00 1.00 0.00
#> TCGA.CA.5256.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.DM.A0X9.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.AY.A69D.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.G4.6626.01 3 0.0000 0.997 0.00 0.00 1.00
#> TCGA.CA.6716.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.A6.2682.01 3 0.0000 0.997 0.00 0.00 1.00
#> TCGA.A6.4107.11 2 0.0000 0.993 0.00 1.00 0.00
#> TCGA.CA.6717.01 3 0.0000 0.997 0.00 0.00 1.00
#> TCGA.G4.6293.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.CK.5916.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.G4.6309.01 2 0.0000 0.993 0.00 1.00 0.00
#> TCGA.AA.3662.01 1 0.5706 0.546 0.68 0.00 0.32
#> TCGA.AF.A56L.01 3 0.0000 0.997 0.00 0.00 1.00
#> TCGA.NH.A6GB.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.AD.5900.01 1 0.1529 0.945 0.96 0.00 0.04
#> TCGA.NH.A50U.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.AA.3712.01 3 0.0000 0.997 0.00 0.00 1.00
#> TCGA.AZ.4614.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.AH.6644.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.AZ.6607.01 1 0.5397 0.625 0.72 0.00 0.28
#> TCGA.AF.2693.01 3 0.0000 0.997 0.00 0.00 1.00
#> TCGA.D5.6924.01 3 0.0000 0.997 0.00 0.00 1.00
#> TCGA.CM.5868.01 3 0.0000 0.997 0.00 0.00 1.00
#> TCGA.AF.4110.01 3 0.0000 0.997 0.00 0.00 1.00
#> TCGA.A6.3809.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.AZ.4313.01 2 0.0000 0.993 0.00 1.00 0.00
#> TCGA.A6.2675.01 3 0.0000 0.997 0.00 0.00 1.00
#> TCGA.AZ.6608.01 3 0.0000 0.997 0.00 0.00 1.00
#> TCGA.CM.5864.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.AA.3494.01 3 0.6126 0.323 0.00 0.40 0.60
#> TCGA.AD.6895.01 1 0.0892 0.967 0.98 0.00 0.02
#> TCGA.CI.6620.01 1 0.5948 0.456 0.64 0.00 0.36
#> TCGA.DC.6156.01 3 0.0000 0.997 0.00 0.00 1.00
#> TCGA.D5.6931.01 3 0.0000 0.997 0.00 0.00 1.00
#> TCGA.CM.6165.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.CM.5861.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.A6.2671.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.DC.6158.01 3 0.0000 0.997 0.00 0.00 1.00
#> TCGA.AG.3742.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.AG.A02N.11 2 0.0000 0.993 0.00 1.00 0.00
#> TCGA.G4.6307.01 2 0.0000 0.993 0.00 1.00 0.00
#> TCGA.A6.5666.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.EI.6511.01 3 0.0000 0.997 0.00 0.00 1.00
#> TCGA.CI.6624.01 2 0.0000 0.993 0.00 1.00 0.00
#> TCGA.AG.3591.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.AY.A8YK.01 2 0.0000 0.993 0.00 1.00 0.00
#> TCGA.F4.6856.01 3 0.0000 0.997 0.00 0.00 1.00
#> TCGA.DM.A1D7.01 3 0.0000 0.997 0.00 0.00 1.00
#> TCGA.A6.2685.01 2 0.0000 0.993 0.00 1.00 0.00
#> TCGA.5M.AAT6.01 2 0.0000 0.993 0.00 1.00 0.00
#> TCGA.AH.6643.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.F4.6569.01 3 0.0000 0.997 0.00 0.00 1.00
#> TCGA.G4.6298.01 3 0.0000 0.997 0.00 0.00 1.00
#> TCGA.AY.6196.01 3 0.0000 0.997 0.00 0.00 1.00
#> TCGA.EI.6510.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.A6.5656.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.A6.2684.11 2 0.0000 0.993 0.00 1.00 0.00
#> TCGA.DY.A1DG.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.AZ.4682.01 3 0.0000 0.997 0.00 0.00 1.00
#> TCGA.EI.6884.01 3 0.0000 0.997 0.00 0.00 1.00
#> TCGA.F4.6806.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.G4.6320.11 2 0.0000 0.993 0.00 1.00 0.00
#> TCGA.G4.6322.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.F5.6810.01 2 0.0000 0.993 0.00 1.00 0.00
#> TCGA.5M.AAT4.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.CL.4957.01 3 0.0000 0.997 0.00 0.00 1.00
#> TCGA.DC.6681.01 3 0.0000 0.997 0.00 0.00 1.00
#> TCGA.CM.6167.01 3 0.0000 0.997 0.00 0.00 1.00
#> TCGA.AG.4022.01 3 0.0000 0.997 0.00 0.00 1.00
#> TCGA.G4.6586.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.EI.6514.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.CK.4950.01 3 0.0000 0.997 0.00 0.00 1.00
#> TCGA.DM.A282.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.DY.A1DC.01 3 0.0000 0.997 0.00 0.00 1.00
#> TCGA.D5.6535.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.DM.A1HA.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.DC.5869.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.AZ.6599.11 2 0.0000 0.993 0.00 1.00 0.00
#> TCGA.CM.4752.01 3 0.0000 0.997 0.00 0.00 1.00
#> TCGA.AZ.4684.01 3 0.0000 0.997 0.00 0.00 1.00
#> TCGA.EI.7004.01 3 0.0000 0.997 0.00 0.00 1.00
#> TCGA.A6.A565.01 2 0.0000 0.993 0.00 1.00 0.00
#> TCGA.D5.6531.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.AZ.6598.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.AD.6890.01 1 0.3686 0.825 0.86 0.00 0.14
#> TCGA.AG.4021.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.A6.6781.01 3 0.0000 0.997 0.00 0.00 1.00
#> TCGA.DM.A1D9.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.CM.4744.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.A6.2679.11 2 0.0000 0.993 0.00 1.00 0.00
#> TCGA.A6.6652.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.AD.6964.01 2 0.0000 0.993 0.00 1.00 0.00
#> TCGA.SS.A7HO.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.A6.6650.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.DM.A0XF.01 3 0.0000 0.997 0.00 0.00 1.00
#> TCGA.G4.6295.01 3 0.0000 0.997 0.00 0.00 1.00
#> TCGA.F4.6461.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.AM.5820.01 1 0.2537 0.900 0.92 0.00 0.08
#> TCGA.G4.6314.11 2 0.0000 0.993 0.00 1.00 0.00
#> TCGA.AD.6889.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.AZ.6605.01 3 0.0000 0.997 0.00 0.00 1.00
#> TCGA.EI.6881.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.NH.A50T.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.AG.3725.11 2 0.0000 0.993 0.00 1.00 0.00
#> TCGA.G4.6323.01 1 0.4555 0.744 0.80 0.00 0.20
#> TCGA.AA.3663.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.AD.6899.01 1 0.0000 0.987 1.00 0.00 0.00
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#> TCGA.DM.A280.01 3 0.0000 0.997 0.00 0.00 1.00
#> TCGA.AG.A020.01 3 0.0000 0.997 0.00 0.00 1.00
#> TCGA.AA.3713.01 3 0.0000 0.997 0.00 0.00 1.00
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#> TCGA.AA.3489.01 3 0.0000 0.997 0.00 0.00 1.00
#> TCGA.AA.3495.01 1 0.0000 0.987 1.00 0.00 0.00
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#> TCGA.AH.6903.01 3 0.0000 0.997 0.00 0.00 1.00
#> TCGA.AZ.6603.01 3 0.0000 0.997 0.00 0.00 1.00
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#> TCGA.NH.A5IV.01 1 0.0000 0.987 1.00 0.00 0.00
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#> TCGA.AD.A5EK.01 1 0.0000 0.987 1.00 0.00 0.00
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#> TCGA.DM.A1DB.01 3 0.0000 0.997 0.00 0.00 1.00
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#> TCGA.F4.6857.01 3 0.0000 0.997 0.00 0.00 1.00
#> TCGA.QG.A5YW.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.A6.5665.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.CM.6168.01 3 0.0000 0.997 0.00 0.00 1.00
#> TCGA.CL.5917.01 3 0.0000 0.997 0.00 0.00 1.00
#> TCGA.AU.6004.01 3 0.0000 0.997 0.00 0.00 1.00
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#> TCGA.G4.6314.01 3 0.0000 0.997 0.00 0.00 1.00
#> TCGA.DC.6683.01 3 0.2066 0.921 0.06 0.00 0.94
#> TCGA.CA.5796.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.AG.A036.11 2 0.0000 0.993 0.00 1.00 0.00
#> TCGA.AZ.4323.01 2 0.0000 0.993 0.00 1.00 0.00
#> TCGA.EI.6882.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.AZ.4315.01 1 0.0892 0.967 0.98 0.00 0.02
#> TCGA.A6.2677.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.DY.A1DF.01 3 0.2066 0.921 0.06 0.00 0.94
#> TCGA.CM.6162.01 2 0.0000 0.993 0.00 1.00 0.00
#> TCGA.F4.6703.01 2 0.0000 0.993 0.00 1.00 0.00
#> TCGA.CM.5349.01 3 0.0000 0.997 0.00 0.00 1.00
#> TCGA.AG.A02N.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.AA.3506.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.D5.6932.01 3 0.0000 0.997 0.00 0.00 1.00
#> TCGA.D5.6538.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.AA.3488.11 2 0.0000 0.993 0.00 1.00 0.00
#> TCGA.AA.3502.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.NH.A8F8.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.AF.A56N.01 3 0.0000 0.997 0.00 0.00 1.00
#> TCGA.AF.6672.01 2 0.0000 0.993 0.00 1.00 0.00
#> TCGA.A6.2685.11 2 0.0000 0.993 0.00 1.00 0.00
#> TCGA.A6.6141.01 3 0.0000 0.997 0.00 0.00 1.00
#> TCGA.AD.6963.01 2 0.0000 0.993 0.00 1.00 0.00
#> TCGA.G4.6298.11 2 0.0000 0.993 0.00 1.00 0.00
#> TCGA.EI.6917.01 3 0.0000 0.997 0.00 0.00 1.00
#> TCGA.QG.A5Z2.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.A6.2684.01 3 0.0000 0.997 0.00 0.00 1.00
#> TCGA.CK.5915.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.CM.6163.01 3 0.0000 0.997 0.00 0.00 1.00
#> TCGA.G4.6322.11 2 0.0000 0.993 0.00 1.00 0.00
#> TCGA.AY.6197.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.D5.6928.01 3 0.0000 0.997 0.00 0.00 1.00
#> TCGA.A6.3810.01 3 0.0000 0.997 0.00 0.00 1.00
#> TCGA.G4.6294.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.AA.3660.11 2 0.0000 0.993 0.00 1.00 0.00
#> TCGA.A6.6137.01 3 0.0000 0.997 0.00 0.00 1.00
#> TCGA.G4.6297.11 2 0.0000 0.993 0.00 1.00 0.00
#> TCGA.AZ.4615.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.CK.4952.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.CM.6172.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.AD.6901.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.AA.3496.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.CK.5913.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.DM.A28A.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.EI.7002.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.D5.6533.01 3 0.0000 0.997 0.00 0.00 1.00
#> TCGA.QG.A5Z1.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.D5.6923.01 3 0.0000 0.997 0.00 0.00 1.00
#> TCGA.AF.2690.01 3 0.0000 0.997 0.00 0.00 1.00
#> TCGA.DM.A28H.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.G4.6320.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.G4.6310.01 1 0.5397 0.625 0.72 0.00 0.28
#> TCGA.DM.A28M.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.DM.A288.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.A6.2681.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.A6.2679.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.4N.A93T.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.NH.A8F7.06 3 0.0000 0.997 0.00 0.00 1.00
#> TCGA.NH.A8F7.01 3 0.0000 0.997 0.00 0.00 1.00
#> TCGA.AZ.6600.11 2 0.0000 0.993 0.00 1.00 0.00
#> TCGA.G5.6572.02 2 0.0000 0.993 0.00 1.00 0.00
#> TCGA.AY.6386.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.G4.6628.01 1 0.0892 0.967 0.98 0.00 0.02
#> TCGA.A6.6653.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.CM.4746.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.F4.6855.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.EF.5830.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.NH.A6GA.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.NH.A50V.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.DY.A0XA.01 3 0.0000 0.997 0.00 0.00 1.00
#> TCGA.DM.A28E.01 3 0.0000 0.997 0.00 0.00 1.00
#> TCGA.AG.3725.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.CK.6747.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.CL.5918.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.CI.6623.01 3 0.0000 0.997 0.00 0.00 1.00
#> TCGA.A6.5667.01 3 0.0000 0.997 0.00 0.00 1.00
#> TCGA.DM.A28K.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.AA.3713.11 2 0.0000 0.993 0.00 1.00 0.00
#> TCGA.AA.3655.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.AU.3779.01 3 0.0000 0.997 0.00 0.00 1.00
#> TCGA.A6.5664.01 3 0.0000 0.997 0.00 0.00 1.00
#> TCGA.AA.3697.11 2 0.0000 0.993 0.00 1.00 0.00
#> TCGA.AZ.5407.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.CM.6169.01 1 0.0892 0.967 0.98 0.00 0.02
#> TCGA.AH.6547.01 3 0.0000 0.997 0.00 0.00 1.00
#> TCGA.AZ.6601.11 2 0.0000 0.993 0.00 1.00 0.00
#> TCGA.A6.5661.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.F4.6807.01 3 0.0000 0.997 0.00 0.00 1.00
#> TCGA.QG.A5YV.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.AA.3509.11 2 0.0000 0.993 0.00 1.00 0.00
#> TCGA.AY.A71X.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.CA.5797.01 2 0.0000 0.993 0.00 1.00 0.00
#> TCGA.F4.6460.01 2 0.0000 0.993 0.00 1.00 0.00
#> TCGA.G4.6302.11 2 0.0000 0.993 0.00 1.00 0.00
#> TCGA.F5.6702.01 2 0.0000 0.993 0.00 1.00 0.00
#> TCGA.AH.6549.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.D5.6927.01 3 0.0000 0.997 0.00 0.00 1.00
#> TCGA.CM.6166.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.AH.6897.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.G4.6304.01 3 0.0000 0.997 0.00 0.00 1.00
#> TCGA.CA.5255.01 3 0.0000 0.997 0.00 0.00 1.00
#> TCGA.EI.6507.01 3 0.0000 0.997 0.00 0.00 1.00
#> TCGA.CK.4947.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.D5.5540.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.DC.6682.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.G4.6321.01 3 0.0000 0.997 0.00 0.00 1.00
#> TCGA.A6.6649.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.CM.5348.01 3 0.0000 0.997 0.00 0.00 1.00
#> TCGA.EI.6513.01 3 0.0000 0.997 0.00 0.00 1.00
#> TCGA.A6.2672.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.D5.6539.01 2 0.0000 0.993 0.00 1.00 0.00
#> TCGA.AA.3510.01 3 0.0000 0.997 0.00 0.00 1.00
#> TCGA.G5.6233.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.BM.6198.01 3 0.0000 0.997 0.00 0.00 1.00
#> TCGA.CA.6719.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.DC.6154.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.DM.A1D6.01 1 0.2959 0.876 0.90 0.00 0.10
#> TCGA.AG.3731.11 2 0.0000 0.993 0.00 1.00 0.00
#> TCGA.CM.6674.01 3 0.0000 0.997 0.00 0.00 1.00
#> TCGA.CM.4743.01 3 0.0000 0.997 0.00 0.00 1.00
#> TCGA.F5.6465.01 3 0.0000 0.997 0.00 0.00 1.00
#> TCGA.D5.5537.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.F4.6463.01 3 0.0000 0.997 0.00 0.00 1.00
#> TCGA.A6.2686.11 2 0.0000 0.993 0.00 1.00 0.00
#> TCGA.4T.AA8H.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.A6.6782.01 3 0.0000 0.997 0.00 0.00 1.00
#> TCGA.AG.3592.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.AD.6888.01 3 0.0000 0.997 0.00 0.00 1.00
#> TCGA.CM.6678.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.CM.5344.01 3 0.0000 0.997 0.00 0.00 1.00
#> TCGA.AA.3495.11 2 0.0000 0.993 0.00 1.00 0.00
#> TCGA.AG.A01W.11 2 0.0000 0.993 0.00 1.00 0.00
#> TCGA.F4.6809.01 3 0.0000 0.997 0.00 0.00 1.00
#> TCGA.CK.5914.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.AZ.4681.01 3 0.0000 0.997 0.00 0.00 1.00
#> TCGA.AA.3492.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.D5.6536.01 3 0.0000 0.997 0.00 0.00 1.00
#> TCGA.AA.3506.11 2 0.0000 0.993 0.00 1.00 0.00
#> TCGA.AA.3488.01 3 0.0000 0.997 0.00 0.00 1.00
#> TCGA.AA.3502.11 2 0.0000 0.993 0.00 1.00 0.00
#> TCGA.A6.6140.01 3 0.0000 0.997 0.00 0.00 1.00
#> TCGA.D5.6529.01 3 0.0000 0.997 0.00 0.00 1.00
#> TCGA.DM.A1D0.01 2 0.0892 0.973 0.00 0.98 0.02
#> TCGA.DM.A1HB.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.D5.6920.01 3 0.0000 0.997 0.00 0.00 1.00
#> TCGA.D5.6922.01 3 0.0000 0.997 0.00 0.00 1.00
#> TCGA.EI.6508.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.D5.6532.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.5M.AATA.01 3 0.0000 0.997 0.00 0.00 1.00
#> TCGA.EI.6509.01 2 0.6280 0.148 0.00 0.54 0.46
#> TCGA.G4.6311.01 3 0.0000 0.997 0.00 0.00 1.00
#> TCGA.A6.A566.01 3 0.0000 0.997 0.00 0.00 1.00
#> TCGA.G4.6625.01 3 0.0000 0.997 0.00 0.00 1.00
#> TCGA.CI.6619.01 2 0.2066 0.931 0.00 0.94 0.06
#> TCGA.F5.6864.01 3 0.0000 0.997 0.00 0.00 1.00
#> TCGA.AA.3492.11 2 0.0000 0.993 0.00 1.00 0.00
#> TCGA.A6.5659.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.WS.AB45.01 3 0.0000 0.997 0.00 0.00 1.00
#> TCGA.G4.6315.01 3 0.0000 0.997 0.00 0.00 1.00
#> TCGA.D5.6541.01 3 0.0000 0.997 0.00 0.00 1.00
#> TCGA.A6.2680.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.CM.4751.01 3 0.0000 0.997 0.00 0.00 1.00
#> TCGA.CM.6680.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.AF.6136.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.AA.3660.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.CM.4747.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.EF.5831.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.DM.A28G.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.G4.6297.01 3 0.0000 0.997 0.00 0.00 1.00
#> TCGA.A6.2682.11 2 0.0000 0.993 0.00 1.00 0.00
#> TCGA.D5.6537.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.CM.6170.01 3 0.0000 0.997 0.00 0.00 1.00
#> TCGA.DY.A1DD.01 1 0.0000 0.987 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.AF.3911.01 3 0.0000 0.993 0.00 0 1.00 0.00
#> TCGA.F4.6459.01 3 0.0000 0.993 0.00 0 1.00 0.00
#> TCGA.AA.3494.11 2 0.0000 1.000 0.00 1 0.00 0.00
#> TCGA.3L.AA1B.01 3 0.0000 0.993 0.00 0 1.00 0.00
#> TCGA.D5.5538.01 3 0.0000 0.993 0.00 0 1.00 0.00
#> TCGA.F4.6854.01 3 0.0000 0.993 0.00 0 1.00 0.00
#> TCGA.AG.A026.01 1 0.0000 0.987 1.00 0 0.00 0.00
#> TCGA.G4.6303.01 1 0.0000 0.987 1.00 0 0.00 0.00
#> TCGA.F5.6464.01 4 0.0000 0.992 0.00 0 0.00 1.00
#> TCGA.T9.A92H.01 1 0.1211 0.944 0.96 0 0.04 0.00
#> TCGA.AA.3712.11 2 0.0000 1.000 0.00 1 0.00 0.00
#> TCGA.CM.5863.01 3 0.0000 0.993 0.00 0 1.00 0.00
#> TCGA.AZ.4308.01 4 0.0000 0.992 0.00 0 0.00 1.00
#> TCGA.AD.6965.01 1 0.0000 0.987 1.00 0 0.00 0.00
#> TCGA.A6.2681.11 2 0.0000 1.000 0.00 1 0.00 0.00
#> TCGA.AD.6548.01 3 0.0000 0.993 0.00 0 1.00 0.00
#> TCGA.A6.5660.01 1 0.0000 0.987 1.00 0 0.00 0.00
#> TCGA.AZ.6600.01 3 0.0000 0.993 0.00 0 1.00 0.00
#> TCGA.F4.6808.01 3 0.0000 0.993 0.00 0 1.00 0.00
#> TCGA.D5.6540.01 1 0.0000 0.987 1.00 0 0.00 0.00
#> TCGA.F5.6571.01 1 0.0707 0.966 0.98 0 0.02 0.00
#> TCGA.D5.6926.01 3 0.0000 0.993 0.00 0 1.00 0.00
#> TCGA.CM.4748.01 3 0.0000 0.993 0.00 0 1.00 0.00
#> TCGA.A6.2675.11 2 0.0000 1.000 0.00 1 0.00 0.00
#> TCGA.5M.AATE.01 3 0.0000 0.993 0.00 0 1.00 0.00
#> TCGA.D5.5541.01 4 0.0000 0.992 0.00 0 0.00 1.00
#> TCGA.CM.5862.01 1 0.0000 0.987 1.00 0 0.00 0.00
#> TCGA.AA.3511.01 3 0.0000 0.993 0.00 0 1.00 0.00
#> TCGA.AA.3663.11 2 0.0000 1.000 0.00 1 0.00 0.00
#> TCGA.CI.6622.01 1 0.4624 0.500 0.66 0 0.34 0.00
#> TCGA.EI.6506.01 3 0.1211 0.952 0.00 0 0.96 0.04
#> TCGA.AM.5821.01 3 0.0000 0.993 0.00 0 1.00 0.00
#> TCGA.F5.6812.01 4 0.0000 0.992 0.00 0 0.00 1.00
#> TCGA.G4.6588.01 1 0.0000 0.987 1.00 0 0.00 0.00
#> TCGA.EI.6512.01 1 0.0000 0.987 1.00 0 0.00 0.00
#> TCGA.A6.6648.01 4 0.0000 0.992 0.00 0 0.00 1.00
#> TCGA.A6.2671.11 2 0.0000 1.000 0.00 1 0.00 0.00
#> TCGA.NH.A6GC.01 3 0.1211 0.948 0.04 0 0.96 0.00
#> TCGA.F4.6805.01 4 0.0000 0.992 0.00 0 0.00 1.00
#> TCGA.AA.3697.01 3 0.0000 0.993 0.00 0 1.00 0.00
#> TCGA.QG.A5YX.01 1 0.0000 0.987 1.00 0 0.00 0.00
#> TCGA.DM.A28C.01 3 0.0000 0.993 0.00 0 1.00 0.00
#> TCGA.AG.A036.01 1 0.4713 0.454 0.64 0 0.36 0.00
#> TCGA.AZ.6606.01 1 0.0000 0.987 1.00 0 0.00 0.00
#> TCGA.F4.6570.01 1 0.0000 0.987 1.00 0 0.00 0.00
#> TCGA.DC.4745.01 3 0.0000 0.993 0.00 0 1.00 0.00
#> TCGA.AF.A56K.01 4 0.0000 0.992 0.00 0 0.00 1.00
#> TCGA.G4.6627.01 4 0.0000 0.992 0.00 0 0.00 1.00
#> TCGA.A6.5657.01 3 0.3400 0.781 0.00 0 0.82 0.18
#> TCGA.A6.5662.01 3 0.0000 0.993 0.00 0 1.00 0.00
#> TCGA.AA.3509.01 1 0.2011 0.896 0.92 0 0.08 0.00
#> TCGA.D5.6929.01 4 0.0000 0.992 0.00 0 0.00 1.00
#> TCGA.CM.6679.01 3 0.0000 0.993 0.00 0 1.00 0.00
#> TCGA.A6.2680.11 2 0.0000 1.000 0.00 1 0.00 0.00
#> TCGA.DC.6157.01 4 0.0000 0.992 0.00 0 0.00 1.00
#> TCGA.AF.6655.01 4 0.0000 0.992 0.00 0 0.00 1.00
#> TCGA.CM.6161.01 3 0.0000 0.993 0.00 0 1.00 0.00
#> TCGA.EI.6883.01 1 0.0000 0.987 1.00 0 0.00 0.00
#> TCGA.F5.6811.01 3 0.0000 0.993 0.00 0 1.00 0.00
#> TCGA.D5.6930.01 3 0.0000 0.993 0.00 0 1.00 0.00
#> TCGA.CM.6164.01 4 0.0000 0.992 0.00 0 0.00 1.00
#> TCGA.AF.2687.01 4 0.0000 0.992 0.00 0 0.00 1.00
#> TCGA.DY.A1H8.01 3 0.0000 0.993 0.00 0 1.00 0.00
#> TCGA.G5.6641.01 3 0.0000 0.993 0.00 0 1.00 0.00
#> TCGA.DC.6155.01 3 0.0000 0.993 0.00 0 1.00 0.00
#> TCGA.RU.A8FL.01 1 0.0000 0.987 1.00 0 0.00 0.00
#> TCGA.CK.4951.01 3 0.0000 0.993 0.00 0 1.00 0.00
#> TCGA.F4.6704.01 4 0.0000 0.992 0.00 0 0.00 1.00
#> TCGA.AZ.6599.01 1 0.0000 0.987 1.00 0 0.00 0.00
#> TCGA.F5.6861.01 3 0.0000 0.993 0.00 0 1.00 0.00
#> TCGA.CM.5860.01 1 0.0000 0.987 1.00 0 0.00 0.00
#> TCGA.A6.6780.01 1 0.0000 0.987 1.00 0 0.00 0.00
#> TCGA.A6.2686.01 1 0.0000 0.987 1.00 0 0.00 0.00
#> TCGA.CM.4750.01 1 0.0000 0.987 1.00 0 0.00 0.00
#> TCGA.CM.6677.01 1 0.0000 0.987 1.00 0 0.00 0.00
#> TCGA.A6.A567.01 4 0.0000 0.992 0.00 0 0.00 1.00
#> TCGA.F5.6814.01 1 0.0000 0.987 1.00 0 0.00 0.00
#> TCGA.D5.6898.01 3 0.0000 0.993 0.00 0 1.00 0.00
#> TCGA.AG.A01W.01 3 0.0000 0.993 0.00 0 1.00 0.00
#> TCGA.AZ.6598.11 2 0.0000 1.000 0.00 1 0.00 0.00
#> TCGA.F5.6813.01 3 0.0000 0.993 0.00 0 1.00 0.00
#> TCGA.AG.3732.01 4 0.0000 0.992 0.00 0 0.00 1.00
#> TCGA.EI.6885.01 4 0.0000 0.992 0.00 0 0.00 1.00
#> TCGA.G4.6299.01 1 0.0000 0.987 1.00 0 0.00 0.00
#> TCGA.A6.4105.01 1 0.0000 0.987 1.00 0 0.00 0.00
#> TCGA.DM.A1D8.01 1 0.0000 0.987 1.00 0 0.00 0.00
#> TCGA.DM.A285.01 3 0.0000 0.993 0.00 0 1.00 0.00
#> TCGA.G4.6295.11 2 0.0000 1.000 0.00 1 0.00 0.00
#> TCGA.DC.4749.01 4 0.0000 0.992 0.00 0 0.00 1.00
#> TCGA.DT.5265.01 1 0.0000 0.987 1.00 0 0.00 0.00
#> TCGA.5M.AAT5.01 4 0.0000 0.992 0.00 0 0.00 1.00
#> TCGA.DM.A0XD.01 1 0.0000 0.987 1.00 0 0.00 0.00
#> TCGA.A6.6138.01 1 0.2921 0.816 0.86 0 0.14 0.00
#> TCGA.D5.7000.01 1 0.0000 0.987 1.00 0 0.00 0.00
#> TCGA.DM.A28F.01 1 0.0000 0.987 1.00 0 0.00 0.00
#> TCGA.DY.A1DE.01 3 0.0000 0.993 0.00 0 1.00 0.00
#> TCGA.A6.6142.01 2 0.0000 1.000 0.00 1 0.00 0.00
#> TCGA.QL.A97D.01 3 0.0000 0.993 0.00 0 1.00 0.00
#> TCGA.CK.6748.01 3 0.0000 0.993 0.00 0 1.00 0.00
#> TCGA.DC.6160.01 4 0.0000 0.992 0.00 0 0.00 1.00
#> TCGA.D5.6534.01 4 0.0000 0.992 0.00 0 0.00 1.00
#> TCGA.AZ.4616.01 3 0.0000 0.993 0.00 0 1.00 0.00
#> TCGA.CK.6751.01 1 0.0000 0.987 1.00 0 0.00 0.00
#> TCGA.CM.6171.01 1 0.0000 0.987 1.00 0 0.00 0.00
#> TCGA.DM.A1DA.01 1 0.0000 0.987 1.00 0 0.00 0.00
#> TCGA.AG.A020.11 2 0.0000 1.000 0.00 1 0.00 0.00
#> TCGA.G4.6311.11 2 0.0000 1.000 0.00 1 0.00 0.00
#> TCGA.G4.6625.11 2 0.0000 1.000 0.00 1 0.00 0.00
#> TCGA.F5.6863.01 4 0.0000 0.992 0.00 0 0.00 1.00
#> TCGA.G4.6317.02 4 0.2921 0.802 0.00 0 0.14 0.86
#> TCGA.G4.6317.01 3 0.0000 0.993 0.00 0 1.00 0.00
#> TCGA.DM.A1D4.01 1 0.0000 0.987 1.00 0 0.00 0.00
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#> TCGA.D5.6530.01 3 0.0000 0.993 0.00 0 1.00 0.00
#> TCGA.CK.4948.01 4 0.0000 0.992 0.00 0 0.00 1.00
#> TCGA.AD.A5EJ.01 1 0.0000 0.987 1.00 0 0.00 0.00
#> TCGA.A6.6651.01 4 0.0000 0.992 0.00 0 0.00 1.00
#> TCGA.CA.5256.01 3 0.0000 0.993 0.00 0 1.00 0.00
#> TCGA.DM.A0X9.01 1 0.0000 0.987 1.00 0 0.00 0.00
#> TCGA.AY.A69D.01 1 0.0000 0.987 1.00 0 0.00 0.00
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#> TCGA.CA.6716.01 1 0.0000 0.987 1.00 0 0.00 0.00
#> TCGA.A6.2682.01 3 0.0000 0.993 0.00 0 1.00 0.00
#> TCGA.A6.4107.11 2 0.0000 1.000 0.00 1 0.00 0.00
#> TCGA.CA.6717.01 3 0.0000 0.993 0.00 0 1.00 0.00
#> TCGA.G4.6293.01 3 0.0000 0.993 0.00 0 1.00 0.00
#> TCGA.CK.5916.01 1 0.0000 0.987 1.00 0 0.00 0.00
#> TCGA.G4.6309.01 4 0.0000 0.992 0.00 0 0.00 1.00
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#> TCGA.AF.A56L.01 3 0.0000 0.993 0.00 0 1.00 0.00
#> TCGA.NH.A6GB.01 1 0.0000 0.987 1.00 0 0.00 0.00
#> TCGA.AD.5900.01 3 0.0000 0.993 0.00 0 1.00 0.00
#> TCGA.NH.A50U.01 1 0.0000 0.987 1.00 0 0.00 0.00
#> TCGA.AA.3712.01 3 0.0000 0.993 0.00 0 1.00 0.00
#> TCGA.AZ.4614.01 1 0.0000 0.987 1.00 0 0.00 0.00
#> TCGA.AH.6644.01 1 0.0000 0.987 1.00 0 0.00 0.00
#> TCGA.AZ.6607.01 3 0.0000 0.993 0.00 0 1.00 0.00
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#> TCGA.CM.5868.01 4 0.0000 0.992 0.00 0 0.00 1.00
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#> TCGA.A6.3809.01 1 0.0000 0.987 1.00 0 0.00 0.00
#> TCGA.AZ.4313.01 4 0.0000 0.992 0.00 0 0.00 1.00
#> TCGA.A6.2675.01 4 0.0000 0.992 0.00 0 0.00 1.00
#> TCGA.AZ.6608.01 3 0.0000 0.993 0.00 0 1.00 0.00
#> TCGA.CM.5864.01 1 0.0000 0.987 1.00 0 0.00 0.00
#> TCGA.AA.3494.01 4 0.0000 0.992 0.00 0 0.00 1.00
#> TCGA.AD.6895.01 3 0.0000 0.993 0.00 0 1.00 0.00
#> TCGA.CI.6620.01 3 0.0000 0.993 0.00 0 1.00 0.00
#> TCGA.DC.6156.01 3 0.0000 0.993 0.00 0 1.00 0.00
#> TCGA.D5.6931.01 3 0.0000 0.993 0.00 0 1.00 0.00
#> TCGA.CM.6165.01 3 0.0000 0.993 0.00 0 1.00 0.00
#> TCGA.CM.5861.01 1 0.0000 0.987 1.00 0 0.00 0.00
#> TCGA.A6.2671.01 3 0.0000 0.993 0.00 0 1.00 0.00
#> TCGA.DC.6158.01 3 0.0000 0.993 0.00 0 1.00 0.00
#> TCGA.AG.3742.01 1 0.0000 0.987 1.00 0 0.00 0.00
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#> TCGA.G4.6307.01 4 0.0000 0.992 0.00 0 0.00 1.00
#> TCGA.A6.5666.01 1 0.0707 0.966 0.98 0 0.02 0.00
#> TCGA.EI.6511.01 3 0.0000 0.993 0.00 0 1.00 0.00
#> TCGA.CI.6624.01 4 0.0000 0.992 0.00 0 0.00 1.00
#> TCGA.AG.3591.01 1 0.0000 0.987 1.00 0 0.00 0.00
#> TCGA.AY.A8YK.01 2 0.0000 1.000 0.00 1 0.00 0.00
#> TCGA.F4.6856.01 3 0.0000 0.993 0.00 0 1.00 0.00
#> TCGA.DM.A1D7.01 3 0.0000 0.993 0.00 0 1.00 0.00
#> TCGA.A6.2685.01 2 0.0000 1.000 0.00 1 0.00 0.00
#> TCGA.5M.AAT6.01 2 0.0000 1.000 0.00 1 0.00 0.00
#> TCGA.AH.6643.01 1 0.0000 0.987 1.00 0 0.00 0.00
#> TCGA.F4.6569.01 3 0.0000 0.993 0.00 0 1.00 0.00
#> TCGA.G4.6298.01 3 0.0000 0.993 0.00 0 1.00 0.00
#> TCGA.AY.6196.01 3 0.4134 0.650 0.00 0 0.74 0.26
#> TCGA.EI.6510.01 1 0.0000 0.987 1.00 0 0.00 0.00
#> TCGA.A6.5656.01 1 0.0000 0.987 1.00 0 0.00 0.00
#> TCGA.A6.2684.11 2 0.0000 1.000 0.00 1 0.00 0.00
#> TCGA.DY.A1DG.01 1 0.0707 0.966 0.98 0 0.02 0.00
#> TCGA.AZ.4682.01 3 0.0000 0.993 0.00 0 1.00 0.00
#> TCGA.EI.6884.01 3 0.0000 0.993 0.00 0 1.00 0.00
#> TCGA.F4.6806.01 1 0.0000 0.987 1.00 0 0.00 0.00
#> TCGA.G4.6320.11 2 0.0000 1.000 0.00 1 0.00 0.00
#> TCGA.G4.6322.01 1 0.0000 0.987 1.00 0 0.00 0.00
#> TCGA.F5.6810.01 4 0.0000 0.992 0.00 0 0.00 1.00
#> TCGA.5M.AAT4.01 1 0.0000 0.987 1.00 0 0.00 0.00
#> TCGA.CL.4957.01 3 0.0000 0.993 0.00 0 1.00 0.00
#> TCGA.DC.6681.01 3 0.0000 0.993 0.00 0 1.00 0.00
#> TCGA.CM.6167.01 4 0.0000 0.992 0.00 0 0.00 1.00
#> TCGA.AG.4022.01 3 0.0000 0.993 0.00 0 1.00 0.00
#> TCGA.G4.6586.01 1 0.0000 0.987 1.00 0 0.00 0.00
#> TCGA.EI.6514.01 1 0.0000 0.987 1.00 0 0.00 0.00
#> TCGA.CK.4950.01 3 0.0000 0.993 0.00 0 1.00 0.00
#> TCGA.DM.A282.01 1 0.0000 0.987 1.00 0 0.00 0.00
#> TCGA.DY.A1DC.01 3 0.0000 0.993 0.00 0 1.00 0.00
#> TCGA.D5.6535.01 3 0.0000 0.993 0.00 0 1.00 0.00
#> TCGA.DM.A1HA.01 1 0.0000 0.987 1.00 0 0.00 0.00
#> TCGA.DC.5869.01 3 0.3172 0.788 0.16 0 0.84 0.00
#> TCGA.AZ.6599.11 2 0.0000 1.000 0.00 1 0.00 0.00
#> TCGA.CM.4752.01 4 0.0000 0.992 0.00 0 0.00 1.00
#> TCGA.AZ.4684.01 3 0.0707 0.973 0.00 0 0.98 0.02
#> TCGA.EI.7004.01 3 0.0000 0.993 0.00 0 1.00 0.00
#> TCGA.A6.A565.01 2 0.0000 1.000 0.00 1 0.00 0.00
#> TCGA.D5.6531.01 1 0.0000 0.987 1.00 0 0.00 0.00
#> TCGA.AZ.6598.01 1 0.0000 0.987 1.00 0 0.00 0.00
#> TCGA.AD.6890.01 3 0.0000 0.993 0.00 0 1.00 0.00
#> TCGA.AG.4021.01 1 0.0000 0.987 1.00 0 0.00 0.00
#> TCGA.A6.6781.01 4 0.0000 0.992 0.00 0 0.00 1.00
#> TCGA.DM.A1D9.01 1 0.0000 0.987 1.00 0 0.00 0.00
#> TCGA.CM.4744.01 1 0.0000 0.987 1.00 0 0.00 0.00
#> TCGA.A6.2679.11 2 0.0000 1.000 0.00 1 0.00 0.00
#> TCGA.A6.6652.01 1 0.0707 0.966 0.98 0 0.02 0.00
#> TCGA.AD.6964.01 2 0.0000 1.000 0.00 1 0.00 0.00
#> TCGA.SS.A7HO.01 1 0.0000 0.987 1.00 0 0.00 0.00
#> TCGA.A6.6650.01 1 0.0000 0.987 1.00 0 0.00 0.00
#> TCGA.DM.A0XF.01 4 0.0000 0.992 0.00 0 0.00 1.00
#> TCGA.G4.6295.01 4 0.0000 0.992 0.00 0 0.00 1.00
#> TCGA.F4.6461.01 1 0.0000 0.987 1.00 0 0.00 0.00
#> TCGA.AM.5820.01 3 0.0000 0.993 0.00 0 1.00 0.00
#> TCGA.G4.6314.11 2 0.0000 1.000 0.00 1 0.00 0.00
#> TCGA.AD.6889.01 1 0.0000 0.987 1.00 0 0.00 0.00
#> TCGA.AZ.6605.01 4 0.2345 0.859 0.00 0 0.10 0.90
#> TCGA.EI.6881.01 3 0.0000 0.993 0.00 0 1.00 0.00
#> TCGA.NH.A50T.01 1 0.0000 0.987 1.00 0 0.00 0.00
#> TCGA.AG.3725.11 2 0.0000 1.000 0.00 1 0.00 0.00
#> TCGA.G4.6323.01 3 0.0000 0.993 0.00 0 1.00 0.00
#> TCGA.AA.3663.01 1 0.0000 0.987 1.00 0 0.00 0.00
#> TCGA.AD.6899.01 1 0.0000 0.987 1.00 0 0.00 0.00
#> TCGA.A6.5667.11 2 0.0000 1.000 0.00 1 0.00 0.00
#> TCGA.A6.A56B.01 1 0.0000 0.987 1.00 0 0.00 0.00
#> TCGA.G5.6572.01 4 0.0000 0.992 0.00 0 0.00 1.00
#> TCGA.DM.A280.01 4 0.0000 0.992 0.00 0 0.00 1.00
#> TCGA.AG.A020.01 3 0.0000 0.993 0.00 0 1.00 0.00
#> TCGA.AA.3713.01 3 0.0000 0.993 0.00 0 1.00 0.00
#> TCGA.D5.5539.01 1 0.3975 0.669 0.76 0 0.24 0.00
#> TCGA.AA.3655.11 2 0.0000 1.000 0.00 1 0.00 0.00
#> TCGA.AA.3489.01 4 0.0000 0.992 0.00 0 0.00 1.00
#> TCGA.AA.3495.01 3 0.0000 0.993 0.00 0 1.00 0.00
#> TCGA.AG.A01Y.01 4 0.0000 0.992 0.00 0 0.00 1.00
#> TCGA.AZ.6601.01 3 0.0000 0.993 0.00 0 1.00 0.00
#> TCGA.AH.6903.01 3 0.0000 0.993 0.00 0 1.00 0.00
#> TCGA.AZ.6603.01 4 0.0000 0.992 0.00 0 0.00 1.00
#> TCGA.CA.5254.01 1 0.0000 0.987 1.00 0 0.00 0.00
#> TCGA.A6.A5ZU.01 3 0.0000 0.993 0.00 0 1.00 0.00
#> TCGA.G4.6302.01 4 0.0000 0.992 0.00 0 0.00 1.00
#> TCGA.AZ.5403.01 2 0.0000 1.000 0.00 1 0.00 0.00
#> TCGA.AY.A54L.01 1 0.0000 0.987 1.00 0 0.00 0.00
#> TCGA.A6.4107.01 1 0.0000 0.987 1.00 0 0.00 0.00
#> TCGA.NH.A5IV.01 1 0.0000 0.987 1.00 0 0.00 0.00
#> TCGA.G4.6306.01 1 0.0000 0.987 1.00 0 0.00 0.00
#> TCGA.AD.A5EK.01 1 0.0000 0.987 1.00 0 0.00 0.00
#> TCGA.G5.6235.01 4 0.0000 0.992 0.00 0 0.00 1.00
#> TCGA.DC.5337.01 1 0.0000 0.987 1.00 0 0.00 0.00
#> TCGA.CM.6675.01 1 0.0000 0.987 1.00 0 0.00 0.00
#> TCGA.AH.6544.01 3 0.0000 0.993 0.00 0 1.00 0.00
#> TCGA.CK.6746.01 1 0.0000 0.987 1.00 0 0.00 0.00
#> TCGA.CA.6718.01 3 0.0000 0.993 0.00 0 1.00 0.00
#> TCGA.CI.6621.01 4 0.0000 0.992 0.00 0 0.00 1.00
#> TCGA.CM.6676.01 3 0.0000 0.993 0.00 0 1.00 0.00
#> TCGA.DM.A1DB.01 3 0.0000 0.993 0.00 0 1.00 0.00
#> TCGA.A6.6654.01 3 0.0000 0.993 0.00 0 1.00 0.00
#> TCGA.AA.3510.11 2 0.0000 1.000 0.00 1 0.00 0.00
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#> TCGA.CM.5341.01 3 0.0000 0.993 0.00 0 1.00 0.00
#> TCGA.CK.5912.01 3 0.0000 0.993 0.00 0 1.00 0.00
#> TCGA.F4.6857.01 4 0.0000 0.992 0.00 0 0.00 1.00
#> TCGA.QG.A5YW.01 1 0.0000 0.987 1.00 0 0.00 0.00
#> TCGA.A6.5665.01 1 0.0000 0.987 1.00 0 0.00 0.00
#> TCGA.CM.6168.01 3 0.0000 0.993 0.00 0 1.00 0.00
#> TCGA.CL.5917.01 3 0.0000 0.993 0.00 0 1.00 0.00
#> TCGA.AU.6004.01 3 0.0000 0.993 0.00 0 1.00 0.00
#> TCGA.AY.5543.01 3 0.0000 0.993 0.00 0 1.00 0.00
#> TCGA.AG.3731.01 3 0.0000 0.993 0.00 0 1.00 0.00
#> TCGA.G4.6314.01 3 0.0000 0.993 0.00 0 1.00 0.00
#> TCGA.DC.6683.01 3 0.0000 0.993 0.00 0 1.00 0.00
#> TCGA.CA.5796.01 3 0.1637 0.924 0.06 0 0.94 0.00
#> TCGA.AG.A036.11 2 0.0000 1.000 0.00 1 0.00 0.00
#> TCGA.AZ.4323.01 4 0.0000 0.992 0.00 0 0.00 1.00
#> TCGA.EI.6882.01 1 0.0000 0.987 1.00 0 0.00 0.00
#> TCGA.AZ.4315.01 3 0.0000 0.993 0.00 0 1.00 0.00
#> TCGA.A6.2677.01 1 0.0000 0.987 1.00 0 0.00 0.00
#> TCGA.DY.A1DF.01 3 0.0000 0.993 0.00 0 1.00 0.00
#> TCGA.CM.6162.01 2 0.0000 1.000 0.00 1 0.00 0.00
#> TCGA.F4.6703.01 2 0.0000 1.000 0.00 1 0.00 0.00
#> TCGA.CM.5349.01 3 0.0000 0.993 0.00 0 1.00 0.00
#> TCGA.AG.A02N.01 3 0.0707 0.971 0.02 0 0.98 0.00
#> TCGA.AA.3506.01 3 0.0707 0.971 0.02 0 0.98 0.00
#> TCGA.D5.6932.01 3 0.0000 0.993 0.00 0 1.00 0.00
#> TCGA.D5.6538.01 1 0.0000 0.987 1.00 0 0.00 0.00
#> TCGA.AA.3488.11 2 0.0000 1.000 0.00 1 0.00 0.00
#> TCGA.AA.3502.01 1 0.0000 0.987 1.00 0 0.00 0.00
#> TCGA.NH.A8F8.01 3 0.0000 0.993 0.00 0 1.00 0.00
#> TCGA.AF.A56N.01 3 0.0000 0.993 0.00 0 1.00 0.00
#> TCGA.AF.6672.01 4 0.0000 0.992 0.00 0 0.00 1.00
#> TCGA.A6.2685.11 2 0.0000 1.000 0.00 1 0.00 0.00
#> TCGA.A6.6141.01 3 0.0000 0.993 0.00 0 1.00 0.00
#> TCGA.AD.6963.01 4 0.0000 0.992 0.00 0 0.00 1.00
#> TCGA.G4.6298.11 2 0.0000 1.000 0.00 1 0.00 0.00
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#> TCGA.QG.A5Z2.01 1 0.0000 0.987 1.00 0 0.00 0.00
#> TCGA.A6.2684.01 3 0.0000 0.993 0.00 0 1.00 0.00
#> TCGA.CK.5915.01 1 0.0000 0.987 1.00 0 0.00 0.00
#> TCGA.CM.6163.01 3 0.0000 0.993 0.00 0 1.00 0.00
#> TCGA.G4.6322.11 2 0.0000 1.000 0.00 1 0.00 0.00
#> TCGA.AY.6197.01 1 0.0000 0.987 1.00 0 0.00 0.00
#> TCGA.D5.6928.01 4 0.0000 0.992 0.00 0 0.00 1.00
#> TCGA.A6.3810.01 4 0.0000 0.992 0.00 0 0.00 1.00
#> TCGA.G4.6294.01 1 0.0000 0.987 1.00 0 0.00 0.00
#> TCGA.AA.3660.11 2 0.0000 1.000 0.00 1 0.00 0.00
#> TCGA.A6.6137.01 3 0.0000 0.993 0.00 0 1.00 0.00
#> TCGA.G4.6297.11 2 0.0000 1.000 0.00 1 0.00 0.00
#> TCGA.AZ.4615.01 3 0.0000 0.993 0.00 0 1.00 0.00
#> TCGA.CK.4952.01 1 0.0000 0.987 1.00 0 0.00 0.00
#> TCGA.CM.6172.01 1 0.1211 0.944 0.96 0 0.04 0.00
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#> TCGA.AA.3496.01 1 0.0000 0.987 1.00 0 0.00 0.00
#> TCGA.CK.5913.01 1 0.0000 0.987 1.00 0 0.00 0.00
#> TCGA.DM.A28A.01 1 0.0000 0.987 1.00 0 0.00 0.00
#> TCGA.EI.7002.01 1 0.0707 0.966 0.98 0 0.02 0.00
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#> TCGA.NH.A6GA.01 1 0.0000 0.987 1.00 0 0.00 0.00
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#> TCGA.AZ.5407.01 1 0.0000 0.987 1.00 0 0.00 0.00
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#> TCGA.AH.6547.01 4 0.0000 0.992 0.00 0 0.00 1.00
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#> TCGA.CM.6166.01 1 0.0000 0.987 1.00 0 0.00 0.00
#> TCGA.AH.6897.01 1 0.0000 0.987 1.00 0 0.00 0.00
#> TCGA.G4.6304.01 4 0.0000 0.992 0.00 0 0.00 1.00
#> TCGA.CA.5255.01 3 0.0000 0.993 0.00 0 1.00 0.00
#> TCGA.EI.6507.01 3 0.0000 0.993 0.00 0 1.00 0.00
#> TCGA.CK.4947.01 3 0.0000 0.993 0.00 0 1.00 0.00
#> TCGA.D5.5540.01 1 0.0000 0.987 1.00 0 0.00 0.00
#> TCGA.DC.6682.01 3 0.0000 0.993 0.00 0 1.00 0.00
#> TCGA.G4.6321.01 3 0.0000 0.993 0.00 0 1.00 0.00
#> TCGA.A6.6649.01 3 0.0000 0.993 0.00 0 1.00 0.00
#> TCGA.CM.5348.01 3 0.0000 0.993 0.00 0 1.00 0.00
#> TCGA.EI.6513.01 4 0.0000 0.992 0.00 0 0.00 1.00
#> TCGA.A6.2672.01 1 0.0000 0.987 1.00 0 0.00 0.00
#> TCGA.D5.6539.01 4 0.0000 0.992 0.00 0 0.00 1.00
#> TCGA.AA.3510.01 3 0.0000 0.993 0.00 0 1.00 0.00
#> TCGA.G5.6233.01 1 0.0000 0.987 1.00 0 0.00 0.00
#> TCGA.BM.6198.01 4 0.0000 0.992 0.00 0 0.00 1.00
#> TCGA.CA.6719.01 1 0.0000 0.987 1.00 0 0.00 0.00
#> TCGA.DC.6154.01 3 0.0000 0.993 0.00 0 1.00 0.00
#> TCGA.DM.A1D6.01 3 0.0000 0.993 0.00 0 1.00 0.00
#> TCGA.AG.3731.11 2 0.0000 1.000 0.00 1 0.00 0.00
#> TCGA.CM.6674.01 4 0.0000 0.992 0.00 0 0.00 1.00
#> TCGA.CM.4743.01 4 0.0000 0.992 0.00 0 0.00 1.00
#> TCGA.F5.6465.01 4 0.0000 0.992 0.00 0 0.00 1.00
#> TCGA.D5.5537.01 1 0.0000 0.987 1.00 0 0.00 0.00
#> TCGA.F4.6463.01 3 0.0000 0.993 0.00 0 1.00 0.00
#> TCGA.A6.2686.11 2 0.0000 1.000 0.00 1 0.00 0.00
#> TCGA.4T.AA8H.01 1 0.0000 0.987 1.00 0 0.00 0.00
#> TCGA.A6.6782.01 3 0.0000 0.993 0.00 0 1.00 0.00
#> TCGA.AG.3592.01 1 0.0000 0.987 1.00 0 0.00 0.00
#> TCGA.AD.6888.01 3 0.0000 0.993 0.00 0 1.00 0.00
#> TCGA.CM.6678.01 1 0.2011 0.896 0.92 0 0.08 0.00
#> TCGA.CM.5344.01 4 0.0000 0.992 0.00 0 0.00 1.00
#> TCGA.AA.3495.11 2 0.0000 1.000 0.00 1 0.00 0.00
#> TCGA.AG.A01W.11 2 0.0000 1.000 0.00 1 0.00 0.00
#> TCGA.F4.6809.01 3 0.0000 0.993 0.00 0 1.00 0.00
#> TCGA.CK.5914.01 1 0.0000 0.987 1.00 0 0.00 0.00
#> TCGA.AZ.4681.01 4 0.0000 0.992 0.00 0 0.00 1.00
#> TCGA.AA.3492.01 1 0.0000 0.987 1.00 0 0.00 0.00
#> TCGA.D5.6536.01 3 0.0000 0.993 0.00 0 1.00 0.00
#> TCGA.AA.3506.11 2 0.0000 1.000 0.00 1 0.00 0.00
#> TCGA.AA.3488.01 3 0.0000 0.993 0.00 0 1.00 0.00
#> TCGA.AA.3502.11 2 0.0000 1.000 0.00 1 0.00 0.00
#> TCGA.A6.6140.01 4 0.0000 0.992 0.00 0 0.00 1.00
#> TCGA.D5.6529.01 3 0.0000 0.993 0.00 0 1.00 0.00
#> TCGA.DM.A1D0.01 4 0.0000 0.992 0.00 0 0.00 1.00
#> TCGA.DM.A1HB.01 1 0.0000 0.987 1.00 0 0.00 0.00
#> TCGA.D5.6920.01 3 0.0000 0.993 0.00 0 1.00 0.00
#> TCGA.D5.6922.01 3 0.0000 0.993 0.00 0 1.00 0.00
#> TCGA.EI.6508.01 1 0.0000 0.987 1.00 0 0.00 0.00
#> TCGA.D5.6532.01 1 0.0000 0.987 1.00 0 0.00 0.00
#> TCGA.5M.AATA.01 3 0.0000 0.993 0.00 0 1.00 0.00
#> TCGA.EI.6509.01 4 0.0000 0.992 0.00 0 0.00 1.00
#> TCGA.G4.6311.01 3 0.0000 0.993 0.00 0 1.00 0.00
#> TCGA.A6.A566.01 3 0.0000 0.993 0.00 0 1.00 0.00
#> TCGA.G4.6625.01 3 0.0000 0.993 0.00 0 1.00 0.00
#> TCGA.CI.6619.01 4 0.0000 0.992 0.00 0 0.00 1.00
#> TCGA.F5.6864.01 3 0.0000 0.993 0.00 0 1.00 0.00
#> TCGA.AA.3492.11 2 0.0000 1.000 0.00 1 0.00 0.00
#> TCGA.A6.5659.01 1 0.0000 0.987 1.00 0 0.00 0.00
#> TCGA.WS.AB45.01 4 0.0000 0.992 0.00 0 0.00 1.00
#> TCGA.G4.6315.01 3 0.0000 0.993 0.00 0 1.00 0.00
#> TCGA.D5.6541.01 3 0.0000 0.993 0.00 0 1.00 0.00
#> TCGA.A6.2680.01 1 0.0000 0.987 1.00 0 0.00 0.00
#> TCGA.CM.4751.01 3 0.0000 0.993 0.00 0 1.00 0.00
#> TCGA.CM.6680.01 1 0.0000 0.987 1.00 0 0.00 0.00
#> TCGA.AF.6136.01 3 0.0000 0.993 0.00 0 1.00 0.00
#> TCGA.AA.3660.01 1 0.0000 0.987 1.00 0 0.00 0.00
#> TCGA.CM.4747.01 1 0.0000 0.987 1.00 0 0.00 0.00
#> TCGA.EF.5831.01 1 0.0000 0.987 1.00 0 0.00 0.00
#> TCGA.DM.A28G.01 1 0.0000 0.987 1.00 0 0.00 0.00
#> TCGA.G4.6297.01 3 0.0000 0.993 0.00 0 1.00 0.00
#> TCGA.A6.2682.11 2 0.0000 1.000 0.00 1 0.00 0.00
#> TCGA.D5.6537.01 1 0.0000 0.987 1.00 0 0.00 0.00
#> TCGA.CM.6170.01 3 0.0000 0.993 0.00 0 1.00 0.00
#> TCGA.DY.A1DD.01 1 0.0000 0.987 1.00 0 0.00 0.00
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> TCGA.AF.3911.01 3 0.2280 0.7807 0.00 0.00 0.88 0.00 0.12
#> TCGA.F4.6459.01 3 0.2280 0.7807 0.00 0.00 0.88 0.00 0.12
#> TCGA.AA.3494.11 2 0.0000 0.9764 0.00 1.00 0.00 0.00 0.00
#> TCGA.3L.AA1B.01 5 0.4287 0.1864 0.00 0.00 0.46 0.00 0.54
#> TCGA.D5.5538.01 5 0.2280 0.8300 0.00 0.00 0.12 0.00 0.88
#> TCGA.F4.6854.01 5 0.0609 0.8403 0.00 0.00 0.02 0.00 0.98
#> TCGA.AG.A026.01 1 0.0000 0.9474 1.00 0.00 0.00 0.00 0.00
#> TCGA.G4.6303.01 5 0.2516 0.8041 0.14 0.00 0.00 0.00 0.86
#> TCGA.F5.6464.01 3 0.1410 0.7685 0.00 0.00 0.94 0.06 0.00
#> TCGA.T9.A92H.01 5 0.0609 0.8365 0.02 0.00 0.00 0.00 0.98
#> TCGA.AA.3712.11 2 0.0000 0.9764 0.00 1.00 0.00 0.00 0.00
#> TCGA.CM.5863.01 3 0.0609 0.7939 0.00 0.00 0.98 0.00 0.02
#> TCGA.AZ.4308.01 4 0.3424 0.7462 0.00 0.00 0.24 0.76 0.00
#> TCGA.AD.6965.01 1 0.0000 0.9474 1.00 0.00 0.00 0.00 0.00
#> TCGA.A6.2681.11 2 0.0000 0.9764 0.00 1.00 0.00 0.00 0.00
#> TCGA.AD.6548.01 5 0.3684 0.6528 0.00 0.00 0.28 0.00 0.72
#> TCGA.A6.5660.01 1 0.0000 0.9474 1.00 0.00 0.00 0.00 0.00
#> TCGA.AZ.6600.01 5 0.2280 0.8300 0.00 0.00 0.12 0.00 0.88
#> TCGA.F4.6808.01 3 0.2732 0.7753 0.00 0.00 0.84 0.00 0.16
#> TCGA.D5.6540.01 1 0.0609 0.9398 0.98 0.00 0.00 0.00 0.02
#> TCGA.F5.6571.01 5 0.1732 0.8367 0.08 0.00 0.00 0.00 0.92
#> TCGA.D5.6926.01 5 0.3684 0.4738 0.00 0.00 0.28 0.00 0.72
#> TCGA.CM.4748.01 3 0.0000 0.7942 0.00 0.00 1.00 0.00 0.00
#> TCGA.A6.2675.11 2 0.0000 0.9764 0.00 1.00 0.00 0.00 0.00
#> TCGA.5M.AATE.01 3 0.4227 0.4656 0.00 0.00 0.58 0.00 0.42
#> TCGA.D5.5541.01 4 0.3796 0.6948 0.00 0.00 0.30 0.70 0.00
#> TCGA.CM.5862.01 1 0.2280 0.8638 0.88 0.00 0.00 0.00 0.12
#> TCGA.AA.3511.01 3 0.1732 0.7931 0.00 0.00 0.92 0.00 0.08
#> TCGA.AA.3663.11 2 0.0000 0.9764 0.00 1.00 0.00 0.00 0.00
#> TCGA.CI.6622.01 5 0.1043 0.8431 0.04 0.00 0.00 0.00 0.96
#> TCGA.EI.6506.01 3 0.0000 0.7942 0.00 0.00 1.00 0.00 0.00
#> TCGA.AM.5821.01 5 0.2280 0.8300 0.00 0.00 0.12 0.00 0.88
#> TCGA.F5.6812.01 4 0.0000 0.8733 0.00 0.00 0.00 1.00 0.00
#> TCGA.G4.6588.01 1 0.1732 0.9047 0.92 0.00 0.00 0.00 0.08
#> TCGA.EI.6512.01 1 0.0609 0.9398 0.98 0.00 0.00 0.00 0.02
#> TCGA.A6.6648.01 4 0.0000 0.8733 0.00 0.00 0.00 1.00 0.00
#> TCGA.A6.2671.11 2 0.0000 0.9764 0.00 1.00 0.00 0.00 0.00
#> TCGA.NH.A6GC.01 5 0.0000 0.8368 0.00 0.00 0.00 0.00 1.00
#> TCGA.F4.6805.01 4 0.3895 0.6725 0.00 0.00 0.32 0.68 0.00
#> TCGA.AA.3697.01 3 0.3983 0.6058 0.00 0.00 0.66 0.00 0.34
#> TCGA.QG.A5YX.01 1 0.3274 0.7499 0.78 0.00 0.00 0.00 0.22
#> TCGA.DM.A28C.01 5 0.1732 0.7957 0.00 0.00 0.08 0.00 0.92
#> TCGA.AG.A036.01 5 0.0609 0.8418 0.02 0.00 0.00 0.00 0.98
#> TCGA.AZ.6606.01 1 0.0000 0.9474 1.00 0.00 0.00 0.00 0.00
#> TCGA.F4.6570.01 1 0.3274 0.7287 0.78 0.00 0.00 0.00 0.22
#> TCGA.DC.4745.01 3 0.2280 0.7807 0.00 0.00 0.88 0.00 0.12
#> TCGA.AF.A56K.01 4 0.0000 0.8733 0.00 0.00 0.00 1.00 0.00
#> TCGA.G4.6627.01 4 0.0000 0.8733 0.00 0.00 0.00 1.00 0.00
#> TCGA.A6.5657.01 3 0.1410 0.7685 0.00 0.00 0.94 0.06 0.00
#> TCGA.A6.5662.01 3 0.2280 0.7807 0.00 0.00 0.88 0.00 0.12
#> TCGA.AA.3509.01 5 0.0609 0.8365 0.02 0.00 0.00 0.00 0.98
#> TCGA.D5.6929.01 4 0.3895 0.6725 0.00 0.00 0.32 0.68 0.00
#> TCGA.CM.6679.01 3 0.0609 0.7964 0.00 0.00 0.98 0.00 0.02
#> TCGA.A6.2680.11 2 0.0000 0.9764 0.00 1.00 0.00 0.00 0.00
#> TCGA.DC.6157.01 4 0.0000 0.8733 0.00 0.00 0.00 1.00 0.00
#> TCGA.AF.6655.01 4 0.0000 0.8733 0.00 0.00 0.00 1.00 0.00
#> TCGA.CM.6161.01 5 0.0609 0.8296 0.00 0.00 0.02 0.00 0.98
#> TCGA.EI.6883.01 1 0.0000 0.9474 1.00 0.00 0.00 0.00 0.00
#> TCGA.F5.6811.01 5 0.0609 0.8418 0.02 0.00 0.00 0.00 0.98
#> TCGA.D5.6930.01 3 0.4182 0.3299 0.00 0.00 0.60 0.00 0.40
#> TCGA.CM.6164.01 4 0.3895 0.6725 0.00 0.00 0.32 0.68 0.00
#> TCGA.AF.2687.01 4 0.0000 0.8733 0.00 0.00 0.00 1.00 0.00
#> TCGA.DY.A1H8.01 5 0.1410 0.8071 0.00 0.00 0.06 0.00 0.94
#> TCGA.G5.6641.01 5 0.3109 0.6537 0.00 0.00 0.20 0.00 0.80
#> TCGA.DC.6155.01 3 0.1732 0.7931 0.00 0.00 0.92 0.00 0.08
#> TCGA.RU.A8FL.01 5 0.2516 0.8041 0.14 0.00 0.00 0.00 0.86
#> TCGA.CK.4951.01 5 0.2280 0.8300 0.00 0.00 0.12 0.00 0.88
#> TCGA.F4.6704.01 4 0.0000 0.8733 0.00 0.00 0.00 1.00 0.00
#> TCGA.AZ.6599.01 1 0.0000 0.9474 1.00 0.00 0.00 0.00 0.00
#> TCGA.F5.6861.01 3 0.1410 0.7857 0.00 0.00 0.94 0.00 0.06
#> TCGA.CM.5860.01 1 0.1732 0.9047 0.92 0.00 0.00 0.00 0.08
#> TCGA.A6.6780.01 1 0.1732 0.9047 0.92 0.00 0.00 0.00 0.08
#> TCGA.A6.2686.01 5 0.4060 0.4640 0.36 0.00 0.00 0.00 0.64
#> TCGA.CM.4750.01 1 0.1732 0.9047 0.92 0.00 0.00 0.00 0.08
#> TCGA.CM.6677.01 1 0.1732 0.9047 0.92 0.00 0.00 0.00 0.08
#> TCGA.A6.A567.01 4 0.0000 0.8733 0.00 0.00 0.00 1.00 0.00
#> TCGA.F5.6814.01 1 0.0000 0.9474 1.00 0.00 0.00 0.00 0.00
#> TCGA.D5.6898.01 3 0.2280 0.7807 0.00 0.00 0.88 0.00 0.12
#> TCGA.AG.A01W.01 5 0.1410 0.8407 0.00 0.00 0.06 0.00 0.94
#> TCGA.AZ.6598.11 2 0.0000 0.9764 0.00 1.00 0.00 0.00 0.00
#> TCGA.F5.6813.01 3 0.1732 0.7931 0.00 0.00 0.92 0.00 0.08
#> TCGA.AG.3732.01 4 0.4262 0.4154 0.00 0.00 0.44 0.56 0.00
#> TCGA.EI.6885.01 4 0.0000 0.8733 0.00 0.00 0.00 1.00 0.00
#> TCGA.G4.6299.01 5 0.2280 0.8228 0.12 0.00 0.00 0.00 0.88
#> TCGA.A6.4105.01 1 0.1732 0.9047 0.92 0.00 0.00 0.00 0.08
#> TCGA.DM.A1D8.01 1 0.0000 0.9474 1.00 0.00 0.00 0.00 0.00
#> TCGA.DM.A285.01 3 0.3983 0.4731 0.00 0.00 0.66 0.00 0.34
#> TCGA.G4.6295.11 2 0.0000 0.9764 0.00 1.00 0.00 0.00 0.00
#> TCGA.DC.4749.01 3 0.3291 0.7083 0.00 0.00 0.84 0.12 0.04
#> TCGA.DT.5265.01 5 0.2280 0.8228 0.12 0.00 0.00 0.00 0.88
#> TCGA.5M.AAT5.01 4 0.0000 0.8733 0.00 0.00 0.00 1.00 0.00
#> TCGA.DM.A0XD.01 5 0.2280 0.8228 0.12 0.00 0.00 0.00 0.88
#> TCGA.A6.6138.01 5 0.2280 0.8228 0.12 0.00 0.00 0.00 0.88
#> TCGA.D5.7000.01 1 0.1732 0.9047 0.92 0.00 0.00 0.00 0.08
#> TCGA.DM.A28F.01 1 0.4287 0.1425 0.54 0.00 0.00 0.00 0.46
#> TCGA.DY.A1DE.01 3 0.1732 0.7931 0.00 0.00 0.92 0.00 0.08
#> TCGA.A6.6142.01 2 0.4060 0.5342 0.00 0.64 0.00 0.36 0.00
#> TCGA.QL.A97D.01 5 0.0000 0.8368 0.00 0.00 0.00 0.00 1.00
#> TCGA.CK.6748.01 3 0.2516 0.7801 0.00 0.00 0.86 0.00 0.14
#> TCGA.DC.6160.01 4 0.3895 0.6725 0.00 0.00 0.32 0.68 0.00
#> TCGA.D5.6534.01 3 0.2516 0.6829 0.00 0.00 0.86 0.14 0.00
#> TCGA.AZ.4616.01 5 0.2280 0.8300 0.00 0.00 0.12 0.00 0.88
#> TCGA.CK.6751.01 1 0.0609 0.9398 0.98 0.00 0.00 0.00 0.02
#> TCGA.CM.6171.01 1 0.0000 0.9474 1.00 0.00 0.00 0.00 0.00
#> TCGA.DM.A1DA.01 1 0.0000 0.9474 1.00 0.00 0.00 0.00 0.00
#> TCGA.AG.A020.11 2 0.0000 0.9764 0.00 1.00 0.00 0.00 0.00
#> TCGA.G4.6311.11 2 0.0000 0.9764 0.00 1.00 0.00 0.00 0.00
#> TCGA.G4.6625.11 2 0.0000 0.9764 0.00 1.00 0.00 0.00 0.00
#> TCGA.F5.6863.01 3 0.4287 -0.1053 0.00 0.00 0.54 0.46 0.00
#> TCGA.G4.6317.02 3 0.2754 0.7708 0.00 0.00 0.88 0.04 0.08
#> TCGA.G4.6317.01 3 0.4302 0.3195 0.00 0.00 0.52 0.00 0.48
#> TCGA.DM.A1D4.01 1 0.0000 0.9474 1.00 0.00 0.00 0.00 0.00
#> TCGA.AG.A01Y.11 2 0.0000 0.9764 0.00 1.00 0.00 0.00 0.00
#> TCGA.D5.6530.01 5 0.2020 0.7612 0.00 0.00 0.10 0.00 0.90
#> TCGA.CK.4948.01 4 0.0609 0.8662 0.00 0.00 0.02 0.98 0.00
#> TCGA.AD.A5EJ.01 1 0.0000 0.9474 1.00 0.00 0.00 0.00 0.00
#> TCGA.A6.6651.01 4 0.0000 0.8733 0.00 0.00 0.00 1.00 0.00
#> TCGA.CA.5256.01 5 0.0000 0.8368 0.00 0.00 0.00 0.00 1.00
#> TCGA.DM.A0X9.01 1 0.0000 0.9474 1.00 0.00 0.00 0.00 0.00
#> TCGA.AY.A69D.01 5 0.2732 0.7964 0.16 0.00 0.00 0.00 0.84
#> TCGA.G4.6626.01 3 0.2516 0.7800 0.00 0.00 0.86 0.00 0.14
#> TCGA.CA.6716.01 1 0.0000 0.9474 1.00 0.00 0.00 0.00 0.00
#> TCGA.A6.2682.01 3 0.0000 0.7942 0.00 0.00 1.00 0.00 0.00
#> TCGA.A6.4107.11 2 0.0000 0.9764 0.00 1.00 0.00 0.00 0.00
#> TCGA.CA.6717.01 3 0.1410 0.7857 0.00 0.00 0.94 0.00 0.06
#> TCGA.G4.6293.01 5 0.2280 0.8300 0.00 0.00 0.12 0.00 0.88
#> TCGA.CK.5916.01 5 0.2280 0.8228 0.12 0.00 0.00 0.00 0.88
#> TCGA.G4.6309.01 4 0.0000 0.8733 0.00 0.00 0.00 1.00 0.00
#> TCGA.AA.3662.01 5 0.0609 0.8296 0.00 0.00 0.02 0.00 0.98
#> TCGA.AF.A56L.01 3 0.0000 0.7942 0.00 0.00 1.00 0.00 0.00
#> TCGA.NH.A6GB.01 1 0.4307 -0.0127 0.50 0.00 0.00 0.00 0.50
#> TCGA.AD.5900.01 5 0.2280 0.8300 0.00 0.00 0.12 0.00 0.88
#> TCGA.NH.A50U.01 1 0.1410 0.9177 0.94 0.00 0.00 0.00 0.06
#> TCGA.AA.3712.01 3 0.2020 0.7881 0.00 0.00 0.90 0.00 0.10
#> TCGA.AZ.4614.01 1 0.0000 0.9474 1.00 0.00 0.00 0.00 0.00
#> TCGA.AH.6644.01 5 0.2516 0.8109 0.14 0.00 0.00 0.00 0.86
#> TCGA.AZ.6607.01 5 0.2280 0.8300 0.00 0.00 0.12 0.00 0.88
#> TCGA.AF.2693.01 3 0.3983 0.3277 0.00 0.00 0.66 0.34 0.00
#> TCGA.D5.6924.01 3 0.4227 0.4649 0.00 0.00 0.58 0.00 0.42
#> TCGA.CM.5868.01 4 0.3796 0.6948 0.00 0.00 0.30 0.70 0.00
#> TCGA.AF.4110.01 4 0.3895 0.6725 0.00 0.00 0.32 0.68 0.00
#> TCGA.A6.3809.01 1 0.1732 0.9047 0.92 0.00 0.00 0.00 0.08
#> TCGA.AZ.4313.01 4 0.0000 0.8733 0.00 0.00 0.00 1.00 0.00
#> TCGA.A6.2675.01 4 0.0000 0.8733 0.00 0.00 0.00 1.00 0.00
#> TCGA.AZ.6608.01 3 0.2280 0.7807 0.00 0.00 0.88 0.00 0.12
#> TCGA.CM.5864.01 1 0.0000 0.9474 1.00 0.00 0.00 0.00 0.00
#> TCGA.AA.3494.01 4 0.0000 0.8733 0.00 0.00 0.00 1.00 0.00
#> TCGA.AD.6895.01 5 0.2280 0.8300 0.00 0.00 0.12 0.00 0.88
#> TCGA.CI.6620.01 5 0.2516 0.8177 0.00 0.00 0.14 0.00 0.86
#> TCGA.DC.6156.01 5 0.3684 0.6528 0.00 0.00 0.28 0.00 0.72
#> TCGA.D5.6931.01 3 0.4060 0.4320 0.00 0.00 0.64 0.00 0.36
#> TCGA.CM.6165.01 5 0.0000 0.8368 0.00 0.00 0.00 0.00 1.00
#> TCGA.CM.5861.01 1 0.0000 0.9474 1.00 0.00 0.00 0.00 0.00
#> TCGA.A6.2671.01 5 0.0609 0.8303 0.00 0.00 0.02 0.00 0.98
#> TCGA.DC.6158.01 3 0.1732 0.7931 0.00 0.00 0.92 0.00 0.08
#> TCGA.AG.3742.01 1 0.0000 0.9474 1.00 0.00 0.00 0.00 0.00
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#> TCGA.AD.6964.01 2 0.3796 0.6391 0.00 0.70 0.00 0.30 0.00
#> TCGA.SS.A7HO.01 5 0.3983 0.5109 0.34 0.00 0.00 0.00 0.66
#> TCGA.A6.6650.01 1 0.0000 0.9474 1.00 0.00 0.00 0.00 0.00
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#> TCGA.G4.6295.01 4 0.3274 0.7611 0.00 0.00 0.22 0.78 0.00
#> TCGA.F4.6461.01 5 0.2280 0.8228 0.12 0.00 0.00 0.00 0.88
#> TCGA.AM.5820.01 5 0.1043 0.8214 0.00 0.00 0.04 0.00 0.96
#> TCGA.G4.6314.11 2 0.0000 0.9764 0.00 1.00 0.00 0.00 0.00
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#> TCGA.AD.6899.01 5 0.2280 0.8228 0.12 0.00 0.00 0.00 0.88
#> TCGA.A6.5667.11 2 0.0000 0.9764 0.00 1.00 0.00 0.00 0.00
#> TCGA.A6.A56B.01 1 0.1732 0.9047 0.92 0.00 0.00 0.00 0.08
#> TCGA.G5.6572.01 3 0.4126 0.2051 0.00 0.00 0.62 0.38 0.00
#> TCGA.DM.A280.01 3 0.1410 0.7685 0.00 0.00 0.94 0.06 0.00
#> TCGA.AG.A020.01 3 0.2280 0.7807 0.00 0.00 0.88 0.00 0.12
#> TCGA.AA.3713.01 3 0.4060 0.4320 0.00 0.00 0.64 0.00 0.36
#> TCGA.D5.5539.01 5 0.1732 0.8367 0.08 0.00 0.00 0.00 0.92
#> TCGA.AA.3655.11 2 0.0000 0.9764 0.00 1.00 0.00 0.00 0.00
#> TCGA.AA.3489.01 4 0.3796 0.6948 0.00 0.00 0.30 0.70 0.00
#> TCGA.AA.3495.01 5 0.2280 0.8300 0.00 0.00 0.12 0.00 0.88
#> TCGA.AG.A01Y.01 4 0.0609 0.8663 0.00 0.00 0.02 0.98 0.00
#> TCGA.AZ.6601.01 5 0.4182 0.3842 0.00 0.00 0.40 0.00 0.60
#> TCGA.AH.6903.01 3 0.4126 0.4574 0.00 0.00 0.62 0.00 0.38
#> TCGA.AZ.6603.01 4 0.3895 0.6725 0.00 0.00 0.32 0.68 0.00
#> TCGA.CA.5254.01 1 0.0000 0.9474 1.00 0.00 0.00 0.00 0.00
#> TCGA.A6.A5ZU.01 5 0.3796 0.4455 0.00 0.00 0.30 0.00 0.70
#> TCGA.G4.6302.01 4 0.0000 0.8733 0.00 0.00 0.00 1.00 0.00
#> TCGA.AZ.5403.01 2 0.4060 0.5342 0.00 0.64 0.00 0.36 0.00
#> TCGA.AY.A54L.01 1 0.0000 0.9474 1.00 0.00 0.00 0.00 0.00
#> TCGA.A6.4107.01 1 0.0000 0.9474 1.00 0.00 0.00 0.00 0.00
#> TCGA.NH.A5IV.01 1 0.0609 0.9398 0.98 0.00 0.00 0.00 0.02
#> TCGA.G4.6306.01 1 0.0000 0.9474 1.00 0.00 0.00 0.00 0.00
#> TCGA.AD.A5EK.01 1 0.0000 0.9474 1.00 0.00 0.00 0.00 0.00
#> TCGA.G5.6235.01 4 0.3895 0.6725 0.00 0.00 0.32 0.68 0.00
#> TCGA.DC.5337.01 5 0.2929 0.7775 0.18 0.00 0.00 0.00 0.82
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#> TCGA.CI.6621.01 4 0.0000 0.8733 0.00 0.00 0.00 1.00 0.00
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#> TCGA.DM.A1DB.01 3 0.2280 0.7807 0.00 0.00 0.88 0.00 0.12
#> TCGA.A6.6654.01 3 0.1648 0.7781 0.00 0.00 0.94 0.04 0.02
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#> TCGA.CK.5912.01 3 0.2280 0.7807 0.00 0.00 0.88 0.00 0.12
#> TCGA.F4.6857.01 3 0.2516 0.6829 0.00 0.00 0.86 0.14 0.00
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#> TCGA.CL.5917.01 3 0.3109 0.7584 0.00 0.00 0.80 0.00 0.20
#> TCGA.AU.6004.01 3 0.1410 0.7857 0.00 0.00 0.94 0.00 0.06
#> TCGA.AY.5543.01 5 0.3983 0.2765 0.00 0.00 0.34 0.00 0.66
#> TCGA.AG.3731.01 3 0.1410 0.7857 0.00 0.00 0.94 0.00 0.06
#> TCGA.G4.6314.01 3 0.1043 0.7912 0.00 0.00 0.96 0.00 0.04
#> TCGA.DC.6683.01 5 0.1410 0.8018 0.00 0.00 0.06 0.00 0.94
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#> TCGA.NH.A8F8.01 5 0.2280 0.8300 0.00 0.00 0.12 0.00 0.88
#> TCGA.AF.A56N.01 3 0.4307 0.2577 0.00 0.00 0.50 0.00 0.50
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#> TCGA.QG.A5Z2.01 1 0.1732 0.9047 0.92 0.00 0.00 0.00 0.08
#> TCGA.A6.2684.01 3 0.3274 0.6572 0.00 0.00 0.78 0.00 0.22
#> TCGA.CK.5915.01 1 0.0000 0.9474 1.00 0.00 0.00 0.00 0.00
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#> TCGA.A6.3810.01 4 0.0000 0.8733 0.00 0.00 0.00 1.00 0.00
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#> TCGA.G4.6297.11 2 0.0000 0.9764 0.00 1.00 0.00 0.00 0.00
#> TCGA.AZ.4615.01 5 0.2280 0.8300 0.00 0.00 0.12 0.00 0.88
#> TCGA.CK.4952.01 1 0.0000 0.9474 1.00 0.00 0.00 0.00 0.00
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#> TCGA.QG.A5Z1.01 1 0.0000 0.9474 1.00 0.00 0.00 0.00 0.00
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#> TCGA.AF.2690.01 4 0.3895 0.6725 0.00 0.00 0.32 0.68 0.00
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#> TCGA.NH.A8F7.06 3 0.2280 0.7807 0.00 0.00 0.88 0.00 0.12
#> TCGA.NH.A8F7.01 3 0.2797 0.7614 0.00 0.00 0.88 0.06 0.06
#> TCGA.AZ.6600.11 2 0.0000 0.9764 0.00 1.00 0.00 0.00 0.00
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#> TCGA.CK.4947.01 5 0.2280 0.8300 0.00 0.00 0.12 0.00 0.88
#> TCGA.D5.5540.01 1 0.0000 0.9474 1.00 0.00 0.00 0.00 0.00
#> TCGA.DC.6682.01 5 0.2280 0.8300 0.00 0.00 0.12 0.00 0.88
#> TCGA.G4.6321.01 5 0.3684 0.6528 0.00 0.00 0.28 0.00 0.72
#> TCGA.A6.6649.01 5 0.2280 0.8300 0.00 0.00 0.12 0.00 0.88
#> TCGA.CM.5348.01 3 0.4060 0.4320 0.00 0.00 0.64 0.00 0.36
#> TCGA.EI.6513.01 4 0.0000 0.8733 0.00 0.00 0.00 1.00 0.00
#> TCGA.A6.2672.01 5 0.4302 0.0780 0.48 0.00 0.00 0.00 0.52
#> TCGA.D5.6539.01 4 0.0000 0.8733 0.00 0.00 0.00 1.00 0.00
#> TCGA.AA.3510.01 3 0.0609 0.7964 0.00 0.00 0.98 0.00 0.02
#> TCGA.G5.6233.01 5 0.2280 0.8228 0.12 0.00 0.00 0.00 0.88
#> TCGA.BM.6198.01 4 0.3109 0.7741 0.00 0.00 0.20 0.80 0.00
#> TCGA.CA.6719.01 1 0.0609 0.9398 0.98 0.00 0.00 0.00 0.02
#> TCGA.DC.6154.01 5 0.1410 0.8071 0.00 0.00 0.06 0.00 0.94
#> TCGA.DM.A1D6.01 5 0.1410 0.8071 0.00 0.00 0.06 0.00 0.94
#> TCGA.AG.3731.11 2 0.0000 0.9764 0.00 1.00 0.00 0.00 0.00
#> TCGA.CM.6674.01 4 0.0000 0.8733 0.00 0.00 0.00 1.00 0.00
#> TCGA.CM.4743.01 3 0.1410 0.7685 0.00 0.00 0.94 0.06 0.00
#> TCGA.F5.6465.01 4 0.3895 0.6725 0.00 0.00 0.32 0.68 0.00
#> TCGA.D5.5537.01 1 0.0000 0.9474 1.00 0.00 0.00 0.00 0.00
#> TCGA.F4.6463.01 3 0.4060 0.4320 0.00 0.00 0.64 0.00 0.36
#> TCGA.A6.2686.11 2 0.0000 0.9764 0.00 1.00 0.00 0.00 0.00
#> TCGA.4T.AA8H.01 1 0.0000 0.9474 1.00 0.00 0.00 0.00 0.00
#> TCGA.A6.6782.01 5 0.2280 0.7371 0.00 0.00 0.12 0.00 0.88
#> TCGA.AG.3592.01 1 0.1732 0.9047 0.92 0.00 0.00 0.00 0.08
#> TCGA.AD.6888.01 3 0.1732 0.7931 0.00 0.00 0.92 0.00 0.08
#> TCGA.CM.6678.01 5 0.1732 0.8367 0.08 0.00 0.00 0.00 0.92
#> TCGA.CM.5344.01 4 0.3684 0.7131 0.00 0.00 0.28 0.72 0.00
#> TCGA.AA.3495.11 2 0.0000 0.9764 0.00 1.00 0.00 0.00 0.00
#> TCGA.AG.A01W.11 2 0.0000 0.9764 0.00 1.00 0.00 0.00 0.00
#> TCGA.F4.6809.01 3 0.4060 0.4320 0.00 0.00 0.64 0.00 0.36
#> TCGA.CK.5914.01 1 0.0000 0.9474 1.00 0.00 0.00 0.00 0.00
#> TCGA.AZ.4681.01 4 0.3796 0.6948 0.00 0.00 0.30 0.70 0.00
#> TCGA.AA.3492.01 1 0.0000 0.9474 1.00 0.00 0.00 0.00 0.00
#> TCGA.D5.6536.01 3 0.1043 0.7967 0.00 0.00 0.96 0.00 0.04
#> TCGA.AA.3506.11 2 0.0000 0.9764 0.00 1.00 0.00 0.00 0.00
#> TCGA.AA.3488.01 5 0.4126 0.1966 0.00 0.00 0.38 0.00 0.62
#> TCGA.AA.3502.11 2 0.0000 0.9764 0.00 1.00 0.00 0.00 0.00
#> TCGA.A6.6140.01 4 0.0000 0.8733 0.00 0.00 0.00 1.00 0.00
#> TCGA.D5.6529.01 3 0.4060 0.4320 0.00 0.00 0.64 0.00 0.36
#> TCGA.DM.A1D0.01 4 0.0000 0.8733 0.00 0.00 0.00 1.00 0.00
#> TCGA.DM.A1HB.01 1 0.1732 0.9047 0.92 0.00 0.00 0.00 0.08
#> TCGA.D5.6920.01 3 0.1043 0.7912 0.00 0.00 0.96 0.00 0.04
#> TCGA.D5.6922.01 3 0.4227 0.4649 0.00 0.00 0.58 0.00 0.42
#> TCGA.EI.6508.01 5 0.2929 0.7775 0.18 0.00 0.00 0.00 0.82
#> TCGA.D5.6532.01 1 0.2929 0.7886 0.82 0.00 0.00 0.00 0.18
#> TCGA.5M.AATA.01 3 0.0000 0.7942 0.00 0.00 1.00 0.00 0.00
#> TCGA.EI.6509.01 4 0.0000 0.8733 0.00 0.00 0.00 1.00 0.00
#> TCGA.G4.6311.01 3 0.0000 0.7942 0.00 0.00 1.00 0.00 0.00
#> TCGA.A6.A566.01 3 0.4126 0.3832 0.00 0.00 0.62 0.00 0.38
#> TCGA.G4.6625.01 3 0.0000 0.7942 0.00 0.00 1.00 0.00 0.00
#> TCGA.CI.6619.01 4 0.0000 0.8733 0.00 0.00 0.00 1.00 0.00
#> TCGA.F5.6864.01 3 0.2280 0.7807 0.00 0.00 0.88 0.00 0.12
#> TCGA.AA.3492.11 2 0.0000 0.9764 0.00 1.00 0.00 0.00 0.00
#> TCGA.A6.5659.01 1 0.0000 0.9474 1.00 0.00 0.00 0.00 0.00
#> TCGA.WS.AB45.01 4 0.0000 0.8733 0.00 0.00 0.00 1.00 0.00
#> TCGA.G4.6315.01 3 0.0000 0.7942 0.00 0.00 1.00 0.00 0.00
#> TCGA.D5.6541.01 3 0.4060 0.4320 0.00 0.00 0.64 0.00 0.36
#> TCGA.A6.2680.01 5 0.2516 0.8109 0.14 0.00 0.00 0.00 0.86
#> TCGA.CM.4751.01 5 0.3684 0.6528 0.00 0.00 0.28 0.00 0.72
#> TCGA.CM.6680.01 1 0.3895 0.5392 0.68 0.00 0.00 0.00 0.32
#> TCGA.AF.6136.01 5 0.0000 0.8368 0.00 0.00 0.00 0.00 1.00
#> TCGA.AA.3660.01 1 0.1732 0.9047 0.92 0.00 0.00 0.00 0.08
#> TCGA.CM.4747.01 5 0.2280 0.8228 0.12 0.00 0.00 0.00 0.88
#> TCGA.EF.5831.01 1 0.0609 0.9398 0.98 0.00 0.00 0.00 0.02
#> TCGA.DM.A28G.01 1 0.0000 0.9474 1.00 0.00 0.00 0.00 0.00
#> TCGA.G4.6297.01 3 0.4126 0.3832 0.00 0.00 0.62 0.00 0.38
#> TCGA.A6.2682.11 2 0.0000 0.9764 0.00 1.00 0.00 0.00 0.00
#> TCGA.D5.6537.01 1 0.0000 0.9474 1.00 0.00 0.00 0.00 0.00
#> TCGA.CM.6170.01 3 0.2280 0.7807 0.00 0.00 0.88 0.00 0.12
#> TCGA.DY.A1DD.01 5 0.3424 0.6809 0.24 0.00 0.00 0.00 0.76
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> TCGA.AF.3911.01 6 0.3156 0.6507 0.00 0.00 0.18 0.00 0.02 0.80
#> TCGA.F4.6459.01 6 0.3592 0.6329 0.00 0.00 0.24 0.00 0.02 0.74
#> TCGA.AA.3494.11 2 0.0000 0.9813 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.3L.AA1B.01 3 0.2260 0.6149 0.00 0.00 0.86 0.00 0.14 0.00
#> TCGA.D5.5538.01 5 0.3309 0.6134 0.00 0.00 0.28 0.00 0.72 0.00
#> TCGA.F4.6854.01 5 0.2941 0.6577 0.00 0.00 0.22 0.00 0.78 0.00
#> TCGA.AG.A026.01 1 0.0000 0.8765 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.G4.6303.01 5 0.2350 0.6890 0.02 0.00 0.00 0.00 0.88 0.10
#> TCGA.F5.6464.01 3 0.4078 0.3893 0.00 0.00 0.64 0.02 0.00 0.34
#> TCGA.T9.A92H.01 5 0.1814 0.6842 0.00 0.00 0.00 0.00 0.90 0.10
#> TCGA.AA.3712.11 2 0.0000 0.9813 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.CM.5863.01 3 0.2631 0.5574 0.00 0.00 0.82 0.00 0.00 0.18
#> TCGA.AZ.4308.01 4 0.4873 0.4956 0.00 0.00 0.06 0.52 0.00 0.42
#> TCGA.AD.6965.01 1 0.0000 0.8765 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.A6.2681.11 2 0.0000 0.9813 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.AD.6548.01 3 0.2260 0.6149 0.00 0.00 0.86 0.00 0.14 0.00
#> TCGA.A6.5660.01 1 0.0000 0.8765 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AZ.6600.01 5 0.3499 0.5705 0.00 0.00 0.32 0.00 0.68 0.00
#> TCGA.F4.6808.01 6 0.4552 0.5697 0.00 0.00 0.30 0.00 0.06 0.64
#> TCGA.D5.6540.01 1 0.3797 0.3216 0.58 0.00 0.00 0.00 0.42 0.00
#> TCGA.F5.6571.01 5 0.2350 0.6873 0.00 0.00 0.02 0.00 0.88 0.10
#> TCGA.D5.6926.01 3 0.5292 0.2782 0.00 0.00 0.60 0.00 0.22 0.18
#> TCGA.CM.4748.01 3 0.2793 0.5617 0.00 0.00 0.80 0.00 0.00 0.20
#> TCGA.A6.2675.11 2 0.0000 0.9813 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.5M.AATE.01 6 0.5364 0.5171 0.00 0.00 0.30 0.00 0.14 0.56
#> TCGA.D5.5541.01 4 0.4892 0.4632 0.00 0.00 0.06 0.50 0.00 0.44
#> TCGA.CM.5862.01 5 0.5195 0.2180 0.36 0.00 0.00 0.00 0.54 0.10
#> TCGA.AA.3511.01 6 0.2941 0.6298 0.00 0.00 0.22 0.00 0.00 0.78
#> TCGA.AA.3663.11 2 0.0000 0.9813 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.CI.6622.01 5 0.1556 0.7023 0.00 0.00 0.08 0.00 0.92 0.00
#> TCGA.EI.6506.01 3 0.3647 0.3858 0.00 0.00 0.64 0.00 0.00 0.36
#> TCGA.AM.5821.01 5 0.3076 0.6475 0.00 0.00 0.24 0.00 0.76 0.00
#> TCGA.F5.6812.01 4 0.0000 0.8046 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.G4.6588.01 5 0.3864 -0.0363 0.48 0.00 0.00 0.00 0.52 0.00
#> TCGA.EI.6512.01 1 0.3756 0.3727 0.60 0.00 0.00 0.00 0.40 0.00
#> TCGA.A6.6648.01 4 0.0000 0.8046 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.A6.2671.11 2 0.0000 0.9813 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.NH.A6GC.01 5 0.1814 0.6842 0.00 0.00 0.00 0.00 0.90 0.10
#> TCGA.F4.6805.01 4 0.5095 0.4723 0.00 0.00 0.08 0.50 0.00 0.42
#> TCGA.AA.3697.01 6 0.5364 0.5119 0.00 0.00 0.30 0.00 0.14 0.56
#> TCGA.QG.A5YX.01 5 0.3985 0.6064 0.14 0.00 0.00 0.00 0.76 0.10
#> TCGA.DM.A28C.01 5 0.5295 -0.0556 0.00 0.00 0.10 0.00 0.46 0.44
#> TCGA.AG.A036.01 5 0.2350 0.6873 0.00 0.00 0.02 0.00 0.88 0.10
#> TCGA.AZ.6606.01 1 0.0000 0.8765 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.F4.6570.01 5 0.3851 0.0358 0.46 0.00 0.00 0.00 0.54 0.00
#> TCGA.DC.4745.01 6 0.3315 0.6471 0.00 0.00 0.20 0.00 0.02 0.78
#> TCGA.AF.A56K.01 4 0.0000 0.8046 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.G4.6627.01 4 0.3544 0.7504 0.00 0.00 0.08 0.80 0.00 0.12
#> TCGA.A6.5657.01 3 0.3499 0.4497 0.00 0.00 0.68 0.00 0.00 0.32
#> TCGA.A6.5662.01 6 0.3156 0.6507 0.00 0.00 0.18 0.00 0.02 0.80
#> TCGA.AA.3509.01 5 0.1814 0.6842 0.00 0.00 0.00 0.00 0.90 0.10
#> TCGA.D5.6929.01 4 0.5095 0.4723 0.00 0.00 0.08 0.50 0.00 0.42
#> TCGA.CM.6679.01 6 0.4199 0.4588 0.00 0.00 0.38 0.00 0.02 0.60
#> TCGA.A6.2680.11 2 0.0000 0.9813 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DC.6157.01 4 0.0000 0.8046 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.AF.6655.01 4 0.0000 0.8046 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.CM.6161.01 5 0.4873 0.4443 0.00 0.00 0.32 0.00 0.60 0.08
#> TCGA.EI.6883.01 1 0.0000 0.8765 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.F5.6811.01 5 0.1814 0.7004 0.00 0.00 0.10 0.00 0.90 0.00
#> TCGA.D5.6930.01 3 0.2260 0.6149 0.00 0.00 0.86 0.00 0.14 0.00
#> TCGA.CM.6164.01 4 0.4902 0.4233 0.00 0.00 0.06 0.48 0.00 0.46
#> TCGA.AF.2687.01 4 0.0000 0.8046 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.DY.A1H8.01 5 0.3797 0.2202 0.00 0.00 0.00 0.00 0.58 0.42
#> TCGA.G5.6641.01 6 0.5769 0.2561 0.00 0.00 0.18 0.00 0.36 0.46
#> TCGA.DC.6155.01 6 0.3819 0.6063 0.00 0.00 0.28 0.00 0.02 0.70
#> TCGA.RU.A8FL.01 5 0.2350 0.6890 0.02 0.00 0.00 0.00 0.88 0.10
#> TCGA.CK.4951.01 5 0.3499 0.5705 0.00 0.00 0.32 0.00 0.68 0.00
#> TCGA.F4.6704.01 4 0.0000 0.8046 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.AZ.6599.01 1 0.0000 0.8765 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.F5.6861.01 3 0.2581 0.6146 0.00 0.00 0.86 0.00 0.02 0.12
#> TCGA.CM.5860.01 5 0.3864 -0.0363 0.48 0.00 0.00 0.00 0.52 0.00
#> TCGA.A6.6780.01 5 0.3864 -0.0363 0.48 0.00 0.00 0.00 0.52 0.00
#> TCGA.A6.2686.01 5 0.3544 0.6732 0.12 0.00 0.08 0.00 0.80 0.00
#> TCGA.CM.4750.01 1 0.3864 0.1452 0.52 0.00 0.00 0.00 0.48 0.00
#> TCGA.CM.6677.01 5 0.3864 -0.0363 0.48 0.00 0.00 0.00 0.52 0.00
#> TCGA.A6.A567.01 4 0.0000 0.8046 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.F5.6814.01 1 0.0000 0.8765 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D5.6898.01 6 0.3592 0.6329 0.00 0.00 0.24 0.00 0.02 0.74
#> TCGA.AG.A01W.01 5 0.2941 0.6577 0.00 0.00 0.22 0.00 0.78 0.00
#> TCGA.AZ.6598.11 2 0.0000 0.9813 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.F5.6813.01 6 0.3076 0.6203 0.00 0.00 0.24 0.00 0.00 0.76
#> TCGA.AG.3732.01 6 0.5295 -0.3779 0.00 0.00 0.10 0.44 0.00 0.46
#> TCGA.EI.6885.01 4 0.0000 0.8046 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.G4.6299.01 5 0.2631 0.6805 0.00 0.00 0.18 0.00 0.82 0.00
#> TCGA.A6.4105.01 5 0.3864 -0.0363 0.48 0.00 0.00 0.00 0.52 0.00
#> TCGA.DM.A1D8.01 1 0.0000 0.8765 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DM.A285.01 3 0.1556 0.6394 0.00 0.00 0.92 0.00 0.08 0.00
#> TCGA.G4.6295.11 2 0.0000 0.9813 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DC.4749.01 6 0.2094 0.5875 0.00 0.00 0.08 0.02 0.00 0.90
#> TCGA.DT.5265.01 5 0.2631 0.6805 0.00 0.00 0.18 0.00 0.82 0.00
#> TCGA.5M.AAT5.01 4 0.3409 0.6727 0.00 0.00 0.00 0.70 0.00 0.30
#> TCGA.DM.A0XD.01 5 0.2631 0.6805 0.00 0.00 0.18 0.00 0.82 0.00
#> TCGA.A6.6138.01 5 0.2454 0.6885 0.00 0.00 0.16 0.00 0.84 0.00
#> TCGA.D5.7000.01 5 0.3864 -0.0363 0.48 0.00 0.00 0.00 0.52 0.00
#> TCGA.DM.A28F.01 5 0.3592 0.5382 0.24 0.00 0.00 0.00 0.74 0.02
#> TCGA.DY.A1DE.01 6 0.3198 0.6086 0.00 0.00 0.26 0.00 0.00 0.74
#> TCGA.A6.6142.01 4 0.3851 -0.0788 0.00 0.46 0.00 0.54 0.00 0.00
#> TCGA.QL.A97D.01 5 0.1814 0.7004 0.00 0.00 0.10 0.00 0.90 0.00
#> TCGA.CK.6748.01 6 0.4462 0.5935 0.00 0.00 0.28 0.00 0.06 0.66
#> TCGA.DC.6160.01 6 0.4902 -0.3964 0.00 0.00 0.06 0.46 0.00 0.48
#> TCGA.D5.6534.01 3 0.4938 0.3021 0.00 0.00 0.58 0.08 0.00 0.34
#> TCGA.AZ.4616.01 5 0.3499 0.5705 0.00 0.00 0.32 0.00 0.68 0.00
#> TCGA.CK.6751.01 1 0.3647 0.4592 0.64 0.00 0.00 0.00 0.36 0.00
#> TCGA.CM.6171.01 1 0.0000 0.8765 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DM.A1DA.01 1 0.0000 0.8765 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AG.A020.11 2 0.0000 0.9813 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.G4.6311.11 2 0.0000 0.9813 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.G4.6625.11 2 0.0000 0.9813 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.F5.6863.01 6 0.5364 0.0394 0.00 0.00 0.14 0.30 0.00 0.56
#> TCGA.G4.6317.02 6 0.1814 0.5985 0.00 0.00 0.10 0.00 0.00 0.90
#> TCGA.G4.6317.01 6 0.5102 0.4082 0.00 0.00 0.14 0.00 0.24 0.62
#> TCGA.DM.A1D4.01 1 0.0000 0.8765 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AG.A01Y.11 2 0.0000 0.9813 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.D5.6530.01 3 0.6095 -0.1191 0.00 0.00 0.36 0.00 0.28 0.36
#> TCGA.CK.4948.01 4 0.4094 0.7116 0.00 0.00 0.08 0.74 0.00 0.18
#> TCGA.AD.A5EJ.01 1 0.0000 0.8765 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.A6.6651.01 4 0.0000 0.8046 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.CA.5256.01 5 0.2048 0.6737 0.00 0.00 0.00 0.00 0.88 0.12
#> TCGA.DM.A0X9.01 1 0.0000 0.8765 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AY.A69D.01 5 0.3321 0.6921 0.08 0.00 0.10 0.00 0.82 0.00
#> TCGA.G4.6626.01 6 0.4360 0.6122 0.00 0.00 0.26 0.00 0.06 0.68
#> TCGA.CA.6716.01 1 0.0000 0.8765 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.A6.2682.01 3 0.3647 0.3283 0.00 0.00 0.64 0.00 0.00 0.36
#> TCGA.A6.4107.11 2 0.0000 0.9813 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.CA.6717.01 3 0.2260 0.5935 0.00 0.00 0.86 0.00 0.00 0.14
#> TCGA.G4.6293.01 5 0.3499 0.5705 0.00 0.00 0.32 0.00 0.68 0.00
#> TCGA.CK.5916.01 5 0.2631 0.6805 0.00 0.00 0.18 0.00 0.82 0.00
#> TCGA.G4.6309.01 4 0.0000 0.8046 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.AA.3662.01 5 0.3706 0.4679 0.00 0.00 0.38 0.00 0.62 0.00
#> TCGA.AF.A56L.01 3 0.2793 0.5615 0.00 0.00 0.80 0.00 0.00 0.20
#> TCGA.NH.A6GB.01 5 0.3198 0.5205 0.26 0.00 0.00 0.00 0.74 0.00
#> TCGA.AD.5900.01 3 0.3499 0.3666 0.00 0.00 0.68 0.00 0.32 0.00
#> TCGA.NH.A50U.01 1 0.4892 0.1285 0.50 0.00 0.00 0.00 0.44 0.06
#> TCGA.AA.3712.01 6 0.3460 0.6392 0.00 0.00 0.22 0.00 0.02 0.76
#> TCGA.AZ.4614.01 1 0.0000 0.8765 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AH.6644.01 5 0.2956 0.6967 0.04 0.00 0.12 0.00 0.84 0.00
#> TCGA.AZ.6607.01 3 0.3828 0.0206 0.00 0.00 0.56 0.00 0.44 0.00
#> TCGA.AF.2693.01 6 0.5364 0.0394 0.00 0.00 0.14 0.30 0.00 0.56
#> TCGA.D5.6924.01 6 0.5447 0.2827 0.00 0.00 0.42 0.00 0.12 0.46
#> TCGA.CM.5868.01 4 0.4873 0.4956 0.00 0.00 0.06 0.52 0.00 0.42
#> TCGA.AF.4110.01 6 0.4892 -0.3493 0.00 0.00 0.06 0.44 0.00 0.50
#> TCGA.A6.3809.01 5 0.3864 -0.0363 0.48 0.00 0.00 0.00 0.52 0.00
#> TCGA.AZ.4313.01 4 0.0000 0.8046 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.A6.2675.01 4 0.3351 0.7523 0.00 0.00 0.04 0.80 0.00 0.16
#> TCGA.AZ.6608.01 6 0.3156 0.6507 0.00 0.00 0.18 0.00 0.02 0.80
#> TCGA.CM.5864.01 1 0.0000 0.8765 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AA.3494.01 4 0.0000 0.8046 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.AD.6895.01 3 0.3499 0.3666 0.00 0.00 0.68 0.00 0.32 0.00
#> TCGA.CI.6620.01 5 0.3851 0.3046 0.00 0.00 0.46 0.00 0.54 0.00
#> TCGA.DC.6156.01 3 0.3198 0.5007 0.00 0.00 0.74 0.00 0.26 0.00
#> TCGA.D5.6931.01 3 0.1556 0.6394 0.00 0.00 0.92 0.00 0.08 0.00
#> TCGA.CM.6165.01 5 0.3787 0.6092 0.00 0.00 0.10 0.00 0.78 0.12
#> TCGA.CM.5861.01 1 0.3409 0.5705 0.70 0.00 0.00 0.00 0.30 0.00
#> TCGA.A6.2671.01 5 0.2793 0.6096 0.00 0.00 0.00 0.00 0.80 0.20
#> TCGA.DC.6158.01 6 0.2454 0.6117 0.00 0.00 0.16 0.00 0.00 0.84
#> TCGA.AG.3742.01 1 0.0000 0.8765 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AG.A02N.11 2 0.0000 0.9813 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.G4.6307.01 4 0.0000 0.8046 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.A6.5666.01 5 0.2581 0.6724 0.02 0.00 0.00 0.00 0.86 0.12
#> TCGA.EI.6511.01 3 0.3270 0.5652 0.00 0.00 0.82 0.00 0.12 0.06
#> TCGA.CI.6624.01 4 0.0000 0.8046 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.AG.3591.01 5 0.3567 0.6447 0.10 0.00 0.00 0.00 0.80 0.10
#> TCGA.AY.A8YK.01 2 0.3864 0.2371 0.00 0.52 0.00 0.48 0.00 0.00
#> TCGA.F4.6856.01 3 0.2454 0.6002 0.00 0.00 0.84 0.00 0.16 0.00
#> TCGA.DM.A1D7.01 3 0.5938 -0.0105 0.00 0.00 0.46 0.00 0.26 0.28
#> TCGA.A6.2685.01 2 0.0000 0.9813 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.5M.AAT6.01 2 0.0000 0.9813 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.AH.6643.01 5 0.3567 0.6447 0.10 0.00 0.00 0.00 0.80 0.10
#> TCGA.F4.6569.01 3 0.1556 0.6246 0.00 0.00 0.92 0.00 0.00 0.08
#> TCGA.G4.6298.01 3 0.2728 0.6259 0.00 0.00 0.86 0.00 0.04 0.10
#> TCGA.AY.6196.01 3 0.3499 0.4497 0.00 0.00 0.68 0.00 0.00 0.32
#> TCGA.EI.6510.01 5 0.3045 0.6788 0.06 0.00 0.00 0.00 0.84 0.10
#> TCGA.A6.5656.01 5 0.2350 0.6890 0.02 0.00 0.00 0.00 0.88 0.10
#> TCGA.A6.2684.11 2 0.0000 0.9813 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DY.A1DG.01 5 0.2454 0.6511 0.00 0.00 0.00 0.00 0.84 0.16
#> TCGA.AZ.4682.01 6 0.2981 0.6439 0.00 0.00 0.16 0.00 0.02 0.82
#> TCGA.EI.6884.01 3 0.2048 0.6046 0.00 0.00 0.88 0.00 0.00 0.12
#> TCGA.F4.6806.01 1 0.3756 0.3727 0.60 0.00 0.00 0.00 0.40 0.00
#> TCGA.G4.6320.11 2 0.0000 0.9813 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.G4.6322.01 1 0.3309 0.5966 0.72 0.00 0.00 0.00 0.28 0.00
#> TCGA.F5.6810.01 4 0.0000 0.8046 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.5M.AAT4.01 5 0.3864 -0.0375 0.48 0.00 0.00 0.00 0.52 0.00
#> TCGA.CL.4957.01 6 0.3819 0.6041 0.00 0.00 0.28 0.00 0.02 0.70
#> TCGA.DC.6681.01 3 0.2581 0.6146 0.00 0.00 0.86 0.00 0.02 0.12
#> TCGA.CM.6167.01 4 0.1480 0.7930 0.00 0.00 0.02 0.94 0.00 0.04
#> TCGA.AG.4022.01 3 0.5791 -0.1698 0.00 0.00 0.44 0.00 0.18 0.38
#> TCGA.G4.6586.01 1 0.2793 0.7129 0.80 0.00 0.00 0.00 0.20 0.00
#> TCGA.EI.6514.01 1 0.4845 0.2387 0.54 0.00 0.00 0.00 0.40 0.06
#> TCGA.CK.4950.01 3 0.2048 0.6086 0.00 0.00 0.88 0.00 0.00 0.12
#> TCGA.DM.A282.01 1 0.2454 0.7499 0.84 0.00 0.00 0.00 0.16 0.00
#> TCGA.DY.A1DC.01 6 0.4711 0.5829 0.00 0.00 0.28 0.00 0.08 0.64
#> TCGA.D5.6535.01 5 0.3409 0.5938 0.00 0.00 0.30 0.00 0.70 0.00
#> TCGA.DM.A1HA.01 1 0.0000 0.8765 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DC.5869.01 5 0.1480 0.7001 0.00 0.00 0.02 0.00 0.94 0.04
#> TCGA.AZ.6599.11 2 0.0000 0.9813 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.CM.4752.01 4 0.5523 0.4777 0.00 0.00 0.14 0.50 0.00 0.36
#> TCGA.AZ.4684.01 6 0.2941 0.5631 0.00 0.00 0.22 0.00 0.00 0.78
#> TCGA.EI.7004.01 3 0.1267 0.6411 0.00 0.00 0.94 0.00 0.06 0.00
#> TCGA.A6.A565.01 2 0.0000 0.9813 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.D5.6531.01 1 0.0000 0.8765 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AZ.6598.01 1 0.0000 0.8765 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AD.6890.01 5 0.4938 0.3808 0.00 0.00 0.34 0.00 0.58 0.08
#> TCGA.AG.4021.01 5 0.2793 0.6063 0.20 0.00 0.00 0.00 0.80 0.00
#> TCGA.A6.6781.01 4 0.3544 0.7504 0.00 0.00 0.08 0.80 0.00 0.12
#> TCGA.DM.A1D9.01 5 0.2094 0.6922 0.08 0.00 0.00 0.00 0.90 0.02
#> TCGA.CM.4744.01 5 0.3864 -0.0363 0.48 0.00 0.00 0.00 0.52 0.00
#> TCGA.A6.2679.11 2 0.0000 0.9813 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.A6.6652.01 5 0.1814 0.6842 0.00 0.00 0.00 0.00 0.90 0.10
#> TCGA.AD.6964.01 2 0.3864 0.2371 0.00 0.52 0.00 0.48 0.00 0.00
#> TCGA.SS.A7HO.01 5 0.3567 0.6447 0.10 0.00 0.00 0.00 0.80 0.10
#> TCGA.A6.6650.01 1 0.0000 0.8765 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DM.A0XF.01 6 0.5289 0.0976 0.00 0.00 0.14 0.28 0.00 0.58
#> TCGA.G4.6295.01 4 0.4806 0.5463 0.00 0.00 0.06 0.56 0.00 0.38
#> TCGA.F4.6461.01 5 0.2631 0.6805 0.00 0.00 0.18 0.00 0.82 0.00
#> TCGA.AM.5820.01 5 0.5285 0.0312 0.00 0.00 0.10 0.00 0.48 0.42
#> TCGA.G4.6314.11 2 0.0000 0.9813 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.AD.6889.01 1 0.0000 0.8765 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AZ.6605.01 3 0.3578 0.4181 0.00 0.00 0.66 0.00 0.00 0.34
#> TCGA.EI.6881.01 5 0.1814 0.6842 0.00 0.00 0.00 0.00 0.90 0.10
#> TCGA.NH.A50T.01 1 0.0000 0.8765 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AG.3725.11 2 0.0000 0.9813 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.G4.6323.01 3 0.3409 0.4124 0.00 0.00 0.70 0.00 0.30 0.00
#> TCGA.AA.3663.01 5 0.3864 -0.0363 0.48 0.00 0.00 0.00 0.52 0.00
#> TCGA.AD.6899.01 5 0.2454 0.6885 0.00 0.00 0.16 0.00 0.84 0.00
#> TCGA.A6.5667.11 2 0.0000 0.9813 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.A6.A56B.01 5 0.4873 0.1294 0.42 0.00 0.00 0.00 0.52 0.06
#> TCGA.G5.6572.01 6 0.5289 0.0976 0.00 0.00 0.14 0.28 0.00 0.58
#> TCGA.DM.A280.01 3 0.4078 0.3903 0.00 0.00 0.64 0.02 0.00 0.34
#> TCGA.AG.A020.01 6 0.3315 0.6472 0.00 0.00 0.20 0.00 0.02 0.78
#> TCGA.AA.3713.01 3 0.1556 0.6394 0.00 0.00 0.92 0.00 0.08 0.00
#> TCGA.D5.5539.01 5 0.2260 0.6935 0.00 0.00 0.14 0.00 0.86 0.00
#> TCGA.AA.3655.11 2 0.0000 0.9813 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.AA.3489.01 4 0.5481 0.5020 0.00 0.00 0.14 0.52 0.00 0.34
#> TCGA.AA.3495.01 5 0.3499 0.5705 0.00 0.00 0.32 0.00 0.68 0.00
#> TCGA.AG.A01Y.01 4 0.3198 0.7068 0.00 0.00 0.00 0.74 0.00 0.26
#> TCGA.AZ.6601.01 3 0.2260 0.6149 0.00 0.00 0.86 0.00 0.14 0.00
#> TCGA.AH.6903.01 3 0.3829 0.4660 0.00 0.00 0.76 0.00 0.06 0.18
#> TCGA.AZ.6603.01 6 0.4902 -0.4029 0.00 0.00 0.06 0.46 0.00 0.48
#> TCGA.CA.5254.01 1 0.0000 0.8765 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.A6.A5ZU.01 6 0.5945 0.2758 0.00 0.00 0.22 0.00 0.36 0.42
#> TCGA.G4.6302.01 4 0.0000 0.8046 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.AZ.5403.01 4 0.3864 -0.1434 0.00 0.48 0.00 0.52 0.00 0.00
#> TCGA.AY.A54L.01 1 0.2260 0.7709 0.86 0.00 0.00 0.00 0.14 0.00
#> TCGA.A6.4107.01 1 0.0000 0.8765 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.NH.A5IV.01 1 0.3756 0.3727 0.60 0.00 0.00 0.00 0.40 0.00
#> TCGA.G4.6306.01 1 0.0000 0.8765 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AD.A5EK.01 1 0.0000 0.8765 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.G5.6235.01 4 0.5888 0.3964 0.00 0.00 0.22 0.46 0.00 0.32
#> TCGA.DC.5337.01 5 0.0547 0.7046 0.02 0.00 0.00 0.00 0.98 0.00
#> TCGA.CM.6675.01 1 0.0000 0.8765 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AH.6544.01 3 0.3499 0.3972 0.00 0.00 0.68 0.00 0.00 0.32
#> TCGA.CK.6746.01 1 0.0000 0.8765 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CA.6718.01 5 0.3499 0.5705 0.00 0.00 0.32 0.00 0.68 0.00
#> TCGA.CI.6621.01 4 0.0000 0.8046 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.CM.6676.01 6 0.3592 0.6282 0.00 0.00 0.24 0.00 0.02 0.74
#> TCGA.DM.A1DB.01 6 0.4462 0.5935 0.00 0.00 0.28 0.00 0.06 0.66
#> TCGA.A6.6654.01 3 0.3499 0.4497 0.00 0.00 0.68 0.00 0.00 0.32
#> TCGA.AA.3510.11 2 0.0000 0.9813 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.CA.6715.01 6 0.3156 0.6507 0.00 0.00 0.18 0.00 0.02 0.80
#> TCGA.CM.5341.01 5 0.2941 0.6603 0.00 0.00 0.22 0.00 0.78 0.00
#> TCGA.CK.5912.01 6 0.3156 0.6507 0.00 0.00 0.18 0.00 0.02 0.80
#> TCGA.F4.6857.01 3 0.4700 0.3236 0.00 0.00 0.60 0.06 0.00 0.34
#> TCGA.QG.A5YW.01 1 0.3756 0.3727 0.60 0.00 0.00 0.00 0.40 0.00
#> TCGA.A6.5665.01 1 0.0000 0.8765 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CM.6168.01 3 0.2793 0.5414 0.00 0.00 0.80 0.00 0.00 0.20
#> TCGA.CL.5917.01 6 0.4926 0.5439 0.00 0.00 0.24 0.00 0.12 0.64
#> TCGA.AU.6004.01 3 0.1814 0.6192 0.00 0.00 0.90 0.00 0.00 0.10
#> TCGA.AY.5543.01 3 0.5992 -0.1656 0.00 0.00 0.42 0.00 0.24 0.34
#> TCGA.AG.3731.01 3 0.1556 0.6246 0.00 0.00 0.92 0.00 0.00 0.08
#> TCGA.G4.6314.01 3 0.2790 0.6021 0.00 0.00 0.84 0.00 0.02 0.14
#> TCGA.DC.6683.01 5 0.6059 -0.0354 0.00 0.00 0.36 0.00 0.38 0.26
#> TCGA.CA.5796.01 5 0.1807 0.6970 0.00 0.00 0.02 0.00 0.92 0.06
#> TCGA.AG.A036.11 2 0.0000 0.9813 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.AZ.4323.01 4 0.0000 0.8046 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.EI.6882.01 1 0.0000 0.8765 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AZ.4315.01 5 0.3647 0.5060 0.00 0.00 0.36 0.00 0.64 0.00
#> TCGA.A6.2677.01 1 0.0000 0.8765 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DY.A1DF.01 6 0.5655 0.2493 0.00 0.00 0.16 0.00 0.36 0.48
#> TCGA.CM.6162.01 2 0.0000 0.9813 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.F4.6703.01 2 0.0000 0.9813 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.CM.5349.01 3 0.2048 0.6086 0.00 0.00 0.88 0.00 0.00 0.12
#> TCGA.AG.A02N.01 5 0.1814 0.6842 0.00 0.00 0.00 0.00 0.90 0.10
#> TCGA.AA.3506.01 5 0.2454 0.6885 0.00 0.00 0.16 0.00 0.84 0.00
#> TCGA.D5.6932.01 6 0.3711 0.6186 0.00 0.00 0.26 0.00 0.02 0.72
#> TCGA.D5.6538.01 1 0.0000 0.8765 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AA.3488.11 2 0.0000 0.9813 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.AA.3502.01 1 0.0000 0.8765 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.NH.A8F8.01 5 0.3499 0.5705 0.00 0.00 0.32 0.00 0.68 0.00
#> TCGA.AF.A56N.01 6 0.5769 0.3372 0.00 0.00 0.36 0.00 0.18 0.46
#> TCGA.AF.6672.01 4 0.0000 0.8046 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.A6.2685.11 2 0.0000 0.9813 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.A6.6141.01 3 0.3315 0.5624 0.00 0.00 0.78 0.00 0.02 0.20
#> TCGA.AD.6963.01 4 0.0000 0.8046 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.G4.6298.11 2 0.0000 0.9813 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.EI.6917.01 3 0.2260 0.6149 0.00 0.00 0.86 0.00 0.14 0.00
#> TCGA.QG.A5Z2.01 5 0.3864 -0.0363 0.48 0.00 0.00 0.00 0.52 0.00
#> TCGA.A6.2684.01 3 0.3315 0.5386 0.00 0.00 0.78 0.00 0.02 0.20
#> TCGA.CK.5915.01 1 0.0000 0.8765 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CM.6163.01 3 0.3460 0.5190 0.00 0.00 0.76 0.00 0.02 0.22
#> TCGA.G4.6322.11 2 0.0000 0.9813 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.AY.6197.01 1 0.1267 0.8402 0.94 0.00 0.00 0.00 0.06 0.00
#> TCGA.D5.6928.01 3 0.5938 0.1175 0.00 0.00 0.46 0.26 0.00 0.28
#> TCGA.A6.3810.01 4 0.2454 0.7663 0.00 0.00 0.00 0.84 0.00 0.16
#> TCGA.G4.6294.01 5 0.1814 0.6842 0.00 0.00 0.00 0.00 0.90 0.10
#> TCGA.AA.3660.11 2 0.0000 0.9813 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.A6.6137.01 6 0.5769 0.3372 0.00 0.00 0.36 0.00 0.18 0.46
#> TCGA.G4.6297.11 2 0.0000 0.9813 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.AZ.4615.01 5 0.3409 0.5938 0.00 0.00 0.30 0.00 0.70 0.00
#> TCGA.CK.4952.01 1 0.0000 0.8765 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CM.6172.01 5 0.1814 0.6842 0.00 0.00 0.00 0.00 0.90 0.10
#> TCGA.AD.6901.01 5 0.3499 0.5705 0.00 0.00 0.32 0.00 0.68 0.00
#> TCGA.AA.3496.01 5 0.3156 0.6256 0.18 0.00 0.02 0.00 0.80 0.00
#> TCGA.CK.5913.01 1 0.0000 0.8765 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DM.A28A.01 1 0.0000 0.8765 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EI.7002.01 5 0.1814 0.6842 0.00 0.00 0.00 0.00 0.90 0.10
#> TCGA.D5.6533.01 6 0.5888 0.3712 0.00 0.00 0.32 0.00 0.22 0.46
#> TCGA.QG.A5Z1.01 1 0.1267 0.8374 0.94 0.00 0.00 0.00 0.06 0.00
#> TCGA.D5.6923.01 4 0.4873 0.4956 0.00 0.00 0.06 0.52 0.00 0.42
#> TCGA.AF.2690.01 6 0.5452 -0.3774 0.00 0.00 0.12 0.44 0.00 0.44
#> TCGA.DM.A28H.01 1 0.1814 0.8066 0.90 0.00 0.00 0.00 0.10 0.00
#> TCGA.G4.6320.01 1 0.0000 0.8765 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.G4.6310.01 5 0.3828 0.3579 0.00 0.00 0.44 0.00 0.56 0.00
#> TCGA.DM.A28M.01 1 0.0000 0.8765 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DM.A288.01 1 0.0000 0.8765 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.A6.2681.01 5 0.3499 0.5705 0.00 0.00 0.32 0.00 0.68 0.00
#> TCGA.A6.2679.01 5 0.3499 0.5705 0.00 0.00 0.32 0.00 0.68 0.00
#> TCGA.4N.A93T.01 5 0.1814 0.6842 0.00 0.00 0.00 0.00 0.90 0.10
#> TCGA.NH.A8F7.06 6 0.3156 0.6507 0.00 0.00 0.18 0.00 0.02 0.80
#> TCGA.NH.A8F7.01 6 0.1814 0.5985 0.00 0.00 0.10 0.00 0.00 0.90
#> TCGA.AZ.6600.11 2 0.0000 0.9813 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.G5.6572.02 4 0.0000 0.8046 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.AY.6386.01 5 0.3076 0.6475 0.00 0.00 0.24 0.00 0.76 0.00
#> TCGA.G4.6628.01 3 0.3499 0.3666 0.00 0.00 0.68 0.00 0.32 0.00
#> TCGA.A6.6653.01 1 0.0000 0.8765 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CM.4746.01 5 0.3819 0.4884 0.00 0.00 0.02 0.00 0.70 0.28
#> TCGA.F4.6855.01 5 0.2454 0.6885 0.00 0.00 0.16 0.00 0.84 0.00
#> TCGA.EF.5830.01 5 0.1814 0.6842 0.00 0.00 0.00 0.00 0.90 0.10
#> TCGA.NH.A6GA.01 5 0.2941 0.5810 0.22 0.00 0.00 0.00 0.78 0.00
#> TCGA.NH.A50V.01 5 0.2454 0.6885 0.00 0.00 0.16 0.00 0.84 0.00
#> TCGA.DY.A0XA.01 4 0.4576 0.5426 0.00 0.00 0.04 0.56 0.00 0.40
#> TCGA.DM.A28E.01 6 0.1814 0.5985 0.00 0.00 0.10 0.00 0.00 0.90
#> TCGA.AG.3725.01 5 0.1814 0.6842 0.00 0.00 0.00 0.00 0.90 0.10
#> TCGA.CK.6747.01 1 0.0000 0.8765 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CL.5918.01 1 0.0000 0.8765 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CI.6623.01 4 0.0000 0.8046 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.A6.5667.01 6 0.2631 0.6425 0.00 0.00 0.18 0.00 0.00 0.82
#> TCGA.DM.A28K.01 1 0.0000 0.8765 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AA.3713.11 2 0.0000 0.9813 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.AA.3655.01 5 0.1814 0.6842 0.00 0.00 0.00 0.00 0.90 0.10
#> TCGA.AU.3779.01 6 0.5289 0.0976 0.00 0.00 0.14 0.28 0.00 0.58
#> TCGA.A6.5664.01 3 0.3499 0.4497 0.00 0.00 0.68 0.00 0.00 0.32
#> TCGA.AA.3697.11 2 0.0000 0.9813 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.AZ.5407.01 1 0.3797 0.3216 0.58 0.00 0.00 0.00 0.42 0.00
#> TCGA.CM.6169.01 5 0.3647 0.5060 0.00 0.00 0.36 0.00 0.64 0.00
#> TCGA.AH.6547.01 4 0.3544 0.7504 0.00 0.00 0.08 0.80 0.00 0.12
#> TCGA.AZ.6601.11 2 0.0000 0.9813 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.A6.5661.01 5 0.3851 0.0358 0.46 0.00 0.00 0.00 0.54 0.00
#> TCGA.F4.6807.01 3 0.1556 0.6394 0.00 0.00 0.92 0.00 0.08 0.00
#> TCGA.QG.A5YV.01 1 0.0000 0.8765 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AA.3509.11 2 0.0000 0.9813 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.AY.A71X.01 1 0.0000 0.8765 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CA.5797.01 4 0.0000 0.8046 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.F4.6460.01 4 0.0000 0.8046 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.G4.6302.11 2 0.0000 0.9813 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.F5.6702.01 4 0.0000 0.8046 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.AH.6549.01 1 0.3851 0.2019 0.54 0.00 0.00 0.00 0.46 0.00
#> TCGA.D5.6927.01 4 0.2350 0.7781 0.00 0.00 0.02 0.88 0.00 0.10
#> TCGA.CM.6166.01 1 0.0000 0.8765 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AH.6897.01 1 0.0000 0.8765 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.G4.6304.01 3 0.5747 0.2119 0.00 0.00 0.50 0.20 0.00 0.30
#> TCGA.CA.5255.01 3 0.2260 0.5935 0.00 0.00 0.86 0.00 0.00 0.14
#> TCGA.EI.6507.01 3 0.2793 0.5349 0.00 0.00 0.80 0.00 0.00 0.20
#> TCGA.CK.4947.01 5 0.3499 0.5705 0.00 0.00 0.32 0.00 0.68 0.00
#> TCGA.D5.5540.01 1 0.0000 0.8765 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DC.6682.01 5 0.3499 0.5705 0.00 0.00 0.32 0.00 0.68 0.00
#> TCGA.G4.6321.01 3 0.2260 0.6149 0.00 0.00 0.86 0.00 0.14 0.00
#> TCGA.A6.6649.01 5 0.3409 0.5925 0.00 0.00 0.30 0.00 0.70 0.00
#> TCGA.CM.5348.01 3 0.1556 0.6394 0.00 0.00 0.92 0.00 0.08 0.00
#> TCGA.EI.6513.01 4 0.0000 0.8046 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.A6.2672.01 5 0.3460 0.5761 0.22 0.00 0.02 0.00 0.76 0.00
#> TCGA.D5.6539.01 4 0.0000 0.8046 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.AA.3510.01 6 0.3309 0.5876 0.00 0.00 0.28 0.00 0.00 0.72
#> TCGA.G5.6233.01 5 0.2454 0.6885 0.00 0.00 0.16 0.00 0.84 0.00
#> TCGA.BM.6198.01 4 0.4938 0.5743 0.00 0.00 0.08 0.58 0.00 0.34
#> TCGA.CA.6719.01 1 0.3499 0.5358 0.68 0.00 0.00 0.00 0.32 0.00
#> TCGA.DC.6154.01 5 0.3828 0.1718 0.00 0.00 0.00 0.00 0.56 0.44
#> TCGA.DM.A1D6.01 5 0.5295 -0.0556 0.00 0.00 0.10 0.00 0.46 0.44
#> TCGA.AG.3731.11 2 0.0000 0.9813 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.CM.6674.01 4 0.3544 0.7504 0.00 0.00 0.08 0.80 0.00 0.12
#> TCGA.CM.4743.01 3 0.3499 0.4497 0.00 0.00 0.68 0.00 0.00 0.32
#> TCGA.F5.6465.01 4 0.5095 0.4723 0.00 0.00 0.08 0.50 0.00 0.42
#> TCGA.D5.5537.01 1 0.0000 0.8765 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.F4.6463.01 3 0.1556 0.6394 0.00 0.00 0.92 0.00 0.08 0.00
#> TCGA.A6.2686.11 2 0.0000 0.9813 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.4T.AA8H.01 1 0.2260 0.7709 0.86 0.00 0.00 0.00 0.14 0.00
#> TCGA.A6.6782.01 6 0.6116 0.1582 0.00 0.00 0.34 0.00 0.30 0.36
#> TCGA.AG.3592.01 1 0.3851 0.2019 0.54 0.00 0.00 0.00 0.46 0.00
#> TCGA.AD.6888.01 6 0.3592 0.6329 0.00 0.00 0.24 0.00 0.02 0.74
#> TCGA.CM.6678.01 5 0.2454 0.6885 0.00 0.00 0.16 0.00 0.84 0.00
#> TCGA.CM.5344.01 4 0.4873 0.4956 0.00 0.00 0.06 0.52 0.00 0.42
#> TCGA.AA.3495.11 2 0.0000 0.9813 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.AG.A01W.11 2 0.0000 0.9813 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.F4.6809.01 3 0.1556 0.6394 0.00 0.00 0.92 0.00 0.08 0.00
#> TCGA.CK.5914.01 1 0.0000 0.8765 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AZ.4681.01 4 0.4609 0.5135 0.00 0.00 0.04 0.54 0.00 0.42
#> TCGA.AA.3492.01 1 0.0000 0.8765 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D5.6536.01 6 0.4246 0.4266 0.00 0.00 0.40 0.00 0.02 0.58
#> TCGA.AA.3506.11 2 0.0000 0.9813 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.AA.3488.01 6 0.5569 0.2952 0.00 0.00 0.16 0.00 0.32 0.52
#> TCGA.AA.3502.11 2 0.0000 0.9813 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.A6.6140.01 4 0.2454 0.7663 0.00 0.00 0.00 0.84 0.00 0.16
#> TCGA.D5.6529.01 3 0.1556 0.6394 0.00 0.00 0.92 0.00 0.08 0.00
#> TCGA.DM.A1D0.01 4 0.0000 0.8046 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.DM.A1HB.01 5 0.3864 -0.0363 0.48 0.00 0.00 0.00 0.52 0.00
#> TCGA.D5.6920.01 3 0.2631 0.5574 0.00 0.00 0.82 0.00 0.00 0.18
#> TCGA.D5.6922.01 6 0.5636 0.4630 0.00 0.00 0.30 0.00 0.18 0.52
#> TCGA.EI.6508.01 5 0.2350 0.6890 0.02 0.00 0.00 0.00 0.88 0.10
#> TCGA.D5.6532.01 5 0.3797 0.1701 0.42 0.00 0.00 0.00 0.58 0.00
#> TCGA.5M.AATA.01 6 0.3756 0.3759 0.00 0.00 0.40 0.00 0.00 0.60
#> TCGA.EI.6509.01 4 0.0000 0.8046 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.G4.6311.01 3 0.3578 0.4181 0.00 0.00 0.66 0.00 0.00 0.34
#> TCGA.A6.A566.01 3 0.2048 0.6246 0.00 0.00 0.88 0.00 0.12 0.00
#> TCGA.G4.6625.01 3 0.2941 0.5163 0.00 0.00 0.78 0.00 0.00 0.22
#> TCGA.CI.6619.01 4 0.0000 0.8046 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.F5.6864.01 6 0.3592 0.6329 0.00 0.00 0.24 0.00 0.02 0.74
#> TCGA.AA.3492.11 2 0.0000 0.9813 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.A6.5659.01 1 0.0000 0.8765 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.WS.AB45.01 4 0.3321 0.7582 0.00 0.00 0.08 0.82 0.00 0.10
#> TCGA.G4.6315.01 3 0.2793 0.5615 0.00 0.00 0.80 0.00 0.00 0.20
#> TCGA.D5.6541.01 3 0.1556 0.6394 0.00 0.00 0.92 0.00 0.08 0.00
#> TCGA.A6.2680.01 5 0.2094 0.7043 0.02 0.00 0.08 0.00 0.90 0.00
#> TCGA.CM.4751.01 3 0.2260 0.6149 0.00 0.00 0.86 0.00 0.14 0.00
#> TCGA.CM.6680.01 5 0.3578 0.3683 0.34 0.00 0.00 0.00 0.66 0.00
#> TCGA.AF.6136.01 5 0.2350 0.6791 0.00 0.00 0.02 0.00 0.88 0.10
#> TCGA.AA.3660.01 1 0.3869 0.0812 0.50 0.00 0.00 0.00 0.50 0.00
#> TCGA.CM.4747.01 5 0.2454 0.6885 0.00 0.00 0.16 0.00 0.84 0.00
#> TCGA.EF.5831.01 1 0.3756 0.3727 0.60 0.00 0.00 0.00 0.40 0.00
#> TCGA.DM.A28G.01 1 0.0000 0.8765 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.G4.6297.01 3 0.1556 0.6394 0.00 0.00 0.92 0.00 0.08 0.00
#> TCGA.A6.2682.11 2 0.0000 0.9813 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.D5.6537.01 1 0.1814 0.8070 0.90 0.00 0.00 0.00 0.10 0.00
#> TCGA.CM.6170.01 6 0.3156 0.6507 0.00 0.00 0.18 0.00 0.02 0.80
#> TCGA.DY.A1DD.01 5 0.3045 0.6694 0.06 0.00 0.00 0.00 0.84 0.10
cbind(get_classes(res, k = 7), get_membership(res, k = 7))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7
#> TCGA.AF.3911.01 6 0.3745 0.62408 0.00 0.00 0.04 0.00 0.00 0.70 0.26
#> TCGA.F4.6459.01 6 0.3911 0.63615 0.00 0.00 0.06 0.00 0.00 0.70 0.24
#> TCGA.AA.3494.11 2 0.0000 0.99420 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.3L.AA1B.01 3 0.0504 0.71623 0.00 0.00 0.98 0.00 0.02 0.00 0.00
#> TCGA.D5.5538.01 5 0.3496 0.26192 0.00 0.00 0.42 0.00 0.58 0.00 0.00
#> TCGA.F4.6854.01 5 0.6450 0.23310 0.00 0.00 0.32 0.08 0.40 0.20 0.00
#> TCGA.AG.A026.01 1 0.0000 0.96854 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.G4.6303.01 5 0.4908 0.46830 0.00 0.00 0.00 0.10 0.62 0.26 0.02
#> TCGA.F5.6464.01 7 0.3558 -0.00916 0.00 0.00 0.48 0.00 0.00 0.00 0.52
#> TCGA.T9.A92H.01 5 0.4992 0.44524 0.00 0.00 0.00 0.10 0.60 0.28 0.02
#> TCGA.AA.3712.11 2 0.0000 0.99420 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CM.5863.01 3 0.2422 0.63583 0.00 0.00 0.82 0.00 0.00 0.00 0.18
#> TCGA.AZ.4308.01 7 0.2803 0.70562 0.00 0.00 0.00 0.06 0.00 0.10 0.84
#> TCGA.AD.6965.01 1 0.0000 0.96854 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.A6.2681.11 2 0.0000 0.99420 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AD.6548.01 3 0.0504 0.71623 0.00 0.00 0.98 0.00 0.02 0.00 0.00
#> TCGA.A6.5660.01 1 0.0000 0.96854 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AZ.6600.01 3 0.3985 0.00544 0.00 0.00 0.52 0.00 0.46 0.02 0.00
#> TCGA.F4.6808.01 6 0.1166 0.65176 0.00 0.00 0.06 0.00 0.00 0.94 0.00
#> TCGA.D5.6540.01 5 0.2832 0.61959 0.24 0.00 0.00 0.00 0.76 0.00 0.00
#> TCGA.F5.6571.01 5 0.4440 0.58753 0.00 0.00 0.02 0.10 0.74 0.12 0.02
#> TCGA.D5.6926.01 3 0.3867 0.28453 0.00 0.00 0.60 0.00 0.02 0.38 0.00
#> TCGA.CM.4748.01 3 0.1664 0.70585 0.00 0.00 0.92 0.00 0.00 0.02 0.06
#> TCGA.A6.2675.11 2 0.0000 0.99420 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.5M.AATE.01 6 0.1664 0.64712 0.00 0.00 0.06 0.00 0.02 0.92 0.00
#> TCGA.D5.5541.01 7 0.3199 0.67269 0.00 0.00 0.00 0.06 0.00 0.14 0.80
#> TCGA.CM.5862.01 5 0.4110 0.62606 0.04 0.00 0.00 0.10 0.78 0.06 0.02
#> TCGA.AA.3511.01 6 0.3927 0.58439 0.00 0.00 0.04 0.00 0.00 0.66 0.30
#> TCGA.AA.3663.11 2 0.0000 0.99420 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CI.6622.01 5 0.2509 0.66524 0.00 0.00 0.06 0.04 0.88 0.02 0.00
#> TCGA.EI.6506.01 7 0.4328 0.30536 0.00 0.00 0.34 0.00 0.00 0.06 0.60
#> TCGA.AM.5821.01 5 0.3496 0.26192 0.00 0.00 0.42 0.00 0.58 0.00 0.00
#> TCGA.F5.6812.01 4 0.2259 0.88431 0.00 0.00 0.00 0.84 0.00 0.00 0.16
#> TCGA.G4.6588.01 5 0.2422 0.66903 0.18 0.00 0.00 0.00 0.82 0.00 0.00
#> TCGA.EI.6512.01 5 0.2832 0.61959 0.24 0.00 0.00 0.00 0.76 0.00 0.00
#> TCGA.A6.6648.01 4 0.1671 0.92805 0.00 0.00 0.00 0.90 0.00 0.00 0.10
#> TCGA.A6.2671.11 2 0.0504 0.98592 0.00 0.98 0.00 0.00 0.00 0.02 0.00
#> TCGA.NH.A6GC.01 5 0.5747 0.42801 0.00 0.00 0.04 0.10 0.56 0.28 0.02
#> TCGA.F4.6805.01 7 0.1363 0.70249 0.00 0.00 0.02 0.04 0.00 0.00 0.94
#> TCGA.AA.3697.01 6 0.1166 0.65176 0.00 0.00 0.06 0.00 0.00 0.94 0.00
#> TCGA.QG.A5YX.01 5 0.4992 0.44524 0.00 0.00 0.00 0.10 0.60 0.28 0.02
#> TCGA.DM.A28C.01 6 0.4945 0.49831 0.00 0.00 0.04 0.10 0.14 0.70 0.02
#> TCGA.AG.A036.01 5 0.5243 0.53298 0.00 0.00 0.04 0.10 0.66 0.18 0.02
#> TCGA.AZ.6606.01 1 0.0000 0.96854 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.F4.6570.01 5 0.2259 0.67934 0.16 0.00 0.00 0.00 0.84 0.00 0.00
#> TCGA.DC.4745.01 6 0.3911 0.63615 0.00 0.00 0.06 0.00 0.00 0.70 0.24
#> TCGA.AF.A56K.01 4 0.1671 0.92805 0.00 0.00 0.00 0.90 0.00 0.00 0.10
#> TCGA.G4.6627.01 7 0.3517 0.44593 0.00 0.00 0.02 0.28 0.00 0.00 0.70
#> TCGA.A6.5657.01 3 0.3558 0.09035 0.00 0.00 0.52 0.00 0.00 0.00 0.48
#> TCGA.A6.5662.01 6 0.3745 0.62408 0.00 0.00 0.04 0.00 0.00 0.70 0.26
#> TCGA.AA.3509.01 5 0.5443 0.43764 0.00 0.00 0.02 0.10 0.58 0.28 0.02
#> TCGA.D5.6929.01 7 0.1166 0.70109 0.00 0.00 0.00 0.06 0.00 0.00 0.94
#> TCGA.CM.6679.01 6 0.4547 0.39863 0.00 0.00 0.34 0.00 0.00 0.58 0.08
#> TCGA.A6.2680.11 2 0.0000 0.99420 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DC.6157.01 4 0.2422 0.86751 0.00 0.00 0.00 0.82 0.00 0.00 0.18
#> TCGA.AF.6655.01 4 0.2422 0.86751 0.00 0.00 0.00 0.82 0.00 0.00 0.18
#> TCGA.CM.6161.01 3 0.5919 0.24482 0.00 0.00 0.50 0.06 0.14 0.30 0.00
#> TCGA.EI.6883.01 1 0.0000 0.96854 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.F5.6811.01 5 0.4187 0.62513 0.00 0.00 0.08 0.08 0.76 0.08 0.00
#> TCGA.D5.6930.01 3 0.0863 0.71985 0.00 0.00 0.96 0.00 0.00 0.00 0.04
#> TCGA.CM.6164.01 7 0.2803 0.70562 0.00 0.00 0.00 0.06 0.00 0.10 0.84
#> TCGA.AF.2687.01 4 0.1671 0.92805 0.00 0.00 0.00 0.90 0.00 0.00 0.10
#> TCGA.DY.A1H8.01 6 0.4813 0.37333 0.00 0.00 0.00 0.10 0.24 0.64 0.02
#> TCGA.G5.6641.01 6 0.4405 0.57622 0.00 0.00 0.10 0.08 0.08 0.74 0.00
#> TCGA.DC.6155.01 6 0.4348 0.58773 0.00 0.00 0.18 0.00 0.00 0.68 0.14
#> TCGA.RU.A8FL.01 5 0.3965 0.59092 0.00 0.00 0.00 0.10 0.76 0.12 0.02
#> TCGA.CK.4951.01 5 0.3525 0.21988 0.00 0.00 0.44 0.00 0.56 0.00 0.00
#> TCGA.F4.6704.01 4 0.2832 0.78870 0.00 0.00 0.00 0.76 0.00 0.00 0.24
#> TCGA.AZ.6599.01 1 0.0000 0.96854 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.F5.6861.01 3 0.0863 0.71985 0.00 0.00 0.96 0.00 0.00 0.00 0.04
#> TCGA.CM.5860.01 5 0.2422 0.66903 0.18 0.00 0.00 0.00 0.82 0.00 0.00
#> TCGA.A6.6780.01 5 0.2422 0.66903 0.18 0.00 0.00 0.00 0.82 0.00 0.00
#> TCGA.A6.2686.01 5 0.2259 0.67934 0.16 0.00 0.00 0.00 0.84 0.00 0.00
#> TCGA.CM.4750.01 5 0.2422 0.67019 0.18 0.00 0.00 0.00 0.82 0.00 0.00
#> TCGA.CM.6677.01 5 0.2422 0.66903 0.18 0.00 0.00 0.00 0.82 0.00 0.00
#> TCGA.A6.A567.01 4 0.2945 0.75677 0.00 0.00 0.00 0.74 0.00 0.00 0.26
#> TCGA.F5.6814.01 1 0.0863 0.93161 0.96 0.00 0.00 0.00 0.04 0.00 0.00
#> TCGA.D5.6898.01 6 0.3911 0.63615 0.00 0.00 0.06 0.00 0.00 0.70 0.24
#> TCGA.AG.A01W.01 3 0.6301 -0.09807 0.00 0.00 0.38 0.06 0.36 0.20 0.00
#> TCGA.AZ.6598.11 2 0.0000 0.99420 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.F5.6813.01 6 0.4146 0.62635 0.00 0.00 0.08 0.00 0.00 0.68 0.24
#> TCGA.AG.3732.01 7 0.0504 0.69645 0.00 0.00 0.02 0.00 0.00 0.00 0.98
#> TCGA.EI.6885.01 4 0.1671 0.92805 0.00 0.00 0.00 0.90 0.00 0.00 0.10
#> TCGA.G4.6299.01 5 0.2572 0.61614 0.00 0.00 0.20 0.00 0.80 0.00 0.00
#> TCGA.A6.4105.01 5 0.2422 0.66903 0.18 0.00 0.00 0.00 0.82 0.00 0.00
#> TCGA.DM.A1D8.01 1 0.0000 0.96854 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DM.A285.01 3 0.0863 0.71985 0.00 0.00 0.96 0.00 0.00 0.00 0.04
#> TCGA.G4.6295.11 2 0.0504 0.98592 0.00 0.98 0.00 0.00 0.00 0.02 0.00
#> TCGA.DC.4749.01 6 0.3496 0.38585 0.00 0.00 0.00 0.00 0.00 0.58 0.42
#> TCGA.DT.5265.01 5 0.2572 0.61614 0.00 0.00 0.20 0.00 0.80 0.00 0.00
#> TCGA.5M.AAT5.01 7 0.3526 0.62004 0.00 0.00 0.00 0.18 0.00 0.06 0.76
#> TCGA.DM.A0XD.01 5 0.2572 0.61614 0.00 0.00 0.20 0.00 0.80 0.00 0.00
#> TCGA.A6.6138.01 5 0.2572 0.61614 0.00 0.00 0.20 0.00 0.80 0.00 0.00
#> TCGA.D5.7000.01 5 0.2422 0.66903 0.18 0.00 0.00 0.00 0.82 0.00 0.00
#> TCGA.DM.A28F.01 5 0.1006 0.68953 0.02 0.00 0.00 0.00 0.96 0.00 0.02
#> TCGA.DY.A1DE.01 6 0.3927 0.58464 0.00 0.00 0.04 0.00 0.00 0.66 0.30
#> TCGA.A6.6142.01 4 0.2569 0.75127 0.00 0.14 0.00 0.84 0.00 0.02 0.00
#> TCGA.QL.A97D.01 5 0.3691 0.63665 0.00 0.00 0.06 0.08 0.80 0.06 0.00
#> TCGA.CK.6748.01 6 0.2313 0.66085 0.00 0.00 0.06 0.00 0.00 0.88 0.06
#> TCGA.DC.6160.01 7 0.2803 0.70562 0.00 0.00 0.00 0.06 0.00 0.10 0.84
#> TCGA.D5.6534.01 3 0.3558 0.09035 0.00 0.00 0.52 0.00 0.00 0.00 0.48
#> TCGA.AZ.4616.01 5 0.3525 0.21988 0.00 0.00 0.44 0.00 0.56 0.00 0.00
#> TCGA.CK.6751.01 5 0.2832 0.61959 0.24 0.00 0.00 0.00 0.76 0.00 0.00
#> TCGA.CM.6171.01 1 0.0000 0.96854 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DM.A1DA.01 1 0.0000 0.96854 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AG.A020.11 2 0.0000 0.99420 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.G4.6311.11 2 0.0504 0.98592 0.00 0.98 0.00 0.00 0.00 0.02 0.00
#> TCGA.G4.6625.11 2 0.0000 0.99420 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.F5.6863.01 7 0.3244 0.62899 0.00 0.00 0.00 0.04 0.00 0.18 0.78
#> TCGA.G4.6317.02 6 0.3413 0.46187 0.00 0.00 0.00 0.00 0.00 0.62 0.38
#> TCGA.G4.6317.01 6 0.1363 0.62587 0.00 0.00 0.02 0.00 0.04 0.94 0.00
#> TCGA.DM.A1D4.01 1 0.0000 0.96854 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AG.A01Y.11 2 0.0000 0.99420 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D5.6530.01 6 0.4941 -0.01701 0.00 0.00 0.46 0.06 0.02 0.46 0.00
#> TCGA.CK.4948.01 7 0.3139 0.42915 0.00 0.00 0.00 0.30 0.00 0.00 0.70
#> TCGA.AD.A5EJ.01 1 0.3221 0.48065 0.68 0.00 0.00 0.00 0.32 0.00 0.00
#> TCGA.A6.6651.01 4 0.1671 0.92805 0.00 0.00 0.00 0.90 0.00 0.00 0.10
#> TCGA.CA.5256.01 5 0.5868 0.36190 0.00 0.00 0.04 0.10 0.52 0.32 0.02
#> TCGA.DM.A0X9.01 1 0.0000 0.96854 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AY.A69D.01 5 0.2016 0.69287 0.06 0.00 0.04 0.00 0.90 0.00 0.00
#> TCGA.G4.6626.01 6 0.2803 0.66022 0.00 0.00 0.06 0.00 0.00 0.84 0.10
#> TCGA.CA.6716.01 1 0.0000 0.96854 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.A6.2682.01 7 0.4381 0.26464 0.00 0.00 0.36 0.00 0.00 0.06 0.58
#> TCGA.A6.4107.11 2 0.0000 0.99420 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CA.6717.01 3 0.2422 0.63583 0.00 0.00 0.82 0.00 0.00 0.00 0.18
#> TCGA.G4.6293.01 3 0.3546 0.03972 0.00 0.00 0.54 0.00 0.46 0.00 0.00
#> TCGA.CK.5916.01 5 0.2572 0.61614 0.00 0.00 0.20 0.00 0.80 0.00 0.00
#> TCGA.G4.6309.01 4 0.1671 0.92805 0.00 0.00 0.00 0.90 0.00 0.00 0.10
#> TCGA.AA.3662.01 3 0.5919 0.24482 0.00 0.00 0.50 0.06 0.14 0.30 0.00
#> TCGA.AF.A56L.01 3 0.2016 0.69752 0.00 0.00 0.90 0.00 0.00 0.04 0.06
#> TCGA.NH.A6GB.01 5 0.2259 0.67934 0.16 0.00 0.00 0.00 0.84 0.00 0.00
#> TCGA.AD.5900.01 3 0.1671 0.68141 0.00 0.00 0.90 0.00 0.10 0.00 0.00
#> TCGA.NH.A50U.01 5 0.3538 0.67730 0.14 0.00 0.00 0.02 0.80 0.02 0.02
#> TCGA.AA.3712.01 6 0.3911 0.63615 0.00 0.00 0.06 0.00 0.00 0.70 0.24
#> TCGA.AZ.4614.01 1 0.0000 0.96854 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AH.6644.01 5 0.0863 0.68249 0.00 0.00 0.04 0.00 0.96 0.00 0.00
#> TCGA.AZ.6607.01 3 0.2081 0.64908 0.00 0.00 0.86 0.00 0.14 0.00 0.00
#> TCGA.AF.2693.01 7 0.2906 0.61999 0.00 0.00 0.00 0.02 0.00 0.18 0.80
#> TCGA.D5.6924.01 6 0.2708 0.56265 0.00 0.00 0.22 0.00 0.00 0.78 0.00
#> TCGA.CM.5868.01 7 0.2803 0.70562 0.00 0.00 0.00 0.06 0.00 0.10 0.84
#> TCGA.AF.4110.01 7 0.3086 0.65395 0.00 0.00 0.00 0.04 0.00 0.16 0.80
#> TCGA.A6.3809.01 5 0.2422 0.66903 0.18 0.00 0.00 0.00 0.82 0.00 0.00
#> TCGA.AZ.4313.01 4 0.1671 0.92805 0.00 0.00 0.00 0.90 0.00 0.00 0.10
#> TCGA.A6.2675.01 7 0.3413 0.30621 0.00 0.00 0.00 0.38 0.00 0.00 0.62
#> TCGA.AZ.6608.01 6 0.3745 0.62408 0.00 0.00 0.04 0.00 0.00 0.70 0.26
#> TCGA.CM.5864.01 1 0.0000 0.96854 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AA.3494.01 4 0.1671 0.92805 0.00 0.00 0.00 0.90 0.00 0.00 0.10
#> TCGA.AD.6895.01 3 0.1671 0.68141 0.00 0.00 0.90 0.00 0.10 0.00 0.00
#> TCGA.CI.6620.01 3 0.4883 0.37916 0.00 0.00 0.60 0.00 0.20 0.20 0.00
#> TCGA.DC.6156.01 3 0.0504 0.71623 0.00 0.00 0.98 0.00 0.02 0.00 0.00
#> TCGA.D5.6931.01 3 0.0863 0.71985 0.00 0.00 0.96 0.00 0.00 0.00 0.04
#> TCGA.CM.6165.01 6 0.7043 -0.02513 0.00 0.00 0.22 0.10 0.30 0.36 0.02
#> TCGA.CM.5861.01 5 0.2832 0.61959 0.24 0.00 0.00 0.00 0.76 0.00 0.00
#> TCGA.A6.2671.01 6 0.5948 0.01686 0.00 0.00 0.04 0.10 0.36 0.48 0.02
#> TCGA.DC.6158.01 6 0.3755 0.52746 0.00 0.00 0.02 0.00 0.00 0.64 0.34
#> TCGA.AG.3742.01 1 0.0000 0.96854 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AG.A02N.11 2 0.0000 0.99420 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.G4.6307.01 4 0.1671 0.92805 0.00 0.00 0.00 0.90 0.00 0.00 0.10
#> TCGA.A6.5666.01 5 0.5065 0.41644 0.00 0.00 0.00 0.10 0.58 0.30 0.02
#> TCGA.EI.6511.01 3 0.2708 0.54182 0.00 0.00 0.78 0.00 0.00 0.22 0.00
#> TCGA.CI.6624.01 4 0.1671 0.92805 0.00 0.00 0.00 0.90 0.00 0.00 0.10
#> TCGA.AG.3591.01 5 0.4992 0.44524 0.00 0.00 0.00 0.10 0.60 0.28 0.02
#> TCGA.AY.A8YK.01 4 0.2745 0.72596 0.00 0.16 0.00 0.82 0.00 0.02 0.00
#> TCGA.F4.6856.01 3 0.0504 0.71623 0.00 0.00 0.98 0.00 0.02 0.00 0.00
#> TCGA.DM.A1D7.01 3 0.4408 0.12160 0.00 0.00 0.52 0.02 0.02 0.44 0.00
#> TCGA.A6.2685.01 2 0.1928 0.90746 0.00 0.90 0.00 0.08 0.00 0.02 0.00
#> TCGA.5M.AAT6.01 2 0.0504 0.98592 0.00 0.98 0.00 0.00 0.00 0.02 0.00
#> TCGA.AH.6643.01 5 0.4992 0.44524 0.00 0.00 0.00 0.10 0.60 0.28 0.02
#> TCGA.F4.6569.01 3 0.1886 0.68227 0.00 0.00 0.88 0.00 0.00 0.00 0.12
#> TCGA.G4.6298.01 3 0.0863 0.71985 0.00 0.00 0.96 0.00 0.00 0.00 0.04
#> TCGA.AY.6196.01 3 0.3558 0.09035 0.00 0.00 0.52 0.00 0.00 0.00 0.48
#> TCGA.EI.6510.01 5 0.3965 0.59085 0.00 0.00 0.00 0.10 0.76 0.12 0.02
#> TCGA.A6.5656.01 5 0.3541 0.61573 0.00 0.00 0.00 0.10 0.80 0.08 0.02
#> TCGA.A6.2684.11 2 0.0000 0.99420 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DY.A1DG.01 5 0.5180 0.34267 0.00 0.00 0.00 0.10 0.54 0.34 0.02
#> TCGA.AZ.4682.01 6 0.3517 0.60053 0.00 0.00 0.02 0.00 0.00 0.70 0.28
#> TCGA.EI.6884.01 3 0.1671 0.69361 0.00 0.00 0.90 0.00 0.00 0.00 0.10
#> TCGA.F4.6806.01 5 0.2832 0.61959 0.24 0.00 0.00 0.00 0.76 0.00 0.00
#> TCGA.G4.6320.11 2 0.0504 0.98592 0.00 0.98 0.00 0.00 0.00 0.02 0.00
#> TCGA.G4.6322.01 5 0.3047 0.57917 0.28 0.00 0.00 0.00 0.72 0.00 0.00
#> TCGA.F5.6810.01 4 0.1671 0.92805 0.00 0.00 0.00 0.90 0.00 0.00 0.10
#> TCGA.5M.AAT4.01 5 0.2422 0.66903 0.18 0.00 0.00 0.00 0.82 0.00 0.00
#> TCGA.CL.4957.01 6 0.3370 0.65533 0.00 0.00 0.06 0.00 0.00 0.78 0.16
#> TCGA.DC.6681.01 3 0.0863 0.71985 0.00 0.00 0.96 0.00 0.00 0.00 0.04
#> TCGA.CM.6167.01 4 0.3546 0.20783 0.00 0.00 0.00 0.54 0.00 0.00 0.46
#> TCGA.AG.4022.01 6 0.3985 0.04933 0.00 0.00 0.46 0.02 0.00 0.52 0.00
#> TCGA.G4.6586.01 5 0.3294 0.48245 0.34 0.00 0.00 0.00 0.66 0.00 0.00
#> TCGA.EI.6514.01 5 0.3780 0.60525 0.24 0.00 0.00 0.02 0.72 0.02 0.00
#> TCGA.CK.4950.01 3 0.2422 0.63583 0.00 0.00 0.82 0.00 0.00 0.00 0.18
#> TCGA.DM.A282.01 5 0.3459 0.37630 0.40 0.00 0.00 0.00 0.60 0.00 0.00
#> TCGA.DY.A1DC.01 6 0.2016 0.65911 0.00 0.00 0.06 0.00 0.00 0.90 0.04
#> TCGA.D5.6535.01 3 0.4421 -0.03156 0.00 0.00 0.50 0.02 0.46 0.02 0.00
#> TCGA.DM.A1HA.01 1 0.0000 0.96854 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DC.5869.01 5 0.4732 0.57159 0.00 0.00 0.04 0.08 0.72 0.14 0.02
#> TCGA.AZ.6599.11 2 0.0000 0.99420 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CM.4752.01 7 0.1363 0.69472 0.00 0.00 0.04 0.02 0.00 0.00 0.94
#> TCGA.AZ.4684.01 7 0.3685 0.30597 0.00 0.00 0.02 0.00 0.00 0.32 0.66
#> TCGA.EI.7004.01 3 0.0863 0.71985 0.00 0.00 0.96 0.00 0.00 0.00 0.04
#> TCGA.A6.A565.01 2 0.0504 0.98592 0.00 0.98 0.00 0.00 0.00 0.02 0.00
#> TCGA.D5.6531.01 1 0.0000 0.96854 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AZ.6598.01 1 0.0000 0.96854 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AD.6890.01 3 0.5983 0.23273 0.00 0.00 0.50 0.08 0.12 0.30 0.00
#> TCGA.AG.4021.01 5 0.1886 0.69250 0.12 0.00 0.00 0.00 0.88 0.00 0.00
#> TCGA.A6.6781.01 7 0.3139 0.42915 0.00 0.00 0.00 0.30 0.00 0.00 0.70
#> TCGA.DM.A1D9.01 5 0.1006 0.67991 0.00 0.00 0.00 0.02 0.96 0.00 0.02
#> TCGA.CM.4744.01 5 0.2422 0.66903 0.18 0.00 0.00 0.00 0.82 0.00 0.00
#> TCGA.A6.2679.11 2 0.0000 0.99420 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.A6.6652.01 5 0.4992 0.44524 0.00 0.00 0.00 0.10 0.60 0.28 0.02
#> TCGA.AD.6964.01 4 0.2745 0.72596 0.00 0.16 0.00 0.82 0.00 0.02 0.00
#> TCGA.SS.A7HO.01 5 0.4308 0.56169 0.00 0.00 0.00 0.10 0.72 0.16 0.02
#> TCGA.A6.6650.01 1 0.0863 0.93161 0.96 0.00 0.00 0.00 0.04 0.00 0.00
#> TCGA.DM.A0XF.01 7 0.2163 0.65364 0.00 0.00 0.02 0.00 0.00 0.10 0.88
#> TCGA.G4.6295.01 7 0.2829 0.70089 0.00 0.00 0.00 0.08 0.00 0.08 0.84
#> TCGA.F4.6461.01 5 0.2572 0.61614 0.00 0.00 0.20 0.00 0.80 0.00 0.00
#> TCGA.AM.5820.01 6 0.5630 0.38758 0.00 0.00 0.06 0.10 0.20 0.62 0.02
#> TCGA.G4.6314.11 2 0.0000 0.99420 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AD.6889.01 1 0.0000 0.96854 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AZ.6605.01 7 0.3562 -0.06464 0.00 0.00 0.50 0.00 0.00 0.00 0.50
#> TCGA.EI.6881.01 5 0.5747 0.42801 0.00 0.00 0.04 0.10 0.56 0.28 0.02
#> TCGA.NH.A50T.01 1 0.0504 0.95077 0.98 0.00 0.00 0.00 0.02 0.00 0.00
#> TCGA.AG.3725.11 2 0.0000 0.99420 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.G4.6323.01 3 0.1671 0.68141 0.00 0.00 0.90 0.00 0.10 0.00 0.00
#> TCGA.AA.3663.01 5 0.2422 0.66903 0.18 0.00 0.00 0.00 0.82 0.00 0.00
#> TCGA.AD.6899.01 5 0.2259 0.64082 0.00 0.00 0.16 0.00 0.84 0.00 0.00
#> TCGA.A6.5667.11 2 0.0000 0.99420 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.A6.A56B.01 5 0.3142 0.68558 0.10 0.00 0.00 0.02 0.84 0.02 0.02
#> TCGA.G5.6572.01 7 0.3388 0.60457 0.00 0.00 0.00 0.04 0.00 0.20 0.76
#> TCGA.DM.A280.01 3 0.3562 0.03096 0.00 0.00 0.50 0.00 0.00 0.00 0.50
#> TCGA.AG.A020.01 6 0.3795 0.64379 0.00 0.00 0.06 0.00 0.00 0.72 0.22
#> TCGA.AA.3713.01 3 0.0863 0.71985 0.00 0.00 0.96 0.00 0.00 0.00 0.04
#> TCGA.D5.5539.01 5 0.1166 0.67546 0.00 0.00 0.06 0.00 0.94 0.00 0.00
#> TCGA.AA.3655.11 2 0.0000 0.99420 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AA.3489.01 7 0.3058 0.64277 0.00 0.00 0.10 0.08 0.00 0.00 0.82
#> TCGA.AA.3495.01 5 0.3562 0.06128 0.00 0.00 0.50 0.00 0.50 0.00 0.00
#> TCGA.AG.A01Y.01 7 0.3186 0.58374 0.00 0.00 0.00 0.22 0.00 0.02 0.76
#> TCGA.AZ.6601.01 3 0.0504 0.71623 0.00 0.00 0.98 0.00 0.02 0.00 0.00
#> TCGA.AH.6903.01 3 0.1886 0.64119 0.00 0.00 0.88 0.00 0.00 0.12 0.00
#> TCGA.AZ.6603.01 7 0.3011 0.69131 0.00 0.00 0.00 0.06 0.00 0.12 0.82
#> TCGA.CA.5254.01 1 0.0000 0.96854 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.A6.A5ZU.01 6 0.3734 0.59497 0.00 0.00 0.14 0.04 0.04 0.78 0.00
#> TCGA.G4.6302.01 4 0.1671 0.92805 0.00 0.00 0.00 0.90 0.00 0.00 0.10
#> TCGA.AZ.5403.01 4 0.2569 0.75127 0.00 0.14 0.00 0.84 0.00 0.02 0.00
#> TCGA.AY.A54L.01 5 0.3496 0.32577 0.42 0.00 0.00 0.00 0.58 0.00 0.00
#> TCGA.A6.4107.01 1 0.0000 0.96854 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.NH.A5IV.01 5 0.3139 0.55618 0.30 0.00 0.00 0.00 0.70 0.00 0.00
#> TCGA.G4.6306.01 1 0.0000 0.96854 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AD.A5EK.01 1 0.0000 0.96854 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.G5.6235.01 7 0.2708 0.54201 0.00 0.00 0.22 0.00 0.00 0.00 0.78
#> TCGA.DC.5337.01 5 0.0000 0.68465 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.CM.6675.01 1 0.0000 0.96854 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AH.6544.01 3 0.4630 0.36843 0.00 0.00 0.62 0.00 0.00 0.26 0.12
#> TCGA.CK.6746.01 1 0.0000 0.96854 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CA.6718.01 5 0.3558 0.11961 0.00 0.00 0.48 0.00 0.52 0.00 0.00
#> TCGA.CI.6621.01 4 0.2422 0.86751 0.00 0.00 0.00 0.82 0.00 0.00 0.18
#> TCGA.CM.6676.01 6 0.4146 0.62635 0.00 0.00 0.08 0.00 0.00 0.68 0.24
#> TCGA.DM.A1DB.01 6 0.2313 0.66075 0.00 0.00 0.06 0.00 0.00 0.88 0.06
#> TCGA.A6.6654.01 3 0.3546 0.14292 0.00 0.00 0.54 0.00 0.00 0.00 0.46
#> TCGA.AA.3510.11 2 0.0000 0.99420 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CA.6715.01 6 0.3745 0.62408 0.00 0.00 0.04 0.00 0.00 0.70 0.26
#> TCGA.CM.5341.01 5 0.3047 0.52223 0.00 0.00 0.28 0.00 0.72 0.00 0.00
#> TCGA.CK.5912.01 6 0.3745 0.62408 0.00 0.00 0.04 0.00 0.00 0.70 0.26
#> TCGA.F4.6857.01 3 0.3562 0.03096 0.00 0.00 0.50 0.00 0.00 0.00 0.50
#> TCGA.QG.A5YW.01 5 0.3047 0.57917 0.28 0.00 0.00 0.00 0.72 0.00 0.00
#> TCGA.A6.5665.01 1 0.3221 0.48065 0.68 0.00 0.00 0.00 0.32 0.00 0.00
#> TCGA.CM.6168.01 3 0.2832 0.56685 0.00 0.00 0.76 0.00 0.00 0.00 0.24
#> TCGA.CL.5917.01 6 0.1664 0.65592 0.00 0.00 0.06 0.00 0.00 0.92 0.02
#> TCGA.AU.6004.01 3 0.2422 0.63583 0.00 0.00 0.82 0.00 0.00 0.00 0.18
#> TCGA.AY.5543.01 6 0.3517 0.45748 0.00 0.00 0.28 0.02 0.00 0.70 0.00
#> TCGA.AG.3731.01 3 0.1886 0.68227 0.00 0.00 0.88 0.00 0.00 0.00 0.12
#> TCGA.G4.6314.01 3 0.0863 0.71985 0.00 0.00 0.96 0.00 0.00 0.00 0.04
#> TCGA.DC.6683.01 3 0.5336 0.11763 0.00 0.00 0.50 0.06 0.02 0.40 0.02
#> TCGA.CA.5796.01 5 0.5036 0.53952 0.00 0.00 0.04 0.08 0.68 0.18 0.02
#> TCGA.AG.A036.11 2 0.0504 0.98592 0.00 0.98 0.00 0.00 0.00 0.02 0.00
#> TCGA.AZ.4323.01 4 0.1671 0.92805 0.00 0.00 0.00 0.90 0.00 0.00 0.10
#> TCGA.EI.6882.01 1 0.0000 0.96854 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AZ.4315.01 3 0.5007 0.28048 0.00 0.00 0.56 0.00 0.28 0.16 0.00
#> TCGA.A6.2677.01 1 0.0000 0.96854 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DY.A1DF.01 6 0.4079 0.53730 0.00 0.00 0.04 0.08 0.12 0.76 0.00
#> TCGA.CM.6162.01 2 0.0504 0.98592 0.00 0.98 0.00 0.00 0.00 0.02 0.00
#> TCGA.F4.6703.01 2 0.0504 0.98592 0.00 0.98 0.00 0.00 0.00 0.02 0.00
#> TCGA.CM.5349.01 3 0.2422 0.63583 0.00 0.00 0.82 0.00 0.00 0.00 0.18
#> TCGA.AG.A02N.01 5 0.5813 0.39839 0.00 0.00 0.04 0.10 0.54 0.30 0.02
#> TCGA.AA.3506.01 5 0.2572 0.61614 0.00 0.00 0.20 0.00 0.80 0.00 0.00
#> TCGA.D5.6932.01 6 0.3795 0.64394 0.00 0.00 0.06 0.00 0.00 0.72 0.22
#> TCGA.D5.6538.01 1 0.0000 0.96854 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AA.3488.11 2 0.0000 0.99420 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AA.3502.01 1 0.0000 0.96854 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.NH.A8F8.01 3 0.3546 0.03972 0.00 0.00 0.54 0.00 0.46 0.00 0.00
#> TCGA.AF.A56N.01 6 0.2745 0.60671 0.00 0.00 0.16 0.02 0.00 0.82 0.00
#> TCGA.AF.6672.01 4 0.1671 0.92805 0.00 0.00 0.00 0.90 0.00 0.00 0.10
#> TCGA.A6.2685.11 2 0.0000 0.99420 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.A6.6141.01 3 0.2016 0.70023 0.00 0.00 0.90 0.00 0.00 0.06 0.04
#> TCGA.AD.6963.01 4 0.1671 0.92805 0.00 0.00 0.00 0.90 0.00 0.00 0.10
#> TCGA.G4.6298.11 2 0.0504 0.98592 0.00 0.98 0.00 0.00 0.00 0.02 0.00
#> TCGA.EI.6917.01 3 0.0504 0.71623 0.00 0.00 0.98 0.00 0.02 0.00 0.00
#> TCGA.QG.A5Z2.01 5 0.2422 0.66903 0.18 0.00 0.00 0.00 0.82 0.00 0.00
#> TCGA.A6.2684.01 3 0.2163 0.66546 0.00 0.00 0.88 0.00 0.00 0.10 0.02
#> TCGA.CK.5915.01 1 0.0000 0.96854 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CM.6163.01 3 0.2278 0.68770 0.00 0.00 0.88 0.00 0.00 0.08 0.04
#> TCGA.G4.6322.11 2 0.0000 0.99420 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AY.6197.01 5 0.3558 0.14500 0.48 0.00 0.00 0.00 0.52 0.00 0.00
#> TCGA.D5.6928.01 7 0.3413 0.26918 0.00 0.00 0.38 0.00 0.00 0.00 0.62
#> TCGA.A6.3810.01 7 0.3413 0.30872 0.00 0.00 0.00 0.38 0.00 0.00 0.62
#> TCGA.G4.6294.01 5 0.4707 0.50708 0.00 0.00 0.00 0.10 0.66 0.22 0.02
#> TCGA.AA.3660.11 2 0.0000 0.99420 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.A6.6137.01 6 0.2259 0.61658 0.00 0.00 0.16 0.00 0.00 0.84 0.00
#> TCGA.G4.6297.11 2 0.0000 0.99420 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AZ.4615.01 5 0.3525 0.21988 0.00 0.00 0.44 0.00 0.56 0.00 0.00
#> TCGA.CK.4952.01 1 0.0000 0.96854 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CM.6172.01 5 0.4992 0.44524 0.00 0.00 0.00 0.10 0.60 0.28 0.02
#> TCGA.AD.6901.01 5 0.3525 0.21988 0.00 0.00 0.44 0.00 0.56 0.00 0.00
#> TCGA.AA.3496.01 5 0.1671 0.69727 0.10 0.00 0.00 0.00 0.90 0.00 0.00
#> TCGA.CK.5913.01 1 0.3047 0.57175 0.72 0.00 0.00 0.00 0.28 0.00 0.00
#> TCGA.DM.A28A.01 1 0.0000 0.96854 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EI.7002.01 5 0.4992 0.44524 0.00 0.00 0.00 0.10 0.60 0.28 0.02
#> TCGA.D5.6533.01 6 0.2259 0.61658 0.00 0.00 0.16 0.00 0.00 0.84 0.00
#> TCGA.QG.A5Z1.01 1 0.2832 0.62437 0.76 0.00 0.00 0.00 0.24 0.00 0.00
#> TCGA.D5.6923.01 7 0.3011 0.69131 0.00 0.00 0.00 0.06 0.00 0.12 0.82
#> TCGA.AF.2690.01 7 0.1006 0.70126 0.00 0.00 0.02 0.02 0.00 0.00 0.96
#> TCGA.DM.A28H.01 5 0.3558 0.15487 0.48 0.00 0.00 0.00 0.52 0.00 0.00
#> TCGA.G4.6320.01 1 0.0000 0.96854 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.G4.6310.01 3 0.4873 0.36340 0.00 0.00 0.60 0.00 0.22 0.18 0.00
#> TCGA.DM.A28M.01 1 0.0000 0.96854 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DM.A288.01 1 0.0000 0.96854 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.A6.2681.01 3 0.4244 0.08853 0.00 0.00 0.54 0.00 0.42 0.04 0.00
#> TCGA.A6.2679.01 5 0.3558 0.11961 0.00 0.00 0.48 0.00 0.52 0.00 0.00
#> TCGA.4N.A93T.01 5 0.5813 0.39839 0.00 0.00 0.04 0.10 0.54 0.30 0.02
#> TCGA.NH.A8F7.06 6 0.3745 0.62408 0.00 0.00 0.04 0.00 0.00 0.70 0.26
#> TCGA.NH.A8F7.01 6 0.3459 0.42593 0.00 0.00 0.00 0.00 0.00 0.60 0.40
#> TCGA.AZ.6600.11 2 0.0000 0.99420 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.G5.6572.02 4 0.1671 0.92805 0.00 0.00 0.00 0.90 0.00 0.00 0.10
#> TCGA.AY.6386.01 5 0.3496 0.26192 0.00 0.00 0.42 0.00 0.58 0.00 0.00
#> TCGA.G4.6628.01 3 0.1671 0.68141 0.00 0.00 0.90 0.00 0.10 0.00 0.00
#> TCGA.A6.6653.01 1 0.0000 0.96854 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CM.4746.01 6 0.6056 0.17007 0.00 0.00 0.06 0.10 0.30 0.52 0.02
#> TCGA.F4.6855.01 5 0.1671 0.66665 0.00 0.00 0.10 0.00 0.90 0.00 0.00
#> TCGA.EF.5830.01 5 0.5747 0.42801 0.00 0.00 0.04 0.10 0.56 0.28 0.02
#> TCGA.NH.A6GA.01 5 0.1671 0.69727 0.10 0.00 0.00 0.00 0.90 0.00 0.00
#> TCGA.NH.A50V.01 5 0.2422 0.62957 0.00 0.00 0.18 0.00 0.82 0.00 0.00
#> TCGA.DY.A0XA.01 7 0.2803 0.70562 0.00 0.00 0.00 0.06 0.00 0.10 0.84
#> TCGA.DM.A28E.01 6 0.3413 0.46240 0.00 0.00 0.00 0.00 0.00 0.62 0.38
#> TCGA.AG.3725.01 5 0.5747 0.42801 0.00 0.00 0.04 0.10 0.56 0.28 0.02
#> TCGA.CK.6747.01 1 0.0000 0.96854 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CL.5918.01 1 0.0000 0.96854 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CI.6623.01 4 0.2259 0.88431 0.00 0.00 0.00 0.84 0.00 0.00 0.16
#> TCGA.A6.5667.01 6 0.3841 0.60608 0.00 0.00 0.04 0.00 0.00 0.68 0.28
#> TCGA.DM.A28K.01 1 0.0000 0.96854 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AA.3713.11 2 0.0000 0.99420 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AA.3655.01 5 0.5443 0.43764 0.00 0.00 0.02 0.10 0.58 0.28 0.02
#> TCGA.AU.3779.01 7 0.3388 0.60457 0.00 0.00 0.00 0.04 0.00 0.20 0.76
#> TCGA.A6.5664.01 3 0.3558 0.09035 0.00 0.00 0.52 0.00 0.00 0.00 0.48
#> TCGA.AA.3697.11 2 0.0000 0.99420 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AZ.5407.01 5 0.2832 0.61959 0.24 0.00 0.00 0.00 0.76 0.00 0.00
#> TCGA.CM.6169.01 3 0.5377 0.28814 0.00 0.00 0.56 0.02 0.26 0.16 0.00
#> TCGA.AH.6547.01 7 0.3517 0.44593 0.00 0.00 0.02 0.28 0.00 0.00 0.70
#> TCGA.AZ.6601.11 2 0.0000 0.99420 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.A6.5661.01 5 0.2422 0.66903 0.18 0.00 0.00 0.00 0.82 0.00 0.00
#> TCGA.F4.6807.01 3 0.0000 0.71860 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.QG.A5YV.01 1 0.0000 0.96854 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AA.3509.11 2 0.0000 0.99420 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AY.A71X.01 1 0.0000 0.96854 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CA.5797.01 4 0.1671 0.92805 0.00 0.00 0.00 0.90 0.00 0.00 0.10
#> TCGA.F4.6460.01 4 0.1671 0.92805 0.00 0.00 0.00 0.90 0.00 0.00 0.10
#> TCGA.G4.6302.11 2 0.0504 0.98592 0.00 0.98 0.00 0.00 0.00 0.02 0.00
#> TCGA.F5.6702.01 4 0.1671 0.92805 0.00 0.00 0.00 0.90 0.00 0.00 0.10
#> TCGA.AH.6549.01 5 0.2572 0.65680 0.20 0.00 0.00 0.00 0.80 0.00 0.00
#> TCGA.D5.6927.01 7 0.3546 0.04080 0.00 0.00 0.00 0.46 0.00 0.00 0.54
#> TCGA.CM.6166.01 1 0.1886 0.83815 0.88 0.00 0.00 0.00 0.12 0.00 0.00
#> TCGA.AH.6897.01 1 0.0000 0.96854 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.G4.6304.01 7 0.3459 0.22273 0.00 0.00 0.40 0.00 0.00 0.00 0.60
#> TCGA.CA.5255.01 3 0.2422 0.63583 0.00 0.00 0.82 0.00 0.00 0.00 0.18
#> TCGA.EI.6507.01 3 0.2906 0.62317 0.00 0.00 0.80 0.00 0.00 0.02 0.18
#> TCGA.CK.4947.01 5 0.3525 0.21988 0.00 0.00 0.44 0.00 0.56 0.00 0.00
#> TCGA.D5.5540.01 1 0.0000 0.96854 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DC.6682.01 3 0.3546 0.03972 0.00 0.00 0.54 0.00 0.46 0.00 0.00
#> TCGA.G4.6321.01 3 0.0504 0.71623 0.00 0.00 0.98 0.00 0.02 0.00 0.00
#> TCGA.A6.6649.01 5 0.3525 0.21988 0.00 0.00 0.44 0.00 0.56 0.00 0.00
#> TCGA.CM.5348.01 3 0.0863 0.71985 0.00 0.00 0.96 0.00 0.00 0.00 0.04
#> TCGA.EI.6513.01 4 0.2422 0.86668 0.00 0.00 0.00 0.82 0.00 0.00 0.18
#> TCGA.A6.2672.01 5 0.2259 0.67934 0.16 0.00 0.00 0.00 0.84 0.00 0.00
#> TCGA.D5.6539.01 4 0.1671 0.92805 0.00 0.00 0.00 0.90 0.00 0.00 0.10
#> TCGA.AA.3510.01 6 0.4146 0.62635 0.00 0.00 0.08 0.00 0.00 0.68 0.24
#> TCGA.G5.6233.01 5 0.2422 0.62957 0.00 0.00 0.18 0.00 0.82 0.00 0.00
#> TCGA.BM.6198.01 7 0.1671 0.68013 0.00 0.00 0.00 0.10 0.00 0.00 0.90
#> TCGA.CA.6719.01 5 0.3047 0.57917 0.28 0.00 0.00 0.00 0.72 0.00 0.00
#> TCGA.DC.6154.01 6 0.4707 0.40900 0.00 0.00 0.00 0.10 0.22 0.66 0.02
#> TCGA.DM.A1D6.01 6 0.5051 0.44344 0.00 0.00 0.02 0.10 0.20 0.66 0.02
#> TCGA.AG.3731.11 2 0.0000 0.99420 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CM.6674.01 7 0.3139 0.42915 0.00 0.00 0.00 0.30 0.00 0.00 0.70
#> TCGA.CM.4743.01 3 0.3558 0.09035 0.00 0.00 0.52 0.00 0.00 0.00 0.48
#> TCGA.F5.6465.01 7 0.1166 0.70109 0.00 0.00 0.00 0.06 0.00 0.00 0.94
#> TCGA.D5.5537.01 1 0.0000 0.96854 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.F4.6463.01 3 0.0863 0.71985 0.00 0.00 0.96 0.00 0.00 0.00 0.04
#> TCGA.A6.2686.11 2 0.0504 0.98592 0.00 0.98 0.00 0.00 0.00 0.02 0.00
#> TCGA.4T.AA8H.01 5 0.3459 0.37081 0.40 0.00 0.00 0.00 0.60 0.00 0.00
#> TCGA.A6.6782.01 6 0.4778 0.29258 0.00 0.00 0.34 0.06 0.02 0.58 0.00
#> TCGA.AG.3592.01 5 0.2572 0.65680 0.20 0.00 0.00 0.00 0.80 0.00 0.00
#> TCGA.AD.6888.01 6 0.3911 0.63615 0.00 0.00 0.06 0.00 0.00 0.70 0.24
#> TCGA.CM.6678.01 5 0.1671 0.66665 0.00 0.00 0.10 0.00 0.90 0.00 0.00
#> TCGA.CM.5344.01 7 0.2803 0.70562 0.00 0.00 0.00 0.06 0.00 0.10 0.84
#> TCGA.AA.3495.11 2 0.0000 0.99420 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AG.A01W.11 2 0.0000 0.99420 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.F4.6809.01 3 0.0000 0.71860 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.CK.5914.01 1 0.0000 0.96854 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AZ.4681.01 7 0.3199 0.67269 0.00 0.00 0.00 0.06 0.00 0.14 0.80
#> TCGA.AA.3492.01 1 0.0000 0.96854 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D5.6536.01 6 0.4127 0.39406 0.00 0.00 0.36 0.00 0.00 0.60 0.04
#> TCGA.AA.3506.11 2 0.0000 0.99420 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AA.3488.01 6 0.3061 0.60633 0.00 0.00 0.06 0.02 0.08 0.84 0.00
#> TCGA.AA.3502.11 2 0.0000 0.99420 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.A6.6140.01 7 0.3221 0.44163 0.00 0.00 0.00 0.32 0.00 0.00 0.68
#> TCGA.D5.6529.01 3 0.0863 0.71985 0.00 0.00 0.96 0.00 0.00 0.00 0.04
#> TCGA.DM.A1D0.01 4 0.1671 0.92805 0.00 0.00 0.00 0.90 0.00 0.00 0.10
#> TCGA.DM.A1HB.01 5 0.2422 0.66903 0.18 0.00 0.00 0.00 0.82 0.00 0.00
#> TCGA.D5.6920.01 3 0.2708 0.59268 0.00 0.00 0.78 0.00 0.00 0.00 0.22
#> TCGA.D5.6922.01 6 0.2081 0.62951 0.00 0.00 0.14 0.00 0.00 0.86 0.00
#> TCGA.EI.6508.01 5 0.2159 0.66237 0.00 0.00 0.00 0.06 0.90 0.02 0.02
#> TCGA.D5.6532.01 5 0.2081 0.68581 0.14 0.00 0.00 0.00 0.86 0.00 0.00
#> TCGA.5M.AATA.01 6 0.5375 0.30179 0.00 0.00 0.20 0.00 0.00 0.46 0.34
#> TCGA.EI.6509.01 4 0.1671 0.92805 0.00 0.00 0.00 0.90 0.00 0.00 0.10
#> TCGA.G4.6311.01 3 0.3562 0.03096 0.00 0.00 0.50 0.00 0.00 0.00 0.50
#> TCGA.A6.A566.01 3 0.0863 0.71985 0.00 0.00 0.96 0.00 0.00 0.00 0.04
#> TCGA.G4.6625.01 3 0.2945 0.53974 0.00 0.00 0.74 0.00 0.00 0.00 0.26
#> TCGA.CI.6619.01 4 0.1671 0.92805 0.00 0.00 0.00 0.90 0.00 0.00 0.10
#> TCGA.F5.6864.01 6 0.3911 0.63615 0.00 0.00 0.06 0.00 0.00 0.70 0.24
#> TCGA.AA.3492.11 2 0.0000 0.99420 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.A6.5659.01 1 0.0000 0.96854 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.WS.AB45.01 7 0.3909 0.18287 0.00 0.00 0.02 0.40 0.00 0.00 0.58
#> TCGA.G4.6315.01 3 0.2016 0.69752 0.00 0.00 0.90 0.00 0.00 0.04 0.06
#> TCGA.D5.6541.01 3 0.0863 0.71985 0.00 0.00 0.96 0.00 0.00 0.00 0.04
#> TCGA.A6.2680.01 5 0.0504 0.68425 0.00 0.00 0.02 0.00 0.98 0.00 0.00
#> TCGA.CM.4751.01 3 0.0504 0.71623 0.00 0.00 0.98 0.00 0.02 0.00 0.00
#> TCGA.CM.6680.01 5 0.1671 0.69727 0.10 0.00 0.00 0.00 0.90 0.00 0.00
#> TCGA.AF.6136.01 5 0.5747 0.42801 0.00 0.00 0.04 0.10 0.56 0.28 0.02
#> TCGA.AA.3660.01 5 0.2422 0.66903 0.18 0.00 0.00 0.00 0.82 0.00 0.00
#> TCGA.CM.4747.01 5 0.1886 0.65985 0.00 0.00 0.12 0.00 0.88 0.00 0.00
#> TCGA.EF.5831.01 5 0.3047 0.57917 0.28 0.00 0.00 0.00 0.72 0.00 0.00
#> TCGA.DM.A28G.01 1 0.1166 0.91158 0.94 0.00 0.00 0.00 0.06 0.00 0.00
#> TCGA.G4.6297.01 3 0.0000 0.71860 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.A6.2682.11 2 0.0000 0.99420 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D5.6537.01 5 0.3558 0.15254 0.48 0.00 0.00 0.00 0.52 0.00 0.00
#> TCGA.CM.6170.01 6 0.3745 0.62408 0.00 0.00 0.04 0.00 0.00 0.70 0.26
#> TCGA.DY.A1DD.01 5 0.4992 0.44524 0.00 0.00 0.00 0.10 0.60 0.28 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.AF.3911.01 6 0.0000 0.8737 0.00 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.F4.6459.01 6 0.0000 0.8737 0.00 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.AA.3494.11 2 0.0000 0.9924 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.3L.AA1B.01 3 0.0000 0.7829 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D5.5538.01 3 0.2406 0.7530 0.00 0.00 0.80 0.00 0.20 0.00 0.00 0.00
#> TCGA.F4.6854.01 3 0.3293 0.7061 0.00 0.00 0.74 0.00 0.22 0.00 0.00 0.04
#> TCGA.AG.A026.01 1 0.2267 0.9951 0.82 0.00 0.00 0.00 0.18 0.00 0.00 0.00
#> TCGA.G4.6303.01 8 0.1765 0.9167 0.00 0.00 0.00 0.00 0.12 0.00 0.00 0.88
#> TCGA.F5.6464.01 7 0.5157 0.6407 0.14 0.00 0.20 0.00 0.00 0.00 0.60 0.06
#> TCGA.T9.A92H.01 8 0.1765 0.9167 0.00 0.00 0.00 0.00 0.12 0.00 0.00 0.88
#> TCGA.AA.3712.11 2 0.0000 0.9924 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CM.5863.01 3 0.5257 0.2988 0.14 0.00 0.58 0.00 0.00 0.00 0.22 0.06
#> TCGA.AZ.4308.01 7 0.3615 0.6364 0.00 0.00 0.00 0.04 0.00 0.20 0.74 0.02
#> TCGA.AD.6965.01 1 0.2267 0.9951 0.82 0.00 0.00 0.00 0.18 0.00 0.00 0.00
#> TCGA.A6.2681.11 2 0.0000 0.9924 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AD.6548.01 3 0.0000 0.7829 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.A6.5660.01 1 0.2267 0.9951 0.82 0.00 0.00 0.00 0.18 0.00 0.00 0.00
#> TCGA.AZ.6600.01 3 0.2406 0.7530 0.00 0.00 0.80 0.00 0.20 0.00 0.00 0.00
#> TCGA.F4.6808.01 6 0.1607 0.8421 0.00 0.00 0.04 0.00 0.00 0.92 0.00 0.04
#> TCGA.D5.6540.01 5 0.0000 0.8457 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.F5.6571.01 8 0.2406 0.8481 0.00 0.00 0.00 0.00 0.20 0.00 0.00 0.80
#> TCGA.D5.6926.01 3 0.2756 0.6242 0.00 0.00 0.74 0.00 0.00 0.26 0.00 0.00
#> TCGA.CM.4748.01 3 0.2547 0.7025 0.04 0.00 0.84 0.00 0.00 0.12 0.00 0.00
#> TCGA.A6.2675.11 2 0.0000 0.9924 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.5M.AATE.01 6 0.1563 0.8212 0.00 0.00 0.00 0.00 0.00 0.90 0.00 0.10
#> TCGA.D5.5541.01 7 0.3843 0.5978 0.00 0.00 0.00 0.04 0.00 0.24 0.70 0.02
#> TCGA.CM.5862.01 8 0.2534 0.8142 0.00 0.00 0.00 0.00 0.22 0.00 0.00 0.78
#> TCGA.AA.3511.01 6 0.0471 0.8680 0.00 0.00 0.00 0.00 0.00 0.98 0.00 0.02
#> TCGA.AA.3663.11 2 0.0000 0.9924 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CI.6622.01 5 0.3514 0.3396 0.00 0.00 0.02 0.00 0.64 0.00 0.00 0.34
#> TCGA.EI.6506.01 7 0.5157 0.6407 0.14 0.00 0.20 0.00 0.00 0.00 0.60 0.06
#> TCGA.AM.5821.01 3 0.2756 0.6825 0.00 0.00 0.74 0.00 0.26 0.00 0.00 0.00
#> TCGA.F5.6812.01 4 0.1563 0.8571 0.00 0.00 0.00 0.90 0.00 0.00 0.10 0.00
#> TCGA.G4.6588.01 5 0.0000 0.8457 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.EI.6512.01 5 0.0000 0.8457 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.A6.6648.01 4 0.0000 0.9282 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.A6.2671.11 2 0.0471 0.9882 0.00 0.98 0.00 0.00 0.00 0.00 0.00 0.02
#> TCGA.NH.A6GC.01 8 0.2484 0.9037 0.00 0.00 0.00 0.00 0.10 0.02 0.02 0.86
#> TCGA.F4.6805.01 7 0.3397 0.7010 0.10 0.00 0.00 0.04 0.00 0.00 0.80 0.06
#> TCGA.AA.3697.01 6 0.1091 0.8496 0.00 0.00 0.00 0.00 0.00 0.94 0.00 0.06
#> TCGA.QG.A5YX.01 8 0.1765 0.9167 0.00 0.00 0.00 0.00 0.12 0.00 0.00 0.88
#> TCGA.DM.A28C.01 8 0.2547 0.7911 0.00 0.00 0.00 0.00 0.00 0.12 0.04 0.84
#> TCGA.AG.A036.01 8 0.1947 0.9054 0.00 0.00 0.00 0.00 0.14 0.00 0.00 0.86
#> TCGA.AZ.6606.01 1 0.2267 0.9951 0.82 0.00 0.00 0.00 0.18 0.00 0.00 0.00
#> TCGA.F4.6570.01 5 0.0000 0.8457 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.DC.4745.01 6 0.0000 0.8737 0.00 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.AF.A56K.01 4 0.0000 0.9282 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.G4.6627.01 7 0.3758 0.6986 0.14 0.00 0.00 0.04 0.00 0.00 0.76 0.06
#> TCGA.A6.5657.01 7 0.5157 0.6407 0.14 0.00 0.20 0.00 0.00 0.00 0.60 0.06
#> TCGA.A6.5662.01 6 0.0471 0.8680 0.00 0.00 0.00 0.00 0.00 0.98 0.00 0.02
#> TCGA.AA.3509.01 8 0.1765 0.9167 0.00 0.00 0.00 0.00 0.12 0.00 0.00 0.88
#> TCGA.D5.6929.01 7 0.1275 0.6873 0.02 0.00 0.00 0.04 0.00 0.00 0.94 0.00
#> TCGA.CM.6679.01 6 0.0808 0.8585 0.00 0.00 0.04 0.00 0.00 0.96 0.00 0.00
#> TCGA.A6.2680.11 2 0.0000 0.9924 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DC.6157.01 4 0.2852 0.6692 0.00 0.00 0.00 0.72 0.00 0.00 0.28 0.00
#> TCGA.AF.6655.01 4 0.2650 0.7177 0.00 0.00 0.00 0.76 0.00 0.00 0.24 0.00
#> TCGA.CM.6161.01 3 0.3586 0.7546 0.00 0.00 0.78 0.00 0.12 0.06 0.00 0.04
#> TCGA.EI.6883.01 1 0.2267 0.9951 0.82 0.00 0.00 0.00 0.18 0.00 0.00 0.00
#> TCGA.F5.6811.01 8 0.3922 0.6273 0.00 0.00 0.06 0.00 0.30 0.00 0.00 0.64
#> TCGA.D5.6930.01 3 0.0000 0.7829 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CM.6164.01 7 0.3615 0.6364 0.00 0.00 0.00 0.04 0.00 0.20 0.74 0.02
#> TCGA.AF.2687.01 4 0.0808 0.9144 0.04 0.00 0.00 0.96 0.00 0.00 0.00 0.00
#> TCGA.DY.A1H8.01 8 0.2547 0.7911 0.00 0.00 0.00 0.00 0.00 0.12 0.04 0.84
#> TCGA.G5.6641.01 6 0.3658 0.3161 0.00 0.00 0.02 0.00 0.00 0.58 0.00 0.40
#> TCGA.DC.6155.01 6 0.0471 0.8688 0.00 0.00 0.02 0.00 0.00 0.98 0.00 0.00
#> TCGA.RU.A8FL.01 8 0.1947 0.9036 0.00 0.00 0.00 0.00 0.14 0.00 0.00 0.86
#> TCGA.CK.4951.01 3 0.2406 0.7530 0.00 0.00 0.80 0.00 0.20 0.00 0.00 0.00
#> TCGA.F4.6704.01 4 0.3142 0.5516 0.00 0.00 0.00 0.64 0.00 0.00 0.36 0.00
#> TCGA.AZ.6599.01 1 0.2267 0.9951 0.82 0.00 0.00 0.00 0.18 0.00 0.00 0.00
#> TCGA.F5.6861.01 3 0.1275 0.7599 0.04 0.00 0.94 0.00 0.00 0.02 0.00 0.00
#> TCGA.CM.5860.01 5 0.0000 0.8457 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.A6.6780.01 5 0.0000 0.8457 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.A6.2686.01 5 0.1765 0.7715 0.00 0.00 0.12 0.00 0.88 0.00 0.00 0.00
#> TCGA.CM.4750.01 5 0.0000 0.8457 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.CM.6677.01 5 0.0000 0.8457 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.A6.A567.01 4 0.3570 0.5368 0.02 0.00 0.00 0.62 0.00 0.00 0.36 0.00
#> TCGA.F5.6814.01 1 0.3083 0.7405 0.66 0.00 0.00 0.00 0.34 0.00 0.00 0.00
#> TCGA.D5.6898.01 6 0.0000 0.8737 0.00 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.AG.A01W.01 3 0.2406 0.7530 0.00 0.00 0.80 0.00 0.20 0.00 0.00 0.00
#> TCGA.AZ.6598.11 2 0.0471 0.9882 0.00 0.98 0.00 0.00 0.00 0.00 0.00 0.02
#> TCGA.F5.6813.01 6 0.0000 0.8737 0.00 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.AG.3732.01 7 0.3397 0.7010 0.10 0.00 0.00 0.04 0.00 0.00 0.80 0.06
#> TCGA.EI.6885.01 4 0.0808 0.9144 0.04 0.00 0.00 0.96 0.00 0.00 0.00 0.00
#> TCGA.G4.6299.01 5 0.2267 0.7198 0.00 0.00 0.18 0.00 0.82 0.00 0.00 0.00
#> TCGA.A6.4105.01 5 0.0000 0.8457 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.DM.A1D8.01 1 0.2267 0.9951 0.82 0.00 0.00 0.00 0.18 0.00 0.00 0.00
#> TCGA.DM.A285.01 3 0.0000 0.7829 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.G4.6295.11 2 0.0471 0.9882 0.00 0.98 0.00 0.00 0.00 0.00 0.00 0.02
#> TCGA.DC.4749.01 6 0.3449 0.4515 0.00 0.00 0.00 0.00 0.00 0.66 0.32 0.02
#> TCGA.DT.5265.01 5 0.2267 0.7198 0.00 0.00 0.18 0.00 0.82 0.00 0.00 0.00
#> TCGA.5M.AAT5.01 7 0.4779 0.5614 0.02 0.00 0.00 0.12 0.00 0.18 0.66 0.02
#> TCGA.DM.A0XD.01 5 0.2267 0.7198 0.00 0.00 0.18 0.00 0.82 0.00 0.00 0.00
#> TCGA.A6.6138.01 5 0.2267 0.7198 0.00 0.00 0.18 0.00 0.82 0.00 0.00 0.00
#> TCGA.D5.7000.01 5 0.0000 0.8457 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.DM.A28F.01 5 0.2534 0.6375 0.00 0.00 0.00 0.00 0.78 0.00 0.00 0.22
#> TCGA.DY.A1DE.01 6 0.0000 0.8737 0.00 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.A6.6142.01 4 0.0808 0.8942 0.00 0.04 0.00 0.96 0.00 0.00 0.00 0.00
#> TCGA.QL.A97D.01 8 0.3746 0.6221 0.00 0.00 0.04 0.00 0.32 0.00 0.00 0.64
#> TCGA.CK.6748.01 6 0.0808 0.8603 0.00 0.00 0.00 0.00 0.00 0.96 0.00 0.04
#> TCGA.DC.6160.01 7 0.3615 0.6364 0.00 0.00 0.00 0.04 0.00 0.20 0.74 0.02
#> TCGA.D5.6534.01 7 0.5157 0.6407 0.14 0.00 0.20 0.00 0.00 0.00 0.60 0.06
#> TCGA.AZ.4616.01 3 0.2406 0.7530 0.00 0.00 0.80 0.00 0.20 0.00 0.00 0.00
#> TCGA.CK.6751.01 5 0.0000 0.8457 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.CM.6171.01 1 0.2267 0.9951 0.82 0.00 0.00 0.00 0.18 0.00 0.00 0.00
#> TCGA.DM.A1DA.01 1 0.2267 0.9951 0.82 0.00 0.00 0.00 0.18 0.00 0.00 0.00
#> TCGA.AG.A020.11 2 0.0000 0.9924 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.G4.6311.11 2 0.0471 0.9882 0.00 0.98 0.00 0.00 0.00 0.00 0.00 0.02
#> TCGA.G4.6625.11 2 0.0000 0.9924 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.F5.6863.01 7 0.3426 0.6225 0.00 0.00 0.00 0.02 0.00 0.22 0.74 0.02
#> TCGA.G4.6317.02 6 0.3036 0.6767 0.00 0.00 0.00 0.00 0.00 0.78 0.18 0.04
#> TCGA.G4.6317.01 6 0.3293 0.6513 0.00 0.00 0.00 0.00 0.00 0.74 0.04 0.22
#> TCGA.DM.A1D4.01 1 0.2267 0.9951 0.82 0.00 0.00 0.00 0.18 0.00 0.00 0.00
#> TCGA.AG.A01Y.11 2 0.0000 0.9924 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D5.6530.01 3 0.3746 0.4953 0.00 0.00 0.64 0.00 0.00 0.32 0.00 0.04
#> TCGA.CK.4948.01 7 0.3758 0.6933 0.14 0.00 0.00 0.04 0.00 0.00 0.76 0.06
#> TCGA.AD.A5EJ.01 5 0.2756 0.5060 0.26 0.00 0.00 0.00 0.74 0.00 0.00 0.00
#> TCGA.A6.6651.01 4 0.0000 0.9282 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.CA.5256.01 8 0.2132 0.8930 0.00 0.00 0.00 0.00 0.08 0.04 0.00 0.88
#> TCGA.DM.A0X9.01 1 0.2267 0.9951 0.82 0.00 0.00 0.00 0.18 0.00 0.00 0.00
#> TCGA.AY.A69D.01 5 0.2404 0.7431 0.00 0.00 0.14 0.00 0.84 0.00 0.00 0.02
#> TCGA.G4.6626.01 6 0.0471 0.8689 0.00 0.00 0.00 0.00 0.00 0.98 0.00 0.02
#> TCGA.CA.6716.01 1 0.2267 0.9951 0.82 0.00 0.00 0.00 0.18 0.00 0.00 0.00
#> TCGA.A6.2682.01 7 0.5157 0.6407 0.14 0.00 0.20 0.00 0.00 0.00 0.60 0.06
#> TCGA.A6.4107.11 2 0.0000 0.9924 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CA.6717.01 3 0.5257 0.2988 0.14 0.00 0.58 0.00 0.00 0.00 0.22 0.06
#> TCGA.G4.6293.01 3 0.2406 0.7530 0.00 0.00 0.80 0.00 0.20 0.00 0.00 0.00
#> TCGA.CK.5916.01 5 0.2267 0.7198 0.00 0.00 0.18 0.00 0.82 0.00 0.00 0.00
#> TCGA.G4.6309.01 4 0.0000 0.9282 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.AA.3662.01 3 0.3337 0.7567 0.00 0.00 0.78 0.00 0.16 0.04 0.00 0.02
#> TCGA.AF.A56L.01 3 0.2404 0.6958 0.02 0.00 0.84 0.00 0.00 0.14 0.00 0.00
#> TCGA.NH.A6GB.01 5 0.0000 0.8457 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.AD.5900.01 3 0.1947 0.7798 0.00 0.00 0.86 0.00 0.14 0.00 0.00 0.00
#> TCGA.NH.A50U.01 5 0.3083 0.4209 0.00 0.00 0.00 0.00 0.66 0.00 0.00 0.34
#> TCGA.AA.3712.01 6 0.0000 0.8737 0.00 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.AZ.4614.01 1 0.2267 0.9951 0.82 0.00 0.00 0.00 0.18 0.00 0.00 0.00
#> TCGA.AH.6644.01 5 0.2725 0.7253 0.00 0.00 0.14 0.00 0.82 0.00 0.00 0.04
#> TCGA.AZ.6607.01 3 0.1765 0.7828 0.00 0.00 0.88 0.00 0.12 0.00 0.00 0.00
#> TCGA.AF.2693.01 7 0.3426 0.6225 0.00 0.00 0.00 0.02 0.00 0.22 0.74 0.02
#> TCGA.D5.6924.01 6 0.3193 0.3220 0.00 0.00 0.38 0.00 0.00 0.62 0.00 0.00
#> TCGA.CM.5868.01 7 0.3735 0.6207 0.00 0.00 0.00 0.04 0.00 0.22 0.72 0.02
#> TCGA.AF.4110.01 7 0.3615 0.6364 0.00 0.00 0.00 0.04 0.00 0.20 0.74 0.02
#> TCGA.A6.3809.01 5 0.0000 0.8457 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.AZ.4313.01 4 0.0000 0.9282 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.A6.2675.01 7 0.2650 0.5064 0.00 0.00 0.00 0.24 0.00 0.00 0.76 0.00
#> TCGA.AZ.6608.01 6 0.0471 0.8680 0.00 0.00 0.00 0.00 0.00 0.98 0.00 0.02
#> TCGA.CM.5864.01 1 0.2267 0.9951 0.82 0.00 0.00 0.00 0.18 0.00 0.00 0.00
#> TCGA.AA.3494.01 4 0.0000 0.9282 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.AD.6895.01 3 0.1947 0.7798 0.00 0.00 0.86 0.00 0.14 0.00 0.00 0.00
#> TCGA.CI.6620.01 3 0.2114 0.7738 0.00 0.00 0.84 0.00 0.16 0.00 0.00 0.00
#> TCGA.DC.6156.01 3 0.0471 0.7849 0.00 0.00 0.98 0.00 0.02 0.00 0.00 0.00
#> TCGA.D5.6931.01 3 0.0000 0.7829 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CM.6165.01 8 0.2591 0.8394 0.00 0.00 0.08 0.00 0.04 0.02 0.00 0.86
#> TCGA.CM.5861.01 5 0.0000 0.8457 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.A6.2671.01 8 0.2025 0.8320 0.00 0.00 0.00 0.00 0.02 0.10 0.00 0.88
#> TCGA.DC.6158.01 6 0.0471 0.8680 0.00 0.00 0.00 0.00 0.00 0.98 0.00 0.02
#> TCGA.AG.3742.01 1 0.2267 0.9951 0.82 0.00 0.00 0.00 0.18 0.00 0.00 0.00
#> TCGA.AG.A02N.11 2 0.0000 0.9924 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.G4.6307.01 4 0.0000 0.9282 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.A6.5666.01 8 0.1765 0.9167 0.00 0.00 0.00 0.00 0.12 0.00 0.00 0.88
#> TCGA.EI.6511.01 3 0.1947 0.7385 0.00 0.00 0.86 0.00 0.00 0.14 0.00 0.00
#> TCGA.CI.6624.01 4 0.0000 0.9282 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.AG.3591.01 8 0.1765 0.9167 0.00 0.00 0.00 0.00 0.12 0.00 0.00 0.88
#> TCGA.AY.A8YK.01 4 0.0808 0.8942 0.00 0.04 0.00 0.96 0.00 0.00 0.00 0.00
#> TCGA.F4.6856.01 3 0.0000 0.7829 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DM.A1D7.01 3 0.3015 0.5403 0.00 0.00 0.68 0.00 0.00 0.32 0.00 0.00
#> TCGA.A6.2685.01 2 0.1804 0.9100 0.00 0.90 0.00 0.08 0.00 0.00 0.00 0.02
#> TCGA.5M.AAT6.01 2 0.0471 0.9882 0.00 0.98 0.00 0.00 0.00 0.00 0.00 0.02
#> TCGA.AH.6643.01 8 0.1765 0.9167 0.00 0.00 0.00 0.00 0.12 0.00 0.00 0.88
#> TCGA.F4.6569.01 3 0.2859 0.6599 0.14 0.00 0.82 0.00 0.00 0.00 0.02 0.02
#> TCGA.G4.6298.01 3 0.0471 0.7747 0.02 0.00 0.98 0.00 0.00 0.00 0.00 0.00
#> TCGA.AY.6196.01 7 0.5157 0.6407 0.14 0.00 0.20 0.00 0.00 0.00 0.60 0.06
#> TCGA.EI.6510.01 8 0.1947 0.9036 0.00 0.00 0.00 0.00 0.14 0.00 0.00 0.86
#> TCGA.A6.5656.01 8 0.2114 0.8843 0.00 0.00 0.00 0.00 0.16 0.00 0.00 0.84
#> TCGA.A6.2684.11 2 0.0000 0.9924 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DY.A1DG.01 8 0.2547 0.9057 0.00 0.00 0.00 0.00 0.12 0.00 0.04 0.84
#> TCGA.AZ.4682.01 6 0.0471 0.8680 0.00 0.00 0.00 0.00 0.00 0.98 0.00 0.02
#> TCGA.EI.6884.01 3 0.2859 0.6599 0.14 0.00 0.82 0.00 0.00 0.00 0.02 0.02
#> TCGA.F4.6806.01 5 0.0000 0.8457 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.G4.6320.11 2 0.0471 0.9882 0.00 0.98 0.00 0.00 0.00 0.00 0.00 0.02
#> TCGA.G4.6322.01 5 0.0808 0.8208 0.04 0.00 0.00 0.00 0.96 0.00 0.00 0.00
#> TCGA.F5.6810.01 4 0.0808 0.9144 0.04 0.00 0.00 0.96 0.00 0.00 0.00 0.00
#> TCGA.5M.AAT4.01 5 0.0000 0.8457 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.CL.4957.01 6 0.0000 0.8737 0.00 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.DC.6681.01 3 0.1607 0.7521 0.04 0.00 0.92 0.00 0.00 0.04 0.00 0.00
#> TCGA.CM.6167.01 7 0.3618 0.3540 0.02 0.00 0.00 0.38 0.00 0.00 0.60 0.00
#> TCGA.AG.4022.01 3 0.3658 0.3544 0.00 0.00 0.58 0.00 0.00 0.40 0.00 0.02
#> TCGA.G4.6586.01 5 0.1341 0.7842 0.08 0.00 0.00 0.00 0.92 0.00 0.00 0.00
#> TCGA.EI.6514.01 5 0.2406 0.6609 0.00 0.00 0.00 0.00 0.80 0.00 0.00 0.20
#> TCGA.CK.4950.01 3 0.5157 0.3433 0.14 0.00 0.60 0.00 0.00 0.00 0.20 0.06
#> TCGA.DM.A282.01 5 0.2406 0.6234 0.20 0.00 0.00 0.00 0.80 0.00 0.00 0.00
#> TCGA.DY.A1DC.01 6 0.0471 0.8689 0.00 0.00 0.00 0.00 0.00 0.98 0.00 0.02
#> TCGA.D5.6535.01 3 0.2406 0.7530 0.00 0.00 0.80 0.00 0.20 0.00 0.00 0.00
#> TCGA.DM.A1HA.01 1 0.2267 0.9951 0.82 0.00 0.00 0.00 0.18 0.00 0.00 0.00
#> TCGA.DC.5869.01 8 0.2267 0.8671 0.00 0.00 0.00 0.00 0.18 0.00 0.00 0.82
#> TCGA.AZ.6599.11 2 0.0000 0.9924 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CM.4752.01 7 0.3758 0.6986 0.14 0.00 0.00 0.04 0.00 0.00 0.76 0.06
#> TCGA.AZ.4684.01 6 0.2719 0.6666 0.00 0.00 0.00 0.00 0.00 0.80 0.18 0.02
#> TCGA.EI.7004.01 3 0.0808 0.7647 0.04 0.00 0.96 0.00 0.00 0.00 0.00 0.00
#> TCGA.A6.A565.01 2 0.0471 0.9882 0.00 0.98 0.00 0.00 0.00 0.00 0.00 0.02
#> TCGA.D5.6531.01 1 0.2267 0.9951 0.82 0.00 0.00 0.00 0.18 0.00 0.00 0.00
#> TCGA.AZ.6598.01 1 0.2267 0.9951 0.82 0.00 0.00 0.00 0.18 0.00 0.00 0.00
#> TCGA.AD.6890.01 3 0.4122 0.7147 0.00 0.00 0.74 0.00 0.08 0.10 0.00 0.08
#> TCGA.AG.4021.01 5 0.0000 0.8457 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.A6.6781.01 7 0.3397 0.7010 0.10 0.00 0.00 0.04 0.00 0.00 0.80 0.06
#> TCGA.DM.A1D9.01 5 0.2650 0.6039 0.00 0.00 0.00 0.00 0.76 0.00 0.00 0.24
#> TCGA.CM.4744.01 5 0.0000 0.8457 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.A6.2679.11 2 0.0471 0.9882 0.00 0.98 0.00 0.00 0.00 0.00 0.00 0.02
#> TCGA.A6.6652.01 8 0.1765 0.9167 0.00 0.00 0.00 0.00 0.12 0.00 0.00 0.88
#> TCGA.AD.6964.01 4 0.0808 0.8942 0.00 0.04 0.00 0.96 0.00 0.00 0.00 0.00
#> TCGA.SS.A7HO.01 8 0.1947 0.9036 0.00 0.00 0.00 0.00 0.14 0.00 0.00 0.86
#> TCGA.A6.6650.01 1 0.2406 0.9665 0.80 0.00 0.00 0.00 0.20 0.00 0.00 0.00
#> TCGA.DM.A0XF.01 7 0.3494 0.6726 0.04 0.00 0.00 0.04 0.00 0.14 0.78 0.00
#> TCGA.G4.6295.01 7 0.4667 0.6114 0.04 0.00 0.00 0.04 0.00 0.20 0.68 0.04
#> TCGA.F4.6461.01 5 0.2267 0.7198 0.00 0.00 0.18 0.00 0.82 0.00 0.00 0.00
#> TCGA.AM.5820.01 8 0.1765 0.8064 0.00 0.00 0.00 0.00 0.00 0.12 0.00 0.88
#> TCGA.G4.6314.11 2 0.0471 0.9882 0.00 0.98 0.00 0.00 0.00 0.00 0.00 0.02
#> TCGA.AD.6889.01 1 0.2267 0.9951 0.82 0.00 0.00 0.00 0.18 0.00 0.00 0.00
#> TCGA.AZ.6605.01 7 0.5157 0.6407 0.14 0.00 0.20 0.00 0.00 0.00 0.60 0.06
#> TCGA.EI.6881.01 8 0.1765 0.9167 0.00 0.00 0.00 0.00 0.12 0.00 0.00 0.88
#> TCGA.NH.A50T.01 1 0.2267 0.9951 0.82 0.00 0.00 0.00 0.18 0.00 0.00 0.00
#> TCGA.AG.3725.11 2 0.0471 0.9882 0.00 0.98 0.00 0.00 0.00 0.00 0.00 0.02
#> TCGA.G4.6323.01 3 0.1765 0.7828 0.00 0.00 0.88 0.00 0.12 0.00 0.00 0.00
#> TCGA.AA.3663.01 5 0.0000 0.8457 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.AD.6899.01 5 0.2569 0.7242 0.00 0.00 0.16 0.00 0.82 0.00 0.00 0.02
#> TCGA.A6.5667.11 2 0.0000 0.9924 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.A6.A56B.01 5 0.3015 0.4673 0.00 0.00 0.00 0.00 0.68 0.00 0.00 0.32
#> TCGA.G5.6572.01 7 0.3537 0.6012 0.00 0.00 0.00 0.02 0.00 0.24 0.72 0.02
#> TCGA.DM.A280.01 7 0.5157 0.6407 0.14 0.00 0.20 0.00 0.00 0.00 0.60 0.06
#> TCGA.AG.A020.01 6 0.0000 0.8737 0.00 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.AA.3713.01 3 0.0000 0.7829 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D5.5539.01 5 0.3227 0.6923 0.00 0.00 0.14 0.00 0.78 0.00 0.00 0.08
#> TCGA.AA.3655.11 2 0.0000 0.9924 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AA.3489.01 7 0.3758 0.6986 0.14 0.00 0.00 0.04 0.00 0.00 0.76 0.06
#> TCGA.AA.3495.01 3 0.2406 0.7530 0.00 0.00 0.80 0.00 0.20 0.00 0.00 0.00
#> TCGA.AG.A01Y.01 7 0.5397 0.5098 0.04 0.00 0.00 0.16 0.00 0.14 0.62 0.04
#> TCGA.AZ.6601.01 3 0.0000 0.7829 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AH.6903.01 3 0.2650 0.6452 0.00 0.00 0.76 0.00 0.00 0.24 0.00 0.00
#> TCGA.AZ.6603.01 7 0.3735 0.6207 0.00 0.00 0.00 0.04 0.00 0.22 0.72 0.02
#> TCGA.CA.5254.01 1 0.2267 0.9951 0.82 0.00 0.00 0.00 0.18 0.00 0.00 0.00
#> TCGA.A6.A5ZU.01 6 0.3589 0.6955 0.00 0.00 0.16 0.00 0.00 0.74 0.00 0.10
#> TCGA.G4.6302.01 4 0.0000 0.9282 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.AZ.5403.01 4 0.0808 0.8942 0.00 0.04 0.00 0.96 0.00 0.00 0.00 0.00
#> TCGA.AY.A54L.01 5 0.2267 0.6558 0.18 0.00 0.00 0.00 0.82 0.00 0.00 0.00
#> TCGA.A6.4107.01 1 0.2267 0.9951 0.82 0.00 0.00 0.00 0.18 0.00 0.00 0.00
#> TCGA.NH.A5IV.01 5 0.2132 0.7617 0.08 0.00 0.00 0.00 0.88 0.00 0.00 0.04
#> TCGA.G4.6306.01 1 0.2267 0.9951 0.82 0.00 0.00 0.00 0.18 0.00 0.00 0.00
#> TCGA.AD.A5EK.01 1 0.2267 0.9951 0.82 0.00 0.00 0.00 0.18 0.00 0.00 0.00
#> TCGA.G5.6235.01 7 0.3758 0.6940 0.14 0.00 0.04 0.00 0.00 0.00 0.76 0.06
#> TCGA.DC.5337.01 5 0.2650 0.5959 0.00 0.00 0.00 0.00 0.76 0.00 0.00 0.24
#> TCGA.CM.6675.01 1 0.2267 0.9951 0.82 0.00 0.00 0.00 0.18 0.00 0.00 0.00
#> TCGA.AH.6544.01 6 0.5208 0.4022 0.04 0.00 0.26 0.00 0.00 0.60 0.06 0.04
#> TCGA.CK.6746.01 1 0.2267 0.9951 0.82 0.00 0.00 0.00 0.18 0.00 0.00 0.00
#> TCGA.CA.6718.01 3 0.2406 0.7530 0.00 0.00 0.80 0.00 0.20 0.00 0.00 0.00
#> TCGA.CI.6621.01 4 0.2756 0.6954 0.00 0.00 0.00 0.74 0.00 0.00 0.26 0.00
#> TCGA.CM.6676.01 6 0.0000 0.8737 0.00 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.DM.A1DB.01 6 0.0808 0.8603 0.00 0.00 0.00 0.00 0.00 0.96 0.00 0.04
#> TCGA.A6.6654.01 7 0.5157 0.6407 0.14 0.00 0.20 0.00 0.00 0.00 0.60 0.06
#> TCGA.AA.3510.11 2 0.0000 0.9924 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CA.6715.01 6 0.0471 0.8680 0.00 0.00 0.00 0.00 0.00 0.98 0.00 0.02
#> TCGA.CM.5341.01 3 0.2406 0.7530 0.00 0.00 0.80 0.00 0.20 0.00 0.00 0.00
#> TCGA.CK.5912.01 6 0.0471 0.8680 0.00 0.00 0.00 0.00 0.00 0.98 0.00 0.02
#> TCGA.F4.6857.01 7 0.5157 0.6407 0.14 0.00 0.20 0.00 0.00 0.00 0.60 0.06
#> TCGA.QG.A5YW.01 5 0.1887 0.7831 0.06 0.00 0.00 0.00 0.90 0.00 0.00 0.04
#> TCGA.A6.5665.01 5 0.2756 0.5060 0.26 0.00 0.00 0.00 0.74 0.00 0.00 0.00
#> TCGA.CM.6168.01 3 0.5617 -0.0536 0.14 0.00 0.46 0.00 0.00 0.00 0.34 0.06
#> TCGA.CL.5917.01 6 0.1275 0.8560 0.00 0.00 0.00 0.00 0.00 0.94 0.02 0.04
#> TCGA.AU.6004.01 3 0.5157 0.3433 0.14 0.00 0.60 0.00 0.00 0.00 0.20 0.06
#> TCGA.AY.5543.01 6 0.3971 0.1439 0.00 0.00 0.42 0.00 0.00 0.54 0.00 0.04
#> TCGA.AG.3731.01 3 0.2404 0.6786 0.14 0.00 0.84 0.00 0.00 0.00 0.00 0.02
#> TCGA.G4.6314.01 3 0.1765 0.7245 0.00 0.00 0.88 0.00 0.00 0.12 0.00 0.00
#> TCGA.DC.6683.01 3 0.3551 0.6271 0.00 0.00 0.72 0.00 0.00 0.22 0.00 0.06
#> TCGA.CA.5796.01 8 0.2114 0.8886 0.00 0.00 0.00 0.00 0.16 0.00 0.00 0.84
#> TCGA.AG.A036.11 2 0.0471 0.9882 0.00 0.98 0.00 0.00 0.00 0.00 0.00 0.02
#> TCGA.AZ.4323.01 4 0.0000 0.9282 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.EI.6882.01 1 0.2267 0.9951 0.82 0.00 0.00 0.00 0.18 0.00 0.00 0.00
#> TCGA.AZ.4315.01 3 0.2406 0.7530 0.00 0.00 0.80 0.00 0.20 0.00 0.00 0.00
#> TCGA.A6.2677.01 1 0.2267 0.9951 0.82 0.00 0.00 0.00 0.18 0.00 0.00 0.00
#> TCGA.DY.A1DF.01 8 0.3971 0.1779 0.00 0.00 0.00 0.00 0.00 0.42 0.04 0.54
#> TCGA.CM.6162.01 2 0.0471 0.9882 0.00 0.98 0.00 0.00 0.00 0.00 0.00 0.02
#> TCGA.F4.6703.01 2 0.0471 0.9882 0.00 0.98 0.00 0.00 0.00 0.00 0.00 0.02
#> TCGA.CM.5349.01 3 0.5157 0.3433 0.14 0.00 0.60 0.00 0.00 0.00 0.20 0.06
#> TCGA.AG.A02N.01 8 0.1765 0.9167 0.00 0.00 0.00 0.00 0.12 0.00 0.00 0.88
#> TCGA.AA.3506.01 5 0.2267 0.7198 0.00 0.00 0.18 0.00 0.82 0.00 0.00 0.00
#> TCGA.D5.6932.01 6 0.0000 0.8737 0.00 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.D5.6538.01 1 0.2267 0.9951 0.82 0.00 0.00 0.00 0.18 0.00 0.00 0.00
#> TCGA.AA.3488.11 2 0.0000 0.9924 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AA.3502.01 1 0.2267 0.9951 0.82 0.00 0.00 0.00 0.18 0.00 0.00 0.00
#> TCGA.NH.A8F8.01 3 0.2406 0.7530 0.00 0.00 0.80 0.00 0.20 0.00 0.00 0.00
#> TCGA.AF.A56N.01 6 0.3404 0.6105 0.00 0.00 0.24 0.00 0.00 0.72 0.00 0.04
#> TCGA.AF.6672.01 4 0.0000 0.9282 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.A6.2685.11 2 0.0000 0.9924 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.A6.6141.01 3 0.2267 0.6756 0.00 0.00 0.82 0.00 0.00 0.18 0.00 0.00
#> TCGA.AD.6963.01 4 0.0000 0.9282 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.G4.6298.11 2 0.0471 0.9882 0.00 0.98 0.00 0.00 0.00 0.00 0.00 0.02
#> TCGA.EI.6917.01 3 0.0000 0.7829 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.QG.A5Z2.01 5 0.0000 0.8457 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.A6.2684.01 3 0.2756 0.6067 0.00 0.00 0.74 0.00 0.00 0.26 0.00 0.00
#> TCGA.CK.5915.01 1 0.2267 0.9951 0.82 0.00 0.00 0.00 0.18 0.00 0.00 0.00
#> TCGA.CM.6163.01 3 0.2534 0.6304 0.00 0.00 0.78 0.00 0.00 0.22 0.00 0.00
#> TCGA.G4.6322.11 2 0.0000 0.9924 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AY.6197.01 5 0.2114 0.6850 0.16 0.00 0.00 0.00 0.84 0.00 0.00 0.00
#> TCGA.D5.6928.01 7 0.4778 0.6636 0.14 0.00 0.14 0.00 0.00 0.00 0.66 0.06
#> TCGA.A6.3810.01 7 0.3291 0.4333 0.00 0.00 0.00 0.28 0.00 0.00 0.70 0.02
#> TCGA.G4.6294.01 8 0.1765 0.9167 0.00 0.00 0.00 0.00 0.12 0.00 0.00 0.88
#> TCGA.AA.3660.11 2 0.0000 0.9924 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.A6.6137.01 6 0.3036 0.7051 0.00 0.00 0.18 0.00 0.00 0.78 0.00 0.04
#> TCGA.G4.6297.11 2 0.0000 0.9924 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AZ.4615.01 3 0.2406 0.7530 0.00 0.00 0.80 0.00 0.20 0.00 0.00 0.00
#> TCGA.CK.4952.01 1 0.2267 0.9951 0.82 0.00 0.00 0.00 0.18 0.00 0.00 0.00
#> TCGA.CM.6172.01 8 0.1765 0.9167 0.00 0.00 0.00 0.00 0.12 0.00 0.00 0.88
#> TCGA.AD.6901.01 3 0.2406 0.7530 0.00 0.00 0.80 0.00 0.20 0.00 0.00 0.00
#> TCGA.AA.3496.01 5 0.0000 0.8457 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.CK.5913.01 5 0.2756 0.5060 0.26 0.00 0.00 0.00 0.74 0.00 0.00 0.00
#> TCGA.DM.A28A.01 1 0.2267 0.9951 0.82 0.00 0.00 0.00 0.18 0.00 0.00 0.00
#> TCGA.EI.7002.01 8 0.1765 0.9167 0.00 0.00 0.00 0.00 0.12 0.00 0.00 0.88
#> TCGA.D5.6533.01 6 0.3036 0.7051 0.00 0.00 0.18 0.00 0.00 0.78 0.00 0.04
#> TCGA.QG.A5Z1.01 5 0.2534 0.5886 0.22 0.00 0.00 0.00 0.78 0.00 0.00 0.00
#> TCGA.D5.6923.01 7 0.3735 0.6207 0.00 0.00 0.00 0.04 0.00 0.22 0.72 0.02
#> TCGA.AF.2690.01 7 0.3758 0.6986 0.14 0.00 0.00 0.04 0.00 0.00 0.76 0.06
#> TCGA.DM.A28H.01 5 0.2406 0.6234 0.20 0.00 0.00 0.00 0.80 0.00 0.00 0.00
#> TCGA.G4.6320.01 1 0.2267 0.9951 0.82 0.00 0.00 0.00 0.18 0.00 0.00 0.00
#> TCGA.G4.6310.01 3 0.2267 0.7640 0.00 0.00 0.82 0.00 0.18 0.00 0.00 0.00
#> TCGA.DM.A28M.01 1 0.2267 0.9951 0.82 0.00 0.00 0.00 0.18 0.00 0.00 0.00
#> TCGA.DM.A288.01 1 0.2267 0.9951 0.82 0.00 0.00 0.00 0.18 0.00 0.00 0.00
#> TCGA.A6.2681.01 3 0.2406 0.7530 0.00 0.00 0.80 0.00 0.20 0.00 0.00 0.00
#> TCGA.A6.2679.01 3 0.2406 0.7530 0.00 0.00 0.80 0.00 0.20 0.00 0.00 0.00
#> TCGA.4N.A93T.01 8 0.2025 0.9072 0.00 0.00 0.00 0.00 0.10 0.02 0.00 0.88
#> TCGA.NH.A8F7.06 6 0.0471 0.8680 0.00 0.00 0.00 0.00 0.00 0.98 0.00 0.02
#> TCGA.NH.A8F7.01 6 0.2981 0.6369 0.00 0.00 0.00 0.00 0.00 0.76 0.22 0.02
#> TCGA.AZ.6600.11 2 0.0000 0.9924 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.G5.6572.02 4 0.0000 0.9282 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.AY.6386.01 3 0.2756 0.6825 0.00 0.00 0.74 0.00 0.26 0.00 0.00 0.00
#> TCGA.G4.6628.01 3 0.1947 0.7798 0.00 0.00 0.86 0.00 0.14 0.00 0.00 0.00
#> TCGA.A6.6653.01 1 0.2267 0.9951 0.82 0.00 0.00 0.00 0.18 0.00 0.00 0.00
#> TCGA.CM.4746.01 8 0.1765 0.8064 0.00 0.00 0.00 0.00 0.00 0.12 0.00 0.88
#> TCGA.F4.6855.01 5 0.2725 0.7253 0.00 0.00 0.14 0.00 0.82 0.00 0.00 0.04
#> TCGA.EF.5830.01 8 0.1765 0.9167 0.00 0.00 0.00 0.00 0.12 0.00 0.00 0.88
#> TCGA.NH.A6GA.01 5 0.0000 0.8457 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.NH.A50V.01 5 0.2267 0.7198 0.00 0.00 0.18 0.00 0.82 0.00 0.00 0.00
#> TCGA.DY.A0XA.01 7 0.3735 0.6207 0.00 0.00 0.00 0.04 0.00 0.22 0.72 0.02
#> TCGA.DM.A28E.01 6 0.2856 0.6669 0.00 0.00 0.00 0.00 0.00 0.78 0.20 0.02
#> TCGA.AG.3725.01 8 0.2025 0.9072 0.00 0.00 0.00 0.00 0.10 0.02 0.00 0.88
#> TCGA.CK.6747.01 1 0.2267 0.9951 0.82 0.00 0.00 0.00 0.18 0.00 0.00 0.00
#> TCGA.CL.5918.01 1 0.2267 0.9951 0.82 0.00 0.00 0.00 0.18 0.00 0.00 0.00
#> TCGA.CI.6623.01 4 0.2267 0.7784 0.00 0.00 0.00 0.82 0.00 0.00 0.18 0.00
#> TCGA.A6.5667.01 6 0.0471 0.8680 0.00 0.00 0.00 0.00 0.00 0.98 0.00 0.02
#> TCGA.DM.A28K.01 1 0.2267 0.9951 0.82 0.00 0.00 0.00 0.18 0.00 0.00 0.00
#> TCGA.AA.3713.11 2 0.0000 0.9924 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AA.3655.01 8 0.1765 0.9167 0.00 0.00 0.00 0.00 0.12 0.00 0.00 0.88
#> TCGA.AU.3779.01 7 0.3615 0.6364 0.00 0.00 0.00 0.04 0.00 0.20 0.74 0.02
#> TCGA.A6.5664.01 7 0.5157 0.6407 0.14 0.00 0.20 0.00 0.00 0.00 0.60 0.06
#> TCGA.AA.3697.11 2 0.0000 0.9924 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AZ.5407.01 5 0.0000 0.8457 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.CM.6169.01 3 0.2406 0.7530 0.00 0.00 0.80 0.00 0.20 0.00 0.00 0.00
#> TCGA.AH.6547.01 7 0.3758 0.6986 0.14 0.00 0.00 0.04 0.00 0.00 0.76 0.06
#> TCGA.AZ.6601.11 2 0.0000 0.9924 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.A6.5661.01 5 0.0000 0.8457 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.F4.6807.01 3 0.0000 0.7829 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.QG.A5YV.01 1 0.2267 0.9951 0.82 0.00 0.00 0.00 0.18 0.00 0.00 0.00
#> TCGA.AA.3509.11 2 0.0000 0.9924 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AY.A71X.01 1 0.2267 0.9951 0.82 0.00 0.00 0.00 0.18 0.00 0.00 0.00
#> TCGA.CA.5797.01 4 0.0000 0.9282 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.F4.6460.01 4 0.0000 0.9282 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.G4.6302.11 2 0.0471 0.9882 0.00 0.98 0.00 0.00 0.00 0.00 0.00 0.02
#> TCGA.F5.6702.01 4 0.0000 0.9282 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.AH.6549.01 5 0.0000 0.8457 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.D5.6927.01 7 0.3758 0.6573 0.06 0.00 0.00 0.14 0.00 0.00 0.76 0.04
#> TCGA.CM.6166.01 5 0.2650 0.5499 0.24 0.00 0.00 0.00 0.76 0.00 0.00 0.00
#> TCGA.AH.6897.01 1 0.2267 0.9951 0.82 0.00 0.00 0.00 0.18 0.00 0.00 0.00
#> TCGA.G4.6304.01 7 0.5045 0.6487 0.14 0.00 0.18 0.00 0.00 0.00 0.62 0.06
#> TCGA.CA.5255.01 3 0.5344 0.2586 0.14 0.00 0.56 0.00 0.00 0.00 0.24 0.06
#> TCGA.EI.6507.01 3 0.5490 0.4089 0.12 0.00 0.62 0.00 0.00 0.04 0.16 0.06
#> TCGA.CK.4947.01 3 0.2406 0.7530 0.00 0.00 0.80 0.00 0.20 0.00 0.00 0.00
#> TCGA.D5.5540.01 1 0.2267 0.9951 0.82 0.00 0.00 0.00 0.18 0.00 0.00 0.00
#> TCGA.DC.6682.01 3 0.2406 0.7530 0.00 0.00 0.80 0.00 0.20 0.00 0.00 0.00
#> TCGA.G4.6321.01 3 0.0000 0.7829 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.A6.6649.01 3 0.2406 0.7530 0.00 0.00 0.80 0.00 0.20 0.00 0.00 0.00
#> TCGA.CM.5348.01 3 0.0000 0.7829 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EI.6513.01 4 0.2807 0.8375 0.04 0.00 0.00 0.84 0.00 0.00 0.10 0.02
#> TCGA.A6.2672.01 5 0.0000 0.8457 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.D5.6539.01 4 0.0000 0.9282 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.AA.3510.01 6 0.0000 0.8737 0.00 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.G5.6233.01 5 0.2267 0.7198 0.00 0.00 0.18 0.00 0.82 0.00 0.00 0.00
#> TCGA.BM.6198.01 7 0.0808 0.6830 0.00 0.00 0.00 0.04 0.00 0.00 0.96 0.00
#> TCGA.CA.6719.01 5 0.1091 0.8042 0.06 0.00 0.00 0.00 0.94 0.00 0.00 0.00
#> TCGA.DC.6154.01 8 0.2547 0.7911 0.00 0.00 0.00 0.00 0.00 0.12 0.04 0.84
#> TCGA.DM.A1D6.01 8 0.2547 0.7911 0.00 0.00 0.00 0.00 0.00 0.12 0.04 0.84
#> TCGA.AG.3731.11 2 0.0000 0.9924 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CM.6674.01 7 0.3397 0.7010 0.10 0.00 0.00 0.04 0.00 0.00 0.80 0.06
#> TCGA.CM.4743.01 7 0.5157 0.6407 0.14 0.00 0.20 0.00 0.00 0.00 0.60 0.06
#> TCGA.F5.6465.01 7 0.0808 0.6830 0.00 0.00 0.00 0.04 0.00 0.00 0.96 0.00
#> TCGA.D5.5537.01 1 0.2267 0.9951 0.82 0.00 0.00 0.00 0.18 0.00 0.00 0.00
#> TCGA.F4.6463.01 3 0.0000 0.7829 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.A6.2686.11 2 0.0471 0.9882 0.00 0.98 0.00 0.00 0.00 0.00 0.00 0.02
#> TCGA.4T.AA8H.01 5 0.2267 0.6558 0.18 0.00 0.00 0.00 0.82 0.00 0.00 0.00
#> TCGA.A6.6782.01 3 0.3907 0.3697 0.00 0.00 0.58 0.00 0.00 0.38 0.00 0.04
#> TCGA.AG.3592.01 5 0.0000 0.8457 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.AD.6888.01 6 0.0000 0.8737 0.00 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.CM.6678.01 5 0.2569 0.7242 0.00 0.00 0.16 0.00 0.82 0.00 0.00 0.02
#> TCGA.CM.5344.01 7 0.3615 0.6364 0.00 0.00 0.00 0.04 0.00 0.20 0.74 0.02
#> TCGA.AA.3495.11 2 0.0471 0.9882 0.00 0.98 0.00 0.00 0.00 0.00 0.00 0.02
#> TCGA.AG.A01W.11 2 0.0000 0.9924 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.F4.6809.01 3 0.0000 0.7829 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CK.5914.01 1 0.2267 0.9951 0.82 0.00 0.00 0.00 0.18 0.00 0.00 0.00
#> TCGA.AZ.4681.01 7 0.3941 0.5711 0.00 0.00 0.00 0.04 0.00 0.26 0.68 0.02
#> TCGA.AA.3492.01 1 0.2267 0.9951 0.82 0.00 0.00 0.00 0.18 0.00 0.00 0.00
#> TCGA.D5.6536.01 6 0.0808 0.8588 0.00 0.00 0.04 0.00 0.00 0.96 0.00 0.00
#> TCGA.AA.3506.11 2 0.0000 0.9924 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AA.3488.01 6 0.2534 0.6817 0.00 0.00 0.00 0.00 0.00 0.78 0.00 0.22
#> TCGA.AA.3502.11 2 0.0000 0.9924 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.A6.6140.01 7 0.4096 0.4754 0.00 0.00 0.00 0.24 0.00 0.06 0.68 0.02
#> TCGA.D5.6529.01 3 0.0000 0.7829 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DM.A1D0.01 4 0.0000 0.9282 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DM.A1HB.01 5 0.0000 0.8457 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.D5.6920.01 3 0.5485 0.1486 0.14 0.00 0.52 0.00 0.00 0.00 0.28 0.06
#> TCGA.D5.6922.01 6 0.2994 0.7451 0.00 0.00 0.14 0.00 0.00 0.80 0.00 0.06
#> TCGA.EI.6508.01 8 0.3015 0.6416 0.00 0.00 0.00 0.00 0.32 0.00 0.00 0.68
#> TCGA.D5.6532.01 5 0.0000 0.8457 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.5M.AATA.01 6 0.0808 0.8529 0.00 0.00 0.04 0.00 0.00 0.96 0.00 0.00
#> TCGA.EI.6509.01 4 0.0000 0.9282 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.G4.6311.01 7 0.5157 0.6407 0.14 0.00 0.20 0.00 0.00 0.00 0.60 0.06
#> TCGA.A6.A566.01 3 0.0000 0.7829 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.G4.6625.01 3 0.5583 0.0195 0.14 0.00 0.48 0.00 0.00 0.00 0.32 0.06
#> TCGA.CI.6619.01 4 0.0808 0.9144 0.04 0.00 0.00 0.96 0.00 0.00 0.00 0.00
#> TCGA.F5.6864.01 6 0.0000 0.8737 0.00 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.AA.3492.11 2 0.0471 0.9882 0.00 0.98 0.00 0.00 0.00 0.00 0.00 0.02
#> TCGA.A6.5659.01 1 0.2267 0.9951 0.82 0.00 0.00 0.00 0.18 0.00 0.00 0.00
#> TCGA.WS.AB45.01 7 0.3758 0.6986 0.14 0.00 0.00 0.04 0.00 0.00 0.76 0.06
#> TCGA.G4.6315.01 3 0.2404 0.6958 0.02 0.00 0.84 0.00 0.00 0.14 0.00 0.00
#> TCGA.D5.6541.01 3 0.0000 0.7829 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.A6.2680.01 5 0.2818 0.7059 0.00 0.00 0.06 0.00 0.82 0.00 0.00 0.12
#> TCGA.CM.4751.01 3 0.0000 0.7829 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CM.6680.01 5 0.0000 0.8457 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.AF.6136.01 8 0.1765 0.9167 0.00 0.00 0.00 0.00 0.12 0.00 0.00 0.88
#> TCGA.AA.3660.01 5 0.0000 0.8457 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.CM.4747.01 5 0.2569 0.7242 0.00 0.00 0.16 0.00 0.82 0.00 0.00 0.02
#> TCGA.EF.5831.01 5 0.0808 0.8208 0.04 0.00 0.00 0.00 0.96 0.00 0.00 0.00
#> TCGA.DM.A28G.01 5 0.2852 0.4557 0.28 0.00 0.00 0.00 0.72 0.00 0.00 0.00
#> TCGA.G4.6297.01 3 0.0000 0.7829 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.A6.2682.11 2 0.0000 0.9924 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D5.6537.01 5 0.2406 0.6234 0.20 0.00 0.00 0.00 0.80 0.00 0.00 0.00
#> TCGA.CM.6170.01 6 0.0471 0.8680 0.00 0.00 0.00 0.00 0.00 0.98 0.00 0.02
#> TCGA.DY.A1DD.01 8 0.1765 0.9167 0.00 0.00 0.00 0.00 0.12 0.00 0.00 0.88
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 , Node021 , Node022-leaf , Node023-leaf , Node041 , Node042 , Node043 .
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 145 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 0.999 1.000 0.4092 0.592 0.592
#> 3 3 1.000 0.946 0.980 0.3386 0.828 0.714
#> 4 4 0.917 0.902 0.955 0.1883 0.863 0.702
#> 5 5 0.928 0.937 0.967 0.0799 0.924 0.786
#> 6 6 0.925 0.855 0.929 0.0386 0.938 0.798
#> 7 7 0.878 0.828 0.903 0.0252 0.995 0.981
#> 8 8 0.863 0.705 0.877 0.0165 0.972 0.893
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.AG.A026.01 1 0.000 1.00 1.00 0.00
#> TCGA.G4.6303.01 1 0.000 1.00 1.00 0.00
#> TCGA.T9.A92H.01 1 0.000 1.00 1.00 0.00
#> TCGA.AD.6965.01 1 0.000 1.00 1.00 0.00
#> TCGA.A6.5660.01 1 0.000 1.00 1.00 0.00
#> TCGA.D5.6540.01 2 0.000 1.00 0.00 1.00
#> TCGA.F5.6571.01 1 0.000 1.00 1.00 0.00
#> TCGA.CM.5862.01 1 0.000 1.00 1.00 0.00
#> TCGA.CI.6622.01 1 0.000 1.00 1.00 0.00
#> TCGA.G4.6588.01 2 0.000 1.00 0.00 1.00
#> TCGA.EI.6512.01 1 0.000 1.00 1.00 0.00
#> TCGA.QG.A5YX.01 1 0.000 1.00 1.00 0.00
#> TCGA.AG.A036.01 1 0.000 1.00 1.00 0.00
#> TCGA.AZ.6606.01 2 0.000 1.00 0.00 1.00
#> TCGA.F4.6570.01 2 0.000 1.00 0.00 1.00
#> TCGA.AA.3509.01 1 0.000 1.00 1.00 0.00
#> TCGA.EI.6883.01 1 0.000 1.00 1.00 0.00
#> TCGA.RU.A8FL.01 1 0.000 1.00 1.00 0.00
#> TCGA.AZ.6599.01 1 0.000 1.00 1.00 0.00
#> TCGA.CM.5860.01 1 0.000 1.00 1.00 0.00
#> TCGA.A6.6780.01 1 0.000 1.00 1.00 0.00
#> TCGA.A6.2686.01 2 0.000 1.00 0.00 1.00
#> TCGA.CM.4750.01 1 0.000 1.00 1.00 0.00
#> TCGA.CM.6677.01 1 0.000 1.00 1.00 0.00
#> TCGA.F5.6814.01 1 0.000 1.00 1.00 0.00
#> TCGA.G4.6299.01 2 0.000 1.00 0.00 1.00
#> TCGA.A6.4105.01 2 0.000 1.00 0.00 1.00
#> TCGA.DM.A1D8.01 1 0.000 1.00 1.00 0.00
#> TCGA.DT.5265.01 2 0.000 1.00 0.00 1.00
#> TCGA.DM.A0XD.01 2 0.000 1.00 0.00 1.00
#> TCGA.A6.6138.01 1 0.000 1.00 1.00 0.00
#> TCGA.D5.7000.01 2 0.000 1.00 0.00 1.00
#> TCGA.DM.A28F.01 1 0.000 1.00 1.00 0.00
#> TCGA.CK.6751.01 2 0.000 1.00 0.00 1.00
#> TCGA.CM.6171.01 2 0.000 1.00 0.00 1.00
#> TCGA.DM.A1DA.01 2 0.000 1.00 0.00 1.00
#> TCGA.DM.A1D4.01 1 0.141 0.98 0.98 0.02
#> TCGA.AD.A5EJ.01 2 0.000 1.00 0.00 1.00
#> TCGA.DM.A0X9.01 1 0.000 1.00 1.00 0.00
#> TCGA.AY.A69D.01 1 0.000 1.00 1.00 0.00
#> TCGA.CA.6716.01 1 0.000 1.00 1.00 0.00
#> TCGA.CK.5916.01 2 0.000 1.00 0.00 1.00
#> TCGA.NH.A6GB.01 1 0.000 1.00 1.00 0.00
#> TCGA.NH.A50U.01 1 0.000 1.00 1.00 0.00
#> TCGA.AZ.4614.01 2 0.000 1.00 0.00 1.00
#> TCGA.AH.6644.01 1 0.000 1.00 1.00 0.00
#> TCGA.A6.3809.01 2 0.000 1.00 0.00 1.00
#> TCGA.CM.5864.01 1 0.000 1.00 1.00 0.00
#> TCGA.CM.5861.01 2 0.000 1.00 0.00 1.00
#> TCGA.AG.3742.01 1 0.000 1.00 1.00 0.00
#> TCGA.A6.5666.01 1 0.000 1.00 1.00 0.00
#> TCGA.AG.3591.01 1 0.000 1.00 1.00 0.00
#> TCGA.AH.6643.01 1 0.000 1.00 1.00 0.00
#> TCGA.EI.6510.01 1 0.000 1.00 1.00 0.00
#> TCGA.A6.5656.01 1 0.000 1.00 1.00 0.00
#> TCGA.DY.A1DG.01 1 0.000 1.00 1.00 0.00
#> TCGA.F4.6806.01 1 0.000 1.00 1.00 0.00
#> TCGA.G4.6322.01 2 0.000 1.00 0.00 1.00
#> TCGA.5M.AAT4.01 1 0.000 1.00 1.00 0.00
#> TCGA.G4.6586.01 2 0.000 1.00 0.00 1.00
#> TCGA.EI.6514.01 1 0.000 1.00 1.00 0.00
#> TCGA.DM.A282.01 1 0.000 1.00 1.00 0.00
#> TCGA.DM.A1HA.01 1 0.000 1.00 1.00 0.00
#> TCGA.D5.6531.01 2 0.000 1.00 0.00 1.00
#> TCGA.AZ.6598.01 2 0.000 1.00 0.00 1.00
#> TCGA.AG.4021.01 1 0.000 1.00 1.00 0.00
#> TCGA.DM.A1D9.01 1 0.000 1.00 1.00 0.00
#> TCGA.CM.4744.01 1 0.000 1.00 1.00 0.00
#> TCGA.A6.6652.01 1 0.000 1.00 1.00 0.00
#> TCGA.SS.A7HO.01 1 0.000 1.00 1.00 0.00
#> TCGA.A6.6650.01 1 0.000 1.00 1.00 0.00
#> TCGA.F4.6461.01 2 0.000 1.00 0.00 1.00
#> TCGA.AD.6889.01 2 0.000 1.00 0.00 1.00
#> TCGA.NH.A50T.01 1 0.000 1.00 1.00 0.00
#> TCGA.AA.3663.01 2 0.000 1.00 0.00 1.00
#> TCGA.AD.6899.01 1 0.000 1.00 1.00 0.00
#> TCGA.A6.A56B.01 1 0.000 1.00 1.00 0.00
#> TCGA.D5.5539.01 1 0.000 1.00 1.00 0.00
#> TCGA.CA.5254.01 2 0.000 1.00 0.00 1.00
#> TCGA.AY.A54L.01 1 0.000 1.00 1.00 0.00
#> TCGA.A6.4107.01 2 0.000 1.00 0.00 1.00
#> TCGA.NH.A5IV.01 1 0.000 1.00 1.00 0.00
#> TCGA.G4.6306.01 1 0.000 1.00 1.00 0.00
#> TCGA.AD.A5EK.01 1 0.000 1.00 1.00 0.00
#> TCGA.DC.5337.01 1 0.000 1.00 1.00 0.00
#> TCGA.CM.6675.01 2 0.000 1.00 0.00 1.00
#> TCGA.CK.6746.01 2 0.000 1.00 0.00 1.00
#> TCGA.QG.A5YW.01 1 0.000 1.00 1.00 0.00
#> TCGA.A6.5665.01 2 0.000 1.00 0.00 1.00
#> TCGA.EI.6882.01 1 0.000 1.00 1.00 0.00
#> TCGA.A6.2677.01 1 0.000 1.00 1.00 0.00
#> TCGA.D5.6538.01 2 0.000 1.00 0.00 1.00
#> TCGA.AA.3502.01 1 0.000 1.00 1.00 0.00
#> TCGA.QG.A5Z2.01 2 0.000 1.00 0.00 1.00
#> TCGA.CK.5915.01 1 0.000 1.00 1.00 0.00
#> TCGA.AY.6197.01 1 0.000 1.00 1.00 0.00
#> TCGA.G4.6294.01 1 0.000 1.00 1.00 0.00
#> TCGA.CK.4952.01 2 0.000 1.00 0.00 1.00
#> TCGA.CM.6172.01 1 0.000 1.00 1.00 0.00
#> TCGA.AA.3496.01 1 0.000 1.00 1.00 0.00
#> TCGA.CK.5913.01 2 0.000 1.00 0.00 1.00
#> TCGA.DM.A28A.01 1 0.000 1.00 1.00 0.00
#> TCGA.EI.7002.01 1 0.000 1.00 1.00 0.00
#> TCGA.QG.A5Z1.01 1 0.000 1.00 1.00 0.00
#> TCGA.DM.A28H.01 1 0.000 1.00 1.00 0.00
#> TCGA.G4.6320.01 2 0.000 1.00 0.00 1.00
#> TCGA.DM.A28M.01 1 0.000 1.00 1.00 0.00
#> TCGA.DM.A288.01 1 0.000 1.00 1.00 0.00
#> TCGA.A6.6653.01 2 0.000 1.00 0.00 1.00
#> TCGA.F4.6855.01 1 0.000 1.00 1.00 0.00
#> TCGA.NH.A6GA.01 1 0.000 1.00 1.00 0.00
#> TCGA.NH.A50V.01 1 0.000 1.00 1.00 0.00
#> TCGA.CK.6747.01 1 0.000 1.00 1.00 0.00
#> TCGA.CL.5918.01 1 0.000 1.00 1.00 0.00
#> TCGA.DM.A28K.01 1 0.000 1.00 1.00 0.00
#> TCGA.AA.3655.01 1 0.000 1.00 1.00 0.00
#> TCGA.AZ.5407.01 1 0.141 0.98 0.98 0.02
#> TCGA.A6.5661.01 2 0.000 1.00 0.00 1.00
#> TCGA.QG.A5YV.01 1 0.000 1.00 1.00 0.00
#> TCGA.AY.A71X.01 1 0.000 1.00 1.00 0.00
#> TCGA.AH.6549.01 1 0.000 1.00 1.00 0.00
#> TCGA.CM.6166.01 1 0.000 1.00 1.00 0.00
#> TCGA.AH.6897.01 1 0.000 1.00 1.00 0.00
#> TCGA.D5.5540.01 1 0.000 1.00 1.00 0.00
#> TCGA.A6.2672.01 2 0.000 1.00 0.00 1.00
#> TCGA.G5.6233.01 1 0.000 1.00 1.00 0.00
#> TCGA.CA.6719.01 1 0.000 1.00 1.00 0.00
#> TCGA.D5.5537.01 1 0.000 1.00 1.00 0.00
#> TCGA.4T.AA8H.01 1 0.000 1.00 1.00 0.00
#> TCGA.AG.3592.01 1 0.000 1.00 1.00 0.00
#> TCGA.CM.6678.01 1 0.000 1.00 1.00 0.00
#> TCGA.CK.5914.01 1 0.000 1.00 1.00 0.00
#> TCGA.AA.3492.01 2 0.000 1.00 0.00 1.00
#> TCGA.DM.A1HB.01 2 0.000 1.00 0.00 1.00
#> TCGA.EI.6508.01 1 0.000 1.00 1.00 0.00
#> TCGA.D5.6532.01 1 0.000 1.00 1.00 0.00
#> TCGA.A6.5659.01 2 0.000 1.00 0.00 1.00
#> TCGA.A6.2680.01 1 0.000 1.00 1.00 0.00
#> TCGA.CM.6680.01 1 0.000 1.00 1.00 0.00
#> TCGA.AA.3660.01 1 0.000 1.00 1.00 0.00
#> TCGA.CM.4747.01 1 0.000 1.00 1.00 0.00
#> TCGA.EF.5831.01 1 0.000 1.00 1.00 0.00
#> TCGA.DM.A28G.01 1 0.000 1.00 1.00 0.00
#> TCGA.D5.6537.01 1 0.000 1.00 1.00 0.00
#> TCGA.DY.A1DD.01 1 0.000 1.00 1.00 0.00
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.AG.A026.01 1 0.000 0.996 1.00 0.00 0.00
#> TCGA.G4.6303.01 1 0.000 0.996 1.00 0.00 0.00
#> TCGA.T9.A92H.01 1 0.000 0.996 1.00 0.00 0.00
#> TCGA.AD.6965.01 1 0.000 0.996 1.00 0.00 0.00
#> TCGA.A6.5660.01 1 0.000 0.996 1.00 0.00 0.00
#> TCGA.D5.6540.01 2 0.000 0.978 0.00 1.00 0.00
#> TCGA.F5.6571.01 1 0.000 0.996 1.00 0.00 0.00
#> TCGA.CM.5862.01 1 0.000 0.996 1.00 0.00 0.00
#> TCGA.CI.6622.01 1 0.000 0.996 1.00 0.00 0.00
#> TCGA.G4.6588.01 2 0.000 0.978 0.00 1.00 0.00
#> TCGA.EI.6512.01 1 0.000 0.996 1.00 0.00 0.00
#> TCGA.QG.A5YX.01 1 0.000 0.996 1.00 0.00 0.00
#> TCGA.AG.A036.01 1 0.000 0.996 1.00 0.00 0.00
#> TCGA.AZ.6606.01 2 0.000 0.978 0.00 1.00 0.00
#> TCGA.F4.6570.01 2 0.000 0.978 0.00 1.00 0.00
#> TCGA.AA.3509.01 1 0.000 0.996 1.00 0.00 0.00
#> TCGA.EI.6883.01 1 0.000 0.996 1.00 0.00 0.00
#> TCGA.RU.A8FL.01 1 0.000 0.996 1.00 0.00 0.00
#> TCGA.AZ.6599.01 3 0.630 0.177 0.48 0.00 0.52
#> TCGA.CM.5860.01 3 0.000 0.883 0.00 0.00 1.00
#> TCGA.A6.6780.01 3 0.000 0.883 0.00 0.00 1.00
#> TCGA.A6.2686.01 2 0.000 0.978 0.00 1.00 0.00
#> TCGA.CM.4750.01 1 0.000 0.996 1.00 0.00 0.00
#> TCGA.CM.6677.01 3 0.628 0.239 0.46 0.00 0.54
#> TCGA.F5.6814.01 1 0.000 0.996 1.00 0.00 0.00
#> TCGA.G4.6299.01 2 0.000 0.978 0.00 1.00 0.00
#> TCGA.A6.4105.01 3 0.000 0.883 0.00 0.00 1.00
#> TCGA.DM.A1D8.01 3 0.000 0.883 0.00 0.00 1.00
#> TCGA.DT.5265.01 2 0.000 0.978 0.00 1.00 0.00
#> TCGA.DM.A0XD.01 3 0.000 0.883 0.00 0.00 1.00
#> TCGA.A6.6138.01 3 0.604 0.434 0.38 0.00 0.62
#> TCGA.D5.7000.01 3 0.000 0.883 0.00 0.00 1.00
#> TCGA.DM.A28F.01 1 0.000 0.996 1.00 0.00 0.00
#> TCGA.CK.6751.01 3 0.000 0.883 0.00 0.00 1.00
#> TCGA.CM.6171.01 2 0.000 0.978 0.00 1.00 0.00
#> TCGA.DM.A1DA.01 2 0.595 0.494 0.00 0.64 0.36
#> TCGA.DM.A1D4.01 3 0.000 0.883 0.00 0.00 1.00
#> TCGA.AD.A5EJ.01 2 0.000 0.978 0.00 1.00 0.00
#> TCGA.DM.A0X9.01 3 0.000 0.883 0.00 0.00 1.00
#> TCGA.AY.A69D.01 1 0.000 0.996 1.00 0.00 0.00
#> TCGA.CA.6716.01 3 0.000 0.883 0.00 0.00 1.00
#> TCGA.CK.5916.01 2 0.000 0.978 0.00 1.00 0.00
#> TCGA.NH.A6GB.01 1 0.000 0.996 1.00 0.00 0.00
#> TCGA.NH.A50U.01 1 0.000 0.996 1.00 0.00 0.00
#> TCGA.AZ.4614.01 2 0.000 0.978 0.00 1.00 0.00
#> TCGA.AH.6644.01 1 0.000 0.996 1.00 0.00 0.00
#> TCGA.A6.3809.01 2 0.000 0.978 0.00 1.00 0.00
#> TCGA.CM.5864.01 1 0.000 0.996 1.00 0.00 0.00
#> TCGA.CM.5861.01 2 0.000 0.978 0.00 1.00 0.00
#> TCGA.AG.3742.01 1 0.000 0.996 1.00 0.00 0.00
#> TCGA.A6.5666.01 1 0.000 0.996 1.00 0.00 0.00
#> TCGA.AG.3591.01 1 0.000 0.996 1.00 0.00 0.00
#> TCGA.AH.6643.01 1 0.000 0.996 1.00 0.00 0.00
#> TCGA.EI.6510.01 1 0.000 0.996 1.00 0.00 0.00
#> TCGA.A6.5656.01 1 0.000 0.996 1.00 0.00 0.00
#> TCGA.DY.A1DG.01 1 0.000 0.996 1.00 0.00 0.00
#> TCGA.F4.6806.01 3 0.000 0.883 0.00 0.00 1.00
#> TCGA.G4.6322.01 3 0.000 0.883 0.00 0.00 1.00
#> TCGA.5M.AAT4.01 1 0.000 0.996 1.00 0.00 0.00
#> TCGA.G4.6586.01 2 0.000 0.978 0.00 1.00 0.00
#> TCGA.EI.6514.01 1 0.000 0.996 1.00 0.00 0.00
#> TCGA.DM.A282.01 1 0.000 0.996 1.00 0.00 0.00
#> TCGA.DM.A1HA.01 3 0.630 0.177 0.48 0.00 0.52
#> TCGA.D5.6531.01 2 0.000 0.978 0.00 1.00 0.00
#> TCGA.AZ.6598.01 2 0.000 0.978 0.00 1.00 0.00
#> TCGA.AG.4021.01 1 0.000 0.996 1.00 0.00 0.00
#> TCGA.DM.A1D9.01 1 0.000 0.996 1.00 0.00 0.00
#> TCGA.CM.4744.01 3 0.000 0.883 0.00 0.00 1.00
#> TCGA.A6.6652.01 1 0.000 0.996 1.00 0.00 0.00
#> TCGA.SS.A7HO.01 1 0.000 0.996 1.00 0.00 0.00
#> TCGA.A6.6650.01 1 0.000 0.996 1.00 0.00 0.00
#> TCGA.F4.6461.01 2 0.000 0.978 0.00 1.00 0.00
#> TCGA.AD.6889.01 2 0.000 0.978 0.00 1.00 0.00
#> TCGA.NH.A50T.01 1 0.000 0.996 1.00 0.00 0.00
#> TCGA.AA.3663.01 3 0.000 0.883 0.00 0.00 1.00
#> TCGA.AD.6899.01 1 0.000 0.996 1.00 0.00 0.00
#> TCGA.A6.A56B.01 1 0.000 0.996 1.00 0.00 0.00
#> TCGA.D5.5539.01 1 0.000 0.996 1.00 0.00 0.00
#> TCGA.CA.5254.01 2 0.000 0.978 0.00 1.00 0.00
#> TCGA.AY.A54L.01 1 0.000 0.996 1.00 0.00 0.00
#> TCGA.A6.4107.01 2 0.595 0.494 0.00 0.64 0.36
#> TCGA.NH.A5IV.01 1 0.000 0.996 1.00 0.00 0.00
#> TCGA.G4.6306.01 1 0.000 0.996 1.00 0.00 0.00
#> TCGA.AD.A5EK.01 1 0.571 0.466 0.68 0.00 0.32
#> TCGA.DC.5337.01 1 0.000 0.996 1.00 0.00 0.00
#> TCGA.CM.6675.01 2 0.000 0.978 0.00 1.00 0.00
#> TCGA.CK.6746.01 2 0.000 0.978 0.00 1.00 0.00
#> TCGA.QG.A5YW.01 1 0.000 0.996 1.00 0.00 0.00
#> TCGA.A6.5665.01 2 0.000 0.978 0.00 1.00 0.00
#> TCGA.EI.6882.01 1 0.000 0.996 1.00 0.00 0.00
#> TCGA.A6.2677.01 1 0.000 0.996 1.00 0.00 0.00
#> TCGA.D5.6538.01 3 0.000 0.883 0.00 0.00 1.00
#> TCGA.AA.3502.01 1 0.000 0.996 1.00 0.00 0.00
#> TCGA.QG.A5Z2.01 2 0.000 0.978 0.00 1.00 0.00
#> TCGA.CK.5915.01 1 0.000 0.996 1.00 0.00 0.00
#> TCGA.AY.6197.01 3 0.000 0.883 0.00 0.00 1.00
#> TCGA.G4.6294.01 1 0.000 0.996 1.00 0.00 0.00
#> TCGA.CK.4952.01 2 0.000 0.978 0.00 1.00 0.00
#> TCGA.CM.6172.01 1 0.000 0.996 1.00 0.00 0.00
#> TCGA.AA.3496.01 1 0.000 0.996 1.00 0.00 0.00
#> TCGA.CK.5913.01 2 0.000 0.978 0.00 1.00 0.00
#> TCGA.DM.A28A.01 1 0.000 0.996 1.00 0.00 0.00
#> TCGA.EI.7002.01 1 0.000 0.996 1.00 0.00 0.00
#> TCGA.QG.A5Z1.01 1 0.000 0.996 1.00 0.00 0.00
#> TCGA.DM.A28H.01 1 0.000 0.996 1.00 0.00 0.00
#> TCGA.G4.6320.01 2 0.000 0.978 0.00 1.00 0.00
#> TCGA.DM.A28M.01 1 0.000 0.996 1.00 0.00 0.00
#> TCGA.DM.A288.01 1 0.000 0.996 1.00 0.00 0.00
#> TCGA.A6.6653.01 2 0.000 0.978 0.00 1.00 0.00
#> TCGA.F4.6855.01 1 0.000 0.996 1.00 0.00 0.00
#> TCGA.NH.A6GA.01 1 0.000 0.996 1.00 0.00 0.00
#> TCGA.NH.A50V.01 3 0.000 0.883 0.00 0.00 1.00
#> TCGA.CK.6747.01 1 0.000 0.996 1.00 0.00 0.00
#> TCGA.CL.5918.01 1 0.000 0.996 1.00 0.00 0.00
#> TCGA.DM.A28K.01 1 0.000 0.996 1.00 0.00 0.00
#> TCGA.AA.3655.01 1 0.000 0.996 1.00 0.00 0.00
#> TCGA.AZ.5407.01 3 0.000 0.883 0.00 0.00 1.00
#> TCGA.A6.5661.01 2 0.000 0.978 0.00 1.00 0.00
#> TCGA.QG.A5YV.01 1 0.000 0.996 1.00 0.00 0.00
#> TCGA.AY.A71X.01 1 0.000 0.996 1.00 0.00 0.00
#> TCGA.AH.6549.01 1 0.000 0.996 1.00 0.00 0.00
#> TCGA.CM.6166.01 1 0.000 0.996 1.00 0.00 0.00
#> TCGA.AH.6897.01 1 0.000 0.996 1.00 0.00 0.00
#> TCGA.D5.5540.01 1 0.000 0.996 1.00 0.00 0.00
#> TCGA.A6.2672.01 2 0.000 0.978 0.00 1.00 0.00
#> TCGA.G5.6233.01 3 0.000 0.883 0.00 0.00 1.00
#> TCGA.CA.6719.01 1 0.000 0.996 1.00 0.00 0.00
#> TCGA.D5.5537.01 1 0.000 0.996 1.00 0.00 0.00
#> TCGA.4T.AA8H.01 1 0.000 0.996 1.00 0.00 0.00
#> TCGA.AG.3592.01 1 0.000 0.996 1.00 0.00 0.00
#> TCGA.CM.6678.01 1 0.000 0.996 1.00 0.00 0.00
#> TCGA.CK.5914.01 1 0.000 0.996 1.00 0.00 0.00
#> TCGA.AA.3492.01 2 0.000 0.978 0.00 1.00 0.00
#> TCGA.DM.A1HB.01 2 0.000 0.978 0.00 1.00 0.00
#> TCGA.EI.6508.01 1 0.000 0.996 1.00 0.00 0.00
#> TCGA.D5.6532.01 1 0.000 0.996 1.00 0.00 0.00
#> TCGA.A6.5659.01 3 0.000 0.883 0.00 0.00 1.00
#> TCGA.A6.2680.01 1 0.000 0.996 1.00 0.00 0.00
#> TCGA.CM.6680.01 1 0.000 0.996 1.00 0.00 0.00
#> TCGA.AA.3660.01 1 0.000 0.996 1.00 0.00 0.00
#> TCGA.CM.4747.01 1 0.000 0.996 1.00 0.00 0.00
#> TCGA.EF.5831.01 1 0.000 0.996 1.00 0.00 0.00
#> TCGA.DM.A28G.01 1 0.000 0.996 1.00 0.00 0.00
#> TCGA.D5.6537.01 1 0.000 0.996 1.00 0.00 0.00
#> TCGA.DY.A1DD.01 1 0.000 0.996 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.AG.A026.01 1 0.0000 0.9853 1.00 0.00 0.00 0.00
#> TCGA.G4.6303.01 1 0.0000 0.9853 1.00 0.00 0.00 0.00
#> TCGA.T9.A92H.01 1 0.0000 0.9853 1.00 0.00 0.00 0.00
#> TCGA.AD.6965.01 1 0.0000 0.9853 1.00 0.00 0.00 0.00
#> TCGA.A6.5660.01 1 0.0000 0.9853 1.00 0.00 0.00 0.00
#> TCGA.D5.6540.01 2 0.0000 0.9777 0.00 1.00 0.00 0.00
#> TCGA.F5.6571.01 1 0.0000 0.9853 1.00 0.00 0.00 0.00
#> TCGA.CM.5862.01 1 0.0000 0.9853 1.00 0.00 0.00 0.00
#> TCGA.CI.6622.01 1 0.0000 0.9853 1.00 0.00 0.00 0.00
#> TCGA.G4.6588.01 2 0.0000 0.9777 0.00 1.00 0.00 0.00
#> TCGA.EI.6512.01 1 0.4977 -0.0789 0.54 0.00 0.00 0.46
#> TCGA.QG.A5YX.01 1 0.0000 0.9853 1.00 0.00 0.00 0.00
#> TCGA.AG.A036.01 1 0.0000 0.9853 1.00 0.00 0.00 0.00
#> TCGA.AZ.6606.01 2 0.0707 0.9639 0.00 0.98 0.02 0.00
#> TCGA.F4.6570.01 2 0.0000 0.9777 0.00 1.00 0.00 0.00
#> TCGA.AA.3509.01 1 0.0000 0.9853 1.00 0.00 0.00 0.00
#> TCGA.EI.6883.01 4 0.1211 0.7605 0.04 0.00 0.00 0.96
#> TCGA.RU.A8FL.01 1 0.0000 0.9853 1.00 0.00 0.00 0.00
#> TCGA.AZ.6599.01 4 0.0000 0.7603 0.00 0.00 0.00 1.00
#> TCGA.CM.5860.01 3 0.4134 0.7944 0.00 0.00 0.74 0.26
#> TCGA.A6.6780.01 4 0.0000 0.7603 0.00 0.00 0.00 1.00
#> TCGA.A6.2686.01 2 0.0000 0.9777 0.00 1.00 0.00 0.00
#> TCGA.CM.4750.01 1 0.0000 0.9853 1.00 0.00 0.00 0.00
#> TCGA.CM.6677.01 4 0.0000 0.7603 0.00 0.00 0.00 1.00
#> TCGA.F5.6814.01 1 0.0000 0.9853 1.00 0.00 0.00 0.00
#> TCGA.G4.6299.01 2 0.0000 0.9777 0.00 1.00 0.00 0.00
#> TCGA.A6.4105.01 3 0.0707 0.8741 0.00 0.00 0.98 0.02
#> TCGA.DM.A1D8.01 4 0.0000 0.7603 0.00 0.00 0.00 1.00
#> TCGA.DT.5265.01 2 0.0000 0.9777 0.00 1.00 0.00 0.00
#> TCGA.DM.A0XD.01 3 0.0707 0.8741 0.00 0.00 0.98 0.02
#> TCGA.A6.6138.01 4 0.0000 0.7603 0.00 0.00 0.00 1.00
#> TCGA.D5.7000.01 3 0.0000 0.8719 0.00 0.00 1.00 0.00
#> TCGA.DM.A28F.01 1 0.0000 0.9853 1.00 0.00 0.00 0.00
#> TCGA.CK.6751.01 3 0.0000 0.8719 0.00 0.00 1.00 0.00
#> TCGA.CM.6171.01 2 0.0000 0.9777 0.00 1.00 0.00 0.00
#> TCGA.DM.A1DA.01 3 0.0000 0.8719 0.00 0.00 1.00 0.00
#> TCGA.DM.A1D4.01 3 0.3801 0.8131 0.00 0.00 0.78 0.22
#> TCGA.AD.A5EJ.01 2 0.0000 0.9777 0.00 1.00 0.00 0.00
#> TCGA.DM.A0X9.01 3 0.4713 0.6687 0.00 0.00 0.64 0.36
#> TCGA.AY.A69D.01 4 0.0707 0.7638 0.02 0.00 0.00 0.98
#> TCGA.CA.6716.01 4 0.3400 0.5127 0.00 0.00 0.18 0.82
#> TCGA.CK.5916.01 2 0.0000 0.9777 0.00 1.00 0.00 0.00
#> TCGA.NH.A6GB.01 4 0.4134 0.6969 0.26 0.00 0.00 0.74
#> TCGA.NH.A50U.01 1 0.0000 0.9853 1.00 0.00 0.00 0.00
#> TCGA.AZ.4614.01 3 0.3610 0.6693 0.00 0.20 0.80 0.00
#> TCGA.AH.6644.01 1 0.0000 0.9853 1.00 0.00 0.00 0.00
#> TCGA.A6.3809.01 2 0.0000 0.9777 0.00 1.00 0.00 0.00
#> TCGA.CM.5864.01 1 0.0000 0.9853 1.00 0.00 0.00 0.00
#> TCGA.CM.5861.01 2 0.0000 0.9777 0.00 1.00 0.00 0.00
#> TCGA.AG.3742.01 1 0.0000 0.9853 1.00 0.00 0.00 0.00
#> TCGA.A6.5666.01 1 0.0000 0.9853 1.00 0.00 0.00 0.00
#> TCGA.AG.3591.01 1 0.0000 0.9853 1.00 0.00 0.00 0.00
#> TCGA.AH.6643.01 1 0.0000 0.9853 1.00 0.00 0.00 0.00
#> TCGA.EI.6510.01 1 0.0000 0.9853 1.00 0.00 0.00 0.00
#> TCGA.A6.5656.01 1 0.0000 0.9853 1.00 0.00 0.00 0.00
#> TCGA.DY.A1DG.01 1 0.0000 0.9853 1.00 0.00 0.00 0.00
#> TCGA.F4.6806.01 4 0.0000 0.7603 0.00 0.00 0.00 1.00
#> TCGA.G4.6322.01 3 0.0000 0.8719 0.00 0.00 1.00 0.00
#> TCGA.5M.AAT4.01 1 0.0000 0.9853 1.00 0.00 0.00 0.00
#> TCGA.G4.6586.01 2 0.0000 0.9777 0.00 1.00 0.00 0.00
#> TCGA.EI.6514.01 1 0.0000 0.9853 1.00 0.00 0.00 0.00
#> TCGA.DM.A282.01 1 0.0000 0.9853 1.00 0.00 0.00 0.00
#> TCGA.DM.A1HA.01 4 0.0000 0.7603 0.00 0.00 0.00 1.00
#> TCGA.D5.6531.01 2 0.0707 0.9639 0.00 0.98 0.02 0.00
#> TCGA.AZ.6598.01 2 0.0000 0.9777 0.00 1.00 0.00 0.00
#> TCGA.AG.4021.01 1 0.0000 0.9853 1.00 0.00 0.00 0.00
#> TCGA.DM.A1D9.01 1 0.0000 0.9853 1.00 0.00 0.00 0.00
#> TCGA.CM.4744.01 3 0.4134 0.7944 0.00 0.00 0.74 0.26
#> TCGA.A6.6652.01 1 0.0000 0.9853 1.00 0.00 0.00 0.00
#> TCGA.SS.A7HO.01 1 0.0000 0.9853 1.00 0.00 0.00 0.00
#> TCGA.A6.6650.01 1 0.0000 0.9853 1.00 0.00 0.00 0.00
#> TCGA.F4.6461.01 2 0.4790 0.4511 0.00 0.62 0.38 0.00
#> TCGA.AD.6889.01 2 0.0000 0.9777 0.00 1.00 0.00 0.00
#> TCGA.NH.A50T.01 1 0.0000 0.9853 1.00 0.00 0.00 0.00
#> TCGA.AA.3663.01 3 0.0707 0.8741 0.00 0.00 0.98 0.02
#> TCGA.AD.6899.01 4 0.4134 0.6969 0.26 0.00 0.00 0.74
#> TCGA.A6.A56B.01 1 0.0000 0.9853 1.00 0.00 0.00 0.00
#> TCGA.D5.5539.01 1 0.0000 0.9853 1.00 0.00 0.00 0.00
#> TCGA.CA.5254.01 2 0.0707 0.9639 0.00 0.98 0.02 0.00
#> TCGA.AY.A54L.01 1 0.0707 0.9634 0.98 0.00 0.00 0.02
#> TCGA.A6.4107.01 3 0.0000 0.8719 0.00 0.00 1.00 0.00
#> TCGA.NH.A5IV.01 1 0.0000 0.9853 1.00 0.00 0.00 0.00
#> TCGA.G4.6306.01 1 0.0000 0.9853 1.00 0.00 0.00 0.00
#> TCGA.AD.A5EK.01 4 0.0000 0.7603 0.00 0.00 0.00 1.00
#> TCGA.DC.5337.01 1 0.0000 0.9853 1.00 0.00 0.00 0.00
#> TCGA.CM.6675.01 2 0.0000 0.9777 0.00 1.00 0.00 0.00
#> TCGA.CK.6746.01 2 0.0000 0.9777 0.00 1.00 0.00 0.00
#> TCGA.QG.A5YW.01 1 0.0000 0.9853 1.00 0.00 0.00 0.00
#> TCGA.A6.5665.01 2 0.0000 0.9777 0.00 1.00 0.00 0.00
#> TCGA.EI.6882.01 1 0.0000 0.9853 1.00 0.00 0.00 0.00
#> TCGA.A6.2677.01 1 0.0000 0.9853 1.00 0.00 0.00 0.00
#> TCGA.D5.6538.01 3 0.0707 0.8741 0.00 0.00 0.98 0.02
#> TCGA.AA.3502.01 4 0.4134 0.6969 0.26 0.00 0.00 0.74
#> TCGA.QG.A5Z2.01 2 0.0000 0.9777 0.00 1.00 0.00 0.00
#> TCGA.CK.5915.01 4 0.4907 0.4396 0.42 0.00 0.00 0.58
#> TCGA.AY.6197.01 3 0.4277 0.7760 0.00 0.00 0.72 0.28
#> TCGA.G4.6294.01 1 0.0000 0.9853 1.00 0.00 0.00 0.00
#> TCGA.CK.4952.01 2 0.3801 0.7414 0.00 0.78 0.22 0.00
#> TCGA.CM.6172.01 1 0.0000 0.9853 1.00 0.00 0.00 0.00
#> TCGA.AA.3496.01 1 0.0000 0.9853 1.00 0.00 0.00 0.00
#> TCGA.CK.5913.01 2 0.0000 0.9777 0.00 1.00 0.00 0.00
#> TCGA.DM.A28A.01 1 0.0000 0.9853 1.00 0.00 0.00 0.00
#> TCGA.EI.7002.01 1 0.0000 0.9853 1.00 0.00 0.00 0.00
#> TCGA.QG.A5Z1.01 1 0.0000 0.9853 1.00 0.00 0.00 0.00
#> TCGA.DM.A28H.01 1 0.4855 0.1684 0.60 0.00 0.00 0.40
#> TCGA.G4.6320.01 2 0.0000 0.9777 0.00 1.00 0.00 0.00
#> TCGA.DM.A28M.01 1 0.0000 0.9853 1.00 0.00 0.00 0.00
#> TCGA.DM.A288.01 4 0.4134 0.6969 0.26 0.00 0.00 0.74
#> TCGA.A6.6653.01 2 0.0000 0.9777 0.00 1.00 0.00 0.00
#> TCGA.F4.6855.01 1 0.0000 0.9853 1.00 0.00 0.00 0.00
#> TCGA.NH.A6GA.01 4 0.4134 0.6969 0.26 0.00 0.00 0.74
#> TCGA.NH.A50V.01 4 0.0000 0.7603 0.00 0.00 0.00 1.00
#> TCGA.CK.6747.01 1 0.0000 0.9853 1.00 0.00 0.00 0.00
#> TCGA.CL.5918.01 1 0.0000 0.9853 1.00 0.00 0.00 0.00
#> TCGA.DM.A28K.01 1 0.0000 0.9853 1.00 0.00 0.00 0.00
#> TCGA.AA.3655.01 1 0.0000 0.9853 1.00 0.00 0.00 0.00
#> TCGA.AZ.5407.01 3 0.4134 0.7944 0.00 0.00 0.74 0.26
#> TCGA.A6.5661.01 2 0.0000 0.9777 0.00 1.00 0.00 0.00
#> TCGA.QG.A5YV.01 1 0.0000 0.9853 1.00 0.00 0.00 0.00
#> TCGA.AY.A71X.01 4 0.0000 0.7603 0.00 0.00 0.00 1.00
#> TCGA.AH.6549.01 1 0.0000 0.9853 1.00 0.00 0.00 0.00
#> TCGA.CM.6166.01 1 0.0000 0.9853 1.00 0.00 0.00 0.00
#> TCGA.AH.6897.01 1 0.0000 0.9853 1.00 0.00 0.00 0.00
#> TCGA.D5.5540.01 1 0.1211 0.9400 0.96 0.00 0.00 0.04
#> TCGA.A6.2672.01 2 0.0000 0.9777 0.00 1.00 0.00 0.00
#> TCGA.G5.6233.01 3 0.4134 0.7944 0.00 0.00 0.74 0.26
#> TCGA.CA.6719.01 4 0.4134 0.6969 0.26 0.00 0.00 0.74
#> TCGA.D5.5537.01 4 0.4277 0.6725 0.28 0.00 0.00 0.72
#> TCGA.4T.AA8H.01 4 0.0707 0.7638 0.02 0.00 0.00 0.98
#> TCGA.AG.3592.01 1 0.0000 0.9853 1.00 0.00 0.00 0.00
#> TCGA.CM.6678.01 1 0.0000 0.9853 1.00 0.00 0.00 0.00
#> TCGA.CK.5914.01 1 0.0000 0.9853 1.00 0.00 0.00 0.00
#> TCGA.AA.3492.01 2 0.0000 0.9777 0.00 1.00 0.00 0.00
#> TCGA.DM.A1HB.01 2 0.0000 0.9777 0.00 1.00 0.00 0.00
#> TCGA.EI.6508.01 1 0.0000 0.9853 1.00 0.00 0.00 0.00
#> TCGA.D5.6532.01 1 0.0000 0.9853 1.00 0.00 0.00 0.00
#> TCGA.A6.5659.01 3 0.0000 0.8719 0.00 0.00 1.00 0.00
#> TCGA.A6.2680.01 1 0.0000 0.9853 1.00 0.00 0.00 0.00
#> TCGA.CM.6680.01 1 0.0000 0.9853 1.00 0.00 0.00 0.00
#> TCGA.AA.3660.01 1 0.0000 0.9853 1.00 0.00 0.00 0.00
#> TCGA.CM.4747.01 4 0.3975 0.7038 0.24 0.00 0.00 0.76
#> TCGA.EF.5831.01 1 0.0000 0.9853 1.00 0.00 0.00 0.00
#> TCGA.DM.A28G.01 1 0.0000 0.9853 1.00 0.00 0.00 0.00
#> TCGA.D5.6537.01 1 0.0000 0.9853 1.00 0.00 0.00 0.00
#> TCGA.DY.A1DD.01 1 0.0000 0.9853 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.AG.A026.01 1 0.0000 0.986 1.00 0.00 0.00 0.00 0.00
#> TCGA.G4.6303.01 1 0.0000 0.986 1.00 0.00 0.00 0.00 0.00
#> TCGA.T9.A92H.01 1 0.0000 0.986 1.00 0.00 0.00 0.00 0.00
#> TCGA.AD.6965.01 1 0.0000 0.986 1.00 0.00 0.00 0.00 0.00
#> TCGA.A6.5660.01 1 0.0000 0.986 1.00 0.00 0.00 0.00 0.00
#> TCGA.D5.6540.01 2 0.0000 1.000 0.00 1.00 0.00 0.00 0.00
#> TCGA.F5.6571.01 1 0.0000 0.986 1.00 0.00 0.00 0.00 0.00
#> TCGA.CM.5862.01 1 0.0000 0.986 1.00 0.00 0.00 0.00 0.00
#> TCGA.CI.6622.01 1 0.0000 0.986 1.00 0.00 0.00 0.00 0.00
#> TCGA.G4.6588.01 2 0.0000 1.000 0.00 1.00 0.00 0.00 0.00
#> TCGA.EI.6512.01 4 0.1216 0.928 0.02 0.00 0.00 0.96 0.02
#> TCGA.QG.A5YX.01 1 0.0000 0.986 1.00 0.00 0.00 0.00 0.00
#> TCGA.AG.A036.01 1 0.0000 0.986 1.00 0.00 0.00 0.00 0.00
#> TCGA.AZ.6606.01 5 0.3274 0.738 0.00 0.22 0.00 0.00 0.78
#> TCGA.F4.6570.01 2 0.0000 1.000 0.00 1.00 0.00 0.00 0.00
#> TCGA.AA.3509.01 1 0.0000 0.986 1.00 0.00 0.00 0.00 0.00
#> TCGA.EI.6883.01 4 0.1216 0.928 0.02 0.00 0.00 0.96 0.02
#> TCGA.RU.A8FL.01 1 0.0000 0.986 1.00 0.00 0.00 0.00 0.00
#> TCGA.AZ.6599.01 4 0.2020 0.874 0.00 0.00 0.10 0.90 0.00
#> TCGA.CM.5860.01 3 0.0000 0.919 0.00 0.00 1.00 0.00 0.00
#> TCGA.A6.6780.01 3 0.0609 0.910 0.00 0.00 0.98 0.00 0.02
#> TCGA.A6.2686.01 2 0.0000 1.000 0.00 1.00 0.00 0.00 0.00
#> TCGA.CM.4750.01 1 0.0000 0.986 1.00 0.00 0.00 0.00 0.00
#> TCGA.CM.6677.01 4 0.2020 0.874 0.00 0.00 0.10 0.90 0.00
#> TCGA.F5.6814.01 1 0.2280 0.867 0.88 0.00 0.00 0.12 0.00
#> TCGA.G4.6299.01 2 0.0000 1.000 0.00 1.00 0.00 0.00 0.00
#> TCGA.A6.4105.01 3 0.3109 0.797 0.00 0.00 0.80 0.00 0.20
#> TCGA.DM.A1D8.01 4 0.3999 0.702 0.00 0.00 0.24 0.74 0.02
#> TCGA.DT.5265.01 2 0.0000 1.000 0.00 1.00 0.00 0.00 0.00
#> TCGA.DM.A0XD.01 3 0.3109 0.797 0.00 0.00 0.80 0.00 0.20
#> TCGA.A6.6138.01 4 0.2020 0.874 0.00 0.00 0.10 0.90 0.00
#> TCGA.D5.7000.01 5 0.0609 0.859 0.00 0.00 0.02 0.00 0.98
#> TCGA.DM.A28F.01 1 0.0000 0.986 1.00 0.00 0.00 0.00 0.00
#> TCGA.CK.6751.01 5 0.0609 0.859 0.00 0.00 0.02 0.00 0.98
#> TCGA.CM.6171.01 2 0.0000 1.000 0.00 1.00 0.00 0.00 0.00
#> TCGA.DM.A1DA.01 5 0.0609 0.859 0.00 0.00 0.02 0.00 0.98
#> TCGA.DM.A1D4.01 3 0.0000 0.919 0.00 0.00 1.00 0.00 0.00
#> TCGA.AD.A5EJ.01 2 0.0000 1.000 0.00 1.00 0.00 0.00 0.00
#> TCGA.DM.A0X9.01 3 0.0000 0.919 0.00 0.00 1.00 0.00 0.00
#> TCGA.AY.A69D.01 4 0.1216 0.919 0.00 0.00 0.02 0.96 0.02
#> TCGA.CA.6716.01 3 0.0609 0.910 0.00 0.00 0.98 0.00 0.02
#> TCGA.CK.5916.01 2 0.0000 1.000 0.00 1.00 0.00 0.00 0.00
#> TCGA.NH.A6GB.01 4 0.0609 0.930 0.02 0.00 0.00 0.98 0.00
#> TCGA.NH.A50U.01 1 0.0000 0.986 1.00 0.00 0.00 0.00 0.00
#> TCGA.AZ.4614.01 5 0.0609 0.859 0.00 0.02 0.00 0.00 0.98
#> TCGA.AH.6644.01 1 0.0000 0.986 1.00 0.00 0.00 0.00 0.00
#> TCGA.A6.3809.01 2 0.0000 1.000 0.00 1.00 0.00 0.00 0.00
#> TCGA.CM.5864.01 1 0.0000 0.986 1.00 0.00 0.00 0.00 0.00
#> TCGA.CM.5861.01 2 0.0000 1.000 0.00 1.00 0.00 0.00 0.00
#> TCGA.AG.3742.01 1 0.0000 0.986 1.00 0.00 0.00 0.00 0.00
#> TCGA.A6.5666.01 1 0.0000 0.986 1.00 0.00 0.00 0.00 0.00
#> TCGA.AG.3591.01 1 0.0000 0.986 1.00 0.00 0.00 0.00 0.00
#> TCGA.AH.6643.01 1 0.0000 0.986 1.00 0.00 0.00 0.00 0.00
#> TCGA.EI.6510.01 1 0.0000 0.986 1.00 0.00 0.00 0.00 0.00
#> TCGA.A6.5656.01 1 0.0000 0.986 1.00 0.00 0.00 0.00 0.00
#> TCGA.DY.A1DG.01 1 0.0000 0.986 1.00 0.00 0.00 0.00 0.00
#> TCGA.F4.6806.01 3 0.2929 0.739 0.00 0.00 0.82 0.18 0.00
#> TCGA.G4.6322.01 5 0.1216 0.855 0.00 0.00 0.02 0.02 0.96
#> TCGA.5M.AAT4.01 1 0.2280 0.868 0.88 0.00 0.00 0.12 0.00
#> TCGA.G4.6586.01 2 0.0000 1.000 0.00 1.00 0.00 0.00 0.00
#> TCGA.EI.6514.01 1 0.0000 0.986 1.00 0.00 0.00 0.00 0.00
#> TCGA.DM.A282.01 1 0.0000 0.986 1.00 0.00 0.00 0.00 0.00
#> TCGA.DM.A1HA.01 4 0.1732 0.889 0.00 0.00 0.08 0.92 0.00
#> TCGA.D5.6531.01 5 0.3895 0.611 0.00 0.32 0.00 0.00 0.68
#> TCGA.AZ.6598.01 2 0.0000 1.000 0.00 1.00 0.00 0.00 0.00
#> TCGA.AG.4021.01 1 0.0000 0.986 1.00 0.00 0.00 0.00 0.00
#> TCGA.DM.A1D9.01 1 0.0000 0.986 1.00 0.00 0.00 0.00 0.00
#> TCGA.CM.4744.01 3 0.0000 0.919 0.00 0.00 1.00 0.00 0.00
#> TCGA.A6.6652.01 1 0.0000 0.986 1.00 0.00 0.00 0.00 0.00
#> TCGA.SS.A7HO.01 1 0.0000 0.986 1.00 0.00 0.00 0.00 0.00
#> TCGA.A6.6650.01 1 0.0000 0.986 1.00 0.00 0.00 0.00 0.00
#> TCGA.F4.6461.01 5 0.1216 0.857 0.00 0.02 0.00 0.02 0.96
#> TCGA.AD.6889.01 2 0.0000 1.000 0.00 1.00 0.00 0.00 0.00
#> TCGA.NH.A50T.01 1 0.0000 0.986 1.00 0.00 0.00 0.00 0.00
#> TCGA.AA.3663.01 3 0.3513 0.800 0.00 0.00 0.80 0.02 0.18
#> TCGA.AD.6899.01 4 0.0609 0.930 0.02 0.00 0.00 0.98 0.00
#> TCGA.A6.A56B.01 1 0.2020 0.889 0.90 0.00 0.00 0.10 0.00
#> TCGA.D5.5539.01 1 0.0000 0.986 1.00 0.00 0.00 0.00 0.00
#> TCGA.CA.5254.01 5 0.4227 0.401 0.00 0.42 0.00 0.00 0.58
#> TCGA.AY.A54L.01 4 0.2516 0.788 0.14 0.00 0.00 0.86 0.00
#> TCGA.A6.4107.01 5 0.0609 0.859 0.00 0.00 0.02 0.00 0.98
#> TCGA.NH.A5IV.01 1 0.2732 0.817 0.84 0.00 0.00 0.16 0.00
#> TCGA.G4.6306.01 1 0.0000 0.986 1.00 0.00 0.00 0.00 0.00
#> TCGA.AD.A5EK.01 4 0.1216 0.919 0.00 0.00 0.02 0.96 0.02
#> TCGA.DC.5337.01 1 0.0000 0.986 1.00 0.00 0.00 0.00 0.00
#> TCGA.CM.6675.01 2 0.0000 1.000 0.00 1.00 0.00 0.00 0.00
#> TCGA.CK.6746.01 2 0.0000 1.000 0.00 1.00 0.00 0.00 0.00
#> TCGA.QG.A5YW.01 1 0.0000 0.986 1.00 0.00 0.00 0.00 0.00
#> TCGA.A6.5665.01 2 0.0000 1.000 0.00 1.00 0.00 0.00 0.00
#> TCGA.EI.6882.01 4 0.3109 0.687 0.20 0.00 0.00 0.80 0.00
#> TCGA.A6.2677.01 1 0.0000 0.986 1.00 0.00 0.00 0.00 0.00
#> TCGA.D5.6538.01 3 0.3109 0.797 0.00 0.00 0.80 0.00 0.20
#> TCGA.AA.3502.01 4 0.0609 0.930 0.02 0.00 0.00 0.98 0.00
#> TCGA.QG.A5Z2.01 2 0.0000 1.000 0.00 1.00 0.00 0.00 0.00
#> TCGA.CK.5915.01 4 0.1043 0.915 0.04 0.00 0.00 0.96 0.00
#> TCGA.AY.6197.01 3 0.0000 0.919 0.00 0.00 1.00 0.00 0.00
#> TCGA.G4.6294.01 1 0.0000 0.986 1.00 0.00 0.00 0.00 0.00
#> TCGA.CK.4952.01 5 0.2280 0.811 0.00 0.12 0.00 0.00 0.88
#> TCGA.CM.6172.01 1 0.0000 0.986 1.00 0.00 0.00 0.00 0.00
#> TCGA.AA.3496.01 1 0.3684 0.619 0.72 0.00 0.00 0.28 0.00
#> TCGA.CK.5913.01 2 0.0000 1.000 0.00 1.00 0.00 0.00 0.00
#> TCGA.DM.A28A.01 1 0.0000 0.986 1.00 0.00 0.00 0.00 0.00
#> TCGA.EI.7002.01 1 0.0000 0.986 1.00 0.00 0.00 0.00 0.00
#> TCGA.QG.A5Z1.01 1 0.0609 0.968 0.98 0.00 0.00 0.02 0.00
#> TCGA.DM.A28H.01 4 0.1216 0.928 0.02 0.00 0.00 0.96 0.02
#> TCGA.G4.6320.01 2 0.0000 1.000 0.00 1.00 0.00 0.00 0.00
#> TCGA.DM.A28M.01 1 0.0000 0.986 1.00 0.00 0.00 0.00 0.00
#> TCGA.DM.A288.01 4 0.1216 0.928 0.02 0.00 0.00 0.96 0.02
#> TCGA.A6.6653.01 2 0.0000 1.000 0.00 1.00 0.00 0.00 0.00
#> TCGA.F4.6855.01 1 0.0000 0.986 1.00 0.00 0.00 0.00 0.00
#> TCGA.NH.A6GA.01 4 0.0609 0.930 0.02 0.00 0.00 0.98 0.00
#> TCGA.NH.A50V.01 3 0.0609 0.908 0.00 0.00 0.98 0.02 0.00
#> TCGA.CK.6747.01 1 0.0000 0.986 1.00 0.00 0.00 0.00 0.00
#> TCGA.CL.5918.01 1 0.0000 0.986 1.00 0.00 0.00 0.00 0.00
#> TCGA.DM.A28K.01 1 0.0000 0.986 1.00 0.00 0.00 0.00 0.00
#> TCGA.AA.3655.01 1 0.0000 0.986 1.00 0.00 0.00 0.00 0.00
#> TCGA.AZ.5407.01 3 0.0000 0.919 0.00 0.00 1.00 0.00 0.00
#> TCGA.A6.5661.01 2 0.0000 1.000 0.00 1.00 0.00 0.00 0.00
#> TCGA.QG.A5YV.01 1 0.0000 0.986 1.00 0.00 0.00 0.00 0.00
#> TCGA.AY.A71X.01 4 0.0609 0.920 0.00 0.00 0.02 0.98 0.00
#> TCGA.AH.6549.01 1 0.0000 0.986 1.00 0.00 0.00 0.00 0.00
#> TCGA.CM.6166.01 1 0.0000 0.986 1.00 0.00 0.00 0.00 0.00
#> TCGA.AH.6897.01 1 0.0000 0.986 1.00 0.00 0.00 0.00 0.00
#> TCGA.D5.5540.01 4 0.2280 0.816 0.12 0.00 0.00 0.88 0.00
#> TCGA.A6.2672.01 2 0.0000 1.000 0.00 1.00 0.00 0.00 0.00
#> TCGA.G5.6233.01 3 0.0000 0.919 0.00 0.00 1.00 0.00 0.00
#> TCGA.CA.6719.01 4 0.0609 0.930 0.02 0.00 0.00 0.98 0.00
#> TCGA.D5.5537.01 4 0.0609 0.930 0.02 0.00 0.00 0.98 0.00
#> TCGA.4T.AA8H.01 4 0.0609 0.920 0.00 0.00 0.02 0.98 0.00
#> TCGA.AG.3592.01 1 0.0000 0.986 1.00 0.00 0.00 0.00 0.00
#> TCGA.CM.6678.01 1 0.0000 0.986 1.00 0.00 0.00 0.00 0.00
#> TCGA.CK.5914.01 1 0.0000 0.986 1.00 0.00 0.00 0.00 0.00
#> TCGA.AA.3492.01 2 0.0000 1.000 0.00 1.00 0.00 0.00 0.00
#> TCGA.DM.A1HB.01 2 0.0000 1.000 0.00 1.00 0.00 0.00 0.00
#> TCGA.EI.6508.01 1 0.0000 0.986 1.00 0.00 0.00 0.00 0.00
#> TCGA.D5.6532.01 1 0.0000 0.986 1.00 0.00 0.00 0.00 0.00
#> TCGA.A6.5659.01 5 0.0609 0.859 0.00 0.00 0.02 0.00 0.98
#> TCGA.A6.2680.01 1 0.0000 0.986 1.00 0.00 0.00 0.00 0.00
#> TCGA.CM.6680.01 1 0.0000 0.986 1.00 0.00 0.00 0.00 0.00
#> TCGA.AA.3660.01 1 0.2280 0.867 0.88 0.00 0.00 0.12 0.00
#> TCGA.CM.4747.01 4 0.0609 0.930 0.02 0.00 0.00 0.98 0.00
#> TCGA.EF.5831.01 1 0.0000 0.986 1.00 0.00 0.00 0.00 0.00
#> TCGA.DM.A28G.01 1 0.0000 0.986 1.00 0.00 0.00 0.00 0.00
#> TCGA.D5.6537.01 1 0.0000 0.986 1.00 0.00 0.00 0.00 0.00
#> TCGA.DY.A1DD.01 1 0.0000 0.986 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.AG.A026.01 1 0.0000 0.992 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.G4.6303.01 1 0.0000 0.992 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.T9.A92H.01 1 0.0000 0.992 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AD.6965.01 1 0.0000 0.992 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.A6.5660.01 1 0.0000 0.992 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D5.6540.01 2 0.0000 0.988 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.F5.6571.01 1 0.0000 0.992 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CM.5862.01 1 0.0000 0.992 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CI.6622.01 1 0.0000 0.992 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.G4.6588.01 2 0.0000 0.988 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.EI.6512.01 4 0.0547 0.682 0.00 0.00 0.00 0.98 0.00 0.02
#> TCGA.QG.A5YX.01 1 0.0000 0.992 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AG.A036.01 1 0.0000 0.992 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AZ.6606.01 5 0.0547 0.871 0.00 0.02 0.00 0.00 0.98 0.00
#> TCGA.F4.6570.01 2 0.0000 0.988 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.AA.3509.01 1 0.0000 0.992 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EI.6883.01 4 0.0547 0.682 0.00 0.00 0.00 0.98 0.00 0.02
#> TCGA.RU.A8FL.01 1 0.0000 0.992 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AZ.6599.01 6 0.3647 0.685 0.00 0.00 0.00 0.36 0.00 0.64
#> TCGA.CM.5860.01 3 0.0937 0.880 0.00 0.00 0.96 0.00 0.00 0.04
#> TCGA.A6.6780.01 6 0.3756 0.279 0.00 0.00 0.40 0.00 0.00 0.60
#> TCGA.A6.2686.01 2 0.0000 0.988 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.CM.4750.01 1 0.0000 0.992 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CM.6677.01 6 0.3706 0.658 0.00 0.00 0.00 0.38 0.00 0.62
#> TCGA.F5.6814.01 4 0.3797 0.392 0.42 0.00 0.00 0.58 0.00 0.00
#> TCGA.G4.6299.01 2 0.0000 0.988 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.A6.4105.01 3 0.3315 0.746 0.00 0.00 0.78 0.00 0.02 0.20
#> TCGA.DM.A1D8.01 6 0.3916 0.700 0.00 0.00 0.02 0.30 0.00 0.68
#> TCGA.DT.5265.01 2 0.1267 0.937 0.00 0.94 0.00 0.00 0.06 0.00
#> TCGA.DM.A0XD.01 3 0.0547 0.882 0.00 0.00 0.98 0.00 0.00 0.02
#> TCGA.A6.6138.01 6 0.3647 0.685 0.00 0.00 0.00 0.36 0.00 0.64
#> TCGA.D5.7000.01 5 0.2981 0.839 0.00 0.00 0.02 0.00 0.82 0.16
#> TCGA.DM.A28F.01 1 0.0000 0.992 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CK.6751.01 5 0.2981 0.839 0.00 0.00 0.02 0.00 0.82 0.16
#> TCGA.CM.6171.01 2 0.0000 0.988 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DM.A1DA.01 5 0.0937 0.875 0.00 0.00 0.00 0.00 0.96 0.04
#> TCGA.DM.A1D4.01 3 0.0937 0.880 0.00 0.00 0.96 0.00 0.00 0.04
#> TCGA.AD.A5EJ.01 2 0.0000 0.988 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DM.A0X9.01 3 0.3578 0.504 0.00 0.00 0.66 0.00 0.00 0.34
#> TCGA.AY.A69D.01 4 0.1267 0.666 0.00 0.00 0.00 0.94 0.00 0.06
#> TCGA.CA.6716.01 6 0.3499 0.388 0.00 0.00 0.32 0.00 0.00 0.68
#> TCGA.CK.5916.01 2 0.0000 0.988 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.NH.A6GB.01 4 0.1267 0.665 0.00 0.00 0.00 0.94 0.00 0.06
#> TCGA.NH.A50U.01 1 0.0000 0.992 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AZ.4614.01 5 0.0547 0.874 0.00 0.00 0.00 0.00 0.98 0.02
#> TCGA.AH.6644.01 1 0.0000 0.992 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.A6.3809.01 2 0.0000 0.988 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.CM.5864.01 1 0.0000 0.992 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CM.5861.01 2 0.0000 0.988 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.AG.3742.01 1 0.0000 0.992 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.A6.5666.01 1 0.0000 0.992 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AG.3591.01 1 0.0000 0.992 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AH.6643.01 1 0.0000 0.992 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EI.6510.01 1 0.0000 0.992 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.A6.5656.01 1 0.0000 0.992 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DY.A1DG.01 1 0.0000 0.992 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.F4.6806.01 6 0.4360 0.546 0.00 0.00 0.26 0.06 0.00 0.68
#> TCGA.G4.6322.01 5 0.5520 0.565 0.00 0.00 0.24 0.00 0.56 0.20
#> TCGA.5M.AAT4.01 4 0.3828 0.346 0.44 0.00 0.00 0.56 0.00 0.00
#> TCGA.G4.6586.01 2 0.0000 0.988 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.EI.6514.01 1 0.0000 0.992 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DM.A282.01 1 0.0000 0.992 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DM.A1HA.01 6 0.3647 0.685 0.00 0.00 0.00 0.36 0.00 0.64
#> TCGA.D5.6531.01 5 0.2048 0.795 0.00 0.12 0.00 0.00 0.88 0.00
#> TCGA.AZ.6598.01 2 0.0000 0.988 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.AG.4021.01 1 0.0000 0.992 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DM.A1D9.01 1 0.0000 0.992 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CM.4744.01 3 0.0937 0.884 0.00 0.00 0.96 0.00 0.00 0.04
#> TCGA.A6.6652.01 1 0.0000 0.992 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.SS.A7HO.01 1 0.0000 0.992 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.A6.6650.01 1 0.0000 0.992 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.F4.6461.01 5 0.0937 0.871 0.00 0.00 0.00 0.00 0.96 0.04
#> TCGA.AD.6889.01 2 0.0000 0.988 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.NH.A50T.01 1 0.0000 0.992 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AA.3663.01 3 0.2048 0.857 0.00 0.00 0.88 0.00 0.00 0.12
#> TCGA.AD.6899.01 4 0.0937 0.677 0.00 0.00 0.00 0.96 0.00 0.04
#> TCGA.A6.A56B.01 4 0.3797 0.392 0.42 0.00 0.00 0.58 0.00 0.00
#> TCGA.D5.5539.01 1 0.0000 0.992 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CA.5254.01 5 0.2454 0.748 0.00 0.16 0.00 0.00 0.84 0.00
#> TCGA.AY.A54L.01 4 0.1556 0.653 0.08 0.00 0.00 0.92 0.00 0.00
#> TCGA.A6.4107.01 5 0.1267 0.874 0.00 0.00 0.00 0.00 0.94 0.06
#> TCGA.NH.A5IV.01 4 0.3756 0.405 0.40 0.00 0.00 0.60 0.00 0.00
#> TCGA.G4.6306.01 1 0.0000 0.992 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AD.A5EK.01 4 0.3869 -0.465 0.00 0.00 0.00 0.50 0.00 0.50
#> TCGA.DC.5337.01 1 0.0000 0.992 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CM.6675.01 2 0.2260 0.851 0.00 0.86 0.00 0.00 0.14 0.00
#> TCGA.CK.6746.01 2 0.0000 0.988 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.QG.A5YW.01 1 0.0000 0.992 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.A6.5665.01 2 0.0000 0.988 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.EI.6882.01 4 0.1556 0.652 0.08 0.00 0.00 0.92 0.00 0.00
#> TCGA.A6.2677.01 1 0.0000 0.992 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D5.6538.01 3 0.2260 0.819 0.00 0.00 0.86 0.00 0.00 0.14
#> TCGA.AA.3502.01 4 0.1267 0.665 0.00 0.00 0.00 0.94 0.00 0.06
#> TCGA.QG.A5Z2.01 2 0.0000 0.988 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.CK.5915.01 4 0.0000 0.684 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.AY.6197.01 3 0.1556 0.871 0.00 0.00 0.92 0.00 0.00 0.08
#> TCGA.G4.6294.01 1 0.0000 0.992 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CK.4952.01 5 0.0547 0.874 0.00 0.00 0.00 0.00 0.98 0.02
#> TCGA.CM.6172.01 1 0.1267 0.929 0.94 0.00 0.00 0.06 0.00 0.00
#> TCGA.AA.3496.01 4 0.3409 0.465 0.30 0.00 0.00 0.70 0.00 0.00
#> TCGA.CK.5913.01 2 0.0000 0.988 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DM.A28A.01 1 0.0547 0.972 0.98 0.00 0.00 0.02 0.00 0.00
#> TCGA.EI.7002.01 1 0.0000 0.992 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.QG.A5Z1.01 1 0.2454 0.788 0.84 0.00 0.00 0.16 0.00 0.00
#> TCGA.DM.A28H.01 4 0.0547 0.682 0.00 0.00 0.00 0.98 0.00 0.02
#> TCGA.G4.6320.01 2 0.1814 0.897 0.00 0.90 0.00 0.00 0.10 0.00
#> TCGA.DM.A28M.01 1 0.0000 0.992 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DM.A288.01 4 0.0547 0.682 0.00 0.00 0.00 0.98 0.00 0.02
#> TCGA.A6.6653.01 2 0.0000 0.988 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.F4.6855.01 1 0.0000 0.992 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.NH.A6GA.01 4 0.0547 0.682 0.00 0.00 0.00 0.98 0.00 0.02
#> TCGA.NH.A50V.01 6 0.3647 0.385 0.00 0.00 0.36 0.00 0.00 0.64
#> TCGA.CK.6747.01 1 0.0547 0.972 0.98 0.00 0.00 0.02 0.00 0.00
#> TCGA.CL.5918.01 1 0.0000 0.992 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DM.A28K.01 1 0.0000 0.992 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AA.3655.01 1 0.0000 0.992 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AZ.5407.01 3 0.0937 0.884 0.00 0.00 0.96 0.00 0.00 0.04
#> TCGA.A6.5661.01 2 0.0000 0.988 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.QG.A5YV.01 1 0.0000 0.992 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AY.A71X.01 4 0.2941 0.406 0.00 0.00 0.00 0.78 0.00 0.22
#> TCGA.AH.6549.01 1 0.0000 0.992 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CM.6166.01 1 0.0000 0.992 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AH.6897.01 1 0.0000 0.992 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D5.5540.01 4 0.1267 0.667 0.06 0.00 0.00 0.94 0.00 0.00
#> TCGA.A6.2672.01 2 0.0000 0.988 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.G5.6233.01 3 0.0937 0.884 0.00 0.00 0.96 0.00 0.00 0.04
#> TCGA.CA.6719.01 4 0.0000 0.684 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.D5.5537.01 4 0.0937 0.677 0.00 0.00 0.00 0.96 0.00 0.04
#> TCGA.4T.AA8H.01 4 0.1267 0.665 0.00 0.00 0.00 0.94 0.00 0.06
#> TCGA.AG.3592.01 1 0.0547 0.972 0.98 0.00 0.00 0.02 0.00 0.00
#> TCGA.CM.6678.01 1 0.0000 0.992 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CK.5914.01 1 0.0000 0.992 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AA.3492.01 2 0.0000 0.988 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DM.A1HB.01 2 0.0000 0.988 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.EI.6508.01 1 0.0000 0.992 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D5.6532.01 1 0.0000 0.992 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.A6.5659.01 5 0.3351 0.829 0.00 0.00 0.04 0.00 0.80 0.16
#> TCGA.A6.2680.01 1 0.0000 0.992 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CM.6680.01 1 0.0000 0.992 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AA.3660.01 4 0.3797 0.392 0.42 0.00 0.00 0.58 0.00 0.00
#> TCGA.CM.4747.01 4 0.0937 0.670 0.00 0.00 0.00 0.96 0.00 0.04
#> TCGA.EF.5831.01 1 0.2631 0.754 0.82 0.00 0.00 0.18 0.00 0.00
#> TCGA.DM.A28G.01 1 0.0000 0.992 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D5.6537.01 1 0.0000 0.992 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DY.A1DD.01 1 0.0000 0.992 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.AG.A026.01 7 0.0000 0.970 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.G4.6303.01 7 0.0000 0.970 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.T9.A92H.01 7 0.0000 0.970 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.AD.6965.01 7 0.0863 0.936 0.00 0.00 0.00 0.04 0.00 0.00 0.96
#> TCGA.A6.5660.01 7 0.0000 0.970 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.D5.6540.01 2 0.0000 0.993 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.F5.6571.01 7 0.0000 0.970 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.CM.5862.01 7 0.0000 0.970 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.CI.6622.01 7 0.0000 0.970 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.G4.6588.01 2 0.0000 0.993 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EI.6512.01 4 0.2745 0.686 0.16 0.00 0.00 0.82 0.00 0.02 0.00
#> TCGA.QG.A5YX.01 7 0.0000 0.970 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.AG.A036.01 7 0.0000 0.970 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.AZ.6606.01 5 0.0863 0.814 0.00 0.04 0.00 0.00 0.96 0.00 0.00
#> TCGA.F4.6570.01 2 0.0000 0.993 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AA.3509.01 7 0.0000 0.970 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.EI.6883.01 4 0.3745 0.632 0.26 0.00 0.00 0.70 0.00 0.04 0.00
#> TCGA.RU.A8FL.01 7 0.0000 0.970 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.AZ.6599.01 6 0.2081 0.671 0.00 0.00 0.00 0.14 0.00 0.86 0.00
#> TCGA.CM.5860.01 3 0.2422 0.756 0.18 0.00 0.82 0.00 0.00 0.00 0.00
#> TCGA.A6.6780.01 6 0.4875 0.111 0.10 0.00 0.44 0.00 0.00 0.46 0.00
#> TCGA.A6.2686.01 2 0.0000 0.993 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CM.4750.01 7 0.0863 0.936 0.00 0.00 0.00 0.04 0.00 0.00 0.96
#> TCGA.CM.6677.01 6 0.2569 0.663 0.02 0.00 0.00 0.14 0.00 0.84 0.00
#> TCGA.F5.6814.01 4 0.2945 0.538 0.00 0.00 0.00 0.74 0.00 0.00 0.26
#> TCGA.G4.6299.01 2 0.0000 0.993 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.A6.4105.01 3 0.3459 0.630 0.40 0.00 0.60 0.00 0.00 0.00 0.00
#> TCGA.DM.A1D8.01 6 0.2159 0.647 0.02 0.00 0.06 0.02 0.00 0.90 0.00
#> TCGA.DT.5265.01 2 0.0000 0.993 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DM.A0XD.01 3 0.2422 0.750 0.18 0.00 0.82 0.00 0.00 0.00 0.00
#> TCGA.A6.6138.01 6 0.1886 0.671 0.00 0.00 0.00 0.12 0.00 0.88 0.00
#> TCGA.D5.7000.01 5 0.3795 0.760 0.22 0.00 0.06 0.00 0.72 0.00 0.00
#> TCGA.DM.A28F.01 7 0.0000 0.970 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.CK.6751.01 5 0.3795 0.760 0.22 0.00 0.06 0.00 0.72 0.00 0.00
#> TCGA.CM.6171.01 2 0.0000 0.993 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DM.A1DA.01 5 0.0863 0.822 0.04 0.00 0.00 0.00 0.96 0.00 0.00
#> TCGA.DM.A1D4.01 3 0.2906 0.761 0.18 0.00 0.80 0.00 0.00 0.02 0.00
#> TCGA.AD.A5EJ.01 2 0.0000 0.993 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DM.A0X9.01 6 0.5517 0.150 0.24 0.00 0.34 0.00 0.00 0.42 0.00
#> TCGA.AY.A69D.01 4 0.4451 0.579 0.26 0.00 0.00 0.64 0.00 0.10 0.00
#> TCGA.CA.6716.01 6 0.4842 0.503 0.24 0.00 0.16 0.00 0.00 0.60 0.00
#> TCGA.CK.5916.01 2 0.0000 0.993 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.NH.A6GB.01 4 0.1671 0.702 0.00 0.00 0.00 0.90 0.00 0.10 0.00
#> TCGA.NH.A50U.01 7 0.0000 0.970 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.AZ.4614.01 5 0.0000 0.819 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.AH.6644.01 7 0.0000 0.970 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.A6.3809.01 2 0.0000 0.993 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CM.5864.01 7 0.0000 0.970 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.CM.5861.01 2 0.0000 0.993 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AG.3742.01 7 0.0000 0.970 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.A6.5666.01 7 0.0000 0.970 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.AG.3591.01 7 0.0000 0.970 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.AH.6643.01 7 0.0000 0.970 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.EI.6510.01 7 0.0000 0.970 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.A6.5656.01 7 0.0000 0.970 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.DY.A1DG.01 7 0.0000 0.970 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.F4.6806.01 6 0.2569 0.620 0.02 0.00 0.14 0.00 0.00 0.84 0.00
#> TCGA.G4.6322.01 5 0.5875 0.325 0.30 0.00 0.24 0.00 0.44 0.02 0.00
#> TCGA.5M.AAT4.01 4 0.2832 0.566 0.00 0.00 0.00 0.76 0.00 0.00 0.24
#> TCGA.G4.6586.01 2 0.0000 0.993 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EI.6514.01 7 0.0000 0.970 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.DM.A282.01 7 0.0000 0.970 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.DM.A1HA.01 6 0.2081 0.671 0.00 0.00 0.00 0.14 0.00 0.86 0.00
#> TCGA.D5.6531.01 5 0.1433 0.790 0.00 0.08 0.00 0.00 0.92 0.00 0.00
#> TCGA.AZ.6598.01 2 0.0000 0.993 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AG.4021.01 7 0.0000 0.970 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.DM.A1D9.01 7 0.0000 0.970 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.CM.4744.01 3 0.1671 0.739 0.00 0.00 0.90 0.00 0.00 0.10 0.00
#> TCGA.A6.6652.01 7 0.0000 0.970 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.SS.A7HO.01 7 0.0000 0.970 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.A6.6650.01 7 0.0000 0.970 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.F4.6461.01 5 0.2376 0.783 0.12 0.00 0.00 0.00 0.86 0.02 0.00
#> TCGA.AD.6889.01 2 0.0000 0.993 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.NH.A50T.01 7 0.0000 0.970 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.AA.3663.01 3 0.4055 0.690 0.18 0.00 0.74 0.00 0.04 0.04 0.00
#> TCGA.AD.6899.01 4 0.3487 0.680 0.10 0.00 0.00 0.78 0.00 0.12 0.00
#> TCGA.A6.A56B.01 4 0.3186 0.587 0.02 0.00 0.00 0.76 0.00 0.00 0.22
#> TCGA.D5.5539.01 7 0.0000 0.970 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.CA.5254.01 5 0.2081 0.724 0.00 0.14 0.00 0.00 0.86 0.00 0.00
#> TCGA.AY.A54L.01 4 0.1166 0.715 0.00 0.00 0.00 0.94 0.00 0.00 0.06
#> TCGA.A6.4107.01 5 0.2259 0.806 0.16 0.00 0.00 0.00 0.84 0.00 0.00
#> TCGA.NH.A5IV.01 4 0.2832 0.566 0.00 0.00 0.00 0.76 0.00 0.00 0.24
#> TCGA.G4.6306.01 7 0.0000 0.970 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.AD.A5EK.01 6 0.5402 0.250 0.24 0.00 0.00 0.28 0.00 0.48 0.00
#> TCGA.DC.5337.01 7 0.0000 0.970 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.CM.6675.01 2 0.2081 0.840 0.00 0.86 0.00 0.00 0.14 0.00 0.00
#> TCGA.CK.6746.01 2 0.0000 0.993 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.QG.A5YW.01 7 0.0000 0.970 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.A6.5665.01 2 0.0000 0.993 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EI.6882.01 4 0.1166 0.716 0.00 0.00 0.00 0.94 0.00 0.00 0.06
#> TCGA.A6.2677.01 7 0.0000 0.970 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.D5.6538.01 3 0.3047 0.721 0.28 0.00 0.72 0.00 0.00 0.00 0.00
#> TCGA.AA.3502.01 4 0.4502 0.597 0.16 0.00 0.00 0.66 0.00 0.18 0.00
#> TCGA.QG.A5Z2.01 2 0.0000 0.993 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CK.5915.01 4 0.0863 0.715 0.04 0.00 0.00 0.96 0.00 0.00 0.00
#> TCGA.AY.6197.01 3 0.3487 0.655 0.10 0.00 0.78 0.00 0.00 0.12 0.00
#> TCGA.G4.6294.01 7 0.0000 0.970 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.CK.4952.01 5 0.0000 0.819 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.CM.6172.01 7 0.3139 0.569 0.00 0.00 0.00 0.30 0.00 0.00 0.70
#> TCGA.AA.3496.01 4 0.2081 0.666 0.00 0.00 0.00 0.86 0.00 0.00 0.14
#> TCGA.CK.5913.01 2 0.0000 0.993 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DM.A28A.01 7 0.1671 0.872 0.00 0.00 0.00 0.10 0.00 0.00 0.90
#> TCGA.EI.7002.01 7 0.0000 0.970 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.QG.A5Z1.01 7 0.3459 0.331 0.00 0.00 0.00 0.40 0.00 0.00 0.60
#> TCGA.DM.A28H.01 4 0.2569 0.692 0.14 0.00 0.00 0.84 0.00 0.02 0.00
#> TCGA.G4.6320.01 2 0.0504 0.975 0.00 0.98 0.00 0.00 0.02 0.00 0.00
#> TCGA.DM.A28M.01 7 0.0000 0.970 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.DM.A288.01 4 0.4015 0.618 0.26 0.00 0.00 0.68 0.00 0.06 0.00
#> TCGA.A6.6653.01 2 0.0000 0.993 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.F4.6855.01 7 0.0000 0.970 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.NH.A6GA.01 4 0.3487 0.681 0.12 0.00 0.00 0.78 0.00 0.10 0.00
#> TCGA.NH.A50V.01 6 0.3770 0.566 0.08 0.00 0.18 0.00 0.00 0.74 0.00
#> TCGA.CK.6747.01 7 0.2572 0.744 0.00 0.00 0.00 0.20 0.00 0.00 0.80
#> TCGA.CL.5918.01 7 0.0000 0.970 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.DM.A28K.01 7 0.0863 0.936 0.00 0.00 0.00 0.04 0.00 0.00 0.96
#> TCGA.AA.3655.01 7 0.0000 0.970 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.AZ.5407.01 3 0.1671 0.739 0.00 0.00 0.90 0.00 0.00 0.10 0.00
#> TCGA.A6.5661.01 2 0.0000 0.993 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.QG.A5YV.01 7 0.0000 0.970 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.AY.A71X.01 4 0.5190 0.373 0.18 0.00 0.00 0.52 0.00 0.30 0.00
#> TCGA.AH.6549.01 7 0.0000 0.970 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.CM.6166.01 7 0.0000 0.970 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.AH.6897.01 7 0.0000 0.970 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.D5.5540.01 4 0.0863 0.719 0.00 0.00 0.00 0.96 0.00 0.00 0.04
#> TCGA.A6.2672.01 2 0.0000 0.993 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.G5.6233.01 3 0.3058 0.687 0.08 0.00 0.82 0.00 0.00 0.10 0.00
#> TCGA.CA.6719.01 4 0.1166 0.716 0.06 0.00 0.00 0.94 0.00 0.00 0.00
#> TCGA.D5.5537.01 4 0.1671 0.699 0.00 0.00 0.00 0.90 0.00 0.10 0.00
#> TCGA.4T.AA8H.01 4 0.4478 0.583 0.14 0.00 0.00 0.66 0.00 0.20 0.00
#> TCGA.AG.3592.01 7 0.2572 0.746 0.00 0.00 0.00 0.20 0.00 0.00 0.80
#> TCGA.CM.6678.01 7 0.0000 0.970 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.CK.5914.01 7 0.0000 0.970 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.AA.3492.01 2 0.0000 0.993 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DM.A1HB.01 2 0.0000 0.993 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EI.6508.01 7 0.0000 0.970 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.D5.6532.01 7 0.0000 0.970 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.A6.5659.01 5 0.4681 0.635 0.32 0.00 0.10 0.00 0.58 0.00 0.00
#> TCGA.A6.2680.01 7 0.0000 0.970 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.CM.6680.01 7 0.0000 0.970 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.AA.3660.01 4 0.3052 0.608 0.02 0.00 0.00 0.78 0.00 0.00 0.20
#> TCGA.CM.4747.01 4 0.4309 0.614 0.20 0.00 0.00 0.68 0.00 0.12 0.00
#> TCGA.EF.5831.01 7 0.3496 0.264 0.00 0.00 0.00 0.42 0.00 0.00 0.58
#> TCGA.DM.A28G.01 7 0.0000 0.970 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.D5.6537.01 7 0.0000 0.970 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.DY.A1DD.01 7 0.0000 0.970 0.00 0.00 0.00 0.00 0.00 0.00 1.00
cbind(get_classes(res, k = 8), get_membership(res, k = 8))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7 p8
#> TCGA.AG.A026.01 7 0.0000 0.96436 0.00 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.G4.6303.01 7 0.0000 0.96436 0.00 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.T9.A92H.01 7 0.0000 0.96436 0.00 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.AD.6965.01 7 0.1341 0.89512 0.00 0.00 0.00 0.08 0.00 0.00 0.92 0.00
#> TCGA.A6.5660.01 7 0.0000 0.96436 0.00 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.D5.6540.01 2 0.0000 0.98827 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.F5.6571.01 7 0.0000 0.96436 0.00 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.CM.5862.01 7 0.0000 0.96436 0.00 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.CI.6622.01 7 0.0000 0.96436 0.00 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.G4.6588.01 2 0.0000 0.98827 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EI.6512.01 4 0.2852 0.18705 0.28 0.00 0.00 0.72 0.00 0.00 0.00 0.00
#> TCGA.QG.A5YX.01 7 0.0000 0.96436 0.00 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.AG.A036.01 7 0.0000 0.96436 0.00 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.AZ.6606.01 5 0.0471 0.81819 0.00 0.02 0.00 0.00 0.98 0.00 0.00 0.00
#> TCGA.F4.6570.01 2 0.0000 0.98827 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AA.3509.01 7 0.0000 0.96436 0.00 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.EI.6883.01 4 0.3737 -0.44042 0.48 0.00 0.00 0.50 0.00 0.02 0.00 0.00
#> TCGA.RU.A8FL.01 7 0.0471 0.94984 0.00 0.00 0.00 0.02 0.00 0.00 0.98 0.00
#> TCGA.AZ.6599.01 6 0.2350 0.54047 0.04 0.00 0.00 0.10 0.00 0.86 0.00 0.00
#> TCGA.CM.5860.01 8 0.3015 0.42950 0.00 0.00 0.32 0.00 0.00 0.00 0.00 0.68
#> TCGA.A6.6780.01 3 0.2981 0.48627 0.02 0.00 0.76 0.00 0.00 0.22 0.00 0.00
#> TCGA.A6.2686.01 2 0.0000 0.98827 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CM.4750.01 7 0.1563 0.87390 0.00 0.00 0.00 0.10 0.00 0.00 0.90 0.00
#> TCGA.CM.6677.01 6 0.2350 0.54047 0.04 0.00 0.00 0.10 0.00 0.86 0.00 0.00
#> TCGA.F5.6814.01 4 0.2267 0.47225 0.00 0.00 0.00 0.82 0.00 0.00 0.18 0.00
#> TCGA.G4.6299.01 2 0.0000 0.98827 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.A6.4105.01 8 0.3471 0.44888 0.02 0.00 0.16 0.00 0.02 0.02 0.00 0.78
#> TCGA.DM.A1D8.01 6 0.4028 0.51464 0.04 0.00 0.28 0.02 0.00 0.66 0.00 0.00
#> TCGA.DT.5265.01 2 0.0808 0.95481 0.00 0.96 0.00 0.00 0.04 0.00 0.00 0.00
#> TCGA.DM.A0XD.01 3 0.3729 -0.06890 0.00 0.00 0.52 0.00 0.02 0.00 0.00 0.46
#> TCGA.A6.6138.01 6 0.2350 0.54077 0.04 0.00 0.00 0.10 0.00 0.86 0.00 0.00
#> TCGA.D5.7000.01 5 0.4053 0.71584 0.06 0.00 0.00 0.00 0.72 0.04 0.00 0.18
#> TCGA.DM.A28F.01 7 0.0000 0.96436 0.00 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.CK.6751.01 5 0.4053 0.71584 0.06 0.00 0.00 0.00 0.72 0.04 0.00 0.18
#> TCGA.CM.6171.01 2 0.0000 0.98827 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DM.A1DA.01 5 0.1741 0.81468 0.02 0.00 0.00 0.00 0.92 0.02 0.00 0.04
#> TCGA.DM.A1D4.01 8 0.3015 0.42082 0.00 0.00 0.32 0.00 0.00 0.00 0.00 0.68
#> TCGA.AD.A5EJ.01 2 0.0000 0.98827 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DM.A0X9.01 8 0.6461 -0.07835 0.14 0.00 0.30 0.00 0.00 0.24 0.00 0.32
#> TCGA.AY.A69D.01 1 0.4216 0.19258 0.50 0.00 0.00 0.44 0.00 0.06 0.00 0.00
#> TCGA.CA.6716.01 6 0.6590 0.06871 0.26 0.00 0.26 0.00 0.00 0.30 0.00 0.18
#> TCGA.CK.5916.01 2 0.0000 0.98827 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.NH.A6GB.01 4 0.3021 0.31191 0.02 0.00 0.00 0.80 0.00 0.16 0.00 0.02
#> TCGA.NH.A50U.01 7 0.0000 0.96436 0.00 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.AZ.4614.01 5 0.0000 0.81728 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.AH.6644.01 7 0.0000 0.96436 0.00 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.A6.3809.01 2 0.0000 0.98827 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CM.5864.01 7 0.0000 0.96436 0.00 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.CM.5861.01 2 0.0000 0.98827 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AG.3742.01 7 0.0471 0.94984 0.00 0.00 0.00 0.02 0.00 0.00 0.98 0.00
#> TCGA.A6.5666.01 7 0.0000 0.96436 0.00 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.AG.3591.01 7 0.0000 0.96436 0.00 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.AH.6643.01 7 0.0000 0.96436 0.00 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.EI.6510.01 7 0.0808 0.93321 0.00 0.00 0.00 0.04 0.00 0.00 0.96 0.00
#> TCGA.A6.5656.01 7 0.0000 0.96436 0.00 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.DY.A1DG.01 7 0.0000 0.96436 0.00 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.F4.6806.01 6 0.3291 0.52256 0.00 0.00 0.28 0.02 0.00 0.70 0.00 0.00
#> TCGA.G4.6322.01 5 0.6462 0.29955 0.16 0.00 0.16 0.00 0.46 0.02 0.00 0.20
#> TCGA.5M.AAT4.01 4 0.2267 0.47126 0.00 0.00 0.00 0.82 0.00 0.00 0.18 0.00
#> TCGA.G4.6586.01 2 0.0000 0.98827 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EI.6514.01 7 0.0000 0.96436 0.00 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.DM.A282.01 7 0.0000 0.96436 0.00 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.DM.A1HA.01 6 0.2864 0.54040 0.06 0.00 0.00 0.08 0.00 0.84 0.00 0.02
#> TCGA.D5.6531.01 5 0.1341 0.77122 0.00 0.08 0.00 0.00 0.92 0.00 0.00 0.00
#> TCGA.AZ.6598.01 2 0.0000 0.98827 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AG.4021.01 7 0.0000 0.96436 0.00 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.DM.A1D9.01 7 0.0000 0.96436 0.00 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.CM.4744.01 3 0.2267 0.62864 0.00 0.00 0.82 0.00 0.00 0.00 0.00 0.18
#> TCGA.A6.6652.01 7 0.0000 0.96436 0.00 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.SS.A7HO.01 7 0.0000 0.96436 0.00 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.A6.6650.01 7 0.0000 0.96436 0.00 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.F4.6461.01 5 0.1563 0.80401 0.10 0.00 0.00 0.00 0.90 0.00 0.00 0.00
#> TCGA.AD.6889.01 2 0.0000 0.98827 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.NH.A50T.01 7 0.0000 0.96436 0.00 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.AA.3663.01 3 0.3270 0.62731 0.12 0.00 0.80 0.00 0.00 0.02 0.00 0.06
#> TCGA.AD.6899.01 4 0.4165 0.03734 0.10 0.00 0.00 0.64 0.00 0.26 0.00 0.00
#> TCGA.A6.A56B.01 4 0.2856 0.45594 0.02 0.00 0.00 0.78 0.00 0.00 0.20 0.00
#> TCGA.D5.5539.01 7 0.0000 0.96436 0.00 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.CA.5254.01 5 0.1341 0.77122 0.00 0.08 0.00 0.00 0.92 0.00 0.00 0.00
#> TCGA.AY.A54L.01 4 0.0808 0.48534 0.00 0.00 0.00 0.96 0.00 0.00 0.04 0.00
#> TCGA.A6.4107.01 5 0.3078 0.78082 0.06 0.00 0.00 0.00 0.82 0.02 0.00 0.10
#> TCGA.NH.A5IV.01 4 0.1765 0.49961 0.00 0.00 0.00 0.88 0.00 0.00 0.12 0.00
#> TCGA.G4.6306.01 7 0.0000 0.96436 0.00 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.AD.A5EK.01 1 0.4693 0.11006 0.46 0.00 0.00 0.12 0.00 0.42 0.00 0.00
#> TCGA.DC.5337.01 7 0.0000 0.96436 0.00 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.CM.6675.01 2 0.2267 0.79698 0.00 0.82 0.00 0.00 0.18 0.00 0.00 0.00
#> TCGA.CK.6746.01 2 0.0000 0.98827 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.QG.A5YW.01 7 0.0000 0.96436 0.00 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.A6.5665.01 2 0.0000 0.98827 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EI.6882.01 4 0.1091 0.49596 0.00 0.00 0.00 0.94 0.00 0.00 0.06 0.00
#> TCGA.A6.2677.01 7 0.0000 0.96436 0.00 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.D5.6538.01 8 0.3291 0.45991 0.00 0.00 0.28 0.00 0.02 0.00 0.00 0.70
#> TCGA.AA.3502.01 4 0.4998 -0.27444 0.24 0.00 0.00 0.50 0.00 0.26 0.00 0.00
#> TCGA.QG.A5Z2.01 2 0.0000 0.98827 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CK.5915.01 4 0.2569 0.33415 0.16 0.00 0.00 0.82 0.00 0.00 0.00 0.02
#> TCGA.AY.6197.01 3 0.0000 0.70503 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.G4.6294.01 7 0.0000 0.96436 0.00 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.CK.4952.01 5 0.0471 0.81819 0.00 0.02 0.00 0.00 0.98 0.00 0.00 0.00
#> TCGA.CM.6172.01 7 0.3333 -0.03633 0.00 0.00 0.00 0.50 0.00 0.00 0.50 0.00
#> TCGA.AA.3496.01 4 0.1563 0.50213 0.00 0.00 0.00 0.90 0.00 0.00 0.10 0.00
#> TCGA.CK.5913.01 2 0.0000 0.98827 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DM.A28A.01 7 0.2114 0.79879 0.00 0.00 0.00 0.16 0.00 0.00 0.84 0.00
#> TCGA.EI.7002.01 7 0.0000 0.96436 0.00 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.QG.A5Z1.01 4 0.3237 0.27010 0.00 0.00 0.00 0.60 0.00 0.00 0.40 0.00
#> TCGA.DM.A28H.01 4 0.2756 0.22406 0.26 0.00 0.00 0.74 0.00 0.00 0.00 0.00
#> TCGA.G4.6320.01 2 0.1091 0.93524 0.00 0.94 0.00 0.00 0.06 0.00 0.00 0.00
#> TCGA.DM.A28M.01 7 0.0808 0.93401 0.00 0.00 0.00 0.04 0.00 0.00 0.96 0.00
#> TCGA.DM.A288.01 4 0.3329 -0.40063 0.48 0.00 0.00 0.52 0.00 0.00 0.00 0.00
#> TCGA.A6.6653.01 2 0.0000 0.98827 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.F4.6855.01 7 0.0000 0.96436 0.00 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.NH.A6GA.01 4 0.4299 -0.00525 0.14 0.00 0.00 0.64 0.00 0.22 0.00 0.00
#> TCGA.NH.A50V.01 6 0.3880 0.46734 0.02 0.00 0.32 0.02 0.00 0.64 0.00 0.00
#> TCGA.CK.6747.01 7 0.3237 0.32143 0.00 0.00 0.00 0.40 0.00 0.00 0.60 0.00
#> TCGA.CL.5918.01 7 0.0000 0.96436 0.00 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.DM.A28K.01 7 0.2267 0.77456 0.00 0.00 0.00 0.18 0.00 0.00 0.82 0.00
#> TCGA.AA.3655.01 7 0.0000 0.96436 0.00 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.AZ.5407.01 3 0.1563 0.70061 0.00 0.00 0.90 0.00 0.00 0.00 0.00 0.10
#> TCGA.A6.5661.01 2 0.0000 0.98827 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.QG.A5YV.01 7 0.0000 0.96436 0.00 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.AY.A71X.01 6 0.5190 -0.38523 0.26 0.00 0.00 0.32 0.00 0.42 0.00 0.00
#> TCGA.AH.6549.01 7 0.0000 0.96436 0.00 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.CM.6166.01 7 0.0000 0.96436 0.00 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.AH.6897.01 7 0.0000 0.96436 0.00 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.D5.5540.01 4 0.1275 0.48230 0.02 0.00 0.00 0.94 0.00 0.00 0.04 0.00
#> TCGA.A6.2672.01 2 0.0000 0.98827 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.G5.6233.01 3 0.0808 0.70977 0.00 0.00 0.96 0.00 0.00 0.00 0.00 0.04
#> TCGA.CA.6719.01 4 0.2025 0.36503 0.10 0.00 0.00 0.88 0.00 0.00 0.00 0.02
#> TCGA.D5.5537.01 4 0.3303 0.26362 0.02 0.00 0.00 0.76 0.00 0.20 0.00 0.02
#> TCGA.4T.AA8H.01 4 0.4832 -0.19628 0.20 0.00 0.00 0.54 0.00 0.26 0.00 0.00
#> TCGA.AG.3592.01 7 0.3193 0.37605 0.00 0.00 0.00 0.38 0.00 0.00 0.62 0.00
#> TCGA.CM.6678.01 7 0.0000 0.96436 0.00 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.CK.5914.01 7 0.0000 0.96436 0.00 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.AA.3492.01 2 0.0000 0.98827 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DM.A1HB.01 2 0.0000 0.98827 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EI.6508.01 7 0.0000 0.96436 0.00 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.D5.6532.01 7 0.0471 0.94984 0.00 0.00 0.00 0.02 0.00 0.00 0.98 0.00
#> TCGA.A6.5659.01 8 0.4877 -0.29922 0.06 0.00 0.00 0.00 0.42 0.04 0.00 0.48
#> TCGA.A6.2680.01 7 0.0000 0.96436 0.00 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.CM.6680.01 7 0.0471 0.94974 0.00 0.00 0.00 0.02 0.00 0.00 0.98 0.00
#> TCGA.AA.3660.01 4 0.2569 0.48604 0.02 0.00 0.00 0.82 0.00 0.00 0.16 0.00
#> TCGA.CM.4747.01 4 0.5035 -0.40087 0.36 0.00 0.00 0.50 0.00 0.12 0.00 0.02
#> TCGA.EF.5831.01 4 0.3237 0.26991 0.00 0.00 0.00 0.60 0.00 0.00 0.40 0.00
#> TCGA.DM.A28G.01 7 0.0000 0.96436 0.00 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.D5.6537.01 7 0.0000 0.96436 0.00 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.DY.A1DD.01 7 0.0000 0.96436 0.00 0.00 0.00 0.00 0.00 0.00 1.00 0.00
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
consensus_heatmap(res, k = 7)
consensus_heatmap(res, k = 8)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
membership_heatmap(res, k = 7)
membership_heatmap(res, k = 8)
As soon as the classes for columns are determined, the signatures that are significantly different between subgroups can be looked for. Following are the heatmaps for signatures.
get_signatures(res, k = 2)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
get_signatures(res, k = 7)
get_signatures(res, k = 8)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. To get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows (which is done by automatically selecting number of clusters).If there are too many signatures, top_signatures = ... can be set to only show the
signatures with the highest FDRs:
# code only for demonstration
# e.g. to show the top 500 most significant rows
tb = get_signature(res, k = ..., top_signatures = 500)
If the signatures are defined as these which are uniquely high in current group, diff_method argument
can be set to "uniquely_high_in_one_group":
# code only for demonstration
tb = get_signature(res, k = ..., diff_method = "uniquely_high_in_one_group")
UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
dimension_reduction(res, k = 7, method = "UMAP")
dimension_reduction(res, k = 8, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
If matrix rows can be associated to genes, consider to use functional_enrichment(res,
...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.
Parent node: Node01. Child nodes: Node0111 , Node0112 , Node0121 , Node0122 , Node0211-leaf , Node0212 , Node0411-leaf , Node0412-leaf , Node0413-leaf , Node0414-leaf , Node0421-leaf , Node0422 , Node0423-leaf , Node0431-leaf , Node0432-leaf , Node0433-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 104 columns.
#> Top rows (1000) are extracted by 'ATC' method.
#> Subgroups are detected by 'kmeans' method.
#> Performed in total 350 partitions by row resampling.
#> Best k for subgroups seems to be 2.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_partitions"
#> [7] "compare_signatures" "consensus_heatmap" "dimension_reduction"
#> [10] "functional_enrichment" "get_anno_col" "get_anno"
#> [13] "get_classes" "get_consensus" "get_matrix"
#> [16] "get_membership" "get_param" "get_signatures"
#> [19] "get_stats" "is_best_k" "is_stable_k"
#> [22] "membership_heatmap" "ncol" "nrow"
#> [25] "plot_ecdf" "predict_classes" "rownames"
#> [28] "select_partition_number" "show" "suggest_best_k"
#> [31] "test_to_known_factors" "top_rows_heatmap"
collect_plots() function collects all the plots made from res for all k (number of subgroups)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
The plots are:
k and the heatmap of
predicted classes for each k.k.k.k.All the plots in panels can be made by individual functions and they are plotted later in this section.
select_partition_number() produces several plots showing different
statistics for choosing “optimized” k. There are following statistics:
k;k, the area increased is defined as \(A_k - A_{k-1}\).The detailed explanations of these statistics can be found in the cola vignette.
Generally speaking, higher 1-PAC score, higher mean silhouette score or higher
concordance corresponds to better partition. Rand index and Jaccard index
measure how similar the current partition is compared to partition with k-1.
If they are too similar, we won't accept k is better than k-1.
select_partition_number(res)
The numeric values for all these statistics can be obtained by get_stats().
get_stats(res)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> 2 2 1.000 0.976 0.989 0.4960 0.502 0.502
#> 3 3 0.640 0.790 0.896 0.3273 0.757 0.550
#> 4 4 0.783 0.897 0.930 0.1307 0.754 0.410
#> 5 5 0.829 0.728 0.852 0.0606 0.941 0.772
#> 6 6 0.799 0.476 0.660 0.0316 0.881 0.520
#> 7 7 0.785 0.558 0.792 0.0306 0.902 0.555
#> 8 8 0.797 0.568 0.729 0.0235 0.955 0.759
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.AG.A026.01 2 0.000 0.978 0.00 1.00
#> TCGA.G4.6303.01 1 0.000 0.998 1.00 0.00
#> TCGA.T9.A92H.01 1 0.000 0.998 1.00 0.00
#> TCGA.AD.6965.01 2 0.000 0.978 0.00 1.00
#> TCGA.A6.5660.01 2 0.722 0.760 0.20 0.80
#> TCGA.F5.6571.01 1 0.000 0.998 1.00 0.00
#> TCGA.CM.5862.01 2 0.000 0.978 0.00 1.00
#> TCGA.CI.6622.01 1 0.000 0.998 1.00 0.00
#> TCGA.EI.6512.01 1 0.000 0.998 1.00 0.00
#> TCGA.QG.A5YX.01 2 0.000 0.978 0.00 1.00
#> TCGA.AG.A036.01 2 0.904 0.554 0.32 0.68
#> TCGA.AA.3509.01 1 0.000 0.998 1.00 0.00
#> TCGA.EI.6883.01 1 0.000 0.998 1.00 0.00
#> TCGA.RU.A8FL.01 2 0.000 0.978 0.00 1.00
#> TCGA.AZ.6599.01 2 0.000 0.978 0.00 1.00
#> TCGA.CM.5860.01 1 0.000 0.998 1.00 0.00
#> TCGA.A6.6780.01 1 0.000 0.998 1.00 0.00
#> TCGA.CM.4750.01 2 0.000 0.978 0.00 1.00
#> TCGA.CM.6677.01 2 0.000 0.978 0.00 1.00
#> TCGA.F5.6814.01 2 0.000 0.978 0.00 1.00
#> TCGA.DM.A1D8.01 1 0.000 0.998 1.00 0.00
#> TCGA.A6.6138.01 1 0.000 0.998 1.00 0.00
#> TCGA.DM.A28F.01 2 0.000 0.978 0.00 1.00
#> TCGA.DM.A1D4.01 1 0.000 0.998 1.00 0.00
#> TCGA.DM.A0X9.01 2 0.000 0.978 0.00 1.00
#> TCGA.AY.A69D.01 1 0.000 0.998 1.00 0.00
#> TCGA.CA.6716.01 1 0.000 0.998 1.00 0.00
#> TCGA.NH.A6GB.01 2 0.000 0.978 0.00 1.00
#> TCGA.NH.A50U.01 2 0.000 0.978 0.00 1.00
#> TCGA.AH.6644.01 1 0.000 0.998 1.00 0.00
#> TCGA.CM.5864.01 2 0.000 0.978 0.00 1.00
#> TCGA.AG.3742.01 2 0.000 0.978 0.00 1.00
#> TCGA.A6.5666.01 2 0.000 0.978 0.00 1.00
#> TCGA.AG.3591.01 2 0.000 0.978 0.00 1.00
#> TCGA.AH.6643.01 1 0.000 0.998 1.00 0.00
#> TCGA.EI.6510.01 2 0.000 0.978 0.00 1.00
#> TCGA.A6.5656.01 1 0.000 0.998 1.00 0.00
#> TCGA.DY.A1DG.01 2 0.000 0.978 0.00 1.00
#> TCGA.F4.6806.01 1 0.000 0.998 1.00 0.00
#> TCGA.5M.AAT4.01 1 0.000 0.998 1.00 0.00
#> TCGA.EI.6514.01 1 0.000 0.998 1.00 0.00
#> TCGA.DM.A282.01 1 0.000 0.998 1.00 0.00
#> TCGA.DM.A1HA.01 1 0.000 0.998 1.00 0.00
#> TCGA.AG.4021.01 2 0.000 0.978 0.00 1.00
#> TCGA.DM.A1D9.01 2 0.000 0.978 0.00 1.00
#> TCGA.CM.4744.01 2 0.000 0.978 0.00 1.00
#> TCGA.A6.6652.01 1 0.000 0.998 1.00 0.00
#> TCGA.SS.A7HO.01 2 0.000 0.978 0.00 1.00
#> TCGA.A6.6650.01 1 0.141 0.978 0.98 0.02
#> TCGA.NH.A50T.01 2 0.000 0.978 0.00 1.00
#> TCGA.AD.6899.01 1 0.000 0.998 1.00 0.00
#> TCGA.A6.A56B.01 1 0.000 0.998 1.00 0.00
#> TCGA.D5.5539.01 2 0.722 0.760 0.20 0.80
#> TCGA.AY.A54L.01 2 0.000 0.978 0.00 1.00
#> TCGA.NH.A5IV.01 1 0.469 0.885 0.90 0.10
#> TCGA.G4.6306.01 1 0.000 0.998 1.00 0.00
#> TCGA.AD.A5EK.01 1 0.000 0.998 1.00 0.00
#> TCGA.DC.5337.01 2 0.000 0.978 0.00 1.00
#> TCGA.QG.A5YW.01 2 0.000 0.978 0.00 1.00
#> TCGA.EI.6882.01 2 0.000 0.978 0.00 1.00
#> TCGA.A6.2677.01 2 0.000 0.978 0.00 1.00
#> TCGA.AA.3502.01 2 0.000 0.978 0.00 1.00
#> TCGA.CK.5915.01 1 0.000 0.998 1.00 0.00
#> TCGA.AY.6197.01 1 0.000 0.998 1.00 0.00
#> TCGA.G4.6294.01 1 0.000 0.998 1.00 0.00
#> TCGA.CM.6172.01 1 0.000 0.998 1.00 0.00
#> TCGA.AA.3496.01 2 0.000 0.978 0.00 1.00
#> TCGA.DM.A28A.01 1 0.000 0.998 1.00 0.00
#> TCGA.EI.7002.01 1 0.000 0.998 1.00 0.00
#> TCGA.QG.A5Z1.01 1 0.000 0.998 1.00 0.00
#> TCGA.DM.A28H.01 1 0.000 0.998 1.00 0.00
#> TCGA.DM.A28M.01 1 0.000 0.998 1.00 0.00
#> TCGA.DM.A288.01 1 0.000 0.998 1.00 0.00
#> TCGA.F4.6855.01 1 0.000 0.998 1.00 0.00
#> TCGA.NH.A6GA.01 1 0.000 0.998 1.00 0.00
#> TCGA.NH.A50V.01 1 0.000 0.998 1.00 0.00
#> TCGA.CK.6747.01 1 0.000 0.998 1.00 0.00
#> TCGA.CL.5918.01 2 0.000 0.978 0.00 1.00
#> TCGA.DM.A28K.01 1 0.000 0.998 1.00 0.00
#> TCGA.AA.3655.01 1 0.000 0.998 1.00 0.00
#> TCGA.AZ.5407.01 1 0.000 0.998 1.00 0.00
#> TCGA.QG.A5YV.01 1 0.000 0.998 1.00 0.00
#> TCGA.AY.A71X.01 2 0.000 0.978 0.00 1.00
#> TCGA.AH.6549.01 2 0.000 0.978 0.00 1.00
#> TCGA.CM.6166.01 1 0.000 0.998 1.00 0.00
#> TCGA.AH.6897.01 2 0.000 0.978 0.00 1.00
#> TCGA.D5.5540.01 1 0.000 0.998 1.00 0.00
#> TCGA.G5.6233.01 1 0.000 0.998 1.00 0.00
#> TCGA.CA.6719.01 1 0.000 0.998 1.00 0.00
#> TCGA.D5.5537.01 1 0.000 0.998 1.00 0.00
#> TCGA.4T.AA8H.01 2 0.000 0.978 0.00 1.00
#> TCGA.AG.3592.01 1 0.000 0.998 1.00 0.00
#> TCGA.CM.6678.01 1 0.000 0.998 1.00 0.00
#> TCGA.CK.5914.01 1 0.000 0.998 1.00 0.00
#> TCGA.EI.6508.01 2 0.000 0.978 0.00 1.00
#> TCGA.D5.6532.01 2 0.000 0.978 0.00 1.00
#> TCGA.A6.2680.01 2 0.827 0.667 0.26 0.74
#> TCGA.CM.6680.01 2 0.000 0.978 0.00 1.00
#> TCGA.AA.3660.01 1 0.000 0.998 1.00 0.00
#> TCGA.CM.4747.01 1 0.000 0.998 1.00 0.00
#> TCGA.EF.5831.01 1 0.000 0.998 1.00 0.00
#> TCGA.DM.A28G.01 2 0.000 0.978 0.00 1.00
#> TCGA.D5.6537.01 2 0.000 0.978 0.00 1.00
#> TCGA.DY.A1DD.01 2 0.000 0.978 0.00 1.00
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.AG.A026.01 2 0.369 0.809 0.00 0.86 0.14
#> TCGA.G4.6303.01 1 0.540 0.745 0.72 0.00 0.28
#> TCGA.T9.A92H.01 1 0.631 0.269 0.50 0.00 0.50
#> TCGA.AD.6965.01 2 0.000 0.899 0.00 1.00 0.00
#> TCGA.A6.5660.01 3 0.000 0.849 0.00 0.00 1.00
#> TCGA.F5.6571.01 1 0.000 0.871 1.00 0.00 0.00
#> TCGA.CM.5862.01 2 0.000 0.899 0.00 1.00 0.00
#> TCGA.CI.6622.01 1 0.000 0.871 1.00 0.00 0.00
#> TCGA.EI.6512.01 1 0.000 0.871 1.00 0.00 0.00
#> TCGA.QG.A5YX.01 2 0.000 0.899 0.00 1.00 0.00
#> TCGA.AG.A036.01 3 0.000 0.849 0.00 0.00 1.00
#> TCGA.AA.3509.01 1 0.000 0.871 1.00 0.00 0.00
#> TCGA.EI.6883.01 1 0.000 0.871 1.00 0.00 0.00
#> TCGA.RU.A8FL.01 3 0.571 0.420 0.00 0.32 0.68
#> TCGA.AZ.6599.01 2 0.000 0.899 0.00 1.00 0.00
#> TCGA.CM.5860.01 1 0.540 0.745 0.72 0.00 0.28
#> TCGA.A6.6780.01 3 0.334 0.791 0.12 0.00 0.88
#> TCGA.CM.4750.01 2 0.624 0.328 0.00 0.56 0.44
#> TCGA.CM.6677.01 2 0.429 0.770 0.00 0.82 0.18
#> TCGA.F5.6814.01 3 0.400 0.720 0.00 0.16 0.84
#> TCGA.DM.A1D8.01 1 0.000 0.871 1.00 0.00 0.00
#> TCGA.A6.6138.01 1 0.000 0.871 1.00 0.00 0.00
#> TCGA.DM.A28F.01 2 0.000 0.899 0.00 1.00 0.00
#> TCGA.DM.A1D4.01 3 0.000 0.849 0.00 0.00 1.00
#> TCGA.DM.A0X9.01 3 0.369 0.742 0.00 0.14 0.86
#> TCGA.AY.A69D.01 1 0.000 0.871 1.00 0.00 0.00
#> TCGA.CA.6716.01 1 0.000 0.871 1.00 0.00 0.00
#> TCGA.NH.A6GB.01 2 0.000 0.899 0.00 1.00 0.00
#> TCGA.NH.A50U.01 2 0.153 0.880 0.00 0.96 0.04
#> TCGA.AH.6644.01 1 0.540 0.745 0.72 0.00 0.28
#> TCGA.CM.5864.01 2 0.153 0.880 0.00 0.96 0.04
#> TCGA.AG.3742.01 2 0.624 0.328 0.00 0.56 0.44
#> TCGA.A6.5666.01 2 0.000 0.899 0.00 1.00 0.00
#> TCGA.AG.3591.01 2 0.000 0.899 0.00 1.00 0.00
#> TCGA.AH.6643.01 1 0.540 0.745 0.72 0.00 0.28
#> TCGA.EI.6510.01 2 0.624 0.328 0.00 0.56 0.44
#> TCGA.A6.5656.01 3 0.334 0.791 0.12 0.00 0.88
#> TCGA.DY.A1DG.01 2 0.400 0.791 0.00 0.84 0.16
#> TCGA.F4.6806.01 1 0.540 0.745 0.72 0.00 0.28
#> TCGA.5M.AAT4.01 3 0.334 0.791 0.12 0.00 0.88
#> TCGA.EI.6514.01 3 0.455 0.670 0.20 0.00 0.80
#> TCGA.DM.A282.01 1 0.000 0.871 1.00 0.00 0.00
#> TCGA.DM.A1HA.01 3 0.207 0.831 0.06 0.00 0.94
#> TCGA.AG.4021.01 2 0.000 0.899 0.00 1.00 0.00
#> TCGA.DM.A1D9.01 3 0.455 0.668 0.00 0.20 0.80
#> TCGA.CM.4744.01 2 0.000 0.899 0.00 1.00 0.00
#> TCGA.A6.6652.01 3 0.455 0.670 0.20 0.00 0.80
#> TCGA.SS.A7HO.01 2 0.000 0.899 0.00 1.00 0.00
#> TCGA.A6.6650.01 3 0.000 0.849 0.00 0.00 1.00
#> TCGA.NH.A50T.01 2 0.000 0.899 0.00 1.00 0.00
#> TCGA.AD.6899.01 1 0.000 0.871 1.00 0.00 0.00
#> TCGA.A6.A56B.01 1 0.000 0.871 1.00 0.00 0.00
#> TCGA.D5.5539.01 3 0.000 0.849 0.00 0.00 1.00
#> TCGA.AY.A54L.01 2 0.000 0.899 0.00 1.00 0.00
#> TCGA.NH.A5IV.01 3 0.000 0.849 0.00 0.00 1.00
#> TCGA.G4.6306.01 3 0.334 0.791 0.12 0.00 0.88
#> TCGA.AD.A5EK.01 1 0.000 0.871 1.00 0.00 0.00
#> TCGA.DC.5337.01 2 0.000 0.899 0.00 1.00 0.00
#> TCGA.QG.A5YW.01 2 0.000 0.899 0.00 1.00 0.00
#> TCGA.EI.6882.01 3 0.455 0.668 0.00 0.20 0.80
#> TCGA.A6.2677.01 3 0.624 0.049 0.00 0.44 0.56
#> TCGA.AA.3502.01 2 0.000 0.899 0.00 1.00 0.00
#> TCGA.CK.5915.01 1 0.000 0.871 1.00 0.00 0.00
#> TCGA.AY.6197.01 1 0.000 0.871 1.00 0.00 0.00
#> TCGA.G4.6294.01 1 0.000 0.871 1.00 0.00 0.00
#> TCGA.CM.6172.01 1 0.000 0.871 1.00 0.00 0.00
#> TCGA.AA.3496.01 2 0.254 0.855 0.00 0.92 0.08
#> TCGA.DM.A28A.01 1 0.000 0.871 1.00 0.00 0.00
#> TCGA.EI.7002.01 1 0.540 0.745 0.72 0.00 0.28
#> TCGA.QG.A5Z1.01 1 0.000 0.871 1.00 0.00 0.00
#> TCGA.DM.A28H.01 1 0.540 0.745 0.72 0.00 0.28
#> TCGA.DM.A28M.01 3 0.334 0.791 0.12 0.00 0.88
#> TCGA.DM.A288.01 1 0.522 0.758 0.74 0.00 0.26
#> TCGA.F4.6855.01 1 0.502 0.770 0.76 0.00 0.24
#> TCGA.NH.A6GA.01 3 0.296 0.807 0.10 0.00 0.90
#> TCGA.NH.A50V.01 1 0.000 0.871 1.00 0.00 0.00
#> TCGA.CK.6747.01 1 0.540 0.745 0.72 0.00 0.28
#> TCGA.CL.5918.01 2 0.624 0.328 0.00 0.56 0.44
#> TCGA.DM.A28K.01 3 0.000 0.849 0.00 0.00 1.00
#> TCGA.AA.3655.01 1 0.000 0.871 1.00 0.00 0.00
#> TCGA.AZ.5407.01 1 0.540 0.745 0.72 0.00 0.28
#> TCGA.QG.A5YV.01 1 0.540 0.745 0.72 0.00 0.28
#> TCGA.AY.A71X.01 3 0.455 0.668 0.00 0.20 0.80
#> TCGA.AH.6549.01 2 0.000 0.899 0.00 1.00 0.00
#> TCGA.CM.6166.01 3 0.334 0.791 0.12 0.00 0.88
#> TCGA.AH.6897.01 2 0.000 0.899 0.00 1.00 0.00
#> TCGA.D5.5540.01 1 0.000 0.871 1.00 0.00 0.00
#> TCGA.G5.6233.01 1 0.000 0.871 1.00 0.00 0.00
#> TCGA.CA.6719.01 3 0.000 0.849 0.00 0.00 1.00
#> TCGA.D5.5537.01 1 0.540 0.745 0.72 0.00 0.28
#> TCGA.4T.AA8H.01 2 0.000 0.899 0.00 1.00 0.00
#> TCGA.AG.3592.01 1 0.400 0.809 0.84 0.00 0.16
#> TCGA.CM.6678.01 1 0.000 0.871 1.00 0.00 0.00
#> TCGA.CK.5914.01 1 0.000 0.871 1.00 0.00 0.00
#> TCGA.EI.6508.01 2 0.000 0.899 0.00 1.00 0.00
#> TCGA.D5.6532.01 2 0.624 0.328 0.00 0.56 0.44
#> TCGA.A6.2680.01 3 0.000 0.849 0.00 0.00 1.00
#> TCGA.CM.6680.01 3 0.455 0.668 0.00 0.20 0.80
#> TCGA.AA.3660.01 1 0.540 0.745 0.72 0.00 0.28
#> TCGA.CM.4747.01 1 0.000 0.871 1.00 0.00 0.00
#> TCGA.EF.5831.01 1 0.540 0.745 0.72 0.00 0.28
#> TCGA.DM.A28G.01 3 0.000 0.849 0.00 0.00 1.00
#> TCGA.D5.6537.01 2 0.000 0.899 0.00 1.00 0.00
#> TCGA.DY.A1DD.01 3 0.000 0.849 0.00 0.00 1.00
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> TCGA.AG.A026.01 4 0.0707 0.8906 0.00 0.02 0.00 0.98
#> TCGA.G4.6303.01 3 0.3400 0.8563 0.18 0.00 0.82 0.00
#> TCGA.T9.A92H.01 3 0.1211 0.8590 0.04 0.00 0.96 0.00
#> TCGA.AD.6965.01 2 0.0000 0.9681 0.00 1.00 0.00 0.00
#> TCGA.A6.5660.01 4 0.3400 0.8835 0.00 0.00 0.18 0.82
#> TCGA.F5.6571.01 1 0.0000 0.9871 1.00 0.00 0.00 0.00
#> TCGA.CM.5862.01 4 0.2647 0.8083 0.00 0.12 0.00 0.88
#> TCGA.CI.6622.01 1 0.0000 0.9871 1.00 0.00 0.00 0.00
#> TCGA.EI.6512.01 1 0.0000 0.9871 1.00 0.00 0.00 0.00
#> TCGA.QG.A5YX.01 2 0.3172 0.8585 0.00 0.84 0.00 0.16
#> TCGA.AG.A036.01 4 0.3400 0.8835 0.00 0.00 0.18 0.82
#> TCGA.AA.3509.01 1 0.0000 0.9871 1.00 0.00 0.00 0.00
#> TCGA.EI.6883.01 1 0.0000 0.9871 1.00 0.00 0.00 0.00
#> TCGA.RU.A8FL.01 4 0.0707 0.8906 0.00 0.02 0.00 0.98
#> TCGA.AZ.6599.01 2 0.0000 0.9681 0.00 1.00 0.00 0.00
#> TCGA.CM.5860.01 3 0.3400 0.8563 0.18 0.00 0.82 0.00
#> TCGA.A6.6780.01 3 0.0000 0.8512 0.00 0.00 1.00 0.00
#> TCGA.CM.4750.01 4 0.0707 0.8906 0.00 0.02 0.00 0.98
#> TCGA.CM.6677.01 4 0.0707 0.8906 0.00 0.02 0.00 0.98
#> TCGA.F5.6814.01 4 0.3400 0.8835 0.00 0.00 0.18 0.82
#> TCGA.DM.A1D8.01 1 0.3801 0.6700 0.78 0.00 0.22 0.00
#> TCGA.A6.6138.01 1 0.0000 0.9871 1.00 0.00 0.00 0.00
#> TCGA.DM.A28F.01 2 0.0000 0.9681 0.00 1.00 0.00 0.00
#> TCGA.DM.A1D4.01 3 0.0707 0.8362 0.00 0.00 0.98 0.02
#> TCGA.DM.A0X9.01 4 0.3400 0.8835 0.00 0.00 0.18 0.82
#> TCGA.AY.A69D.01 1 0.0000 0.9871 1.00 0.00 0.00 0.00
#> TCGA.CA.6716.01 1 0.0000 0.9871 1.00 0.00 0.00 0.00
#> TCGA.NH.A6GB.01 2 0.0000 0.9681 0.00 1.00 0.00 0.00
#> TCGA.NH.A50U.01 4 0.2647 0.8083 0.00 0.12 0.00 0.88
#> TCGA.AH.6644.01 3 0.3400 0.8563 0.18 0.00 0.82 0.00
#> TCGA.CM.5864.01 4 0.2647 0.8083 0.00 0.12 0.00 0.88
#> TCGA.AG.3742.01 4 0.0707 0.8906 0.00 0.02 0.00 0.98
#> TCGA.A6.5666.01 2 0.3172 0.8585 0.00 0.84 0.00 0.16
#> TCGA.AG.3591.01 2 0.3172 0.8585 0.00 0.84 0.00 0.16
#> TCGA.AH.6643.01 3 0.3400 0.8563 0.18 0.00 0.82 0.00
#> TCGA.EI.6510.01 4 0.0707 0.8906 0.00 0.02 0.00 0.98
#> TCGA.A6.5656.01 3 0.0000 0.8512 0.00 0.00 1.00 0.00
#> TCGA.DY.A1DG.01 4 0.0707 0.8906 0.00 0.02 0.00 0.98
#> TCGA.F4.6806.01 3 0.3400 0.8563 0.18 0.00 0.82 0.00
#> TCGA.5M.AAT4.01 3 0.0000 0.8512 0.00 0.00 1.00 0.00
#> TCGA.EI.6514.01 3 0.0000 0.8512 0.00 0.00 1.00 0.00
#> TCGA.DM.A282.01 1 0.0000 0.9871 1.00 0.00 0.00 0.00
#> TCGA.DM.A1HA.01 3 0.0707 0.8504 0.00 0.00 0.98 0.02
#> TCGA.AG.4021.01 2 0.0000 0.9681 0.00 1.00 0.00 0.00
#> TCGA.DM.A1D9.01 4 0.3400 0.8835 0.00 0.00 0.18 0.82
#> TCGA.CM.4744.01 2 0.0000 0.9681 0.00 1.00 0.00 0.00
#> TCGA.A6.6652.01 3 0.0000 0.8512 0.00 0.00 1.00 0.00
#> TCGA.SS.A7HO.01 2 0.0000 0.9681 0.00 1.00 0.00 0.00
#> TCGA.A6.6650.01 3 0.3975 0.5259 0.00 0.00 0.76 0.24
#> TCGA.NH.A50T.01 2 0.0000 0.9681 0.00 1.00 0.00 0.00
#> TCGA.AD.6899.01 1 0.0000 0.9871 1.00 0.00 0.00 0.00
#> TCGA.A6.A56B.01 1 0.0000 0.9871 1.00 0.00 0.00 0.00
#> TCGA.D5.5539.01 4 0.3400 0.8835 0.00 0.00 0.18 0.82
#> TCGA.AY.A54L.01 2 0.0000 0.9681 0.00 1.00 0.00 0.00
#> TCGA.NH.A5IV.01 3 0.4855 0.0651 0.00 0.00 0.60 0.40
#> TCGA.G4.6306.01 3 0.0000 0.8512 0.00 0.00 1.00 0.00
#> TCGA.AD.A5EK.01 1 0.0000 0.9871 1.00 0.00 0.00 0.00
#> TCGA.DC.5337.01 2 0.0000 0.9681 0.00 1.00 0.00 0.00
#> TCGA.QG.A5YW.01 2 0.0000 0.9681 0.00 1.00 0.00 0.00
#> TCGA.EI.6882.01 4 0.3400 0.8835 0.00 0.00 0.18 0.82
#> TCGA.A6.2677.01 4 0.0707 0.8906 0.00 0.02 0.00 0.98
#> TCGA.AA.3502.01 2 0.0000 0.9681 0.00 1.00 0.00 0.00
#> TCGA.CK.5915.01 1 0.0000 0.9871 1.00 0.00 0.00 0.00
#> TCGA.AY.6197.01 1 0.0000 0.9871 1.00 0.00 0.00 0.00
#> TCGA.G4.6294.01 1 0.0000 0.9871 1.00 0.00 0.00 0.00
#> TCGA.CM.6172.01 1 0.0000 0.9871 1.00 0.00 0.00 0.00
#> TCGA.AA.3496.01 4 0.0707 0.8906 0.00 0.02 0.00 0.98
#> TCGA.DM.A28A.01 1 0.0000 0.9871 1.00 0.00 0.00 0.00
#> TCGA.EI.7002.01 3 0.3400 0.8563 0.18 0.00 0.82 0.00
#> TCGA.QG.A5Z1.01 1 0.0000 0.9871 1.00 0.00 0.00 0.00
#> TCGA.DM.A28H.01 3 0.3400 0.8563 0.18 0.00 0.82 0.00
#> TCGA.DM.A28M.01 3 0.0000 0.8512 0.00 0.00 1.00 0.00
#> TCGA.DM.A288.01 3 0.3400 0.8563 0.18 0.00 0.82 0.00
#> TCGA.F4.6855.01 3 0.3400 0.8563 0.18 0.00 0.82 0.00
#> TCGA.NH.A6GA.01 3 0.0000 0.8512 0.00 0.00 1.00 0.00
#> TCGA.NH.A50V.01 1 0.0707 0.9678 0.98 0.00 0.02 0.00
#> TCGA.CK.6747.01 3 0.3400 0.8563 0.18 0.00 0.82 0.00
#> TCGA.CL.5918.01 4 0.0707 0.8906 0.00 0.02 0.00 0.98
#> TCGA.DM.A28K.01 3 0.0000 0.8512 0.00 0.00 1.00 0.00
#> TCGA.AA.3655.01 1 0.0000 0.9871 1.00 0.00 0.00 0.00
#> TCGA.AZ.5407.01 3 0.3400 0.8563 0.18 0.00 0.82 0.00
#> TCGA.QG.A5YV.01 3 0.3400 0.8563 0.18 0.00 0.82 0.00
#> TCGA.AY.A71X.01 4 0.3400 0.8835 0.00 0.00 0.18 0.82
#> TCGA.AH.6549.01 2 0.0000 0.9681 0.00 1.00 0.00 0.00
#> TCGA.CM.6166.01 3 0.0000 0.8512 0.00 0.00 1.00 0.00
#> TCGA.AH.6897.01 2 0.0000 0.9681 0.00 1.00 0.00 0.00
#> TCGA.D5.5540.01 1 0.0000 0.9871 1.00 0.00 0.00 0.00
#> TCGA.G5.6233.01 1 0.0000 0.9871 1.00 0.00 0.00 0.00
#> TCGA.CA.6719.01 3 0.0000 0.8512 0.00 0.00 1.00 0.00
#> TCGA.D5.5537.01 3 0.3400 0.8563 0.18 0.00 0.82 0.00
#> TCGA.4T.AA8H.01 2 0.0000 0.9681 0.00 1.00 0.00 0.00
#> TCGA.AG.3592.01 3 0.3400 0.8563 0.18 0.00 0.82 0.00
#> TCGA.CM.6678.01 1 0.0000 0.9871 1.00 0.00 0.00 0.00
#> TCGA.CK.5914.01 1 0.0000 0.9871 1.00 0.00 0.00 0.00
#> TCGA.EI.6508.01 2 0.0000 0.9681 0.00 1.00 0.00 0.00
#> TCGA.D5.6532.01 4 0.0707 0.8906 0.00 0.02 0.00 0.98
#> TCGA.A6.2680.01 4 0.3400 0.8835 0.00 0.00 0.18 0.82
#> TCGA.CM.6680.01 4 0.3172 0.8858 0.00 0.00 0.16 0.84
#> TCGA.AA.3660.01 3 0.3400 0.8563 0.18 0.00 0.82 0.00
#> TCGA.CM.4747.01 1 0.1211 0.9455 0.96 0.00 0.04 0.00
#> TCGA.EF.5831.01 3 0.3400 0.8563 0.18 0.00 0.82 0.00
#> TCGA.DM.A28G.01 4 0.3400 0.8835 0.00 0.00 0.18 0.82
#> TCGA.D5.6537.01 2 0.3172 0.8585 0.00 0.84 0.00 0.16
#> TCGA.DY.A1DD.01 4 0.3400 0.8835 0.00 0.00 0.18 0.82
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> TCGA.AG.A026.01 4 0.0000 0.730 0.00 0.00 0.00 1.00 0.00
#> TCGA.G4.6303.01 3 0.1410 0.827 0.00 0.00 0.94 0.00 0.06
#> TCGA.T9.A92H.01 3 0.2516 0.809 0.00 0.00 0.86 0.00 0.14
#> TCGA.AD.6965.01 2 0.0000 0.896 0.00 1.00 0.00 0.00 0.00
#> TCGA.A6.5660.01 5 0.3983 0.413 0.00 0.00 0.00 0.34 0.66
#> TCGA.F5.6571.01 1 0.0000 0.944 1.00 0.00 0.00 0.00 0.00
#> TCGA.CM.5862.01 4 0.0609 0.714 0.00 0.02 0.00 0.98 0.00
#> TCGA.CI.6622.01 1 0.0000 0.944 1.00 0.00 0.00 0.00 0.00
#> TCGA.EI.6512.01 1 0.0000 0.944 1.00 0.00 0.00 0.00 0.00
#> TCGA.QG.A5YX.01 2 0.4302 0.404 0.00 0.52 0.00 0.48 0.00
#> TCGA.AG.A036.01 5 0.3895 0.444 0.00 0.00 0.00 0.32 0.68
#> TCGA.AA.3509.01 1 0.0609 0.932 0.98 0.00 0.02 0.00 0.00
#> TCGA.EI.6883.01 1 0.0609 0.944 0.98 0.00 0.00 0.00 0.02
#> TCGA.RU.A8FL.01 4 0.1043 0.739 0.00 0.00 0.00 0.96 0.04
#> TCGA.AZ.6599.01 2 0.0000 0.896 0.00 1.00 0.00 0.00 0.00
#> TCGA.CM.5860.01 3 0.0000 0.847 0.00 0.00 1.00 0.00 0.00
#> TCGA.A6.6780.01 3 0.3561 0.697 0.00 0.00 0.74 0.00 0.26
#> TCGA.CM.4750.01 4 0.1043 0.739 0.00 0.00 0.00 0.96 0.04
#> TCGA.CM.6677.01 4 0.1043 0.739 0.00 0.00 0.00 0.96 0.04
#> TCGA.F5.6814.01 4 0.4262 0.365 0.00 0.00 0.00 0.56 0.44
#> TCGA.DM.A1D8.01 3 0.4227 0.122 0.42 0.00 0.58 0.00 0.00
#> TCGA.A6.6138.01 1 0.0000 0.944 1.00 0.00 0.00 0.00 0.00
#> TCGA.DM.A28F.01 2 0.0000 0.896 0.00 1.00 0.00 0.00 0.00
#> TCGA.DM.A1D4.01 5 0.2732 0.501 0.00 0.00 0.16 0.00 0.84
#> TCGA.DM.A0X9.01 4 0.4262 0.365 0.00 0.00 0.00 0.56 0.44
#> TCGA.AY.A69D.01 1 0.0609 0.944 0.98 0.00 0.00 0.00 0.02
#> TCGA.CA.6716.01 1 0.0609 0.944 0.98 0.00 0.00 0.00 0.02
#> TCGA.NH.A6GB.01 2 0.0000 0.896 0.00 1.00 0.00 0.00 0.00
#> TCGA.NH.A50U.01 4 0.1216 0.726 0.00 0.02 0.00 0.96 0.02
#> TCGA.AH.6644.01 3 0.0000 0.847 0.00 0.00 1.00 0.00 0.00
#> TCGA.CM.5864.01 4 0.0609 0.714 0.00 0.02 0.00 0.98 0.00
#> TCGA.AG.3742.01 4 0.3109 0.651 0.00 0.00 0.00 0.80 0.20
#> TCGA.A6.5666.01 2 0.4262 0.478 0.00 0.56 0.00 0.44 0.00
#> TCGA.AG.3591.01 2 0.4302 0.404 0.00 0.52 0.00 0.48 0.00
#> TCGA.AH.6643.01 3 0.1410 0.827 0.00 0.00 0.94 0.00 0.06
#> TCGA.EI.6510.01 4 0.3109 0.651 0.00 0.00 0.00 0.80 0.20
#> TCGA.A6.5656.01 3 0.3684 0.716 0.00 0.00 0.72 0.00 0.28
#> TCGA.DY.A1DG.01 4 0.0000 0.730 0.00 0.00 0.00 1.00 0.00
#> TCGA.F4.6806.01 3 0.0000 0.847 0.00 0.00 1.00 0.00 0.00
#> TCGA.5M.AAT4.01 3 0.3424 0.715 0.00 0.00 0.76 0.00 0.24
#> TCGA.EI.6514.01 3 0.3274 0.767 0.00 0.00 0.78 0.00 0.22
#> TCGA.DM.A282.01 1 0.0000 0.944 1.00 0.00 0.00 0.00 0.00
#> TCGA.DM.A1HA.01 5 0.4287 -0.410 0.00 0.00 0.46 0.00 0.54
#> TCGA.AG.4021.01 2 0.0000 0.896 0.00 1.00 0.00 0.00 0.00
#> TCGA.DM.A1D9.01 4 0.4262 0.365 0.00 0.00 0.00 0.56 0.44
#> TCGA.CM.4744.01 2 0.0000 0.896 0.00 1.00 0.00 0.00 0.00
#> TCGA.A6.6652.01 3 0.3424 0.757 0.00 0.00 0.76 0.00 0.24
#> TCGA.SS.A7HO.01 2 0.0000 0.896 0.00 1.00 0.00 0.00 0.00
#> TCGA.A6.6650.01 5 0.5083 0.558 0.00 0.00 0.16 0.14 0.70
#> TCGA.NH.A50T.01 2 0.0000 0.896 0.00 1.00 0.00 0.00 0.00
#> TCGA.AD.6899.01 1 0.1410 0.900 0.94 0.00 0.06 0.00 0.00
#> TCGA.A6.A56B.01 1 0.4252 0.634 0.70 0.00 0.28 0.00 0.02
#> TCGA.D5.5539.01 5 0.3895 0.445 0.00 0.00 0.00 0.32 0.68
#> TCGA.AY.A54L.01 2 0.0000 0.896 0.00 1.00 0.00 0.00 0.00
#> TCGA.NH.A5IV.01 5 0.5083 0.557 0.00 0.00 0.14 0.16 0.70
#> TCGA.G4.6306.01 3 0.3424 0.715 0.00 0.00 0.76 0.00 0.24
#> TCGA.AD.A5EK.01 1 0.0609 0.944 0.98 0.00 0.00 0.00 0.02
#> TCGA.DC.5337.01 2 0.1043 0.876 0.00 0.96 0.00 0.04 0.00
#> TCGA.QG.A5YW.01 2 0.0000 0.896 0.00 1.00 0.00 0.00 0.00
#> TCGA.EI.6882.01 4 0.4262 0.365 0.00 0.00 0.00 0.56 0.44
#> TCGA.A6.2677.01 4 0.0000 0.730 0.00 0.00 0.00 1.00 0.00
#> TCGA.AA.3502.01 2 0.0000 0.896 0.00 1.00 0.00 0.00 0.00
#> TCGA.CK.5915.01 1 0.0609 0.944 0.98 0.00 0.00 0.00 0.02
#> TCGA.AY.6197.01 1 0.0000 0.944 1.00 0.00 0.00 0.00 0.00
#> TCGA.G4.6294.01 1 0.0609 0.944 0.98 0.00 0.00 0.00 0.02
#> TCGA.CM.6172.01 1 0.0609 0.944 0.98 0.00 0.00 0.00 0.02
#> TCGA.AA.3496.01 4 0.0000 0.730 0.00 0.00 0.00 1.00 0.00
#> TCGA.DM.A28A.01 1 0.0609 0.944 0.98 0.00 0.00 0.00 0.02
#> TCGA.EI.7002.01 3 0.1732 0.817 0.00 0.00 0.92 0.00 0.08
#> TCGA.QG.A5Z1.01 1 0.0000 0.944 1.00 0.00 0.00 0.00 0.00
#> TCGA.DM.A28H.01 3 0.0000 0.847 0.00 0.00 1.00 0.00 0.00
#> TCGA.DM.A28M.01 3 0.3561 0.697 0.00 0.00 0.74 0.00 0.26
#> TCGA.DM.A288.01 3 0.0000 0.847 0.00 0.00 1.00 0.00 0.00
#> TCGA.F4.6855.01 3 0.0609 0.836 0.02 0.00 0.98 0.00 0.00
#> TCGA.NH.A6GA.01 3 0.3561 0.697 0.00 0.00 0.74 0.00 0.26
#> TCGA.NH.A50V.01 1 0.3796 0.628 0.70 0.00 0.30 0.00 0.00
#> TCGA.CK.6747.01 3 0.0000 0.847 0.00 0.00 1.00 0.00 0.00
#> TCGA.CL.5918.01 4 0.1043 0.739 0.00 0.00 0.00 0.96 0.04
#> TCGA.DM.A28K.01 5 0.4307 -0.173 0.00 0.00 0.50 0.00 0.50
#> TCGA.AA.3655.01 1 0.0000 0.944 1.00 0.00 0.00 0.00 0.00
#> TCGA.AZ.5407.01 3 0.0000 0.847 0.00 0.00 1.00 0.00 0.00
#> TCGA.QG.A5YV.01 3 0.0000 0.847 0.00 0.00 1.00 0.00 0.00
#> TCGA.AY.A71X.01 4 0.4262 0.365 0.00 0.00 0.00 0.56 0.44
#> TCGA.AH.6549.01 2 0.1043 0.876 0.00 0.96 0.00 0.04 0.00
#> TCGA.CM.6166.01 3 0.3274 0.733 0.00 0.00 0.78 0.00 0.22
#> TCGA.AH.6897.01 2 0.0000 0.896 0.00 1.00 0.00 0.00 0.00
#> TCGA.D5.5540.01 1 0.0609 0.944 0.98 0.00 0.00 0.00 0.02
#> TCGA.G5.6233.01 1 0.0609 0.944 0.98 0.00 0.00 0.00 0.02
#> TCGA.CA.6719.01 3 0.3561 0.693 0.00 0.00 0.74 0.00 0.26
#> TCGA.D5.5537.01 3 0.0000 0.847 0.00 0.00 1.00 0.00 0.00
#> TCGA.4T.AA8H.01 2 0.0000 0.896 0.00 1.00 0.00 0.00 0.00
#> TCGA.AG.3592.01 3 0.0609 0.836 0.02 0.00 0.98 0.00 0.00
#> TCGA.CM.6678.01 1 0.0000 0.944 1.00 0.00 0.00 0.00 0.00
#> TCGA.CK.5914.01 1 0.0609 0.944 0.98 0.00 0.00 0.00 0.02
#> TCGA.EI.6508.01 2 0.0000 0.896 0.00 1.00 0.00 0.00 0.00
#> TCGA.D5.6532.01 4 0.1043 0.739 0.00 0.00 0.00 0.96 0.04
#> TCGA.A6.2680.01 5 0.4456 0.452 0.00 0.00 0.02 0.32 0.66
#> TCGA.CM.6680.01 4 0.4262 0.365 0.00 0.00 0.00 0.56 0.44
#> TCGA.AA.3660.01 3 0.1410 0.827 0.00 0.00 0.94 0.00 0.06
#> TCGA.CM.4747.01 1 0.4126 0.470 0.62 0.00 0.38 0.00 0.00
#> TCGA.EF.5831.01 3 0.0000 0.847 0.00 0.00 1.00 0.00 0.00
#> TCGA.DM.A28G.01 4 0.4287 0.304 0.00 0.00 0.00 0.54 0.46
#> TCGA.D5.6537.01 2 0.4262 0.478 0.00 0.56 0.00 0.44 0.00
#> TCGA.DY.A1DD.01 5 0.4126 0.298 0.00 0.00 0.00 0.38 0.62
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> TCGA.AG.A026.01 4 0.4646 0.52528 0.00 0.00 0.00 0.50 0.46 0.04
#> TCGA.G4.6303.01 6 0.4632 0.54704 0.00 0.00 0.44 0.04 0.00 0.52
#> TCGA.T9.A92H.01 3 0.5371 -0.19754 0.00 0.00 0.52 0.12 0.00 0.36
#> TCGA.AD.6965.01 2 0.0000 0.95551 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.A6.5660.01 5 0.6158 0.39714 0.00 0.00 0.36 0.04 0.48 0.12
#> TCGA.F5.6571.01 1 0.0547 0.98083 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.CM.5862.01 4 0.4646 0.49547 0.00 0.00 0.00 0.50 0.46 0.04
#> TCGA.CI.6622.01 1 0.0547 0.98083 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.EI.6512.01 1 0.0547 0.98083 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.QG.A5YX.01 4 0.5115 0.04070 0.00 0.46 0.00 0.48 0.02 0.04
#> TCGA.AG.A036.01 5 0.6519 0.37619 0.00 0.00 0.34 0.06 0.46 0.14
#> TCGA.AA.3509.01 1 0.1814 0.90186 0.90 0.00 0.00 0.00 0.00 0.10
#> TCGA.EI.6883.01 1 0.0000 0.98202 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.RU.A8FL.01 4 0.4646 0.49547 0.00 0.00 0.00 0.50 0.46 0.04
#> TCGA.AZ.6599.01 2 0.0000 0.95551 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.CM.5860.01 3 0.3851 -0.51876 0.00 0.00 0.54 0.00 0.00 0.46
#> TCGA.A6.6780.01 3 0.2094 0.33227 0.00 0.00 0.90 0.02 0.00 0.08
#> TCGA.CM.4750.01 4 0.4646 0.49547 0.00 0.00 0.00 0.50 0.46 0.04
#> TCGA.CM.6677.01 5 0.4609 -0.41314 0.00 0.00 0.00 0.42 0.54 0.04
#> TCGA.F5.6814.01 5 0.2581 0.49334 0.00 0.00 0.00 0.02 0.86 0.12
#> TCGA.DM.A1D8.01 6 0.5406 0.50686 0.12 0.00 0.38 0.00 0.00 0.50
#> TCGA.A6.6138.01 1 0.0547 0.98083 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.DM.A28F.01 2 0.0000 0.95551 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DM.A1D4.01 3 0.7208 -0.06301 0.00 0.00 0.44 0.14 0.22 0.20
#> TCGA.DM.A0X9.01 5 0.0000 0.49225 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.AY.A69D.01 1 0.0000 0.98202 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CA.6716.01 1 0.0000 0.98202 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.NH.A6GB.01 2 0.0000 0.95551 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.NH.A50U.01 5 0.4609 -0.41314 0.00 0.00 0.00 0.42 0.54 0.04
#> TCGA.AH.6644.01 6 0.3869 0.54235 0.00 0.00 0.50 0.00 0.00 0.50
#> TCGA.CM.5864.01 4 0.4646 0.52528 0.00 0.00 0.00 0.50 0.46 0.04
#> TCGA.AG.3742.01 5 0.3950 0.01624 0.00 0.00 0.00 0.24 0.72 0.04
#> TCGA.A6.5666.01 4 0.4651 -0.03308 0.00 0.48 0.00 0.48 0.00 0.04
#> TCGA.AG.3591.01 4 0.5660 0.16174 0.00 0.42 0.00 0.48 0.06 0.04
#> TCGA.AH.6643.01 3 0.4902 -0.50777 0.00 0.00 0.48 0.06 0.00 0.46
#> TCGA.EI.6510.01 5 0.3950 0.01624 0.00 0.00 0.00 0.24 0.72 0.04
#> TCGA.A6.5656.01 3 0.3787 0.26260 0.00 0.00 0.78 0.10 0.00 0.12
#> TCGA.DY.A1DG.01 4 0.3851 0.51459 0.00 0.00 0.00 0.54 0.46 0.00
#> TCGA.F4.6806.01 3 0.3864 -0.55956 0.00 0.00 0.52 0.00 0.00 0.48
#> TCGA.5M.AAT4.01 3 0.0000 0.36809 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.EI.6514.01 3 0.5364 -0.08500 0.00 0.00 0.56 0.14 0.00 0.30
#> TCGA.DM.A282.01 1 0.0547 0.98083 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.DM.A1HA.01 4 0.5865 -0.37397 0.00 0.00 0.36 0.44 0.00 0.20
#> TCGA.AG.4021.01 2 0.0000 0.95551 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DM.A1D9.01 5 0.0000 0.49225 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.CM.4744.01 2 0.0000 0.95551 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.A6.6652.01 3 0.5428 -0.10566 0.00 0.00 0.54 0.14 0.00 0.32
#> TCGA.SS.A7HO.01 2 0.0000 0.95551 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.A6.6650.01 3 0.6323 -0.28007 0.00 0.00 0.44 0.04 0.38 0.14
#> TCGA.NH.A50T.01 2 0.0000 0.95551 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.AD.6899.01 1 0.2048 0.88153 0.88 0.00 0.00 0.00 0.00 0.12
#> TCGA.A6.A56B.01 6 0.5873 0.25011 0.42 0.00 0.08 0.04 0.00 0.46
#> TCGA.D5.5539.01 5 0.6120 0.41055 0.00 0.00 0.34 0.04 0.50 0.12
#> TCGA.AY.A54L.01 2 0.0000 0.95551 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.NH.A5IV.01 3 0.5896 -0.26893 0.00 0.00 0.46 0.02 0.40 0.12
#> TCGA.G4.6306.01 3 0.0000 0.36809 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.AD.A5EK.01 1 0.0000 0.98202 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DC.5337.01 2 0.1480 0.90817 0.00 0.94 0.00 0.02 0.00 0.04
#> TCGA.QG.A5YW.01 2 0.0000 0.95551 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.EI.6882.01 5 0.0000 0.49225 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.A6.2677.01 4 0.4646 0.52528 0.00 0.00 0.00 0.50 0.46 0.04
#> TCGA.AA.3502.01 2 0.0000 0.95551 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.CK.5915.01 1 0.0000 0.98202 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AY.6197.01 1 0.0547 0.98083 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.G4.6294.01 1 0.0000 0.98202 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CM.6172.01 1 0.0000 0.98202 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AA.3496.01 4 0.4646 0.52528 0.00 0.00 0.00 0.50 0.46 0.04
#> TCGA.DM.A28A.01 1 0.0000 0.98202 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EI.7002.01 6 0.5447 0.35287 0.00 0.00 0.42 0.12 0.00 0.46
#> TCGA.QG.A5Z1.01 1 0.0547 0.98083 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.DM.A28H.01 3 0.3851 -0.51876 0.00 0.00 0.54 0.00 0.00 0.46
#> TCGA.DM.A28M.01 3 0.1092 0.35844 0.00 0.00 0.96 0.02 0.00 0.02
#> TCGA.DM.A288.01 3 0.3851 -0.51876 0.00 0.00 0.54 0.00 0.00 0.46
#> TCGA.F4.6855.01 6 0.3851 0.57061 0.00 0.00 0.46 0.00 0.00 0.54
#> TCGA.NH.A6GA.01 3 0.1480 0.35976 0.00 0.00 0.94 0.02 0.00 0.04
#> TCGA.NH.A50V.01 6 0.5523 0.33317 0.36 0.00 0.14 0.00 0.00 0.50
#> TCGA.CK.6747.01 3 0.3851 -0.51876 0.00 0.00 0.54 0.00 0.00 0.46
#> TCGA.CL.5918.01 4 0.4646 0.49547 0.00 0.00 0.00 0.50 0.46 0.04
#> TCGA.DM.A28K.01 3 0.5774 0.00101 0.00 0.00 0.56 0.02 0.28 0.14
#> TCGA.AA.3655.01 1 0.0547 0.98083 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.AZ.5407.01 3 0.3851 -0.51876 0.00 0.00 0.54 0.00 0.00 0.46
#> TCGA.QG.A5YV.01 6 0.3869 0.54235 0.00 0.00 0.50 0.00 0.00 0.50
#> TCGA.AY.A71X.01 5 0.0000 0.49225 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.AH.6549.01 2 0.1480 0.90817 0.00 0.94 0.00 0.02 0.00 0.04
#> TCGA.CM.6166.01 3 0.1267 0.33011 0.00 0.00 0.94 0.00 0.00 0.06
#> TCGA.AH.6897.01 2 0.0000 0.95551 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.D5.5540.01 1 0.0000 0.98202 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.G5.6233.01 1 0.0000 0.98202 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CA.6719.01 3 0.2882 0.35607 0.00 0.00 0.86 0.02 0.02 0.10
#> TCGA.D5.5537.01 6 0.3869 0.54235 0.00 0.00 0.50 0.00 0.00 0.50
#> TCGA.4T.AA8H.01 2 0.0000 0.95551 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.AG.3592.01 6 0.3828 0.57767 0.00 0.00 0.44 0.00 0.00 0.56
#> TCGA.CM.6678.01 1 0.0547 0.98083 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.CK.5914.01 1 0.0000 0.98202 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EI.6508.01 2 0.0000 0.95551 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.D5.6532.01 5 0.4576 -0.37899 0.00 0.00 0.00 0.40 0.56 0.04
#> TCGA.A6.2680.01 5 0.6120 0.41055 0.00 0.00 0.34 0.04 0.50 0.12
#> TCGA.CM.6680.01 5 0.0547 0.49466 0.00 0.00 0.00 0.00 0.98 0.02
#> TCGA.AA.3660.01 6 0.4632 0.54704 0.00 0.00 0.44 0.04 0.00 0.52
#> TCGA.CM.4747.01 6 0.5684 0.39600 0.28 0.00 0.20 0.00 0.00 0.52
#> TCGA.EF.5831.01 6 0.3864 0.55474 0.00 0.00 0.48 0.00 0.00 0.52
#> TCGA.DM.A28G.01 5 0.5184 0.49318 0.00 0.00 0.20 0.02 0.66 0.12
#> TCGA.D5.6537.01 2 0.4651 -0.10150 0.00 0.48 0.00 0.48 0.00 0.04
#> TCGA.DY.A1DD.01 5 0.7048 0.44129 0.00 0.00 0.24 0.12 0.46 0.18
cbind(get_classes(res, k = 7), get_membership(res, k = 7))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7
#> TCGA.AG.A026.01 4 0.1664 5.41e-01 0.00 0.00 0.00 0.92 0.00 0.02 0.06
#> TCGA.G4.6303.01 3 0.3546 -7.20e-02 0.00 0.00 0.54 0.00 0.00 0.46 0.00
#> TCGA.T9.A92H.01 6 0.4426 5.50e-01 0.00 0.00 0.38 0.00 0.00 0.56 0.06
#> TCGA.AD.6965.01 2 0.0000 9.59e-01 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.A6.5660.01 5 0.1006 6.62e-01 0.00 0.00 0.00 0.02 0.96 0.02 0.00
#> TCGA.F5.6571.01 1 0.0863 9.04e-01 0.96 0.00 0.00 0.00 0.00 0.00 0.04
#> TCGA.CM.5862.01 4 0.3307 4.13e-01 0.00 0.00 0.00 0.74 0.00 0.02 0.24
#> TCGA.CI.6622.01 1 0.2512 8.48e-01 0.86 0.00 0.00 0.00 0.00 0.10 0.04
#> TCGA.EI.6512.01 1 0.0863 9.04e-01 0.96 0.00 0.00 0.00 0.00 0.00 0.04
#> TCGA.QG.A5YX.01 4 0.4667 4.60e-01 0.00 0.14 0.00 0.70 0.00 0.04 0.12
#> TCGA.AG.A036.01 5 0.3965 5.84e-01 0.00 0.00 0.00 0.02 0.76 0.12 0.10
#> TCGA.AA.3509.01 1 0.3208 8.12e-01 0.82 0.00 0.02 0.00 0.00 0.12 0.04
#> TCGA.EI.6883.01 1 0.0863 9.10e-01 0.96 0.00 0.00 0.00 0.00 0.00 0.04
#> TCGA.RU.A8FL.01 4 0.2422 4.32e-01 0.00 0.00 0.00 0.82 0.00 0.00 0.18
#> TCGA.AZ.6599.01 2 0.0000 9.59e-01 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CM.5860.01 3 0.0000 4.57e-01 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.A6.6780.01 3 0.4812 2.14e-01 0.00 0.00 0.66 0.00 0.18 0.14 0.02
#> TCGA.CM.4750.01 4 0.2422 4.32e-01 0.00 0.00 0.00 0.82 0.00 0.00 0.18
#> TCGA.CM.6677.01 4 0.3358 -1.58e-01 0.00 0.00 0.00 0.64 0.00 0.00 0.36
#> TCGA.F5.6814.01 5 0.4030 5.48e-01 0.00 0.00 0.00 0.16 0.72 0.00 0.12
#> TCGA.DM.A1D8.01 3 0.3848 3.61e-01 0.06 0.00 0.76 0.00 0.00 0.16 0.02
#> TCGA.A6.6138.01 1 0.0863 9.04e-01 0.96 0.00 0.00 0.00 0.00 0.00 0.04
#> TCGA.DM.A28F.01 2 0.1363 9.35e-01 0.00 0.94 0.00 0.00 0.00 0.04 0.02
#> TCGA.DM.A1D4.01 5 0.6852 1.02e-01 0.00 0.00 0.16 0.00 0.34 0.32 0.18
#> TCGA.DM.A0X9.01 5 0.4842 4.64e-01 0.00 0.00 0.00 0.16 0.60 0.00 0.24
#> TCGA.AY.A69D.01 1 0.0863 9.10e-01 0.96 0.00 0.00 0.00 0.00 0.00 0.04
#> TCGA.CA.6716.01 1 0.0863 9.10e-01 0.96 0.00 0.00 0.00 0.00 0.00 0.04
#> TCGA.NH.A6GB.01 2 0.0000 9.59e-01 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.NH.A50U.01 4 0.3867 -1.48e-01 0.00 0.00 0.00 0.60 0.00 0.02 0.38
#> TCGA.AH.6644.01 3 0.3047 3.19e-01 0.00 0.00 0.72 0.00 0.00 0.28 0.00
#> TCGA.CM.5864.01 4 0.2278 5.27e-01 0.00 0.00 0.00 0.88 0.00 0.04 0.08
#> TCGA.AG.3742.01 7 0.4875 1.00e+00 0.00 0.00 0.00 0.44 0.10 0.00 0.46
#> TCGA.A6.5666.01 4 0.4422 4.54e-01 0.00 0.16 0.00 0.72 0.00 0.04 0.08
#> TCGA.AG.3591.01 4 0.4492 4.75e-01 0.00 0.12 0.00 0.72 0.00 0.04 0.12
#> TCGA.AH.6643.01 3 0.4505 -4.35e-01 0.00 0.00 0.50 0.00 0.00 0.44 0.06
#> TCGA.EI.6510.01 7 0.4875 1.00e+00 0.00 0.00 0.00 0.44 0.10 0.00 0.46
#> TCGA.A6.5656.01 3 0.6290 -2.66e-01 0.00 0.00 0.40 0.00 0.20 0.34 0.06
#> TCGA.DY.A1DG.01 4 0.1433 5.20e-01 0.00 0.00 0.00 0.92 0.00 0.00 0.08
#> TCGA.F4.6806.01 3 0.0504 4.56e-01 0.00 0.00 0.98 0.00 0.00 0.02 0.00
#> TCGA.5M.AAT4.01 3 0.5007 1.23e-01 0.00 0.00 0.56 0.00 0.28 0.16 0.00
#> TCGA.EI.6514.01 6 0.4875 4.76e-01 0.00 0.00 0.44 0.00 0.00 0.46 0.10
#> TCGA.DM.A282.01 1 0.2278 8.63e-01 0.88 0.00 0.00 0.00 0.00 0.08 0.04
#> TCGA.DM.A1HA.01 6 0.4832 2.44e-01 0.00 0.00 0.04 0.00 0.04 0.58 0.34
#> TCGA.AG.4021.01 2 0.0000 9.59e-01 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DM.A1D9.01 5 0.4930 4.36e-01 0.00 0.00 0.00 0.16 0.58 0.00 0.26
#> TCGA.CM.4744.01 2 0.2769 8.73e-01 0.00 0.86 0.00 0.02 0.00 0.04 0.08
#> TCGA.A6.6652.01 6 0.4945 5.66e-01 0.00 0.00 0.36 0.00 0.00 0.52 0.12
#> TCGA.SS.A7HO.01 2 0.0000 9.59e-01 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.A6.6650.01 5 0.2376 6.17e-01 0.00 0.00 0.02 0.00 0.86 0.12 0.00
#> TCGA.NH.A50T.01 2 0.1006 9.44e-01 0.00 0.96 0.00 0.00 0.00 0.02 0.02
#> TCGA.AD.6899.01 1 0.4703 5.62e-01 0.62 0.00 0.04 0.00 0.00 0.30 0.04
#> TCGA.A6.A56B.01 1 0.6010 7.70e-02 0.42 0.00 0.18 0.00 0.00 0.36 0.04
#> TCGA.D5.5539.01 5 0.1363 6.64e-01 0.00 0.00 0.00 0.02 0.94 0.00 0.04
#> TCGA.AY.A54L.01 2 0.0000 9.59e-01 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.NH.A5IV.01 5 0.1363 6.64e-01 0.00 0.00 0.02 0.00 0.94 0.00 0.04
#> TCGA.G4.6306.01 3 0.4930 1.35e-01 0.00 0.00 0.58 0.00 0.26 0.16 0.00
#> TCGA.AD.A5EK.01 1 0.0863 9.10e-01 0.96 0.00 0.00 0.00 0.00 0.00 0.04
#> TCGA.DC.5337.01 2 0.3691 8.24e-01 0.00 0.80 0.00 0.06 0.00 0.06 0.08
#> TCGA.QG.A5YW.01 2 0.1006 9.44e-01 0.00 0.96 0.00 0.00 0.00 0.02 0.02
#> TCGA.EI.6882.01 5 0.4842 4.64e-01 0.00 0.00 0.00 0.16 0.60 0.00 0.24
#> TCGA.A6.2677.01 4 0.1664 5.41e-01 0.00 0.00 0.00 0.92 0.00 0.02 0.06
#> TCGA.AA.3502.01 2 0.0000 9.59e-01 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CK.5915.01 1 0.0863 9.10e-01 0.96 0.00 0.00 0.00 0.00 0.00 0.04
#> TCGA.AY.6197.01 1 0.0000 9.10e-01 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.G4.6294.01 1 0.0863 9.10e-01 0.96 0.00 0.00 0.00 0.00 0.00 0.04
#> TCGA.CM.6172.01 1 0.0863 9.10e-01 0.96 0.00 0.00 0.00 0.00 0.00 0.04
#> TCGA.AA.3496.01 4 0.1664 5.41e-01 0.00 0.00 0.00 0.92 0.00 0.02 0.06
#> TCGA.DM.A28A.01 1 0.0863 9.10e-01 0.96 0.00 0.00 0.00 0.00 0.00 0.04
#> TCGA.EI.7002.01 6 0.4487 3.69e-01 0.00 0.00 0.42 0.00 0.00 0.52 0.06
#> TCGA.QG.A5Z1.01 1 0.2278 8.63e-01 0.88 0.00 0.00 0.00 0.00 0.08 0.04
#> TCGA.DM.A28H.01 3 0.0863 4.56e-01 0.00 0.00 0.96 0.00 0.00 0.04 0.00
#> TCGA.DM.A28M.01 3 0.4204 2.48e-01 0.00 0.00 0.70 0.00 0.16 0.14 0.00
#> TCGA.DM.A288.01 3 0.0000 4.57e-01 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.F4.6855.01 3 0.3517 2.90e-01 0.02 0.00 0.70 0.00 0.00 0.28 0.00
#> TCGA.NH.A6GA.01 3 0.5324 1.24e-01 0.00 0.00 0.58 0.00 0.18 0.22 0.02
#> TCGA.NH.A50V.01 3 0.5655 5.51e-02 0.38 0.00 0.44 0.00 0.00 0.16 0.02
#> TCGA.CK.6747.01 3 0.0000 4.57e-01 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.CL.5918.01 4 0.2422 4.32e-01 0.00 0.00 0.00 0.82 0.00 0.00 0.18
#> TCGA.DM.A28K.01 5 0.3052 5.08e-01 0.00 0.00 0.20 0.00 0.78 0.02 0.00
#> TCGA.AA.3655.01 1 0.0863 9.04e-01 0.96 0.00 0.00 0.00 0.00 0.00 0.04
#> TCGA.AZ.5407.01 3 0.0000 4.57e-01 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.QG.A5YV.01 3 0.3047 3.19e-01 0.00 0.00 0.72 0.00 0.00 0.28 0.00
#> TCGA.AY.A71X.01 5 0.4842 4.64e-01 0.00 0.00 0.00 0.16 0.60 0.00 0.24
#> TCGA.AH.6549.01 2 0.3691 8.24e-01 0.00 0.80 0.00 0.06 0.00 0.06 0.08
#> TCGA.CM.6166.01 3 0.4883 1.33e-01 0.00 0.00 0.60 0.00 0.20 0.20 0.00
#> TCGA.AH.6897.01 2 0.0000 9.59e-01 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D5.5540.01 1 0.0863 9.10e-01 0.96 0.00 0.00 0.00 0.00 0.00 0.04
#> TCGA.G5.6233.01 1 0.0504 9.11e-01 0.98 0.00 0.00 0.00 0.00 0.00 0.02
#> TCGA.CA.6719.01 3 0.5665 -9.17e-05 0.00 0.00 0.42 0.00 0.40 0.16 0.02
#> TCGA.D5.5537.01 3 0.1886 4.19e-01 0.00 0.00 0.88 0.00 0.00 0.12 0.00
#> TCGA.4T.AA8H.01 2 0.0000 9.59e-01 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AG.3592.01 3 0.3388 3.59e-01 0.04 0.00 0.76 0.00 0.00 0.20 0.00
#> TCGA.CM.6678.01 1 0.0863 9.04e-01 0.96 0.00 0.00 0.00 0.00 0.00 0.04
#> TCGA.CK.5914.01 1 0.0504 9.11e-01 0.98 0.00 0.00 0.00 0.00 0.00 0.02
#> TCGA.EI.6508.01 2 0.0000 9.59e-01 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D5.6532.01 4 0.3413 -2.61e-01 0.00 0.00 0.00 0.62 0.00 0.00 0.38
#> TCGA.A6.2680.01 5 0.1006 6.62e-01 0.00 0.00 0.00 0.02 0.96 0.02 0.00
#> TCGA.CM.6680.01 5 0.4842 4.64e-01 0.00 0.00 0.00 0.16 0.60 0.00 0.24
#> TCGA.AA.3660.01 3 0.3562 -1.89e-01 0.00 0.00 0.50 0.00 0.00 0.50 0.00
#> TCGA.CM.4747.01 3 0.5334 1.76e-01 0.20 0.00 0.58 0.00 0.00 0.20 0.02
#> TCGA.EF.5831.01 3 0.2081 3.85e-01 0.00 0.00 0.86 0.00 0.00 0.14 0.00
#> TCGA.DM.A28G.01 5 0.2803 6.34e-01 0.00 0.00 0.00 0.06 0.84 0.00 0.10
#> TCGA.D5.6537.01 4 0.5091 4.46e-01 0.00 0.16 0.00 0.66 0.00 0.06 0.12
#> TCGA.DY.A1DD.01 5 0.5833 3.69e-01 0.00 0.00 0.00 0.14 0.56 0.08 0.22
cbind(get_classes(res, k = 8), get_membership(res, k = 8))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7 p8
#> TCGA.AG.A026.01 4 0.3291 0.7579 0.00 0.00 0.00 0.70 0.00 0.00 0.02 0.28
#> TCGA.G4.6303.01 6 0.4370 0.2350 0.00 0.00 0.40 0.00 0.00 0.52 0.00 0.08
#> TCGA.T9.A92H.01 6 0.2888 0.5636 0.00 0.00 0.16 0.00 0.00 0.80 0.04 0.00
#> TCGA.AD.6965.01 2 0.0000 0.9517 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.A6.5660.01 5 0.3299 -0.0885 0.00 0.00 0.00 0.00 0.56 0.00 0.44 0.00
#> TCGA.F5.6571.01 1 0.1557 0.8371 0.92 0.00 0.00 0.00 0.00 0.02 0.00 0.06
#> TCGA.CM.5862.01 4 0.2020 0.7799 0.00 0.00 0.00 0.90 0.02 0.00 0.02 0.06
#> TCGA.CI.6622.01 1 0.2569 0.7686 0.82 0.00 0.00 0.00 0.00 0.02 0.00 0.16
#> TCGA.EI.6512.01 1 0.0471 0.8557 0.98 0.00 0.00 0.00 0.00 0.02 0.00 0.00
#> TCGA.QG.A5YX.01 4 0.1607 0.7720 0.00 0.04 0.00 0.92 0.00 0.00 0.00 0.04
#> TCGA.AG.A036.01 7 0.3971 0.1765 0.00 0.00 0.00 0.00 0.42 0.00 0.54 0.04
#> TCGA.AA.3509.01 1 0.3909 0.6183 0.70 0.00 0.00 0.00 0.00 0.12 0.00 0.18
#> TCGA.EI.6883.01 1 0.2224 0.8599 0.86 0.00 0.00 0.00 0.00 0.00 0.02 0.12
#> TCGA.RU.A8FL.01 4 0.4593 0.7468 0.00 0.00 0.00 0.66 0.04 0.00 0.10 0.20
#> TCGA.AZ.6599.01 2 0.0000 0.9517 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CM.5860.01 3 0.0000 0.5494 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.A6.6780.01 3 0.4593 0.3398 0.00 0.00 0.62 0.00 0.00 0.10 0.26 0.02
#> TCGA.CM.4750.01 4 0.4180 0.7611 0.00 0.00 0.00 0.70 0.04 0.00 0.06 0.20
#> TCGA.CM.6677.01 4 0.4672 0.6728 0.00 0.00 0.00 0.66 0.16 0.00 0.04 0.14
#> TCGA.F5.6814.01 5 0.2719 0.4162 0.00 0.00 0.00 0.02 0.80 0.00 0.18 0.00
#> TCGA.DM.A1D8.01 3 0.4590 0.3745 0.16 0.00 0.68 0.00 0.00 0.10 0.00 0.06
#> TCGA.A6.6138.01 1 0.0471 0.8557 0.98 0.00 0.00 0.00 0.00 0.02 0.00 0.00
#> TCGA.DM.A28F.01 2 0.0471 0.9442 0.00 0.98 0.00 0.02 0.00 0.00 0.00 0.00
#> TCGA.DM.A1D4.01 7 0.6664 0.1528 0.00 0.00 0.06 0.00 0.26 0.10 0.44 0.14
#> TCGA.DM.A0X9.01 5 0.1275 0.5183 0.00 0.00 0.00 0.04 0.94 0.00 0.00 0.02
#> TCGA.AY.A69D.01 1 0.2569 0.8615 0.82 0.00 0.00 0.00 0.00 0.00 0.02 0.16
#> TCGA.CA.6716.01 1 0.2224 0.8599 0.86 0.00 0.00 0.00 0.00 0.00 0.02 0.12
#> TCGA.NH.A6GB.01 2 0.0000 0.9517 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.NH.A50U.01 4 0.3675 0.6950 0.00 0.00 0.00 0.76 0.14 0.00 0.02 0.08
#> TCGA.AH.6644.01 3 0.4740 0.2089 0.00 0.00 0.58 0.00 0.00 0.30 0.02 0.10
#> TCGA.CM.5864.01 4 0.0808 0.7891 0.00 0.00 0.00 0.96 0.00 0.00 0.00 0.04
#> TCGA.AG.3742.01 5 0.5061 -0.1840 0.00 0.00 0.00 0.42 0.46 0.00 0.04 0.08
#> TCGA.A6.5666.01 4 0.3170 0.7268 0.00 0.04 0.00 0.76 0.00 0.00 0.00 0.20
#> TCGA.AG.3591.01 4 0.1607 0.7720 0.00 0.04 0.00 0.92 0.00 0.00 0.00 0.04
#> TCGA.AH.6643.01 6 0.2534 0.5473 0.00 0.00 0.22 0.00 0.00 0.78 0.00 0.00
#> TCGA.EI.6510.01 5 0.5207 -0.1945 0.00 0.00 0.00 0.40 0.46 0.00 0.04 0.10
#> TCGA.A6.5656.01 6 0.5165 0.2363 0.00 0.00 0.28 0.00 0.00 0.44 0.28 0.00
#> TCGA.DY.A1DG.01 4 0.1091 0.7983 0.00 0.00 0.00 0.94 0.00 0.00 0.00 0.06
#> TCGA.F4.6806.01 3 0.0471 0.5473 0.00 0.00 0.98 0.00 0.00 0.02 0.00 0.00
#> TCGA.5M.AAT4.01 3 0.5131 0.1560 0.00 0.00 0.50 0.00 0.02 0.14 0.34 0.00
#> TCGA.EI.6514.01 6 0.4538 0.3863 0.00 0.00 0.32 0.00 0.00 0.56 0.12 0.00
#> TCGA.DM.A282.01 1 0.2404 0.7868 0.84 0.00 0.00 0.00 0.00 0.02 0.00 0.14
#> TCGA.DM.A1HA.01 6 0.5903 0.0437 0.00 0.00 0.02 0.00 0.02 0.42 0.26 0.28
#> TCGA.AG.4021.01 2 0.0000 0.9517 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DM.A1D9.01 5 0.1275 0.5183 0.00 0.00 0.00 0.04 0.94 0.00 0.00 0.02
#> TCGA.CM.4744.01 2 0.1091 0.9151 0.00 0.94 0.00 0.06 0.00 0.00 0.00 0.00
#> TCGA.A6.6652.01 6 0.3879 0.5394 0.00 0.00 0.14 0.00 0.00 0.74 0.10 0.02
#> TCGA.SS.A7HO.01 2 0.0000 0.9517 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.A6.6650.01 7 0.3329 0.0916 0.00 0.00 0.00 0.00 0.48 0.00 0.52 0.00
#> TCGA.NH.A50T.01 2 0.0471 0.9442 0.00 0.98 0.00 0.02 0.00 0.00 0.00 0.00
#> TCGA.AD.6899.01 1 0.4904 0.1900 0.50 0.00 0.00 0.00 0.00 0.32 0.00 0.18
#> TCGA.A6.A56B.01 6 0.6241 0.1203 0.34 0.00 0.12 0.00 0.00 0.36 0.00 0.18
#> TCGA.D5.5539.01 5 0.2938 0.2644 0.00 0.00 0.00 0.00 0.70 0.00 0.30 0.00
#> TCGA.AY.A54L.01 2 0.0000 0.9517 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.NH.A5IV.01 5 0.3142 0.1417 0.00 0.00 0.00 0.00 0.64 0.00 0.36 0.00
#> TCGA.G4.6306.01 3 0.4943 0.1198 0.00 0.00 0.48 0.00 0.00 0.18 0.34 0.00
#> TCGA.AD.A5EK.01 1 0.2224 0.8599 0.86 0.00 0.00 0.00 0.00 0.00 0.02 0.12
#> TCGA.DC.5337.01 2 0.3909 0.6794 0.00 0.70 0.00 0.12 0.00 0.00 0.00 0.18
#> TCGA.QG.A5YW.01 2 0.0471 0.9442 0.00 0.98 0.00 0.02 0.00 0.00 0.00 0.00
#> TCGA.EI.6882.01 5 0.1275 0.5183 0.00 0.00 0.00 0.04 0.94 0.00 0.00 0.02
#> TCGA.A6.2677.01 4 0.3291 0.7579 0.00 0.00 0.00 0.70 0.00 0.00 0.02 0.28
#> TCGA.AA.3502.01 2 0.0000 0.9517 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CK.5915.01 1 0.2224 0.8599 0.86 0.00 0.00 0.00 0.00 0.00 0.02 0.12
#> TCGA.AY.6197.01 1 0.0941 0.8526 0.96 0.00 0.00 0.00 0.00 0.02 0.00 0.02
#> TCGA.G4.6294.01 1 0.2224 0.8599 0.86 0.00 0.00 0.00 0.00 0.00 0.02 0.12
#> TCGA.CM.6172.01 1 0.2224 0.8599 0.86 0.00 0.00 0.00 0.00 0.00 0.02 0.12
#> TCGA.AA.3496.01 4 0.3374 0.7479 0.00 0.00 0.00 0.68 0.00 0.00 0.02 0.30
#> TCGA.DM.A28A.01 1 0.2569 0.8615 0.82 0.00 0.00 0.00 0.00 0.00 0.02 0.16
#> TCGA.EI.7002.01 6 0.3036 0.5509 0.00 0.00 0.18 0.00 0.00 0.78 0.00 0.04
#> TCGA.QG.A5Z1.01 1 0.1804 0.8265 0.90 0.00 0.00 0.00 0.00 0.02 0.00 0.08
#> TCGA.DM.A28H.01 3 0.0941 0.5479 0.00 0.00 0.96 0.00 0.00 0.00 0.02 0.02
#> TCGA.DM.A28M.01 3 0.4406 0.3563 0.00 0.00 0.64 0.00 0.00 0.08 0.26 0.02
#> TCGA.DM.A288.01 3 0.0000 0.5494 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.F4.6855.01 3 0.5126 0.0678 0.04 0.00 0.52 0.00 0.00 0.34 0.00 0.10
#> TCGA.NH.A6GA.01 3 0.5073 0.1250 0.00 0.00 0.46 0.00 0.00 0.22 0.32 0.00
#> TCGA.NH.A50V.01 3 0.5451 0.2008 0.30 0.00 0.52 0.00 0.00 0.10 0.00 0.08
#> TCGA.CK.6747.01 3 0.0471 0.5479 0.00 0.00 0.98 0.00 0.00 0.00 0.02 0.00
#> TCGA.CL.5918.01 4 0.4294 0.7647 0.00 0.00 0.00 0.68 0.04 0.00 0.06 0.22
#> TCGA.DM.A28K.01 7 0.5200 0.2425 0.00 0.00 0.14 0.00 0.40 0.00 0.44 0.02
#> TCGA.AA.3655.01 1 0.0941 0.8526 0.96 0.00 0.00 0.00 0.00 0.02 0.00 0.02
#> TCGA.AZ.5407.01 3 0.0000 0.5494 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.QG.A5YV.01 3 0.4758 0.2638 0.00 0.00 0.60 0.00 0.00 0.26 0.02 0.12
#> TCGA.AY.A71X.01 5 0.1275 0.5183 0.00 0.00 0.00 0.04 0.94 0.00 0.00 0.02
#> TCGA.AH.6549.01 2 0.4069 0.6497 0.00 0.68 0.00 0.14 0.00 0.00 0.00 0.18
#> TCGA.CM.6166.01 3 0.5123 0.0758 0.00 0.00 0.42 0.00 0.00 0.22 0.36 0.00
#> TCGA.AH.6897.01 2 0.0000 0.9517 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D5.5540.01 1 0.2224 0.8599 0.86 0.00 0.00 0.00 0.00 0.00 0.02 0.12
#> TCGA.G5.6233.01 1 0.1563 0.8656 0.90 0.00 0.00 0.00 0.00 0.00 0.00 0.10
#> TCGA.CA.6719.01 7 0.5701 0.0215 0.00 0.00 0.36 0.00 0.08 0.12 0.44 0.00
#> TCGA.D5.5537.01 3 0.3601 0.4454 0.00 0.00 0.76 0.00 0.00 0.16 0.02 0.06
#> TCGA.4T.AA8H.01 2 0.0000 0.9517 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AG.3592.01 3 0.4245 0.4042 0.06 0.00 0.72 0.00 0.00 0.14 0.00 0.08
#> TCGA.CM.6678.01 1 0.0808 0.8544 0.96 0.00 0.00 0.00 0.00 0.00 0.00 0.04
#> TCGA.CK.5914.01 1 0.1563 0.8656 0.90 0.00 0.00 0.00 0.00 0.00 0.00 0.10
#> TCGA.EI.6508.01 2 0.0000 0.9517 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D5.6532.01 4 0.4764 0.6957 0.00 0.00 0.00 0.64 0.12 0.00 0.04 0.20
#> TCGA.A6.2680.01 5 0.3272 -0.0307 0.00 0.00 0.00 0.00 0.58 0.00 0.42 0.00
#> TCGA.CM.6680.01 5 0.1275 0.5085 0.00 0.00 0.00 0.04 0.94 0.00 0.02 0.00
#> TCGA.AA.3660.01 6 0.3746 0.4307 0.00 0.00 0.32 0.00 0.00 0.64 0.00 0.04
#> TCGA.CM.4747.01 3 0.6211 0.1316 0.22 0.00 0.44 0.00 0.00 0.20 0.00 0.14
#> TCGA.EF.5831.01 3 0.1947 0.5016 0.00 0.00 0.86 0.00 0.00 0.14 0.00 0.00
#> TCGA.DM.A28G.01 5 0.2756 0.3261 0.00 0.00 0.00 0.00 0.74 0.00 0.26 0.00
#> TCGA.D5.6537.01 4 0.3299 0.7170 0.00 0.06 0.00 0.76 0.00 0.00 0.00 0.18
#> TCGA.DY.A1DD.01 7 0.5355 0.1520 0.00 0.00 0.00 0.02 0.30 0.00 0.48 0.20
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
consensus_heatmap(res, k = 7)
consensus_heatmap(res, k = 8)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
membership_heatmap(res, k = 7)
membership_heatmap(res, k = 8)
As soon as the classes for columns are determined, the signatures that are significantly different between subgroups can be looked for. Following are the heatmaps for signatures.
get_signatures(res, k = 2)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
get_signatures(res, k = 7)
get_signatures(res, k = 8)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. To get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows (which is done by automatically selecting number of clusters).If there are too many signatures, top_signatures = ... can be set to only show the
signatures with the highest FDRs:
# code only for demonstration
# e.g. to show the top 500 most significant rows
tb = get_signature(res, k = ..., top_signatures = 500)
If the signatures are defined as these which are uniquely high in current group, diff_method argument
can be set to "uniquely_high_in_one_group":
# code only for demonstration
tb = get_signature(res, k = ..., diff_method = "uniquely_high_in_one_group")
UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
dimension_reduction(res, k = 7, method = "UMAP")
dimension_reduction(res, k = 8, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
If matrix rows can be associated to genes, consider to use functional_enrichment(res,
...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.
Parent node: Node011. Child nodes: Node01111 , Node01112-leaf , Node01113-leaf , Node01114-leaf , Node01121-leaf , Node01122-leaf , Node01123-leaf , Node01124-leaf , Node01211-leaf , Node01212-leaf , Node01213-leaf , Node01221-leaf , Node01222-leaf , Node01223-leaf , Node01224-leaf , Node02121-leaf , Node02122-leaf , Node02123-leaf , Node04221-leaf , Node04222-leaf , Node04223-leaf .
The object with results only for a single top-value method and a single partitioning method can be extracted as:
res = res_rh["0111"]
A summary of res and all the functions that can be applied to it:
res
#> A 'ConsensusPartition' object with k = 2, 3, 4, 5, 6, 7, 8.
#> On a matrix with 30000 rows and 58 columns.
#> Top rows (1000) are extracted by 'ATC' method.
#> Subgroups are detected by 'kmeans' method.
#> Performed in total 350 partitions by row resampling.
#> Best k for subgroups seems to be 4.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_partitions"
#> [7] "compare_signatures" "consensus_heatmap" "dimension_reduction"
#> [10] "functional_enrichment" "get_anno_col" "get_anno"
#> [13] "get_classes" "get_consensus" "get_matrix"
#> [16] "get_membership" "get_param" "get_signatures"
#> [19] "get_stats" "is_best_k" "is_stable_k"
#> [22] "membership_heatmap" "ncol" "nrow"
#> [25] "plot_ecdf" "predict_classes" "rownames"
#> [28] "select_partition_number" "show" "suggest_best_k"
#> [31] "test_to_known_factors" "top_rows_heatmap"
collect_plots() function collects all the plots made from res for all k (number of subgroups)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
The plots are:
k and the heatmap of
predicted classes for each k.k.k.k.All the plots in panels can be made by individual functions and they are plotted later in this section.
select_partition_number() produces several plots showing different
statistics for choosing “optimized” k. There are following statistics:
k;k, the area increased is defined as \(A_k - A_{k-1}\).The detailed explanations of these statistics can be found in the cola vignette.
Generally speaking, higher 1-PAC score, higher mean silhouette score or higher
concordance corresponds to better partition. Rand index and Jaccard index
measure how similar the current partition is compared to partition with k-1.
If they are too similar, we won't accept k is better than k-1.
select_partition_number(res)
The numeric values for all these statistics can be obtained by get_stats().
get_stats(res)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> 2 2 0.998 0.965 0.985 0.5074 0.492 0.492
#> 3 3 0.827 0.823 0.920 0.3084 0.749 0.539
#> 4 4 0.900 0.954 0.962 0.1243 0.831 0.557
#> 5 5 0.815 0.806 0.853 0.0598 0.984 0.939
#> 6 6 0.801 0.696 0.824 0.0379 0.920 0.690
#> 7 7 0.783 0.593 0.777 0.0265 0.940 0.712
#> 8 8 0.819 0.694 0.835 0.0303 0.935 0.640
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.G4.6303.01 1 0.000 0.974 1.00 0.00
#> TCGA.T9.A92H.01 1 0.000 0.974 1.00 0.00
#> TCGA.F5.6571.01 1 0.000 0.974 1.00 0.00
#> TCGA.CI.6622.01 1 0.000 0.974 1.00 0.00
#> TCGA.EI.6512.01 2 0.000 0.994 0.00 1.00
#> TCGA.AA.3509.01 1 0.000 0.974 1.00 0.00
#> TCGA.EI.6883.01 2 0.000 0.994 0.00 1.00
#> TCGA.CM.5860.01 2 0.000 0.994 0.00 1.00
#> TCGA.A6.6780.01 2 0.000 0.994 0.00 1.00
#> TCGA.DM.A1D8.01 2 0.000 0.994 0.00 1.00
#> TCGA.A6.6138.01 2 0.000 0.994 0.00 1.00
#> TCGA.DM.A1D4.01 2 0.000 0.994 0.00 1.00
#> TCGA.AY.A69D.01 2 0.000 0.994 0.00 1.00
#> TCGA.CA.6716.01 2 0.000 0.994 0.00 1.00
#> TCGA.AH.6644.01 1 0.000 0.974 1.00 0.00
#> TCGA.AH.6643.01 1 0.000 0.974 1.00 0.00
#> TCGA.A6.5656.01 1 0.000 0.974 1.00 0.00
#> TCGA.F4.6806.01 2 0.000 0.994 0.00 1.00
#> TCGA.5M.AAT4.01 1 0.990 0.246 0.56 0.44
#> TCGA.EI.6514.01 1 0.000 0.974 1.00 0.00
#> TCGA.DM.A282.01 1 0.000 0.974 1.00 0.00
#> TCGA.DM.A1HA.01 2 0.000 0.994 0.00 1.00
#> TCGA.A6.6652.01 1 0.000 0.974 1.00 0.00
#> TCGA.A6.6650.01 1 0.000 0.974 1.00 0.00
#> TCGA.AD.6899.01 2 0.000 0.994 0.00 1.00
#> TCGA.A6.A56B.01 2 0.327 0.937 0.06 0.94
#> TCGA.NH.A5IV.01 1 0.000 0.974 1.00 0.00
#> TCGA.G4.6306.01 1 0.000 0.974 1.00 0.00
#> TCGA.AD.A5EK.01 2 0.000 0.994 0.00 1.00
#> TCGA.CK.5915.01 2 0.000 0.994 0.00 1.00
#> TCGA.AY.6197.01 2 0.000 0.994 0.00 1.00
#> TCGA.G4.6294.01 1 0.000 0.974 1.00 0.00
#> TCGA.CM.6172.01 1 0.000 0.974 1.00 0.00
#> TCGA.DM.A28A.01 2 0.000 0.994 0.00 1.00
#> TCGA.EI.7002.01 1 0.000 0.974 1.00 0.00
#> TCGA.QG.A5Z1.01 1 0.242 0.943 0.96 0.04
#> TCGA.DM.A28H.01 2 0.000 0.994 0.00 1.00
#> TCGA.DM.A28M.01 1 0.469 0.887 0.90 0.10
#> TCGA.DM.A288.01 2 0.000 0.994 0.00 1.00
#> TCGA.F4.6855.01 1 0.000 0.974 1.00 0.00
#> TCGA.NH.A6GA.01 2 0.000 0.994 0.00 1.00
#> TCGA.NH.A50V.01 2 0.000 0.994 0.00 1.00
#> TCGA.CK.6747.01 2 0.000 0.994 0.00 1.00
#> TCGA.DM.A28K.01 1 0.469 0.887 0.90 0.10
#> TCGA.AA.3655.01 1 0.000 0.974 1.00 0.00
#> TCGA.AZ.5407.01 2 0.000 0.994 0.00 1.00
#> TCGA.QG.A5YV.01 1 0.000 0.974 1.00 0.00
#> TCGA.CM.6166.01 1 0.000 0.974 1.00 0.00
#> TCGA.D5.5540.01 2 0.000 0.994 0.00 1.00
#> TCGA.G5.6233.01 2 0.000 0.994 0.00 1.00
#> TCGA.CA.6719.01 2 0.000 0.994 0.00 1.00
#> TCGA.D5.5537.01 2 0.000 0.994 0.00 1.00
#> TCGA.AG.3592.01 1 0.000 0.974 1.00 0.00
#> TCGA.CM.6678.01 1 0.000 0.974 1.00 0.00
#> TCGA.CK.5914.01 2 0.402 0.915 0.08 0.92
#> TCGA.AA.3660.01 1 0.141 0.959 0.98 0.02
#> TCGA.CM.4747.01 2 0.000 0.994 0.00 1.00
#> TCGA.EF.5831.01 2 0.242 0.957 0.04 0.96
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.G4.6303.01 1 0.0000 0.934 1.00 0.00 0.00
#> TCGA.T9.A92H.01 1 0.0000 0.934 1.00 0.00 0.00
#> TCGA.F5.6571.01 1 0.0000 0.934 1.00 0.00 0.00
#> TCGA.CI.6622.01 1 0.0000 0.934 1.00 0.00 0.00
#> TCGA.EI.6512.01 2 0.0000 0.860 0.00 1.00 0.00
#> TCGA.AA.3509.01 1 0.0000 0.934 1.00 0.00 0.00
#> TCGA.EI.6883.01 3 0.0892 0.942 0.00 0.02 0.98
#> TCGA.CM.5860.01 2 0.0892 0.854 0.00 0.98 0.02
#> TCGA.A6.6780.01 2 0.6126 0.532 0.00 0.60 0.40
#> TCGA.DM.A1D8.01 2 0.5706 0.628 0.00 0.68 0.32
#> TCGA.A6.6138.01 2 0.6045 0.559 0.00 0.62 0.38
#> TCGA.DM.A1D4.01 2 0.0892 0.854 0.00 0.98 0.02
#> TCGA.AY.A69D.01 3 0.0892 0.942 0.00 0.02 0.98
#> TCGA.CA.6716.01 3 0.0000 0.930 0.00 0.00 1.00
#> TCGA.AH.6644.01 1 0.0000 0.934 1.00 0.00 0.00
#> TCGA.AH.6643.01 1 0.0000 0.934 1.00 0.00 0.00
#> TCGA.A6.5656.01 1 0.0000 0.934 1.00 0.00 0.00
#> TCGA.F4.6806.01 2 0.0000 0.860 0.00 1.00 0.00
#> TCGA.5M.AAT4.01 2 0.0000 0.860 0.00 1.00 0.00
#> TCGA.EI.6514.01 1 0.0000 0.934 1.00 0.00 0.00
#> TCGA.DM.A282.01 1 0.0000 0.934 1.00 0.00 0.00
#> TCGA.DM.A1HA.01 3 0.0000 0.930 0.00 0.00 1.00
#> TCGA.A6.6652.01 1 0.0000 0.934 1.00 0.00 0.00
#> TCGA.A6.6650.01 1 0.0000 0.934 1.00 0.00 0.00
#> TCGA.AD.6899.01 2 0.0000 0.860 0.00 1.00 0.00
#> TCGA.A6.A56B.01 3 0.0892 0.942 0.00 0.02 0.98
#> TCGA.NH.A5IV.01 2 0.0000 0.860 0.00 1.00 0.00
#> TCGA.G4.6306.01 1 0.6126 0.424 0.60 0.40 0.00
#> TCGA.AD.A5EK.01 3 0.0000 0.930 0.00 0.00 1.00
#> TCGA.CK.5915.01 3 0.0892 0.942 0.00 0.02 0.98
#> TCGA.AY.6197.01 2 0.6126 0.532 0.00 0.60 0.40
#> TCGA.G4.6294.01 1 0.0000 0.934 1.00 0.00 0.00
#> TCGA.CM.6172.01 3 0.6244 0.153 0.44 0.00 0.56
#> TCGA.DM.A28A.01 3 0.0892 0.942 0.00 0.02 0.98
#> TCGA.EI.7002.01 1 0.0000 0.934 1.00 0.00 0.00
#> TCGA.QG.A5Z1.01 1 0.6387 0.506 0.68 0.02 0.30
#> TCGA.DM.A28H.01 2 0.6192 0.494 0.00 0.58 0.42
#> TCGA.DM.A28M.01 2 0.0000 0.860 0.00 1.00 0.00
#> TCGA.DM.A288.01 2 0.0892 0.854 0.00 0.98 0.02
#> TCGA.F4.6855.01 1 0.0000 0.934 1.00 0.00 0.00
#> TCGA.NH.A6GA.01 2 0.0000 0.860 0.00 1.00 0.00
#> TCGA.NH.A50V.01 2 0.6126 0.532 0.00 0.60 0.40
#> TCGA.CK.6747.01 2 0.0000 0.860 0.00 1.00 0.00
#> TCGA.DM.A28K.01 2 0.0000 0.860 0.00 1.00 0.00
#> TCGA.AA.3655.01 1 0.0000 0.934 1.00 0.00 0.00
#> TCGA.AZ.5407.01 2 0.0892 0.854 0.00 0.98 0.02
#> TCGA.QG.A5YV.01 1 0.0000 0.934 1.00 0.00 0.00
#> TCGA.CM.6166.01 1 0.0000 0.934 1.00 0.00 0.00
#> TCGA.D5.5540.01 3 0.0892 0.942 0.00 0.02 0.98
#> TCGA.G5.6233.01 2 0.6126 0.532 0.00 0.60 0.40
#> TCGA.CA.6719.01 2 0.0000 0.860 0.00 1.00 0.00
#> TCGA.D5.5537.01 2 0.0000 0.860 0.00 1.00 0.00
#> TCGA.AG.3592.01 1 0.3340 0.826 0.88 0.12 0.00
#> TCGA.CM.6678.01 1 0.0000 0.934 1.00 0.00 0.00
#> TCGA.CK.5914.01 3 0.0892 0.942 0.00 0.02 0.98
#> TCGA.AA.3660.01 1 0.6302 0.218 0.52 0.48 0.00
#> TCGA.CM.4747.01 2 0.0000 0.860 0.00 1.00 0.00
#> TCGA.EF.5831.01 3 0.0892 0.942 0.00 0.02 0.98
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> TCGA.G4.6303.01 1 0.000 1.000 1.00 0.00 0.00 0.00
#> TCGA.T9.A92H.01 1 0.000 1.000 1.00 0.00 0.00 0.00
#> TCGA.F5.6571.01 1 0.000 1.000 1.00 0.00 0.00 0.00
#> TCGA.CI.6622.01 1 0.000 1.000 1.00 0.00 0.00 0.00
#> TCGA.EI.6512.01 2 0.000 0.945 0.00 1.00 0.00 0.00
#> TCGA.AA.3509.01 1 0.000 1.000 1.00 0.00 0.00 0.00
#> TCGA.EI.6883.01 3 0.201 0.965 0.00 0.00 0.92 0.08
#> TCGA.CM.5860.01 4 0.234 0.988 0.00 0.10 0.00 0.90
#> TCGA.A6.6780.01 4 0.234 0.988 0.00 0.10 0.00 0.90
#> TCGA.DM.A1D8.01 4 0.234 0.988 0.00 0.10 0.00 0.90
#> TCGA.A6.6138.01 4 0.234 0.988 0.00 0.10 0.00 0.90
#> TCGA.DM.A1D4.01 4 0.234 0.988 0.00 0.10 0.00 0.90
#> TCGA.AY.A69D.01 3 0.201 0.965 0.00 0.00 0.92 0.08
#> TCGA.CA.6716.01 3 0.234 0.960 0.00 0.00 0.90 0.10
#> TCGA.AH.6644.01 1 0.000 1.000 1.00 0.00 0.00 0.00
#> TCGA.AH.6643.01 1 0.000 1.000 1.00 0.00 0.00 0.00
#> TCGA.A6.5656.01 1 0.000 1.000 1.00 0.00 0.00 0.00
#> TCGA.F4.6806.01 2 0.000 0.945 0.00 1.00 0.00 0.00
#> TCGA.5M.AAT4.01 2 0.000 0.945 0.00 1.00 0.00 0.00
#> TCGA.EI.6514.01 1 0.000 1.000 1.00 0.00 0.00 0.00
#> TCGA.DM.A282.01 1 0.000 1.000 1.00 0.00 0.00 0.00
#> TCGA.DM.A1HA.01 4 0.000 0.877 0.00 0.00 0.00 1.00
#> TCGA.A6.6652.01 1 0.000 1.000 1.00 0.00 0.00 0.00
#> TCGA.A6.6650.01 1 0.000 1.000 1.00 0.00 0.00 0.00
#> TCGA.AD.6899.01 2 0.000 0.945 0.00 1.00 0.00 0.00
#> TCGA.A6.A56B.01 3 0.000 0.961 0.00 0.00 1.00 0.00
#> TCGA.NH.A5IV.01 2 0.000 0.945 0.00 1.00 0.00 0.00
#> TCGA.G4.6306.01 2 0.234 0.843 0.10 0.90 0.00 0.00
#> TCGA.AD.A5EK.01 3 0.234 0.960 0.00 0.00 0.90 0.10
#> TCGA.CK.5915.01 3 0.234 0.960 0.00 0.00 0.90 0.10
#> TCGA.AY.6197.01 4 0.234 0.988 0.00 0.10 0.00 0.90
#> TCGA.G4.6294.01 1 0.000 1.000 1.00 0.00 0.00 0.00
#> TCGA.CM.6172.01 3 0.000 0.961 0.00 0.00 1.00 0.00
#> TCGA.DM.A28A.01 3 0.164 0.967 0.00 0.00 0.94 0.06
#> TCGA.EI.7002.01 1 0.000 1.000 1.00 0.00 0.00 0.00
#> TCGA.QG.A5Z1.01 3 0.000 0.961 0.00 0.00 1.00 0.00
#> TCGA.DM.A28H.01 4 0.234 0.988 0.00 0.10 0.00 0.90
#> TCGA.DM.A28M.01 2 0.000 0.945 0.00 1.00 0.00 0.00
#> TCGA.DM.A288.01 2 0.491 0.123 0.00 0.58 0.00 0.42
#> TCGA.F4.6855.01 1 0.000 1.000 1.00 0.00 0.00 0.00
#> TCGA.NH.A6GA.01 2 0.000 0.945 0.00 1.00 0.00 0.00
#> TCGA.NH.A50V.01 4 0.234 0.988 0.00 0.10 0.00 0.90
#> TCGA.CK.6747.01 2 0.000 0.945 0.00 1.00 0.00 0.00
#> TCGA.DM.A28K.01 2 0.000 0.945 0.00 1.00 0.00 0.00
#> TCGA.AA.3655.01 1 0.000 1.000 1.00 0.00 0.00 0.00
#> TCGA.AZ.5407.01 4 0.234 0.988 0.00 0.10 0.00 0.90
#> TCGA.QG.A5YV.01 1 0.000 1.000 1.00 0.00 0.00 0.00
#> TCGA.CM.6166.01 1 0.000 1.000 1.00 0.00 0.00 0.00
#> TCGA.D5.5540.01 3 0.164 0.967 0.00 0.00 0.94 0.06
#> TCGA.G5.6233.01 4 0.234 0.988 0.00 0.10 0.00 0.90
#> TCGA.CA.6719.01 2 0.000 0.945 0.00 1.00 0.00 0.00
#> TCGA.D5.5537.01 2 0.000 0.945 0.00 1.00 0.00 0.00
#> TCGA.AG.3592.01 2 0.283 0.867 0.04 0.90 0.06 0.00
#> TCGA.CM.6678.01 1 0.000 1.000 1.00 0.00 0.00 0.00
#> TCGA.CK.5914.01 3 0.000 0.961 0.00 0.00 1.00 0.00
#> TCGA.AA.3660.01 2 0.234 0.885 0.02 0.92 0.06 0.00
#> TCGA.CM.4747.01 2 0.000 0.945 0.00 1.00 0.00 0.00
#> TCGA.EF.5831.01 3 0.000 0.961 0.00 0.00 1.00 0.00
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> TCGA.G4.6303.01 5 0.1732 0.88976 0.08 0.00 0.00 0.00 0.92
#> TCGA.T9.A92H.01 5 0.1410 0.89573 0.06 0.00 0.00 0.00 0.94
#> TCGA.F5.6571.01 5 0.0000 0.90228 0.00 0.00 0.00 0.00 1.00
#> TCGA.CI.6622.01 5 0.0000 0.90228 0.00 0.00 0.00 0.00 1.00
#> TCGA.EI.6512.01 2 0.1043 0.80952 0.04 0.96 0.00 0.00 0.00
#> TCGA.AA.3509.01 5 0.0000 0.90228 0.00 0.00 0.00 0.00 1.00
#> TCGA.EI.6883.01 3 0.0000 0.86365 0.00 0.00 1.00 0.00 0.00
#> TCGA.CM.5860.01 4 0.2754 0.86549 0.08 0.04 0.00 0.88 0.00
#> TCGA.A6.6780.01 4 0.0000 0.90265 0.00 0.00 0.00 1.00 0.00
#> TCGA.DM.A1D8.01 4 0.0609 0.90046 0.02 0.00 0.00 0.98 0.00
#> TCGA.A6.6138.01 4 0.3513 0.76305 0.02 0.18 0.00 0.80 0.00
#> TCGA.DM.A1D4.01 4 0.0609 0.90000 0.02 0.00 0.00 0.98 0.00
#> TCGA.AY.A69D.01 3 0.0000 0.86365 0.00 0.00 1.00 0.00 0.00
#> TCGA.CA.6716.01 3 0.5013 0.70365 0.24 0.00 0.68 0.08 0.00
#> TCGA.AH.6644.01 5 0.2732 0.85649 0.16 0.00 0.00 0.00 0.84
#> TCGA.AH.6643.01 5 0.1732 0.88976 0.08 0.00 0.00 0.00 0.92
#> TCGA.A6.5656.01 5 0.1732 0.88976 0.08 0.00 0.00 0.00 0.92
#> TCGA.F4.6806.01 2 0.2516 0.77890 0.14 0.86 0.00 0.00 0.00
#> TCGA.5M.AAT4.01 2 0.1732 0.80728 0.08 0.92 0.00 0.00 0.00
#> TCGA.EI.6514.01 5 0.0000 0.90228 0.00 0.00 0.00 0.00 1.00
#> TCGA.DM.A282.01 5 0.2280 0.87303 0.12 0.00 0.00 0.00 0.88
#> TCGA.DM.A1HA.01 4 0.3274 0.74561 0.22 0.00 0.00 0.78 0.00
#> TCGA.A6.6652.01 5 0.1732 0.88976 0.08 0.00 0.00 0.00 0.92
#> TCGA.A6.6650.01 5 0.4726 0.58562 0.40 0.02 0.00 0.00 0.58
#> TCGA.AD.6899.01 2 0.0609 0.81190 0.02 0.98 0.00 0.00 0.00
#> TCGA.A6.A56B.01 3 0.0000 0.86365 0.00 0.00 1.00 0.00 0.00
#> TCGA.NH.A5IV.01 2 0.4262 0.68177 0.44 0.56 0.00 0.00 0.00
#> TCGA.G4.6306.01 2 0.4227 0.68895 0.42 0.58 0.00 0.00 0.00
#> TCGA.AD.A5EK.01 3 0.3274 0.78110 0.22 0.00 0.78 0.00 0.00
#> TCGA.CK.5915.01 3 0.3424 0.77126 0.24 0.00 0.76 0.00 0.00
#> TCGA.AY.6197.01 4 0.0000 0.90265 0.00 0.00 0.00 1.00 0.00
#> TCGA.G4.6294.01 5 0.1410 0.89573 0.06 0.00 0.00 0.00 0.94
#> TCGA.CM.6172.01 3 0.3946 0.73427 0.08 0.00 0.80 0.00 0.12
#> TCGA.DM.A28A.01 3 0.0000 0.86365 0.00 0.00 1.00 0.00 0.00
#> TCGA.EI.7002.01 5 0.1410 0.89573 0.06 0.00 0.00 0.00 0.94
#> TCGA.QG.A5Z1.01 3 0.6555 -0.00927 0.20 0.40 0.40 0.00 0.00
#> TCGA.DM.A28H.01 4 0.0609 0.90046 0.02 0.00 0.00 0.98 0.00
#> TCGA.DM.A28M.01 2 0.4262 0.68177 0.44 0.56 0.00 0.00 0.00
#> TCGA.DM.A288.01 4 0.6111 0.45381 0.18 0.26 0.00 0.56 0.00
#> TCGA.F4.6855.01 5 0.2732 0.85649 0.16 0.00 0.00 0.00 0.84
#> TCGA.NH.A6GA.01 2 0.0000 0.81402 0.00 1.00 0.00 0.00 0.00
#> TCGA.NH.A50V.01 4 0.0000 0.90265 0.00 0.00 0.00 1.00 0.00
#> TCGA.CK.6747.01 2 0.4182 0.69306 0.40 0.60 0.00 0.00 0.00
#> TCGA.DM.A28K.01 2 0.4262 0.68177 0.44 0.56 0.00 0.00 0.00
#> TCGA.AA.3655.01 5 0.3684 0.76344 0.28 0.00 0.00 0.00 0.72
#> TCGA.AZ.5407.01 4 0.2754 0.86549 0.08 0.04 0.00 0.88 0.00
#> TCGA.QG.A5YV.01 5 0.2516 0.86443 0.14 0.00 0.00 0.00 0.86
#> TCGA.CM.6166.01 5 0.3106 0.85647 0.14 0.02 0.00 0.00 0.84
#> TCGA.D5.5540.01 3 0.0000 0.86365 0.00 0.00 1.00 0.00 0.00
#> TCGA.G5.6233.01 4 0.0000 0.90265 0.00 0.00 0.00 1.00 0.00
#> TCGA.CA.6719.01 2 0.1043 0.80952 0.04 0.96 0.00 0.00 0.00
#> TCGA.D5.5537.01 2 0.0609 0.81190 0.02 0.98 0.00 0.00 0.00
#> TCGA.AG.3592.01 2 0.3274 0.73395 0.22 0.78 0.00 0.00 0.00
#> TCGA.CM.6678.01 5 0.0609 0.89987 0.02 0.00 0.00 0.00 0.98
#> TCGA.CK.5914.01 3 0.0609 0.85880 0.02 0.00 0.98 0.00 0.00
#> TCGA.AA.3660.01 2 0.3274 0.73395 0.22 0.78 0.00 0.00 0.00
#> TCGA.CM.4747.01 2 0.0609 0.81190 0.02 0.98 0.00 0.00 0.00
#> TCGA.EF.5831.01 3 0.1410 0.84496 0.06 0.00 0.94 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.G4.6303.01 5 0.1267 0.787 0.06 0.00 0.00 0.00 0.94 0.00
#> TCGA.T9.A92H.01 5 0.1267 0.787 0.06 0.00 0.00 0.00 0.94 0.00
#> TCGA.F5.6571.01 5 0.0000 0.790 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.CI.6622.01 5 0.0000 0.790 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.EI.6512.01 2 0.0547 0.794 0.02 0.98 0.00 0.00 0.00 0.00
#> TCGA.AA.3509.01 5 0.0000 0.790 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.EI.6883.01 3 0.1556 0.821 0.08 0.00 0.92 0.00 0.00 0.00
#> TCGA.CM.5860.01 4 0.3156 0.737 0.00 0.18 0.00 0.80 0.00 0.02
#> TCGA.A6.6780.01 4 0.0000 0.876 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.DM.A1D8.01 4 0.0000 0.876 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.A6.6138.01 4 0.4078 0.527 0.02 0.34 0.00 0.64 0.00 0.00
#> TCGA.DM.A1D4.01 4 0.0000 0.876 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.AY.A69D.01 3 0.1267 0.828 0.06 0.00 0.94 0.00 0.00 0.00
#> TCGA.CA.6716.01 1 0.4078 0.674 0.64 0.00 0.34 0.02 0.00 0.00
#> TCGA.AH.6644.01 5 0.5520 0.564 0.24 0.00 0.00 0.00 0.56 0.20
#> TCGA.AH.6643.01 5 0.1267 0.787 0.06 0.00 0.00 0.00 0.94 0.00
#> TCGA.A6.5656.01 5 0.1267 0.787 0.06 0.00 0.00 0.00 0.94 0.00
#> TCGA.F4.6806.01 2 0.2048 0.676 0.00 0.88 0.00 0.00 0.00 0.12
#> TCGA.5M.AAT4.01 2 0.2190 0.756 0.04 0.90 0.00 0.00 0.00 0.06
#> TCGA.EI.6514.01 5 0.0000 0.790 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.DM.A282.01 5 0.5173 0.609 0.20 0.00 0.00 0.00 0.62 0.18
#> TCGA.DM.A1HA.01 1 0.3828 0.128 0.56 0.00 0.00 0.44 0.00 0.00
#> TCGA.A6.6652.01 5 0.1267 0.787 0.06 0.00 0.00 0.00 0.94 0.00
#> TCGA.A6.6650.01 6 0.5938 -0.146 0.26 0.00 0.00 0.00 0.28 0.46
#> TCGA.AD.6899.01 2 0.0547 0.796 0.02 0.98 0.00 0.00 0.00 0.00
#> TCGA.A6.A56B.01 3 0.0000 0.848 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.NH.A5IV.01 6 0.3409 0.671 0.00 0.30 0.00 0.00 0.00 0.70
#> TCGA.G4.6306.01 6 0.5841 0.350 0.22 0.30 0.00 0.00 0.00 0.48
#> TCGA.AD.A5EK.01 1 0.3706 0.646 0.62 0.00 0.38 0.00 0.00 0.00
#> TCGA.CK.5915.01 1 0.3647 0.667 0.64 0.00 0.36 0.00 0.00 0.00
#> TCGA.AY.6197.01 4 0.0000 0.876 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.G4.6294.01 5 0.1267 0.787 0.06 0.00 0.00 0.00 0.94 0.00
#> TCGA.CM.6172.01 3 0.3829 0.527 0.06 0.00 0.76 0.00 0.18 0.00
#> TCGA.DM.A28A.01 3 0.0937 0.841 0.04 0.00 0.96 0.00 0.00 0.00
#> TCGA.EI.7002.01 5 0.1267 0.787 0.06 0.00 0.00 0.00 0.94 0.00
#> TCGA.QG.A5Z1.01 2 0.6777 0.323 0.14 0.48 0.28 0.00 0.00 0.10
#> TCGA.DM.A28H.01 4 0.0547 0.866 0.00 0.00 0.00 0.98 0.00 0.02
#> TCGA.DM.A28M.01 6 0.3409 0.671 0.00 0.30 0.00 0.00 0.00 0.70
#> TCGA.DM.A288.01 4 0.5202 0.510 0.00 0.26 0.00 0.60 0.00 0.14
#> TCGA.F4.6855.01 5 0.5520 0.564 0.24 0.00 0.00 0.00 0.56 0.20
#> TCGA.NH.A6GA.01 2 0.0547 0.789 0.00 0.98 0.00 0.00 0.00 0.02
#> TCGA.NH.A50V.01 4 0.0000 0.876 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.CK.6747.01 6 0.3409 0.671 0.00 0.30 0.00 0.00 0.00 0.70
#> TCGA.DM.A28K.01 6 0.3409 0.671 0.00 0.30 0.00 0.00 0.00 0.70
#> TCGA.AA.3655.01 5 0.5867 0.444 0.24 0.00 0.00 0.00 0.48 0.28
#> TCGA.AZ.5407.01 4 0.1092 0.858 0.00 0.02 0.00 0.96 0.00 0.02
#> TCGA.QG.A5YV.01 5 0.5520 0.564 0.24 0.00 0.00 0.00 0.56 0.20
#> TCGA.CM.6166.01 5 0.5608 0.542 0.26 0.00 0.00 0.00 0.54 0.20
#> TCGA.D5.5540.01 3 0.0000 0.848 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.G5.6233.01 4 0.0000 0.876 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.CA.6719.01 2 0.1480 0.782 0.02 0.94 0.00 0.00 0.00 0.04
#> TCGA.D5.5537.01 2 0.0547 0.796 0.02 0.98 0.00 0.00 0.00 0.00
#> TCGA.AG.3592.01 2 0.4723 0.574 0.14 0.68 0.00 0.00 0.00 0.18
#> TCGA.CM.6678.01 5 0.3045 0.733 0.06 0.00 0.00 0.00 0.84 0.10
#> TCGA.CK.5914.01 3 0.1865 0.815 0.04 0.00 0.92 0.00 0.00 0.04
#> TCGA.AA.3660.01 2 0.4566 0.588 0.14 0.70 0.00 0.00 0.00 0.16
#> TCGA.CM.4747.01 2 0.0547 0.796 0.02 0.98 0.00 0.00 0.00 0.00
#> TCGA.EF.5831.01 3 0.3697 0.711 0.06 0.04 0.82 0.00 0.00 0.08
cbind(get_classes(res, k = 7), get_membership(res, k = 7))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7
#> TCGA.G4.6303.01 5 0.1433 0.7763 0.08 0.00 0.00 0.00 0.92 0.00 0.00
#> TCGA.T9.A92H.01 5 0.1433 0.7763 0.08 0.00 0.00 0.00 0.92 0.00 0.00
#> TCGA.F5.6571.01 5 0.0000 0.7826 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.CI.6622.01 5 0.0000 0.7826 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.EI.6512.01 2 0.2832 0.5423 0.00 0.76 0.00 0.00 0.00 0.00 0.24
#> TCGA.AA.3509.01 5 0.0000 0.7826 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.EI.6883.01 3 0.3011 0.4207 0.12 0.00 0.82 0.00 0.00 0.00 0.06
#> TCGA.CM.5860.01 2 0.5773 0.0689 0.08 0.50 0.00 0.36 0.00 0.04 0.02
#> TCGA.A6.6780.01 4 0.0000 0.8565 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.DM.A1D8.01 4 0.0000 0.8565 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.A6.6138.01 2 0.3139 0.4860 0.00 0.70 0.00 0.30 0.00 0.00 0.00
#> TCGA.DM.A1D4.01 4 0.2421 0.8061 0.08 0.00 0.00 0.88 0.00 0.02 0.02
#> TCGA.AY.A69D.01 3 0.1664 0.5451 0.06 0.00 0.92 0.00 0.00 0.02 0.00
#> TCGA.CA.6716.01 1 0.3525 0.9087 0.56 0.00 0.44 0.00 0.00 0.00 0.00
#> TCGA.AH.6644.01 5 0.5913 0.4157 0.12 0.02 0.00 0.00 0.54 0.04 0.28
#> TCGA.AH.6643.01 5 0.2422 0.7443 0.18 0.00 0.00 0.00 0.82 0.00 0.00
#> TCGA.A6.5656.01 5 0.1433 0.7763 0.08 0.00 0.00 0.00 0.92 0.00 0.00
#> TCGA.F4.6806.01 2 0.1860 0.7013 0.02 0.92 0.00 0.02 0.00 0.04 0.00
#> TCGA.5M.AAT4.01 2 0.3745 0.4682 0.00 0.70 0.00 0.00 0.00 0.04 0.26
#> TCGA.EI.6514.01 5 0.0000 0.7826 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.DM.A282.01 5 0.5091 0.5376 0.12 0.00 0.00 0.00 0.64 0.04 0.20
#> TCGA.DM.A1HA.01 4 0.3546 0.2253 0.46 0.00 0.00 0.54 0.00 0.00 0.00
#> TCGA.A6.6652.01 5 0.2081 0.7571 0.14 0.00 0.00 0.00 0.86 0.00 0.00
#> TCGA.A6.6650.01 7 0.7066 -0.0501 0.12 0.02 0.00 0.00 0.18 0.34 0.34
#> TCGA.AD.6899.01 2 0.0504 0.7322 0.00 0.98 0.00 0.02 0.00 0.00 0.00
#> TCGA.A6.A56B.01 3 0.1664 0.6021 0.00 0.00 0.92 0.00 0.00 0.02 0.06
#> TCGA.NH.A5IV.01 6 0.1671 0.8344 0.00 0.10 0.00 0.00 0.00 0.90 0.00
#> TCGA.G4.6306.01 6 0.6572 0.1302 0.12 0.16 0.00 0.00 0.00 0.40 0.32
#> TCGA.AD.A5EK.01 1 0.3525 0.9087 0.56 0.00 0.44 0.00 0.00 0.00 0.00
#> TCGA.CK.5915.01 1 0.4669 0.8120 0.52 0.00 0.40 0.00 0.00 0.00 0.08
#> TCGA.AY.6197.01 4 0.0000 0.8565 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.G4.6294.01 5 0.1671 0.7722 0.10 0.00 0.00 0.00 0.90 0.00 0.00
#> TCGA.CM.6172.01 3 0.5549 0.3469 0.20 0.00 0.62 0.00 0.12 0.02 0.04
#> TCGA.DM.A28A.01 3 0.1166 0.5420 0.06 0.00 0.94 0.00 0.00 0.00 0.00
#> TCGA.EI.7002.01 5 0.1166 0.7793 0.06 0.00 0.00 0.00 0.94 0.00 0.00
#> TCGA.QG.A5Z1.01 7 0.4500 0.1745 0.02 0.22 0.08 0.00 0.00 0.00 0.68
#> TCGA.DM.A28H.01 4 0.0504 0.8481 0.00 0.00 0.00 0.98 0.00 0.02 0.00
#> TCGA.DM.A28M.01 6 0.1671 0.8344 0.00 0.10 0.00 0.00 0.00 0.90 0.00
#> TCGA.DM.A288.01 4 0.6261 0.2670 0.08 0.30 0.00 0.50 0.00 0.10 0.02
#> TCGA.F4.6855.01 5 0.6585 0.2740 0.12 0.02 0.00 0.00 0.46 0.10 0.30
#> TCGA.NH.A6GA.01 2 0.0504 0.7322 0.00 0.98 0.00 0.02 0.00 0.00 0.00
#> TCGA.NH.A50V.01 4 0.0000 0.8565 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.CK.6747.01 6 0.2081 0.8018 0.00 0.14 0.00 0.00 0.00 0.86 0.00
#> TCGA.DM.A28K.01 6 0.1671 0.8344 0.00 0.10 0.00 0.00 0.00 0.90 0.00
#> TCGA.AA.3655.01 7 0.7215 -0.0369 0.12 0.02 0.00 0.00 0.28 0.26 0.32
#> TCGA.AZ.5407.01 4 0.3887 0.7508 0.08 0.06 0.00 0.80 0.00 0.04 0.02
#> TCGA.QG.A5YV.01 5 0.5755 0.4683 0.12 0.02 0.00 0.00 0.58 0.04 0.24
#> TCGA.CM.6166.01 5 0.5840 0.4418 0.12 0.02 0.00 0.00 0.56 0.04 0.26
#> TCGA.D5.5540.01 3 0.0504 0.6010 0.00 0.00 0.98 0.00 0.00 0.00 0.02
#> TCGA.G5.6233.01 4 0.0000 0.8565 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.CA.6719.01 2 0.3221 0.4395 0.00 0.68 0.00 0.00 0.00 0.00 0.32
#> TCGA.D5.5537.01 2 0.0504 0.7322 0.00 0.98 0.00 0.02 0.00 0.00 0.00
#> TCGA.AG.3592.01 7 0.3413 0.1237 0.00 0.38 0.00 0.00 0.00 0.00 0.62
#> TCGA.CM.6678.01 5 0.3061 0.7195 0.06 0.00 0.00 0.00 0.84 0.02 0.08
#> TCGA.CK.5914.01 3 0.3606 0.4655 0.02 0.00 0.68 0.00 0.00 0.00 0.30
#> TCGA.AA.3660.01 7 0.3459 0.0843 0.00 0.40 0.00 0.00 0.00 0.00 0.60
#> TCGA.CM.4747.01 2 0.0504 0.7322 0.00 0.98 0.00 0.02 0.00 0.00 0.00
#> TCGA.EF.5831.01 3 0.3994 0.3036 0.02 0.00 0.50 0.00 0.00 0.00 0.48
cbind(get_classes(res, k = 8), get_membership(res, k = 8))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7 p8
#> TCGA.G4.6303.01 5 0.0471 0.93540 0.00 0.00 0.00 0.00 0.98 0.00 0.02 0.00
#> TCGA.T9.A92H.01 5 0.0000 0.93813 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.F5.6571.01 5 0.1557 0.92258 0.00 0.00 0.00 0.00 0.92 0.02 0.00 0.06
#> TCGA.CI.6622.01 5 0.2348 0.91134 0.00 0.00 0.00 0.00 0.88 0.04 0.02 0.06
#> TCGA.EI.6512.01 2 0.3808 0.12789 0.02 0.66 0.00 0.00 0.00 0.00 0.30 0.02
#> TCGA.AA.3509.01 5 0.2348 0.91134 0.00 0.00 0.00 0.00 0.88 0.04 0.02 0.06
#> TCGA.EI.6883.01 3 0.3170 0.62306 0.20 0.00 0.76 0.00 0.00 0.00 0.04 0.00
#> TCGA.CM.5860.01 2 0.5859 0.00218 0.06 0.48 0.00 0.32 0.00 0.00 0.12 0.02
#> TCGA.A6.6780.01 4 0.0000 0.86738 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DM.A1D8.01 4 0.0808 0.85880 0.00 0.00 0.00 0.96 0.00 0.00 0.04 0.00
#> TCGA.A6.6138.01 2 0.2406 0.49246 0.00 0.80 0.00 0.20 0.00 0.00 0.00 0.00
#> TCGA.DM.A1D4.01 4 0.3270 0.77910 0.06 0.00 0.00 0.80 0.00 0.00 0.12 0.02
#> TCGA.AY.A69D.01 3 0.1765 0.70075 0.12 0.00 0.88 0.00 0.00 0.00 0.00 0.00
#> TCGA.CA.6716.01 1 0.2406 0.73600 0.80 0.00 0.20 0.00 0.00 0.00 0.00 0.00
#> TCGA.AH.6644.01 8 0.1563 0.84497 0.00 0.00 0.00 0.00 0.10 0.00 0.00 0.90
#> TCGA.AH.6643.01 5 0.1557 0.90278 0.06 0.00 0.00 0.00 0.92 0.00 0.02 0.00
#> TCGA.A6.5656.01 5 0.0941 0.93451 0.02 0.00 0.00 0.00 0.96 0.00 0.02 0.00
#> TCGA.F4.6806.01 2 0.0471 0.63312 0.00 0.98 0.00 0.00 0.00 0.00 0.02 0.00
#> TCGA.5M.AAT4.01 2 0.4968 -0.30145 0.02 0.52 0.00 0.00 0.00 0.06 0.38 0.02
#> TCGA.EI.6514.01 5 0.1275 0.92788 0.02 0.00 0.00 0.00 0.94 0.00 0.00 0.04
#> TCGA.DM.A282.01 8 0.2025 0.83693 0.00 0.00 0.00 0.00 0.10 0.02 0.00 0.88
#> TCGA.DM.A1HA.01 1 0.4994 0.24011 0.50 0.00 0.00 0.40 0.00 0.02 0.06 0.02
#> TCGA.A6.6652.01 5 0.0471 0.93540 0.00 0.00 0.00 0.00 0.98 0.00 0.02 0.00
#> TCGA.A6.6650.01 8 0.3131 0.77347 0.06 0.00 0.00 0.00 0.04 0.04 0.02 0.84
#> TCGA.AD.6899.01 2 0.0000 0.64094 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.A6.A56B.01 3 0.0941 0.74814 0.00 0.00 0.96 0.00 0.00 0.02 0.02 0.00
#> TCGA.NH.A5IV.01 6 0.1341 1.00000 0.00 0.08 0.00 0.00 0.00 0.92 0.00 0.00
#> TCGA.G4.6306.01 8 0.6053 0.31273 0.06 0.08 0.00 0.00 0.00 0.12 0.18 0.56
#> TCGA.AD.A5EK.01 1 0.2406 0.73600 0.80 0.00 0.20 0.00 0.00 0.00 0.00 0.00
#> TCGA.CK.5915.01 1 0.3431 0.69657 0.74 0.00 0.20 0.00 0.00 0.00 0.06 0.00
#> TCGA.AY.6197.01 4 0.0000 0.86738 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.G4.6294.01 5 0.1275 0.93329 0.00 0.00 0.00 0.00 0.94 0.04 0.02 0.00
#> TCGA.CM.6172.01 3 0.3078 0.65485 0.06 0.00 0.82 0.00 0.10 0.02 0.00 0.00
#> TCGA.DM.A28A.01 3 0.1563 0.71613 0.10 0.00 0.90 0.00 0.00 0.00 0.00 0.00
#> TCGA.EI.7002.01 5 0.1275 0.93329 0.00 0.00 0.00 0.00 0.94 0.04 0.02 0.00
#> TCGA.QG.A5Z1.01 7 0.4224 0.58309 0.00 0.14 0.14 0.00 0.00 0.02 0.70 0.00
#> TCGA.DM.A28H.01 4 0.1607 0.83887 0.00 0.00 0.00 0.92 0.00 0.00 0.04 0.04
#> TCGA.DM.A28M.01 6 0.1341 1.00000 0.00 0.08 0.00 0.00 0.00 0.92 0.00 0.00
#> TCGA.DM.A288.01 4 0.6219 0.54901 0.08 0.18 0.00 0.54 0.00 0.02 0.16 0.02
#> TCGA.F4.6855.01 8 0.1563 0.84497 0.00 0.00 0.00 0.00 0.10 0.00 0.00 0.90
#> TCGA.NH.A6GA.01 2 0.0471 0.63223 0.02 0.98 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.NH.A50V.01 4 0.0000 0.86738 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.CK.6747.01 6 0.1341 1.00000 0.00 0.08 0.00 0.00 0.00 0.92 0.00 0.00
#> TCGA.DM.A28K.01 6 0.1341 1.00000 0.00 0.08 0.00 0.00 0.00 0.92 0.00 0.00
#> TCGA.AA.3655.01 8 0.2807 0.82839 0.04 0.00 0.00 0.00 0.10 0.00 0.02 0.84
#> TCGA.AZ.5407.01 4 0.4202 0.74778 0.06 0.04 0.00 0.74 0.00 0.00 0.14 0.02
#> TCGA.QG.A5YV.01 8 0.1563 0.84497 0.00 0.00 0.00 0.00 0.10 0.00 0.00 0.90
#> TCGA.CM.6166.01 8 0.2025 0.83986 0.02 0.00 0.00 0.00 0.10 0.00 0.00 0.88
#> TCGA.D5.5540.01 3 0.0000 0.74897 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.G5.6233.01 4 0.0000 0.86738 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.CA.6719.01 2 0.4105 -0.27768 0.02 0.54 0.00 0.00 0.00 0.00 0.42 0.02
#> TCGA.D5.5537.01 2 0.0000 0.64094 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AG.3592.01 7 0.3922 0.70379 0.00 0.30 0.00 0.00 0.00 0.00 0.64 0.06
#> TCGA.CM.6678.01 8 0.4886 0.05239 0.06 0.00 0.00 0.00 0.44 0.04 0.00 0.46
#> TCGA.CK.5914.01 3 0.3095 0.64680 0.00 0.00 0.74 0.00 0.00 0.02 0.24 0.00
#> TCGA.AA.3660.01 7 0.4518 0.61321 0.02 0.36 0.00 0.00 0.00 0.00 0.56 0.06
#> TCGA.CM.4747.01 2 0.0000 0.64094 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EF.5831.01 3 0.3737 0.26528 0.00 0.00 0.50 0.00 0.00 0.02 0.48 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: Node0111. Child nodes: Node011111-leaf , Node011112-leaf .
The object with results only for a single top-value method and a single partitioning method can be extracted as:
res = res_rh["01111"]
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 19 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 0.5268 0.474 0.474
#> 3 3 0.713 0.784 0.866 0.2128 0.906 0.802
#> 4 4 0.649 0.699 0.819 0.1330 0.801 0.507
#> 5 5 0.596 0.813 0.768 0.0647 0.889 0.578
#> 6 6 0.760 0.727 0.792 0.0662 0.965 0.824
#> 7 7 0.813 0.628 0.819 0.0404 0.971 0.833
#> 8 8 0.801 0.567 0.785 0.0253 0.965 0.760
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.G4.6303.01 2 0 1 0 1
#> TCGA.T9.A92H.01 1 0 1 1 0
#> TCGA.F5.6571.01 2 0 1 0 1
#> TCGA.CI.6622.01 1 0 1 1 0
#> TCGA.AA.3509.01 2 0 1 0 1
#> TCGA.AH.6644.01 1 0 1 1 0
#> TCGA.AH.6643.01 1 0 1 1 0
#> TCGA.A6.5656.01 1 0 1 1 0
#> TCGA.EI.6514.01 2 0 1 0 1
#> TCGA.DM.A282.01 2 0 1 0 1
#> TCGA.A6.6652.01 1 0 1 1 0
#> TCGA.A6.6650.01 2 0 1 0 1
#> TCGA.G4.6294.01 1 0 1 1 0
#> TCGA.EI.7002.01 1 0 1 1 0
#> TCGA.F4.6855.01 2 0 1 0 1
#> TCGA.AA.3655.01 1 0 1 1 0
#> TCGA.QG.A5YV.01 2 0 1 0 1
#> TCGA.CM.6166.01 2 0 1 0 1
#> TCGA.CM.6678.01 2 0 1 0 1
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.G4.6303.01 3 0.583 1.000 0.00 0.34 0.66
#> TCGA.T9.A92H.01 1 0.000 0.885 1.00 0.00 0.00
#> TCGA.F5.6571.01 2 0.540 0.474 0.00 0.72 0.28
#> TCGA.CI.6622.01 1 0.583 0.750 0.66 0.00 0.34
#> TCGA.AA.3509.01 2 0.540 0.474 0.00 0.72 0.28
#> TCGA.AH.6644.01 1 0.583 0.750 0.66 0.00 0.34
#> TCGA.AH.6643.01 1 0.000 0.885 1.00 0.00 0.00
#> TCGA.A6.5656.01 1 0.000 0.885 1.00 0.00 0.00
#> TCGA.EI.6514.01 3 0.583 1.000 0.00 0.34 0.66
#> TCGA.DM.A282.01 2 0.000 0.784 0.00 1.00 0.00
#> TCGA.A6.6652.01 1 0.000 0.885 1.00 0.00 0.00
#> TCGA.A6.6650.01 2 0.000 0.784 0.00 1.00 0.00
#> TCGA.G4.6294.01 1 0.000 0.885 1.00 0.00 0.00
#> TCGA.EI.7002.01 1 0.000 0.885 1.00 0.00 0.00
#> TCGA.F4.6855.01 2 0.540 0.474 0.00 0.72 0.28
#> TCGA.AA.3655.01 1 0.583 0.750 0.66 0.00 0.34
#> TCGA.QG.A5YV.01 2 0.000 0.784 0.00 1.00 0.00
#> TCGA.CM.6166.01 2 0.000 0.784 0.00 1.00 0.00
#> TCGA.CM.6678.01 2 0.000 0.784 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.G4.6303.01 3 0.700 0.528 0.00 0.20 0.58 0.22
#> TCGA.T9.A92H.01 1 0.000 0.963 1.00 0.00 0.00 0.00
#> TCGA.F5.6571.01 2 0.499 -0.402 0.00 0.52 0.48 0.00
#> TCGA.CI.6622.01 4 0.380 0.984 0.22 0.00 0.00 0.78
#> TCGA.AA.3509.01 3 0.499 0.169 0.00 0.48 0.52 0.00
#> TCGA.AH.6644.01 4 0.447 0.980 0.22 0.00 0.02 0.76
#> TCGA.AH.6643.01 1 0.000 0.963 1.00 0.00 0.00 0.00
#> TCGA.A6.5656.01 1 0.234 0.895 0.90 0.00 0.10 0.00
#> TCGA.EI.6514.01 3 0.700 0.528 0.00 0.20 0.58 0.22
#> TCGA.DM.A282.01 2 0.292 0.713 0.00 0.86 0.14 0.00
#> TCGA.A6.6652.01 1 0.000 0.963 1.00 0.00 0.00 0.00
#> TCGA.A6.6650.01 2 0.000 0.756 0.00 1.00 0.00 0.00
#> TCGA.G4.6294.01 1 0.201 0.914 0.92 0.00 0.08 0.00
#> TCGA.EI.7002.01 1 0.000 0.963 1.00 0.00 0.00 0.00
#> TCGA.F4.6855.01 3 0.499 0.169 0.00 0.48 0.52 0.00
#> TCGA.AA.3655.01 4 0.447 0.980 0.22 0.00 0.02 0.76
#> TCGA.QG.A5YV.01 2 0.000 0.756 0.00 1.00 0.00 0.00
#> TCGA.CM.6166.01 2 0.292 0.713 0.00 0.86 0.14 0.00
#> TCGA.CM.6678.01 2 0.000 0.756 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.G4.6303.01 3 0.2732 0.899 0.00 0.16 0.84 0.00 0.00
#> TCGA.T9.A92H.01 1 0.0000 0.911 1.00 0.00 0.00 0.00 0.00
#> TCGA.F5.6571.01 2 0.6788 0.512 0.00 0.60 0.14 0.08 0.18
#> TCGA.CI.6622.01 4 0.2280 0.946 0.12 0.00 0.00 0.88 0.00
#> TCGA.AA.3509.01 2 0.3521 0.646 0.00 0.82 0.14 0.04 0.00
#> TCGA.AH.6644.01 4 0.4794 0.902 0.12 0.00 0.02 0.76 0.10
#> TCGA.AH.6643.01 1 0.0609 0.905 0.98 0.00 0.02 0.00 0.00
#> TCGA.A6.5656.01 1 0.4637 0.741 0.74 0.00 0.10 0.00 0.16
#> TCGA.EI.6514.01 3 0.5055 0.897 0.00 0.16 0.74 0.06 0.04
#> TCGA.DM.A282.01 2 0.2516 0.437 0.00 0.86 0.00 0.00 0.14
#> TCGA.A6.6652.01 1 0.0000 0.911 1.00 0.00 0.00 0.00 0.00
#> TCGA.A6.6650.01 5 0.4287 1.000 0.00 0.46 0.00 0.00 0.54
#> TCGA.G4.6294.01 1 0.3109 0.796 0.80 0.00 0.00 0.00 0.20
#> TCGA.EI.7002.01 1 0.0000 0.911 1.00 0.00 0.00 0.00 0.00
#> TCGA.F4.6855.01 2 0.3521 0.646 0.00 0.82 0.14 0.04 0.00
#> TCGA.AA.3655.01 4 0.2873 0.943 0.12 0.00 0.02 0.86 0.00
#> TCGA.QG.A5YV.01 5 0.4287 1.000 0.00 0.46 0.00 0.00 0.54
#> TCGA.CM.6166.01 2 0.2516 0.437 0.00 0.86 0.00 0.00 0.14
#> TCGA.CM.6678.01 5 0.4287 1.000 0.00 0.46 0.00 0.00 0.54
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> TCGA.G4.6303.01 3 0.4420 0.4830 0.00 0.00 0.62 0.00 0.34 0.04
#> TCGA.T9.A92H.01 1 0.0000 0.8491 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.F5.6571.01 3 0.6764 -0.0519 0.00 0.22 0.44 0.02 0.02 0.30
#> TCGA.CI.6622.01 4 0.0937 0.9347 0.04 0.00 0.00 0.96 0.00 0.00
#> TCGA.AA.3509.01 2 0.5239 0.6401 0.00 0.68 0.12 0.00 0.04 0.16
#> TCGA.AH.6644.01 4 0.3258 0.8918 0.04 0.10 0.02 0.84 0.00 0.00
#> TCGA.AH.6643.01 1 0.0937 0.8388 0.96 0.04 0.00 0.00 0.00 0.00
#> TCGA.A6.5656.01 1 0.4926 0.6315 0.64 0.12 0.00 0.00 0.24 0.00
#> TCGA.EI.6514.01 3 0.0937 0.5464 0.00 0.00 0.96 0.00 0.00 0.04
#> TCGA.DM.A282.01 2 0.4310 0.6043 0.00 0.54 0.00 0.02 0.00 0.44
#> TCGA.A6.6652.01 1 0.0547 0.8502 0.98 0.00 0.00 0.00 0.02 0.00
#> TCGA.A6.6650.01 6 0.0000 1.0000 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.G4.6294.01 1 0.3797 0.5760 0.58 0.00 0.00 0.00 0.42 0.00
#> TCGA.EI.7002.01 1 0.0547 0.8502 0.98 0.00 0.00 0.00 0.02 0.00
#> TCGA.F4.6855.01 2 0.5239 0.6401 0.00 0.68 0.12 0.00 0.04 0.16
#> TCGA.AA.3655.01 4 0.2020 0.9265 0.04 0.02 0.02 0.92 0.00 0.00
#> TCGA.QG.A5YV.01 6 0.0000 1.0000 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.CM.6166.01 2 0.4310 0.6043 0.00 0.54 0.00 0.02 0.00 0.44
#> TCGA.CM.6678.01 6 0.0000 1.0000 0.00 0.00 0.00 0.00 0.00 1.00
cbind(get_classes(res, k = 7), get_membership(res, k = 7))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7
#> TCGA.G4.6303.01 3 0.5678 0.3482 0.00 0.26 0.54 0.04 0.00 0.00 0.16
#> TCGA.T9.A92H.01 1 0.0000 0.7811 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.F5.6571.01 3 0.5223 0.0123 0.00 0.00 0.52 0.00 0.36 0.10 0.02
#> TCGA.CI.6622.01 4 0.0863 0.9090 0.04 0.00 0.00 0.96 0.00 0.00 0.00
#> TCGA.AA.3509.01 5 0.3911 0.6635 0.00 0.24 0.06 0.00 0.70 0.00 0.00
#> TCGA.AH.6644.01 4 0.4421 0.8389 0.04 0.08 0.00 0.78 0.04 0.04 0.02
#> TCGA.AH.6643.01 1 0.1363 0.7337 0.94 0.00 0.00 0.00 0.02 0.00 0.04
#> TCGA.A6.5656.01 1 0.4244 -0.0113 0.54 0.42 0.00 0.00 0.00 0.00 0.04
#> TCGA.EI.6514.01 3 0.0000 0.4893 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DM.A282.01 5 0.2259 0.6694 0.00 0.00 0.00 0.00 0.84 0.16 0.00
#> TCGA.A6.6652.01 1 0.0000 0.7811 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.A6.6650.01 6 0.3086 0.8514 0.00 0.00 0.00 0.00 0.04 0.80 0.16
#> TCGA.G4.6294.01 7 0.3496 0.0000 0.42 0.00 0.00 0.00 0.00 0.00 0.58
#> TCGA.EI.7002.01 1 0.0000 0.7811 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.F4.6855.01 5 0.3911 0.6635 0.00 0.24 0.06 0.00 0.70 0.00 0.00
#> TCGA.AA.3655.01 4 0.1718 0.9048 0.04 0.00 0.00 0.92 0.00 0.00 0.04
#> TCGA.QG.A5YV.01 6 0.0863 0.9286 0.00 0.00 0.00 0.00 0.04 0.96 0.00
#> TCGA.CM.6166.01 5 0.2745 0.6590 0.00 0.00 0.00 0.00 0.82 0.16 0.02
#> TCGA.CM.6678.01 6 0.0863 0.9286 0.00 0.00 0.00 0.00 0.04 0.96 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.G4.6303.01 3 0.0471 0.402 0.00 0.00 0.98 0.00 0.00 0.02 0.00 0.00
#> TCGA.T9.A92H.01 1 0.0000 0.934 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.F5.6571.01 8 0.3528 0.000 0.00 0.00 0.00 0.00 0.18 0.08 0.00 0.74
#> TCGA.CI.6622.01 4 0.0471 0.826 0.02 0.00 0.00 0.98 0.00 0.00 0.00 0.00
#> TCGA.AA.3509.01 5 0.0471 0.469 0.00 0.00 0.00 0.00 0.98 0.02 0.00 0.00
#> TCGA.AH.6644.01 4 0.4713 0.705 0.02 0.04 0.00 0.68 0.00 0.00 0.08 0.18
#> TCGA.AH.6643.01 1 0.2591 0.783 0.86 0.00 0.02 0.00 0.00 0.00 0.08 0.04
#> TCGA.A6.5656.01 2 0.3449 0.000 0.32 0.66 0.00 0.00 0.00 0.00 0.02 0.00
#> TCGA.EI.6514.01 3 0.5465 0.130 0.00 0.04 0.44 0.02 0.00 0.02 0.04 0.44
#> TCGA.DM.A282.01 5 0.6745 0.419 0.00 0.20 0.00 0.00 0.42 0.22 0.04 0.12
#> TCGA.A6.6652.01 1 0.0000 0.934 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.A6.6650.01 6 0.3503 0.761 0.00 0.02 0.00 0.00 0.00 0.78 0.12 0.08
#> TCGA.G4.6294.01 7 0.3746 0.000 0.32 0.04 0.00 0.00 0.00 0.00 0.64 0.00
#> TCGA.EI.7002.01 1 0.0000 0.934 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.F4.6855.01 5 0.0471 0.469 0.00 0.00 0.00 0.00 0.98 0.02 0.00 0.00
#> TCGA.AA.3655.01 4 0.2532 0.811 0.02 0.04 0.00 0.88 0.02 0.00 0.00 0.04
#> TCGA.QG.A5YV.01 6 0.0000 0.891 0.00 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.CM.6166.01 5 0.6745 0.419 0.00 0.20 0.00 0.00 0.42 0.22 0.04 0.12
#> TCGA.CM.6678.01 6 0.0000 0.891 0.00 0.00 0.00 0.00 0.00 1.00 0.00 0.00
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
consensus_heatmap(res, k = 7)
consensus_heatmap(res, k = 8)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
membership_heatmap(res, k = 7)
membership_heatmap(res, k = 8)
As soon as the classes for columns are determined, the signatures that are significantly different between subgroups can be looked for. Following are the heatmaps for signatures.
get_signatures(res, k = 2)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
get_signatures(res, k = 7)
get_signatures(res, k = 8)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. To get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows (which is done by automatically selecting number of clusters).If there are too many signatures, top_signatures = ... can be set to only show the
signatures with the highest FDRs:
# code only for demonstration
# e.g. to show the top 500 most significant rows
tb = get_signature(res, k = ..., top_signatures = 500)
If the signatures are defined as these which are uniquely high in current group, diff_method argument
can be set to "uniquely_high_in_one_group":
# code only for demonstration
tb = get_signature(res, k = ..., diff_method = "uniquely_high_in_one_group")
UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
dimension_reduction(res, k = 7, method = "UMAP")
dimension_reduction(res, k = 8, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
If matrix rows can be associated to genes, consider to use functional_enrichment(res,
...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.
Parent node: Node011. Child nodes: Node01111 , Node01112-leaf , Node01113-leaf , Node01114-leaf , Node01121-leaf , Node01122-leaf , Node01123-leaf , Node01124-leaf , Node01211-leaf , Node01212-leaf , Node01213-leaf , Node01221-leaf , Node01222-leaf , Node01223-leaf , Node01224-leaf , Node02121-leaf , Node02122-leaf , Node02123-leaf , Node04221-leaf , Node04222-leaf , Node04223-leaf .
The object with results only for a single top-value method and a single partitioning method can be extracted as:
res = res_rh["0112"]
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 46 columns.
#> Top rows (1000) are extracted by 'ATC' method.
#> Subgroups are detected by 'kmeans' method.
#> Performed in total 350 partitions by row resampling.
#> Best k for subgroups seems to be 4.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_partitions"
#> [7] "compare_signatures" "consensus_heatmap" "dimension_reduction"
#> [10] "functional_enrichment" "get_anno_col" "get_anno"
#> [13] "get_classes" "get_consensus" "get_matrix"
#> [16] "get_membership" "get_param" "get_signatures"
#> [19] "get_stats" "is_best_k" "is_stable_k"
#> [22] "membership_heatmap" "ncol" "nrow"
#> [25] "plot_ecdf" "predict_classes" "rownames"
#> [28] "select_partition_number" "show" "suggest_best_k"
#> [31] "test_to_known_factors" "top_rows_heatmap"
collect_plots() function collects all the plots made from res for all k (number of subgroups)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
The plots are:
k and the heatmap of
predicted classes for each k.k.k.k.All the plots in panels can be made by individual functions and they are plotted later in this section.
select_partition_number() produces several plots showing different
statistics for choosing “optimized” k. There are following statistics:
k;k, the area increased is defined as \(A_k - A_{k-1}\).The detailed explanations of these statistics can be found in the cola vignette.
Generally speaking, higher 1-PAC score, higher mean silhouette score or higher
concordance corresponds to better partition. Rand index and Jaccard index
measure how similar the current partition is compared to partition with k-1.
If they are too similar, we won't accept k is better than k-1.
select_partition_number(res)
The numeric values for all these statistics can be obtained by get_stats().
get_stats(res)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> 2 2 1.000 0.980 0.991 0.4826 0.513 0.513
#> 3 3 0.762 0.785 0.904 0.3148 0.768 0.577
#> 4 4 0.928 0.953 0.959 0.1704 0.784 0.470
#> 5 5 0.815 0.720 0.806 0.0630 0.969 0.876
#> 6 6 0.762 0.694 0.764 0.0396 0.954 0.799
#> 7 7 0.811 0.637 0.790 0.0266 0.947 0.737
#> 8 8 0.766 0.621 0.789 0.0262 0.957 0.743
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.AG.A026.01 1 0.000 1.000 1.00 0.00
#> TCGA.AD.6965.01 2 0.722 0.763 0.20 0.80
#> TCGA.A6.5660.01 1 0.000 1.000 1.00 0.00
#> TCGA.CM.5862.01 1 0.000 1.000 1.00 0.00
#> TCGA.QG.A5YX.01 1 0.000 1.000 1.00 0.00
#> TCGA.AG.A036.01 1 0.000 1.000 1.00 0.00
#> TCGA.RU.A8FL.01 1 0.000 1.000 1.00 0.00
#> TCGA.AZ.6599.01 2 0.000 0.975 0.00 1.00
#> TCGA.CM.4750.01 1 0.000 1.000 1.00 0.00
#> TCGA.CM.6677.01 1 0.000 1.000 1.00 0.00
#> TCGA.F5.6814.01 1 0.000 1.000 1.00 0.00
#> TCGA.DM.A28F.01 1 0.000 1.000 1.00 0.00
#> TCGA.DM.A0X9.01 2 0.000 0.975 0.00 1.00
#> TCGA.NH.A6GB.01 2 0.760 0.734 0.22 0.78
#> TCGA.NH.A50U.01 2 0.000 0.975 0.00 1.00
#> TCGA.CM.5864.01 1 0.000 1.000 1.00 0.00
#> TCGA.AG.3742.01 1 0.000 1.000 1.00 0.00
#> TCGA.A6.5666.01 1 0.000 1.000 1.00 0.00
#> TCGA.AG.3591.01 2 0.000 0.975 0.00 1.00
#> TCGA.EI.6510.01 2 0.000 0.975 0.00 1.00
#> TCGA.DY.A1DG.01 1 0.000 1.000 1.00 0.00
#> TCGA.AG.4021.01 2 0.000 0.975 0.00 1.00
#> TCGA.DM.A1D9.01 2 0.000 0.975 0.00 1.00
#> TCGA.CM.4744.01 2 0.000 0.975 0.00 1.00
#> TCGA.SS.A7HO.01 1 0.000 1.000 1.00 0.00
#> TCGA.NH.A50T.01 1 0.000 1.000 1.00 0.00
#> TCGA.D5.5539.01 2 0.000 0.975 0.00 1.00
#> TCGA.AY.A54L.01 2 0.000 0.975 0.00 1.00
#> TCGA.DC.5337.01 1 0.000 1.000 1.00 0.00
#> TCGA.QG.A5YW.01 1 0.000 1.000 1.00 0.00
#> TCGA.EI.6882.01 2 0.000 0.975 0.00 1.00
#> TCGA.A6.2677.01 1 0.000 1.000 1.00 0.00
#> TCGA.AA.3502.01 2 0.000 0.975 0.00 1.00
#> TCGA.AA.3496.01 1 0.000 1.000 1.00 0.00
#> TCGA.CL.5918.01 1 0.000 1.000 1.00 0.00
#> TCGA.AY.A71X.01 2 0.000 0.975 0.00 1.00
#> TCGA.AH.6549.01 1 0.000 1.000 1.00 0.00
#> TCGA.AH.6897.01 1 0.000 1.000 1.00 0.00
#> TCGA.4T.AA8H.01 2 0.000 0.975 0.00 1.00
#> TCGA.EI.6508.01 1 0.000 1.000 1.00 0.00
#> TCGA.D5.6532.01 1 0.000 1.000 1.00 0.00
#> TCGA.A6.2680.01 1 0.000 1.000 1.00 0.00
#> TCGA.CM.6680.01 2 0.000 0.975 0.00 1.00
#> TCGA.DM.A28G.01 2 0.000 0.975 0.00 1.00
#> TCGA.D5.6537.01 1 0.000 1.000 1.00 0.00
#> TCGA.DY.A1DD.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.AG.A026.01 1 0.0000 0.916 1.00 0.00 0.00
#> TCGA.AD.6965.01 3 0.0000 0.745 0.00 0.00 1.00
#> TCGA.A6.5660.01 1 0.0000 0.916 1.00 0.00 0.00
#> TCGA.CM.5862.01 1 0.0000 0.916 1.00 0.00 0.00
#> TCGA.QG.A5YX.01 3 0.6651 0.606 0.34 0.02 0.64
#> TCGA.AG.A036.01 1 0.0000 0.916 1.00 0.00 0.00
#> TCGA.RU.A8FL.01 1 0.0000 0.916 1.00 0.00 0.00
#> TCGA.AZ.6599.01 2 0.0892 0.914 0.00 0.98 0.02
#> TCGA.CM.4750.01 1 0.0000 0.916 1.00 0.00 0.00
#> TCGA.CM.6677.01 3 0.5016 0.727 0.24 0.00 0.76
#> TCGA.F5.6814.01 3 0.5948 0.581 0.36 0.00 0.64
#> TCGA.DM.A28F.01 1 0.6302 -0.188 0.52 0.00 0.48
#> TCGA.DM.A0X9.01 2 0.5216 0.803 0.00 0.74 0.26
#> TCGA.NH.A6GB.01 3 0.0000 0.745 0.00 0.00 1.00
#> TCGA.NH.A50U.01 2 0.4796 0.822 0.00 0.78 0.22
#> TCGA.CM.5864.01 1 0.5948 0.276 0.64 0.00 0.36
#> TCGA.AG.3742.01 3 0.5016 0.727 0.24 0.00 0.76
#> TCGA.A6.5666.01 1 0.0000 0.916 1.00 0.00 0.00
#> TCGA.AG.3591.01 2 0.0000 0.911 0.00 1.00 0.00
#> TCGA.EI.6510.01 2 0.4796 0.822 0.00 0.78 0.22
#> TCGA.DY.A1DG.01 1 0.0000 0.916 1.00 0.00 0.00
#> TCGA.AG.4021.01 3 0.1529 0.720 0.00 0.04 0.96
#> TCGA.DM.A1D9.01 2 0.5016 0.806 0.00 0.76 0.24
#> TCGA.CM.4744.01 3 0.0000 0.745 0.00 0.00 1.00
#> TCGA.SS.A7HO.01 1 0.0000 0.916 1.00 0.00 0.00
#> TCGA.NH.A50T.01 1 0.0000 0.916 1.00 0.00 0.00
#> TCGA.D5.5539.01 2 0.0000 0.911 0.00 1.00 0.00
#> TCGA.AY.A54L.01 3 0.1529 0.720 0.00 0.04 0.96
#> TCGA.DC.5337.01 1 0.0892 0.899 0.98 0.00 0.02
#> TCGA.QG.A5YW.01 3 0.5948 0.581 0.36 0.00 0.64
#> TCGA.EI.6882.01 2 0.0892 0.914 0.00 0.98 0.02
#> TCGA.A6.2677.01 1 0.0000 0.916 1.00 0.00 0.00
#> TCGA.AA.3502.01 2 0.0892 0.914 0.00 0.98 0.02
#> TCGA.AA.3496.01 1 0.0000 0.916 1.00 0.00 0.00
#> TCGA.CL.5918.01 1 0.0000 0.916 1.00 0.00 0.00
#> TCGA.AY.A71X.01 2 0.0892 0.914 0.00 0.98 0.02
#> TCGA.AH.6549.01 1 0.0000 0.916 1.00 0.00 0.00
#> TCGA.AH.6897.01 1 0.0000 0.916 1.00 0.00 0.00
#> TCGA.4T.AA8H.01 2 0.0892 0.914 0.00 0.98 0.02
#> TCGA.EI.6508.01 1 0.6302 -0.184 0.52 0.00 0.48
#> TCGA.D5.6532.01 1 0.2066 0.859 0.94 0.00 0.06
#> TCGA.A6.2680.01 3 0.5216 0.710 0.26 0.00 0.74
#> TCGA.CM.6680.01 2 0.0000 0.911 0.00 1.00 0.00
#> TCGA.DM.A28G.01 3 0.2066 0.717 0.00 0.06 0.94
#> TCGA.D5.6537.01 1 0.0000 0.916 1.00 0.00 0.00
#> TCGA.DY.A1DD.01 1 0.0000 0.916 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.AG.A026.01 1 0.0707 0.982 0.98 0.00 0.02 0.00
#> TCGA.AD.6965.01 4 0.2011 0.919 0.00 0.00 0.08 0.92
#> TCGA.A6.5660.01 1 0.0707 0.982 0.98 0.00 0.02 0.00
#> TCGA.CM.5862.01 1 0.0000 0.986 1.00 0.00 0.00 0.00
#> TCGA.QG.A5YX.01 3 0.3198 0.892 0.04 0.00 0.88 0.08
#> TCGA.AG.A036.01 1 0.0000 0.986 1.00 0.00 0.00 0.00
#> TCGA.RU.A8FL.01 1 0.0000 0.986 1.00 0.00 0.00 0.00
#> TCGA.AZ.6599.01 2 0.0000 0.994 0.00 1.00 0.00 0.00
#> TCGA.CM.4750.01 1 0.0707 0.982 0.98 0.00 0.02 0.00
#> TCGA.CM.6677.01 3 0.2830 0.904 0.04 0.00 0.90 0.06
#> TCGA.F5.6814.01 3 0.1913 0.930 0.04 0.00 0.94 0.02
#> TCGA.DM.A28F.01 3 0.2011 0.930 0.08 0.00 0.92 0.00
#> TCGA.DM.A0X9.01 4 0.1637 0.935 0.00 0.06 0.00 0.94
#> TCGA.NH.A6GB.01 4 0.2011 0.919 0.00 0.00 0.08 0.92
#> TCGA.NH.A50U.01 4 0.1637 0.935 0.00 0.06 0.00 0.94
#> TCGA.CM.5864.01 3 0.2011 0.928 0.08 0.00 0.92 0.00
#> TCGA.AG.3742.01 3 0.2830 0.904 0.04 0.00 0.90 0.06
#> TCGA.A6.5666.01 1 0.0707 0.976 0.98 0.00 0.02 0.00
#> TCGA.AG.3591.01 2 0.0707 0.990 0.00 0.98 0.02 0.00
#> TCGA.EI.6510.01 4 0.1637 0.935 0.00 0.06 0.00 0.94
#> TCGA.DY.A1DG.01 1 0.0000 0.986 1.00 0.00 0.00 0.00
#> TCGA.AG.4021.01 4 0.0000 0.944 0.00 0.00 0.00 1.00
#> TCGA.DM.A1D9.01 4 0.1637 0.935 0.00 0.06 0.00 0.94
#> TCGA.CM.4744.01 4 0.2011 0.919 0.00 0.00 0.08 0.92
#> TCGA.SS.A7HO.01 1 0.0707 0.976 0.98 0.00 0.02 0.00
#> TCGA.NH.A50T.01 1 0.0000 0.986 1.00 0.00 0.00 0.00
#> TCGA.D5.5539.01 2 0.0707 0.990 0.00 0.98 0.02 0.00
#> TCGA.AY.A54L.01 4 0.0000 0.944 0.00 0.00 0.00 1.00
#> TCGA.DC.5337.01 3 0.2647 0.906 0.12 0.00 0.88 0.00
#> TCGA.QG.A5YW.01 3 0.1913 0.930 0.04 0.00 0.94 0.02
#> TCGA.EI.6882.01 2 0.0000 0.994 0.00 1.00 0.00 0.00
#> TCGA.A6.2677.01 1 0.0707 0.982 0.98 0.00 0.02 0.00
#> TCGA.AA.3502.01 2 0.0000 0.994 0.00 1.00 0.00 0.00
#> TCGA.AA.3496.01 1 0.0707 0.982 0.98 0.00 0.02 0.00
#> TCGA.CL.5918.01 3 0.3975 0.766 0.24 0.00 0.76 0.00
#> TCGA.AY.A71X.01 2 0.0000 0.994 0.00 1.00 0.00 0.00
#> TCGA.AH.6549.01 1 0.0707 0.976 0.98 0.00 0.02 0.00
#> TCGA.AH.6897.01 1 0.0707 0.976 0.98 0.00 0.02 0.00
#> TCGA.4T.AA8H.01 2 0.0000 0.994 0.00 1.00 0.00 0.00
#> TCGA.EI.6508.01 3 0.2011 0.930 0.08 0.00 0.92 0.00
#> TCGA.D5.6532.01 3 0.2011 0.928 0.08 0.00 0.92 0.00
#> TCGA.A6.2680.01 3 0.1411 0.918 0.02 0.00 0.96 0.02
#> TCGA.CM.6680.01 2 0.0707 0.990 0.00 0.98 0.02 0.00
#> TCGA.DM.A28G.01 4 0.0000 0.944 0.00 0.00 0.00 1.00
#> TCGA.D5.6537.01 1 0.0707 0.982 0.98 0.00 0.02 0.00
#> TCGA.DY.A1DD.01 1 0.0000 0.986 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.AG.A026.01 1 0.000 0.9005 1.00 0.00 0.00 0.00 0.00
#> TCGA.AD.6965.01 4 0.633 0.6934 0.00 0.00 0.28 0.52 0.20
#> TCGA.A6.5660.01 1 0.327 0.6705 0.78 0.00 0.22 0.00 0.00
#> TCGA.CM.5862.01 1 0.000 0.9005 1.00 0.00 0.00 0.00 0.00
#> TCGA.QG.A5YX.01 5 0.387 0.6067 0.00 0.00 0.14 0.06 0.80
#> TCGA.AG.A036.01 1 0.000 0.9005 1.00 0.00 0.00 0.00 0.00
#> TCGA.RU.A8FL.01 1 0.000 0.9005 1.00 0.00 0.00 0.00 0.00
#> TCGA.AZ.6599.01 2 0.000 0.9837 0.00 1.00 0.00 0.00 0.00
#> TCGA.CM.4750.01 1 0.000 0.9005 1.00 0.00 0.00 0.00 0.00
#> TCGA.CM.6677.01 3 0.000 0.4736 0.00 0.00 1.00 0.00 0.00
#> TCGA.F5.6814.01 3 0.429 -0.0886 0.00 0.00 0.54 0.00 0.46
#> TCGA.DM.A28F.01 5 0.413 0.4995 0.00 0.00 0.38 0.00 0.62
#> TCGA.DM.A0X9.01 4 0.228 0.8253 0.00 0.00 0.00 0.88 0.12
#> TCGA.NH.A6GB.01 4 0.633 0.6934 0.00 0.00 0.28 0.52 0.20
#> TCGA.NH.A50U.01 4 0.000 0.8160 0.00 0.00 0.00 1.00 0.00
#> TCGA.CM.5864.01 3 0.311 0.4782 0.00 0.00 0.80 0.00 0.20
#> TCGA.AG.3742.01 3 0.000 0.4736 0.00 0.00 1.00 0.00 0.00
#> TCGA.A6.5666.01 1 0.356 0.7702 0.74 0.00 0.00 0.00 0.26
#> TCGA.AG.3591.01 2 0.141 0.9501 0.00 0.94 0.00 0.06 0.00
#> TCGA.EI.6510.01 4 0.000 0.8160 0.00 0.00 0.00 1.00 0.00
#> TCGA.DY.A1DG.01 1 0.000 0.9005 1.00 0.00 0.00 0.00 0.00
#> TCGA.AG.4021.01 4 0.369 0.8170 0.00 0.00 0.02 0.78 0.20
#> TCGA.DM.A1D9.01 4 0.000 0.8160 0.00 0.00 0.00 1.00 0.00
#> TCGA.CM.4744.01 4 0.633 0.6934 0.00 0.00 0.28 0.52 0.20
#> TCGA.SS.A7HO.01 1 0.356 0.7702 0.74 0.00 0.00 0.00 0.26
#> TCGA.NH.A50T.01 1 0.000 0.9005 1.00 0.00 0.00 0.00 0.00
#> TCGA.D5.5539.01 2 0.141 0.9501 0.00 0.94 0.00 0.06 0.00
#> TCGA.AY.A54L.01 4 0.351 0.8207 0.00 0.00 0.02 0.80 0.18
#> TCGA.DC.5337.01 5 0.373 0.6053 0.04 0.00 0.16 0.00 0.80
#> TCGA.QG.A5YW.01 5 0.418 0.4425 0.00 0.00 0.40 0.00 0.60
#> TCGA.EI.6882.01 2 0.000 0.9837 0.00 1.00 0.00 0.00 0.00
#> TCGA.A6.2677.01 1 0.000 0.9005 1.00 0.00 0.00 0.00 0.00
#> TCGA.AA.3502.01 2 0.000 0.9837 0.00 1.00 0.00 0.00 0.00
#> TCGA.AA.3496.01 1 0.327 0.7992 0.78 0.00 0.00 0.00 0.22
#> TCGA.CL.5918.01 3 0.380 0.2377 0.30 0.00 0.70 0.00 0.00
#> TCGA.AY.A71X.01 2 0.000 0.9837 0.00 1.00 0.00 0.00 0.00
#> TCGA.AH.6549.01 1 0.356 0.7702 0.74 0.00 0.00 0.00 0.26
#> TCGA.AH.6897.01 1 0.342 0.7854 0.76 0.00 0.00 0.00 0.24
#> TCGA.4T.AA8H.01 2 0.000 0.9837 0.00 1.00 0.00 0.00 0.00
#> TCGA.EI.6508.01 3 0.431 -0.2282 0.00 0.00 0.50 0.00 0.50
#> TCGA.D5.6532.01 3 0.311 0.4782 0.00 0.00 0.80 0.00 0.20
#> TCGA.A6.2680.01 3 0.426 -0.0156 0.00 0.00 0.56 0.00 0.44
#> TCGA.CM.6680.01 2 0.000 0.9837 0.00 1.00 0.00 0.00 0.00
#> TCGA.DM.A28G.01 4 0.000 0.8160 0.00 0.00 0.00 1.00 0.00
#> TCGA.D5.6537.01 1 0.000 0.9005 1.00 0.00 0.00 0.00 0.00
#> TCGA.DY.A1DD.01 1 0.000 0.9005 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.AG.A026.01 1 0.1480 0.775 0.94 0.00 0.00 0.00 0.02 0.04
#> TCGA.AD.6965.01 6 0.5837 0.900 0.00 0.00 0.20 0.34 0.00 0.46
#> TCGA.A6.5660.01 1 0.2790 0.610 0.84 0.00 0.14 0.00 0.00 0.02
#> TCGA.CM.5862.01 1 0.2631 0.787 0.82 0.00 0.00 0.00 0.00 0.18
#> TCGA.QG.A5YX.01 5 0.1807 0.562 0.00 0.00 0.02 0.06 0.92 0.00
#> TCGA.AG.A036.01 1 0.2048 0.786 0.88 0.00 0.00 0.00 0.00 0.12
#> TCGA.RU.A8FL.01 1 0.3315 0.783 0.78 0.00 0.00 0.00 0.02 0.20
#> TCGA.AZ.6599.01 2 0.0000 0.950 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.CM.4750.01 1 0.0000 0.765 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CM.6677.01 3 0.0000 0.638 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.F5.6814.01 5 0.4337 0.421 0.00 0.00 0.48 0.00 0.50 0.02
#> TCGA.DM.A28F.01 5 0.2454 0.622 0.00 0.00 0.16 0.00 0.84 0.00
#> TCGA.DM.A0X9.01 4 0.2260 0.628 0.00 0.00 0.00 0.86 0.00 0.14
#> TCGA.NH.A6GB.01 6 0.6047 0.951 0.00 0.00 0.26 0.34 0.00 0.40
#> TCGA.NH.A50U.01 4 0.0000 0.747 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.CM.5864.01 3 0.4879 0.629 0.12 0.00 0.72 0.00 0.12 0.04
#> TCGA.AG.3742.01 3 0.0000 0.638 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.A6.5666.01 1 0.5285 0.658 0.48 0.00 0.00 0.00 0.10 0.42
#> TCGA.AG.3591.01 2 0.3382 0.900 0.00 0.84 0.00 0.04 0.04 0.08
#> TCGA.EI.6510.01 4 0.0000 0.747 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.DY.A1DG.01 1 0.3315 0.783 0.78 0.00 0.00 0.00 0.02 0.20
#> TCGA.AG.4021.01 4 0.4310 -0.284 0.00 0.00 0.00 0.54 0.02 0.44
#> TCGA.DM.A1D9.01 4 0.0000 0.747 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.CM.4744.01 6 0.6047 0.951 0.00 0.00 0.26 0.34 0.00 0.40
#> TCGA.SS.A7HO.01 1 0.5037 0.658 0.54 0.00 0.00 0.00 0.08 0.38
#> TCGA.NH.A50T.01 1 0.3315 0.783 0.78 0.00 0.00 0.00 0.02 0.20
#> TCGA.D5.5539.01 2 0.3382 0.900 0.00 0.84 0.00 0.04 0.04 0.08
#> TCGA.AY.A54L.01 4 0.3578 0.159 0.00 0.00 0.00 0.66 0.00 0.34
#> TCGA.DC.5337.01 5 0.4495 0.410 0.06 0.00 0.02 0.00 0.72 0.20
#> TCGA.QG.A5YW.01 5 0.2454 0.622 0.00 0.00 0.16 0.00 0.84 0.00
#> TCGA.EI.6882.01 2 0.0000 0.950 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.A6.2677.01 1 0.0547 0.754 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.AA.3502.01 2 0.0000 0.950 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.AA.3496.01 1 0.4503 0.623 0.68 0.00 0.00 0.00 0.08 0.24
#> TCGA.CL.5918.01 3 0.4002 0.503 0.32 0.00 0.66 0.00 0.00 0.02
#> TCGA.AY.A71X.01 2 0.0000 0.950 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.AH.6549.01 1 0.4503 0.623 0.68 0.00 0.00 0.00 0.08 0.24
#> TCGA.AH.6897.01 1 0.5095 0.671 0.50 0.00 0.00 0.00 0.08 0.42
#> TCGA.4T.AA8H.01 2 0.0000 0.950 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.EI.6508.01 5 0.4337 0.421 0.00 0.00 0.48 0.00 0.50 0.02
#> TCGA.D5.6532.01 3 0.4520 0.641 0.12 0.00 0.74 0.00 0.12 0.02
#> TCGA.A6.2680.01 5 0.4337 0.421 0.00 0.00 0.48 0.00 0.50 0.02
#> TCGA.CM.6680.01 2 0.2474 0.916 0.00 0.88 0.00 0.00 0.04 0.08
#> TCGA.DM.A28G.01 4 0.0000 0.747 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.D5.6537.01 1 0.0937 0.774 0.96 0.00 0.00 0.00 0.00 0.04
#> TCGA.DY.A1DD.01 1 0.3315 0.783 0.78 0.00 0.00 0.00 0.02 0.20
cbind(get_classes(res, k = 7), get_membership(res, k = 7))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7
#> TCGA.AG.A026.01 1 0.0863 0.541 0.96 0.00 0.00 0.00 0.00 0.00 0.04
#> TCGA.AD.6965.01 6 0.1671 0.857 0.00 0.00 0.00 0.10 0.00 0.90 0.00
#> TCGA.A6.5660.01 1 0.2906 0.323 0.80 0.00 0.18 0.00 0.00 0.00 0.02
#> TCGA.CM.5862.01 1 0.2906 0.482 0.80 0.00 0.00 0.00 0.00 0.02 0.18
#> TCGA.QG.A5YX.01 5 0.1718 0.621 0.00 0.00 0.00 0.04 0.92 0.00 0.04
#> TCGA.AG.A036.01 1 0.2745 0.498 0.82 0.00 0.00 0.00 0.00 0.02 0.16
#> TCGA.RU.A8FL.01 1 0.3307 0.434 0.74 0.00 0.00 0.00 0.00 0.02 0.24
#> TCGA.AZ.6599.01 2 0.0000 0.879 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CM.4750.01 1 0.0000 0.535 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CM.6677.01 3 0.3630 0.748 0.00 0.00 0.80 0.00 0.04 0.10 0.06
#> TCGA.F5.6814.01 5 0.4923 0.425 0.00 0.00 0.38 0.00 0.54 0.04 0.04
#> TCGA.DM.A28F.01 5 0.1363 0.639 0.00 0.00 0.04 0.00 0.94 0.02 0.00
#> TCGA.DM.A0X9.01 4 0.3047 0.466 0.00 0.00 0.00 0.72 0.00 0.28 0.00
#> TCGA.NH.A6GB.01 6 0.3289 0.855 0.00 0.00 0.06 0.10 0.00 0.82 0.02
#> TCGA.NH.A50U.01 4 0.0000 0.908 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.CM.5864.01 3 0.3546 0.754 0.06 0.00 0.82 0.00 0.08 0.02 0.02
#> TCGA.AG.3742.01 3 0.3630 0.748 0.00 0.00 0.80 0.00 0.04 0.10 0.06
#> TCGA.A6.5666.01 7 0.3525 0.916 0.44 0.00 0.00 0.00 0.00 0.00 0.56
#> TCGA.AG.3591.01 2 0.4895 0.772 0.00 0.66 0.04 0.04 0.02 0.00 0.24
#> TCGA.EI.6510.01 4 0.0000 0.908 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.DY.A1DG.01 1 0.3307 0.434 0.74 0.00 0.00 0.00 0.00 0.02 0.24
#> TCGA.AG.4021.01 6 0.2906 0.817 0.00 0.00 0.00 0.18 0.00 0.80 0.02
#> TCGA.DM.A1D9.01 4 0.0000 0.908 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.CM.4744.01 6 0.3289 0.855 0.00 0.00 0.06 0.10 0.00 0.82 0.02
#> TCGA.SS.A7HO.01 7 0.3562 0.825 0.50 0.00 0.00 0.00 0.00 0.00 0.50
#> TCGA.NH.A50T.01 1 0.2832 0.443 0.76 0.00 0.00 0.00 0.00 0.00 0.24
#> TCGA.D5.5539.01 2 0.4895 0.772 0.00 0.66 0.04 0.04 0.02 0.00 0.24
#> TCGA.AY.A54L.01 6 0.3221 0.656 0.00 0.00 0.00 0.32 0.00 0.68 0.00
#> TCGA.DC.5337.01 5 0.4447 0.440 0.02 0.00 0.02 0.00 0.66 0.02 0.28
#> TCGA.QG.A5YW.01 5 0.0504 0.640 0.00 0.00 0.02 0.00 0.98 0.00 0.00
#> TCGA.EI.6882.01 2 0.0000 0.879 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.A6.2677.01 1 0.0000 0.535 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AA.3502.01 2 0.0000 0.879 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AA.3496.01 1 0.3221 -0.384 0.68 0.00 0.00 0.00 0.00 0.00 0.32
#> TCGA.CL.5918.01 3 0.3244 0.702 0.18 0.00 0.78 0.00 0.00 0.00 0.04
#> TCGA.AY.A71X.01 2 0.0000 0.879 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AH.6549.01 1 0.4146 -0.336 0.64 0.00 0.02 0.00 0.00 0.02 0.32
#> TCGA.AH.6897.01 7 0.3525 0.916 0.44 0.00 0.00 0.00 0.00 0.00 0.56
#> TCGA.4T.AA8H.01 2 0.0000 0.879 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EI.6508.01 5 0.5194 0.401 0.00 0.00 0.40 0.00 0.50 0.04 0.06
#> TCGA.D5.6532.01 3 0.3061 0.765 0.06 0.00 0.84 0.00 0.08 0.00 0.02
#> TCGA.A6.2680.01 5 0.4923 0.425 0.00 0.00 0.38 0.00 0.54 0.04 0.04
#> TCGA.CM.6680.01 2 0.4107 0.789 0.00 0.70 0.04 0.00 0.02 0.00 0.24
#> TCGA.DM.A28G.01 4 0.0000 0.908 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.D5.6537.01 1 0.0863 0.541 0.96 0.00 0.00 0.00 0.00 0.00 0.04
#> TCGA.DY.A1DD.01 1 0.3307 0.434 0.74 0.00 0.00 0.00 0.00 0.02 0.24
cbind(get_classes(res, k = 8), get_membership(res, k = 8))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7 p8
#> TCGA.AG.A026.01 1 0.1341 0.7478 0.92 0.00 0.08 0.00 0.00 0.00 0.00 0.00
#> TCGA.AD.6965.01 6 0.0000 0.8365 0.00 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.A6.5660.01 1 0.2719 0.6496 0.80 0.00 0.18 0.00 0.02 0.00 0.00 0.00
#> TCGA.CM.5862.01 1 0.4236 0.7339 0.72 0.00 0.04 0.02 0.00 0.00 0.18 0.04
#> TCGA.QG.A5YX.01 8 0.3299 0.0000 0.00 0.00 0.00 0.00 0.44 0.00 0.00 0.56
#> TCGA.AG.A036.01 1 0.3986 0.7455 0.74 0.00 0.08 0.00 0.00 0.00 0.14 0.04
#> TCGA.RU.A8FL.01 1 0.3178 0.7432 0.80 0.00 0.00 0.02 0.00 0.00 0.14 0.04
#> TCGA.AZ.6599.01 2 0.0000 0.8593 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CM.4750.01 1 0.1341 0.7478 0.92 0.00 0.08 0.00 0.00 0.00 0.00 0.00
#> TCGA.CM.6677.01 3 0.5540 0.6429 0.00 0.00 0.56 0.00 0.20 0.10 0.00 0.14
#> TCGA.F5.6814.01 5 0.1091 0.4940 0.00 0.00 0.06 0.00 0.94 0.00 0.00 0.00
#> TCGA.DM.A28F.01 5 0.3299 -0.6402 0.00 0.00 0.00 0.00 0.56 0.00 0.00 0.44
#> TCGA.DM.A0X9.01 4 0.4798 0.3198 0.00 0.00 0.02 0.56 0.00 0.32 0.00 0.10
#> TCGA.NH.A6GB.01 6 0.1804 0.8320 0.00 0.00 0.08 0.00 0.00 0.90 0.00 0.02
#> TCGA.NH.A50U.01 4 0.0808 0.8896 0.00 0.00 0.00 0.96 0.00 0.04 0.00 0.00
#> TCGA.CM.5864.01 3 0.3618 0.6149 0.02 0.00 0.60 0.00 0.38 0.00 0.00 0.00
#> TCGA.AG.3742.01 3 0.5540 0.6429 0.00 0.00 0.56 0.00 0.20 0.10 0.00 0.14
#> TCGA.A6.5666.01 7 0.4622 0.5884 0.26 0.00 0.02 0.02 0.00 0.00 0.64 0.06
#> TCGA.AG.3591.01 2 0.5530 0.6968 0.00 0.60 0.02 0.12 0.00 0.00 0.18 0.08
#> TCGA.EI.6510.01 4 0.0808 0.8896 0.00 0.00 0.00 0.96 0.00 0.04 0.00 0.00
#> TCGA.DY.A1DG.01 1 0.4313 0.6341 0.70 0.00 0.02 0.02 0.00 0.00 0.20 0.06
#> TCGA.AG.4021.01 6 0.3319 0.7733 0.00 0.00 0.06 0.08 0.00 0.82 0.02 0.02
#> TCGA.DM.A1D9.01 4 0.0808 0.8896 0.00 0.00 0.00 0.96 0.00 0.04 0.00 0.00
#> TCGA.CM.4744.01 6 0.1804 0.8320 0.00 0.00 0.08 0.00 0.00 0.90 0.00 0.02
#> TCGA.SS.A7HO.01 7 0.2406 0.6674 0.20 0.00 0.00 0.00 0.00 0.00 0.80 0.00
#> TCGA.NH.A50T.01 1 0.2404 0.7558 0.84 0.00 0.00 0.02 0.00 0.00 0.14 0.00
#> TCGA.D5.5539.01 2 0.5530 0.6968 0.00 0.60 0.02 0.12 0.00 0.00 0.18 0.08
#> TCGA.AY.A54L.01 6 0.2981 0.6487 0.00 0.00 0.00 0.22 0.00 0.76 0.00 0.02
#> TCGA.DC.5337.01 7 0.4588 0.0358 0.00 0.00 0.00 0.00 0.12 0.00 0.54 0.34
#> TCGA.QG.A5YW.01 5 0.3272 -0.6518 0.00 0.00 0.00 0.00 0.58 0.00 0.00 0.42
#> TCGA.EI.6882.01 2 0.0471 0.8551 0.00 0.98 0.02 0.00 0.00 0.00 0.00 0.00
#> TCGA.A6.2677.01 1 0.1765 0.7196 0.88 0.00 0.12 0.00 0.00 0.00 0.00 0.00
#> TCGA.AA.3502.01 2 0.0000 0.8593 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AA.3496.01 7 0.4174 0.6265 0.32 0.00 0.04 0.00 0.00 0.00 0.62 0.02
#> TCGA.CL.5918.01 3 0.4033 0.5455 0.20 0.00 0.68 0.00 0.12 0.00 0.00 0.00
#> TCGA.AY.A71X.01 2 0.0000 0.8593 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AH.6549.01 7 0.4570 0.6322 0.28 0.00 0.06 0.00 0.00 0.00 0.62 0.04
#> TCGA.AH.6897.01 7 0.4375 0.6089 0.26 0.00 0.02 0.02 0.00 0.00 0.66 0.04
#> TCGA.4T.AA8H.01 2 0.0000 0.8593 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EI.6508.01 5 0.2348 0.4156 0.00 0.00 0.06 0.02 0.88 0.00 0.00 0.04
#> TCGA.D5.6532.01 3 0.3514 0.6445 0.02 0.00 0.64 0.00 0.34 0.00 0.00 0.00
#> TCGA.A6.2680.01 5 0.1091 0.4940 0.00 0.00 0.06 0.00 0.94 0.00 0.00 0.00
#> TCGA.CM.6680.01 2 0.3970 0.7649 0.00 0.72 0.02 0.00 0.00 0.00 0.18 0.08
#> TCGA.DM.A28G.01 4 0.0808 0.8896 0.00 0.00 0.00 0.96 0.00 0.04 0.00 0.00
#> TCGA.D5.6537.01 1 0.1275 0.7415 0.94 0.00 0.04 0.00 0.00 0.00 0.02 0.00
#> TCGA.DY.A1DD.01 1 0.3178 0.7432 0.80 0.00 0.00 0.02 0.00 0.00 0.14 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: Node01. Child nodes: Node0111 , Node0112 , Node0121 , Node0122 , Node0211-leaf , Node0212 , Node0411-leaf , Node0412-leaf , Node0413-leaf , Node0414-leaf , Node0421-leaf , Node0422 , Node0423-leaf , Node0431-leaf , Node0432-leaf , Node0433-leaf .
The object with results only for a single top-value method and a single partitioning method can be extracted as:
res = res_rh["012"]
A summary of res and all the functions that can be applied to it:
res
#> A 'ConsensusPartition' object with k = 2, 3, 4, 5, 6, 7, 8.
#> On a matrix with 30000 rows and 41 columns.
#> Top rows (1000) are extracted by 'ATC' method.
#> Subgroups are detected by 'kmeans' method.
#> Performed in total 350 partitions by row resampling.
#> Best k for subgroups seems to be 4.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_partitions"
#> [7] "compare_signatures" "consensus_heatmap" "dimension_reduction"
#> [10] "functional_enrichment" "get_anno_col" "get_anno"
#> [13] "get_classes" "get_consensus" "get_matrix"
#> [16] "get_membership" "get_param" "get_signatures"
#> [19] "get_stats" "is_best_k" "is_stable_k"
#> [22] "membership_heatmap" "ncol" "nrow"
#> [25] "plot_ecdf" "predict_classes" "rownames"
#> [28] "select_partition_number" "show" "suggest_best_k"
#> [31] "test_to_known_factors" "top_rows_heatmap"
collect_plots() function collects all the plots made from res for all k (number of subgroups)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
The plots are:
k and the heatmap of
predicted classes for each k.k.k.k.All the plots in panels can be made by individual functions and they are plotted later in this section.
select_partition_number() produces several plots showing different
statistics for choosing “optimized” k. There are following statistics:
k;k, the area increased is defined as \(A_k - A_{k-1}\).The detailed explanations of these statistics can be found in the cola vignette.
Generally speaking, higher 1-PAC score, higher mean silhouette score or higher
concordance corresponds to better partition. Rand index and Jaccard index
measure how similar the current partition is compared to partition with k-1.
If they are too similar, we won't accept k is better than k-1.
select_partition_number(res)
The numeric values for all these statistics can be obtained by get_stats().
get_stats(res)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> 2 2 1.000 0.999 1.000 0.4885 0.512 0.512
#> 3 3 0.637 0.561 0.611 0.3653 1.000 1.000
#> 4 4 0.978 0.903 0.951 0.1157 0.718 0.460
#> 5 5 0.869 0.889 0.902 0.0733 0.879 0.566
#> 6 6 0.881 0.848 0.887 0.0268 1.000 1.000
#> 7 7 0.870 0.713 0.865 0.0259 0.991 0.954
#> 8 8 0.881 0.840 0.891 0.0182 0.944 0.697
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.D5.6540.01 2 0.000 0.999 0.00 1.00
#> TCGA.G4.6588.01 2 0.000 0.999 0.00 1.00
#> TCGA.AZ.6606.01 2 0.000 0.999 0.00 1.00
#> TCGA.F4.6570.01 2 0.000 0.999 0.00 1.00
#> TCGA.A6.2686.01 1 0.000 1.000 1.00 0.00
#> TCGA.G4.6299.01 2 0.000 0.999 0.00 1.00
#> TCGA.A6.4105.01 2 0.000 0.999 0.00 1.00
#> TCGA.DT.5265.01 2 0.000 0.999 0.00 1.00
#> TCGA.DM.A0XD.01 1 0.000 1.000 1.00 0.00
#> TCGA.D5.7000.01 1 0.000 1.000 1.00 0.00
#> TCGA.CK.6751.01 1 0.000 1.000 1.00 0.00
#> TCGA.CM.6171.01 2 0.000 0.999 0.00 1.00
#> TCGA.DM.A1DA.01 1 0.000 1.000 1.00 0.00
#> TCGA.AD.A5EJ.01 2 0.000 0.999 0.00 1.00
#> TCGA.CK.5916.01 2 0.000 0.999 0.00 1.00
#> TCGA.AZ.4614.01 1 0.000 1.000 1.00 0.00
#> TCGA.A6.3809.01 1 0.000 1.000 1.00 0.00
#> TCGA.CM.5861.01 2 0.000 0.999 0.00 1.00
#> TCGA.G4.6322.01 1 0.000 1.000 1.00 0.00
#> TCGA.G4.6586.01 2 0.000 0.999 0.00 1.00
#> TCGA.D5.6531.01 1 0.000 1.000 1.00 0.00
#> TCGA.AZ.6598.01 2 0.000 0.999 0.00 1.00
#> TCGA.F4.6461.01 2 0.000 0.999 0.00 1.00
#> TCGA.AD.6889.01 2 0.000 0.999 0.00 1.00
#> TCGA.AA.3663.01 2 0.000 0.999 0.00 1.00
#> TCGA.CA.5254.01 2 0.141 0.980 0.02 0.98
#> TCGA.A6.4107.01 2 0.000 0.999 0.00 1.00
#> TCGA.CM.6675.01 1 0.000 1.000 1.00 0.00
#> TCGA.CK.6746.01 1 0.000 1.000 1.00 0.00
#> TCGA.A6.5665.01 2 0.000 0.999 0.00 1.00
#> TCGA.D5.6538.01 1 0.000 1.000 1.00 0.00
#> TCGA.QG.A5Z2.01 2 0.000 0.999 0.00 1.00
#> TCGA.CK.4952.01 1 0.000 1.000 1.00 0.00
#> TCGA.CK.5913.01 1 0.000 1.000 1.00 0.00
#> TCGA.G4.6320.01 1 0.000 1.000 1.00 0.00
#> TCGA.A6.6653.01 2 0.000 0.999 0.00 1.00
#> TCGA.A6.5661.01 2 0.000 0.999 0.00 1.00
#> TCGA.A6.2672.01 2 0.000 0.999 0.00 1.00
#> TCGA.AA.3492.01 2 0.000 0.999 0.00 1.00
#> TCGA.DM.A1HB.01 2 0.000 0.999 0.00 1.00
#> TCGA.A6.5659.01 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.D5.6540.01 2 0.5560 0.495 0.00 0.70 0.30
#> TCGA.G4.6588.01 2 0.0000 0.522 0.00 1.00 0.00
#> TCGA.AZ.6606.01 2 0.6244 0.464 0.00 0.56 0.44
#> TCGA.F4.6570.01 2 0.7091 0.479 0.04 0.64 0.32
#> TCGA.A6.2686.01 1 0.5706 0.452 0.68 0.00 0.32
#> TCGA.G4.6299.01 2 0.6244 0.464 0.00 0.56 0.44
#> TCGA.A6.4105.01 2 0.9602 0.417 0.22 0.46 0.32
#> TCGA.DT.5265.01 2 0.0000 0.522 0.00 1.00 0.00
#> TCGA.DM.A0XD.01 1 0.0000 0.768 1.00 0.00 0.00
#> TCGA.D5.7000.01 1 0.0000 0.768 1.00 0.00 0.00
#> TCGA.CK.6751.01 1 0.0892 0.761 0.98 0.00 0.02
#> TCGA.CM.6171.01 2 0.5560 0.495 0.00 0.70 0.30
#> TCGA.DM.A1DA.01 1 0.5016 0.799 0.76 0.00 0.24
#> TCGA.AD.A5EJ.01 2 0.6244 0.464 0.00 0.56 0.44
#> TCGA.CK.5916.01 2 0.6244 0.464 0.00 0.56 0.44
#> TCGA.AZ.4614.01 1 0.5016 0.799 0.76 0.00 0.24
#> TCGA.A6.3809.01 1 0.5706 0.452 0.68 0.00 0.32
#> TCGA.CM.5861.01 2 0.9725 0.409 0.24 0.44 0.32
#> TCGA.G4.6322.01 1 0.5016 0.799 0.76 0.00 0.24
#> TCGA.G4.6586.01 2 0.9725 0.409 0.24 0.44 0.32
#> TCGA.D5.6531.01 1 0.0892 0.761 0.98 0.00 0.02
#> TCGA.AZ.6598.01 2 0.6244 0.464 0.00 0.56 0.44
#> TCGA.F4.6461.01 2 0.0000 0.522 0.00 1.00 0.00
#> TCGA.AD.6889.01 2 0.6244 0.464 0.00 0.56 0.44
#> TCGA.AA.3663.01 2 0.9725 0.409 0.24 0.44 0.32
#> TCGA.CA.5254.01 2 0.9725 0.409 0.24 0.44 0.32
#> TCGA.A6.4107.01 2 0.9725 0.409 0.24 0.44 0.32
#> TCGA.CM.6675.01 1 0.5016 0.799 0.76 0.00 0.24
#> TCGA.CK.6746.01 1 0.5016 0.799 0.76 0.00 0.24
#> TCGA.A6.5665.01 2 0.6244 0.464 0.00 0.56 0.44
#> TCGA.D5.6538.01 1 0.5016 0.799 0.76 0.00 0.24
#> TCGA.QG.A5Z2.01 2 0.0000 0.522 0.00 1.00 0.00
#> TCGA.CK.4952.01 1 0.5016 0.799 0.76 0.00 0.24
#> TCGA.CK.5913.01 1 0.5706 0.452 0.68 0.00 0.32
#> TCGA.G4.6320.01 1 0.0892 0.761 0.98 0.00 0.02
#> TCGA.A6.6653.01 2 0.6244 0.464 0.00 0.56 0.44
#> TCGA.A6.5661.01 2 0.6244 0.464 0.00 0.56 0.44
#> TCGA.A6.2672.01 2 0.9725 0.409 0.24 0.44 0.32
#> TCGA.AA.3492.01 2 0.9725 0.409 0.24 0.44 0.32
#> TCGA.DM.A1HB.01 2 0.9725 0.409 0.24 0.44 0.32
#> TCGA.A6.5659.01 1 0.5016 0.799 0.76 0.00 0.24
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> TCGA.D5.6540.01 2 0.0000 0.978 0.00 1.00 0 0.00
#> TCGA.G4.6588.01 2 0.0000 0.978 0.00 1.00 0 0.00
#> TCGA.AZ.6606.01 3 0.0000 1.000 0.00 0.00 1 0.00
#> TCGA.F4.6570.01 2 0.0000 0.978 0.00 1.00 0 0.00
#> TCGA.A6.2686.01 4 0.0000 0.891 0.00 0.00 0 1.00
#> TCGA.G4.6299.01 3 0.0000 1.000 0.00 0.00 1 0.00
#> TCGA.A6.4105.01 2 0.0707 0.972 0.02 0.98 0 0.00
#> TCGA.DT.5265.01 2 0.0000 0.978 0.00 1.00 0 0.00
#> TCGA.DM.A0XD.01 4 0.1211 0.892 0.04 0.00 0 0.96
#> TCGA.D5.7000.01 4 0.1211 0.892 0.04 0.00 0 0.96
#> TCGA.CK.6751.01 4 0.0707 0.895 0.02 0.00 0 0.98
#> TCGA.CM.6171.01 2 0.0707 0.970 0.02 0.98 0 0.00
#> TCGA.DM.A1DA.01 1 0.1211 0.874 0.96 0.00 0 0.04
#> TCGA.AD.A5EJ.01 3 0.0000 1.000 0.00 0.00 1 0.00
#> TCGA.CK.5916.01 3 0.0000 1.000 0.00 0.00 1 0.00
#> TCGA.AZ.4614.01 1 0.4855 0.465 0.60 0.00 0 0.40
#> TCGA.A6.3809.01 4 0.0000 0.891 0.00 0.00 0 1.00
#> TCGA.CM.5861.01 2 0.0000 0.978 0.00 1.00 0 0.00
#> TCGA.G4.6322.01 1 0.1211 0.874 0.96 0.00 0 0.04
#> TCGA.G4.6586.01 2 0.1211 0.971 0.00 0.96 0 0.04
#> TCGA.D5.6531.01 4 0.1211 0.892 0.04 0.00 0 0.96
#> TCGA.AZ.6598.01 3 0.0000 1.000 0.00 0.00 1 0.00
#> TCGA.F4.6461.01 2 0.0707 0.970 0.02 0.98 0 0.00
#> TCGA.AD.6889.01 3 0.0000 1.000 0.00 0.00 1 0.00
#> TCGA.AA.3663.01 2 0.1211 0.971 0.00 0.96 0 0.04
#> TCGA.CA.5254.01 4 0.5428 0.275 0.02 0.38 0 0.60
#> TCGA.A6.4107.01 2 0.2335 0.945 0.02 0.92 0 0.06
#> TCGA.CM.6675.01 1 0.1211 0.874 0.96 0.00 0 0.04
#> TCGA.CK.6746.01 1 0.4977 0.328 0.54 0.00 0 0.46
#> TCGA.A6.5665.01 3 0.0000 1.000 0.00 0.00 1 0.00
#> TCGA.D5.6538.01 1 0.1211 0.874 0.96 0.00 0 0.04
#> TCGA.QG.A5Z2.01 2 0.0000 0.978 0.00 1.00 0 0.00
#> TCGA.CK.4952.01 1 0.1211 0.874 0.96 0.00 0 0.04
#> TCGA.CK.5913.01 4 0.0000 0.891 0.00 0.00 0 1.00
#> TCGA.G4.6320.01 4 0.1211 0.892 0.04 0.00 0 0.96
#> TCGA.A6.6653.01 3 0.0000 1.000 0.00 0.00 1 0.00
#> TCGA.A6.5661.01 3 0.0000 1.000 0.00 0.00 1 0.00
#> TCGA.A6.2672.01 2 0.1211 0.971 0.00 0.96 0 0.04
#> TCGA.AA.3492.01 2 0.1211 0.971 0.00 0.96 0 0.04
#> TCGA.DM.A1HB.01 2 0.1211 0.971 0.00 0.96 0 0.04
#> TCGA.A6.5659.01 1 0.1211 0.874 0.96 0.00 0 0.04
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> TCGA.D5.6540.01 2 0.3424 0.916 0.00 0.76 0 0.00 0.24
#> TCGA.G4.6588.01 2 0.3424 0.916 0.00 0.76 0 0.00 0.24
#> TCGA.AZ.6606.01 3 0.0000 1.000 0.00 0.00 1 0.00 0.00
#> TCGA.F4.6570.01 2 0.3561 0.907 0.00 0.74 0 0.00 0.26
#> TCGA.A6.2686.01 4 0.0609 0.917 0.00 0.00 0 0.98 0.02
#> TCGA.G4.6299.01 3 0.0000 1.000 0.00 0.00 1 0.00 0.00
#> TCGA.A6.4105.01 5 0.2929 0.571 0.00 0.18 0 0.00 0.82
#> TCGA.DT.5265.01 2 0.3424 0.916 0.00 0.76 0 0.00 0.24
#> TCGA.DM.A0XD.01 4 0.0609 0.931 0.02 0.00 0 0.98 0.00
#> TCGA.D5.7000.01 4 0.0609 0.931 0.02 0.00 0 0.98 0.00
#> TCGA.CK.6751.01 4 0.0609 0.931 0.02 0.00 0 0.98 0.00
#> TCGA.CM.6171.01 2 0.3106 0.822 0.02 0.84 0 0.00 0.14
#> TCGA.DM.A1DA.01 1 0.0609 1.000 0.98 0.00 0 0.02 0.00
#> TCGA.AD.A5EJ.01 3 0.0000 1.000 0.00 0.00 1 0.00 0.00
#> TCGA.CK.5916.01 3 0.0000 1.000 0.00 0.00 1 0.00 0.00
#> TCGA.AZ.4614.01 4 0.5050 0.696 0.18 0.12 0 0.70 0.00
#> TCGA.A6.3809.01 4 0.0609 0.917 0.00 0.00 0 0.98 0.02
#> TCGA.CM.5861.01 2 0.3424 0.879 0.00 0.76 0 0.00 0.24
#> TCGA.G4.6322.01 1 0.0609 1.000 0.98 0.00 0 0.02 0.00
#> TCGA.G4.6586.01 5 0.3690 0.749 0.00 0.20 0 0.02 0.78
#> TCGA.D5.6531.01 4 0.0609 0.931 0.02 0.00 0 0.98 0.00
#> TCGA.AZ.6598.01 3 0.0000 1.000 0.00 0.00 1 0.00 0.00
#> TCGA.F4.6461.01 2 0.3106 0.822 0.02 0.84 0 0.00 0.14
#> TCGA.AD.6889.01 3 0.0000 1.000 0.00 0.00 1 0.00 0.00
#> TCGA.AA.3663.01 5 0.3319 0.736 0.00 0.16 0 0.02 0.82
#> TCGA.CA.5254.01 5 0.3852 0.503 0.00 0.02 0 0.22 0.76
#> TCGA.A6.4107.01 5 0.1043 0.692 0.00 0.04 0 0.00 0.96
#> TCGA.CM.6675.01 1 0.0609 1.000 0.98 0.00 0 0.02 0.00
#> TCGA.CK.6746.01 4 0.4458 0.770 0.12 0.12 0 0.76 0.00
#> TCGA.A6.5665.01 3 0.0000 1.000 0.00 0.00 1 0.00 0.00
#> TCGA.D5.6538.01 1 0.0609 1.000 0.98 0.00 0 0.02 0.00
#> TCGA.QG.A5Z2.01 2 0.3424 0.916 0.00 0.76 0 0.00 0.24
#> TCGA.CK.4952.01 1 0.0609 1.000 0.98 0.00 0 0.02 0.00
#> TCGA.CK.5913.01 4 0.0609 0.917 0.00 0.00 0 0.98 0.02
#> TCGA.G4.6320.01 4 0.0609 0.931 0.02 0.00 0 0.98 0.00
#> TCGA.A6.6653.01 3 0.0000 1.000 0.00 0.00 1 0.00 0.00
#> TCGA.A6.5661.01 3 0.0000 1.000 0.00 0.00 1 0.00 0.00
#> TCGA.A6.2672.01 5 0.3852 0.742 0.00 0.22 0 0.02 0.76
#> TCGA.AA.3492.01 5 0.3690 0.749 0.00 0.20 0 0.02 0.78
#> TCGA.DM.A1HB.01 5 0.3690 0.749 0.00 0.20 0 0.02 0.78
#> TCGA.A6.5659.01 1 0.0609 1.000 0.98 0.00 0 0.02 0.00
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> TCGA.D5.6540.01 6 0.0000 0.864 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.G4.6588.01 6 0.0000 0.864 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.AZ.6606.01 3 0.0937 0.977 0.00 0.04 0.96 0.00 0.00 0.00
#> TCGA.F4.6570.01 6 0.0547 0.858 0.00 0.02 0.00 0.00 0.00 0.98
#> TCGA.A6.2686.01 4 0.0000 0.888 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.G4.6299.01 3 0.0547 0.987 0.00 0.02 0.98 0.00 0.00 0.00
#> TCGA.A6.4105.01 5 0.5555 0.351 0.00 0.14 0.00 0.00 0.48 0.38
#> TCGA.DT.5265.01 6 0.0000 0.864 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.DM.A0XD.01 4 0.0937 0.902 0.04 0.00 0.00 0.96 0.00 0.00
#> TCGA.D5.7000.01 4 0.0937 0.902 0.04 0.00 0.00 0.96 0.00 0.00
#> TCGA.CK.6751.01 4 0.0937 0.902 0.04 0.00 0.00 0.96 0.00 0.00
#> TCGA.CM.6171.01 6 0.4758 0.564 0.00 0.36 0.00 0.00 0.06 0.58
#> TCGA.DM.A1DA.01 1 0.0000 0.991 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AD.A5EJ.01 3 0.0000 0.989 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.CK.5916.01 3 0.0547 0.987 0.00 0.02 0.98 0.00 0.00 0.00
#> TCGA.AZ.4614.01 4 0.5037 0.596 0.08 0.38 0.00 0.54 0.00 0.00
#> TCGA.A6.3809.01 4 0.0000 0.888 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.CM.5861.01 6 0.2956 0.720 0.00 0.04 0.00 0.00 0.12 0.84
#> TCGA.G4.6322.01 1 0.0000 0.991 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.G4.6586.01 5 0.4265 0.746 0.00 0.00 0.00 0.04 0.66 0.30
#> TCGA.D5.6531.01 4 0.0937 0.902 0.04 0.00 0.00 0.96 0.00 0.00
#> TCGA.AZ.6598.01 3 0.0547 0.980 0.00 0.02 0.98 0.00 0.00 0.00
#> TCGA.F4.6461.01 6 0.3829 0.720 0.00 0.18 0.00 0.00 0.06 0.76
#> TCGA.AD.6889.01 3 0.0000 0.989 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.AA.3663.01 5 0.4403 0.725 0.00 0.04 0.00 0.04 0.74 0.18
#> TCGA.CA.5254.01 5 0.4393 0.560 0.00 0.14 0.00 0.14 0.72 0.00
#> TCGA.A6.4107.01 5 0.4393 0.653 0.00 0.14 0.00 0.00 0.72 0.14
#> TCGA.CM.6675.01 1 0.0000 0.991 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CK.6746.01 4 0.5570 0.605 0.06 0.36 0.00 0.54 0.04 0.00
#> TCGA.A6.5665.01 3 0.0547 0.987 0.00 0.02 0.98 0.00 0.00 0.00
#> TCGA.D5.6538.01 1 0.1480 0.954 0.94 0.04 0.00 0.00 0.02 0.00
#> TCGA.QG.A5Z2.01 6 0.0000 0.864 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.CK.4952.01 1 0.0000 0.991 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CK.5913.01 4 0.0000 0.888 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.G4.6320.01 4 0.0937 0.902 0.04 0.00 0.00 0.96 0.00 0.00
#> TCGA.A6.6653.01 3 0.0000 0.989 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.A6.5661.01 3 0.0000 0.989 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.A6.2672.01 5 0.4265 0.746 0.00 0.00 0.00 0.04 0.66 0.30
#> TCGA.AA.3492.01 5 0.4265 0.746 0.00 0.00 0.00 0.04 0.66 0.30
#> TCGA.DM.A1HB.01 5 0.4265 0.746 0.00 0.00 0.00 0.04 0.66 0.30
#> TCGA.A6.5659.01 1 0.0000 0.991 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.D5.6540.01 7 0.0000 0.830 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.G4.6588.01 7 0.0000 0.830 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.AZ.6606.01 3 0.1671 0.916 0.00 0.00 0.90 0.00 0.00 0.10 0.00
#> TCGA.F4.6570.01 7 0.0504 0.823 0.00 0.00 0.00 0.00 0.02 0.00 0.98
#> TCGA.A6.2686.01 4 0.1363 0.879 0.00 0.02 0.00 0.94 0.04 0.00 0.00
#> TCGA.G4.6299.01 3 0.2422 0.905 0.00 0.00 0.82 0.00 0.00 0.18 0.00
#> TCGA.A6.4105.01 2 0.4710 0.000 0.00 0.46 0.00 0.00 0.46 0.00 0.08
#> TCGA.DT.5265.01 7 0.0000 0.830 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.DM.A0XD.01 4 0.0000 0.894 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.D5.7000.01 4 0.0000 0.894 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.CK.6751.01 4 0.0000 0.894 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.CM.6171.01 7 0.5467 0.453 0.00 0.28 0.00 0.00 0.00 0.26 0.46
#> TCGA.DM.A1DA.01 1 0.0000 0.997 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AD.A5EJ.01 3 0.0000 0.931 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.CK.5916.01 3 0.2422 0.905 0.00 0.00 0.82 0.00 0.00 0.18 0.00
#> TCGA.AZ.4614.01 4 0.5300 0.585 0.04 0.10 0.00 0.58 0.00 0.28 0.00
#> TCGA.A6.3809.01 4 0.1363 0.879 0.00 0.02 0.00 0.94 0.04 0.00 0.00
#> TCGA.CM.5861.01 7 0.3047 0.517 0.00 0.00 0.00 0.00 0.28 0.00 0.72
#> TCGA.G4.6322.01 1 0.0000 0.997 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.G4.6586.01 5 0.2422 0.571 0.00 0.00 0.00 0.00 0.82 0.00 0.18
#> TCGA.D5.6531.01 4 0.1166 0.875 0.00 0.06 0.00 0.94 0.00 0.00 0.00
#> TCGA.AZ.6598.01 3 0.1671 0.920 0.00 0.00 0.90 0.00 0.00 0.10 0.00
#> TCGA.F4.6461.01 7 0.3867 0.695 0.00 0.12 0.00 0.00 0.00 0.14 0.74
#> TCGA.AD.6889.01 3 0.0000 0.931 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.AA.3663.01 5 0.4969 0.227 0.00 0.08 0.00 0.00 0.66 0.20 0.06
#> TCGA.CA.5254.01 5 0.3558 -0.799 0.00 0.48 0.00 0.00 0.52 0.00 0.00
#> TCGA.A6.4107.01 5 0.3558 -0.799 0.00 0.48 0.00 0.00 0.52 0.00 0.00
#> TCGA.CM.6675.01 1 0.0000 0.997 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CK.6746.01 4 0.4070 0.628 0.00 0.04 0.00 0.62 0.00 0.34 0.00
#> TCGA.A6.5665.01 3 0.2081 0.919 0.00 0.00 0.86 0.00 0.00 0.14 0.00
#> TCGA.D5.6538.01 1 0.0504 0.983 0.98 0.02 0.00 0.00 0.00 0.00 0.00
#> TCGA.QG.A5Z2.01 7 0.1166 0.802 0.00 0.00 0.00 0.00 0.00 0.06 0.94
#> TCGA.CK.4952.01 1 0.0000 0.997 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CK.5913.01 4 0.1363 0.879 0.00 0.02 0.00 0.94 0.04 0.00 0.00
#> TCGA.G4.6320.01 4 0.0000 0.894 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.A6.6653.01 3 0.0000 0.931 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.A6.5661.01 3 0.0000 0.931 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.A6.2672.01 5 0.2422 0.571 0.00 0.00 0.00 0.00 0.82 0.00 0.18
#> TCGA.AA.3492.01 5 0.2422 0.571 0.00 0.00 0.00 0.00 0.82 0.00 0.18
#> TCGA.DM.A1HB.01 5 0.2422 0.571 0.00 0.00 0.00 0.00 0.82 0.00 0.18
#> TCGA.A6.5659.01 1 0.0000 0.997 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.D5.6540.01 7 0.0000 0.907 0.00 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.G4.6588.01 7 0.0000 0.907 0.00 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.AZ.6606.01 3 0.2674 0.873 0.00 0.04 0.86 0.00 0.00 0.04 0.00 0.06
#> TCGA.F4.6570.01 7 0.1341 0.819 0.00 0.00 0.00 0.00 0.08 0.00 0.92 0.00
#> TCGA.A6.2686.01 4 0.0941 0.951 0.00 0.02 0.00 0.96 0.02 0.00 0.00 0.00
#> TCGA.G4.6299.01 3 0.2947 0.899 0.00 0.06 0.84 0.00 0.00 0.04 0.00 0.06
#> TCGA.A6.4105.01 2 0.3856 0.825 0.00 0.70 0.00 0.00 0.20 0.00 0.10 0.00
#> TCGA.DT.5265.01 7 0.0000 0.907 0.00 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.DM.A0XD.01 4 0.0000 0.961 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.D5.7000.01 4 0.0000 0.961 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.CK.6751.01 4 0.0000 0.961 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.CM.6171.01 8 0.3015 0.000 0.00 0.00 0.00 0.00 0.00 0.00 0.32 0.68
#> TCGA.DM.A1DA.01 1 0.0000 0.974 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AD.A5EJ.01 3 0.0000 0.920 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CK.5916.01 3 0.2947 0.899 0.00 0.06 0.84 0.00 0.00 0.04 0.00 0.06
#> TCGA.AZ.4614.01 6 0.5486 0.843 0.04 0.04 0.00 0.28 0.00 0.56 0.00 0.08
#> TCGA.A6.3809.01 4 0.0941 0.951 0.00 0.02 0.00 0.96 0.02 0.00 0.00 0.00
#> TCGA.CM.5861.01 5 0.3329 0.141 0.00 0.00 0.00 0.00 0.52 0.00 0.48 0.00
#> TCGA.G4.6322.01 1 0.0000 0.974 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.G4.6586.01 5 0.1091 0.748 0.00 0.00 0.00 0.00 0.94 0.00 0.06 0.00
#> TCGA.D5.6531.01 4 0.1408 0.915 0.00 0.00 0.00 0.94 0.02 0.02 0.00 0.02
#> TCGA.AZ.6598.01 3 0.3454 0.857 0.00 0.06 0.80 0.00 0.00 0.06 0.00 0.08
#> TCGA.F4.6461.01 7 0.2267 0.663 0.00 0.00 0.00 0.00 0.00 0.00 0.82 0.18
#> TCGA.AD.6889.01 3 0.0000 0.920 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AA.3663.01 5 0.5470 0.419 0.00 0.14 0.00 0.00 0.60 0.18 0.02 0.06
#> TCGA.CA.5254.01 2 0.2852 0.914 0.00 0.72 0.00 0.00 0.28 0.00 0.00 0.00
#> TCGA.A6.4107.01 2 0.2852 0.914 0.00 0.72 0.00 0.00 0.28 0.00 0.00 0.00
#> TCGA.CM.6675.01 1 0.0000 0.974 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CK.6746.01 6 0.2938 0.844 0.00 0.00 0.00 0.30 0.00 0.70 0.00 0.00
#> TCGA.A6.5665.01 3 0.2348 0.909 0.00 0.06 0.88 0.00 0.00 0.04 0.00 0.02
#> TCGA.D5.6538.01 1 0.2350 0.857 0.86 0.04 0.00 0.00 0.00 0.00 0.00 0.10
#> TCGA.QG.A5Z2.01 7 0.0471 0.889 0.00 0.00 0.00 0.00 0.00 0.00 0.98 0.02
#> TCGA.CK.4952.01 1 0.0000 0.974 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CK.5913.01 4 0.0941 0.951 0.00 0.02 0.00 0.96 0.02 0.00 0.00 0.00
#> TCGA.G4.6320.01 4 0.0471 0.950 0.00 0.00 0.00 0.98 0.00 0.02 0.00 0.00
#> TCGA.A6.6653.01 3 0.0000 0.920 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.A6.5661.01 3 0.0000 0.920 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.A6.2672.01 5 0.1091 0.748 0.00 0.00 0.00 0.00 0.94 0.00 0.06 0.00
#> TCGA.AA.3492.01 5 0.1804 0.748 0.00 0.00 0.00 0.00 0.90 0.00 0.08 0.02
#> TCGA.DM.A1HB.01 5 0.1341 0.748 0.00 0.00 0.00 0.00 0.92 0.00 0.08 0.00
#> TCGA.A6.5659.01 1 0.0000 0.974 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: Node012. Child nodes: Node01111 , Node01112-leaf , Node01113-leaf , Node01114-leaf , Node01121-leaf , Node01122-leaf , Node01123-leaf , Node01124-leaf , Node01211-leaf , Node01212-leaf , Node01213-leaf , Node01221-leaf , Node01222-leaf , Node01223-leaf , Node01224-leaf , Node02121-leaf , Node02122-leaf , Node02123-leaf , Node04221-leaf , Node04222-leaf , Node04223-leaf .
The object with results only for a single top-value method and a single partitioning method can be extracted as:
res = res_rh["0121"]
A summary of res and all the functions that can be applied to it:
res
#> A 'ConsensusPartition' object with k = 2, 3, 4, 5, 6, 7, 8.
#> On a matrix with 30000 rows and 16 columns.
#> Top rows (1000) are extracted by 'ATC' method.
#> Subgroups are detected by 'skmeans' method.
#> Performed in total 350 partitions by row resampling.
#> Best k for subgroups seems to be 5.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_partitions"
#> [7] "compare_signatures" "consensus_heatmap" "dimension_reduction"
#> [10] "functional_enrichment" "get_anno_col" "get_anno"
#> [13] "get_classes" "get_consensus" "get_matrix"
#> [16] "get_membership" "get_param" "get_signatures"
#> [19] "get_stats" "is_best_k" "is_stable_k"
#> [22] "membership_heatmap" "ncol" "nrow"
#> [25] "plot_ecdf" "predict_classes" "rownames"
#> [28] "select_partition_number" "show" "suggest_best_k"
#> [31] "test_to_known_factors" "top_rows_heatmap"
collect_plots() function collects all the plots made from res for all k (number of subgroups)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
The plots are:
k and the heatmap of
predicted classes for each k.k.k.k.All the plots in panels can be made by individual functions and they are plotted later in this section.
select_partition_number() produces several plots showing different
statistics for choosing “optimized” k. There are following statistics:
k;k, the area increased is defined as \(A_k - A_{k-1}\).The detailed explanations of these statistics can be found in the cola vignette.
Generally speaking, higher 1-PAC score, higher mean silhouette score or higher
concordance corresponds to better partition. Rand index and Jaccard index
measure how similar the current partition is compared to partition with k-1.
If they are too similar, we won't accept k is better than k-1.
select_partition_number(res)
The numeric values for all these statistics can be obtained by get_stats().
get_stats(res)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> 2 2 1.000 1.000 1.000 0.5005 0.500 0.500
#> 3 3 0.892 0.953 0.981 0.1580 0.933 0.867
#> 4 4 0.908 0.978 0.988 0.2130 0.867 0.692
#> 5 5 0.917 0.913 0.985 0.0870 0.942 0.806
#> 6 6 0.892 0.822 0.963 0.0656 0.950 0.793
#> 7 7 0.900 0.668 0.911 0.0325 0.992 0.957
#> 8 8 0.875 0.514 0.899 0.0357 0.958 0.773
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.A6.2686.01 2 0 1 0 1
#> TCGA.DM.A0XD.01 1 0 1 1 0
#> TCGA.D5.7000.01 1 0 1 1 0
#> TCGA.CK.6751.01 1 0 1 1 0
#> TCGA.DM.A1DA.01 1 0 1 1 0
#> TCGA.AZ.4614.01 1 0 1 1 0
#> TCGA.A6.3809.01 2 0 1 0 1
#> TCGA.G4.6322.01 2 0 1 0 1
#> TCGA.D5.6531.01 1 0 1 1 0
#> TCGA.CM.6675.01 1 0 1 1 0
#> TCGA.CK.6746.01 2 0 1 0 1
#> TCGA.D5.6538.01 1 0 1 1 0
#> TCGA.CK.4952.01 2 0 1 0 1
#> TCGA.CK.5913.01 2 0 1 0 1
#> TCGA.G4.6320.01 1 0 1 1 0
#> TCGA.A6.5659.01 1 0 1 1 0
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.A6.2686.01 2 0.000 1.000 0.0 1.0 0
#> TCGA.DM.A0XD.01 1 0.000 0.963 1.0 0.0 0
#> TCGA.D5.7000.01 1 0.000 0.963 1.0 0.0 0
#> TCGA.CK.6751.01 1 0.000 0.963 1.0 0.0 0
#> TCGA.DM.A1DA.01 1 0.000 0.963 1.0 0.0 0
#> TCGA.AZ.4614.01 1 0.556 0.571 0.7 0.3 0
#> TCGA.A6.3809.01 2 0.000 1.000 0.0 1.0 0
#> TCGA.G4.6322.01 3 0.000 1.000 0.0 0.0 1
#> TCGA.D5.6531.01 1 0.000 0.963 1.0 0.0 0
#> TCGA.CM.6675.01 1 0.000 0.963 1.0 0.0 0
#> TCGA.CK.6746.01 2 0.000 1.000 0.0 1.0 0
#> TCGA.D5.6538.01 1 0.000 0.963 1.0 0.0 0
#> TCGA.CK.4952.01 3 0.000 1.000 0.0 0.0 1
#> TCGA.CK.5913.01 2 0.000 1.000 0.0 1.0 0
#> TCGA.G4.6320.01 1 0.000 0.963 1.0 0.0 0
#> TCGA.A6.5659.01 1 0.000 0.963 1.0 0.0 0
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> TCGA.A6.2686.01 2 0.0000 1.000 0.00 1.00 0 0.00
#> TCGA.DM.A0XD.01 1 0.0000 0.975 1.00 0.00 0 0.00
#> TCGA.D5.7000.01 1 0.0000 0.975 1.00 0.00 0 0.00
#> TCGA.CK.6751.01 1 0.0000 0.975 1.00 0.00 0 0.00
#> TCGA.DM.A1DA.01 1 0.0707 0.961 0.98 0.00 0 0.02
#> TCGA.AZ.4614.01 1 0.3335 0.836 0.86 0.12 0 0.02
#> TCGA.A6.3809.01 2 0.0000 1.000 0.00 1.00 0 0.00
#> TCGA.G4.6322.01 3 0.0000 1.000 0.00 0.00 1 0.00
#> TCGA.D5.6531.01 1 0.0000 0.975 1.00 0.00 0 0.00
#> TCGA.CM.6675.01 1 0.0000 0.975 1.00 0.00 0 0.00
#> TCGA.CK.6746.01 2 0.0000 1.000 0.00 1.00 0 0.00
#> TCGA.D5.6538.01 4 0.0707 1.000 0.02 0.00 0 0.98
#> TCGA.CK.4952.01 3 0.0000 1.000 0.00 0.00 1 0.00
#> TCGA.CK.5913.01 2 0.0000 1.000 0.00 1.00 0 0.00
#> TCGA.G4.6320.01 1 0.0000 0.975 1.00 0.00 0 0.00
#> TCGA.A6.5659.01 4 0.0707 1.000 0.02 0.00 0 0.98
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> TCGA.A6.2686.01 2 0.000 1.000 0.00 1 0 0.0 0.00
#> TCGA.DM.A0XD.01 1 0.000 0.964 1.00 0 0 0.0 0.00
#> TCGA.D5.7000.01 1 0.141 0.927 0.94 0 0 0.0 0.06
#> TCGA.CK.6751.01 1 0.000 0.964 1.00 0 0 0.0 0.00
#> TCGA.DM.A1DA.01 1 0.202 0.884 0.90 0 0 0.1 0.00
#> TCGA.AZ.4614.01 5 0.104 0.000 0.04 0 0 0.0 0.96
#> TCGA.A6.3809.01 2 0.000 1.000 0.00 1 0 0.0 0.00
#> TCGA.G4.6322.01 3 0.000 1.000 0.00 0 1 0.0 0.00
#> TCGA.D5.6531.01 1 0.000 0.964 1.00 0 0 0.0 0.00
#> TCGA.CM.6675.01 1 0.104 0.942 0.96 0 0 0.0 0.04
#> TCGA.CK.6746.01 2 0.000 1.000 0.00 1 0 0.0 0.00
#> TCGA.D5.6538.01 4 0.000 1.000 0.00 0 0 1.0 0.00
#> TCGA.CK.4952.01 3 0.000 1.000 0.00 0 1 0.0 0.00
#> TCGA.CK.5913.01 2 0.000 1.000 0.00 1 0 0.0 0.00
#> TCGA.G4.6320.01 1 0.000 0.964 1.00 0 0 0.0 0.00
#> TCGA.A6.5659.01 4 0.000 1.000 0.00 0 0 1.0 0.00
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> TCGA.A6.2686.01 2 0.0000 1.000 0.00 1 0.00 0.00 0.00 0.00
#> TCGA.DM.A0XD.01 1 0.0547 0.914 0.98 0 0.00 0.00 0.00 0.02
#> TCGA.D5.7000.01 1 0.1807 0.884 0.92 0 0.00 0.00 0.02 0.06
#> TCGA.CK.6751.01 1 0.1267 0.894 0.94 0 0.00 0.00 0.00 0.06
#> TCGA.DM.A1DA.01 1 0.3073 0.768 0.84 0 0.00 0.08 0.00 0.08
#> TCGA.AZ.4614.01 5 0.0000 0.000 0.00 0 0.00 0.00 1.00 0.00
#> TCGA.A6.3809.01 2 0.0000 1.000 0.00 1 0.00 0.00 0.00 0.00
#> TCGA.G4.6322.01 3 0.1556 0.933 0.00 0 0.92 0.00 0.00 0.08
#> TCGA.D5.6531.01 1 0.0547 0.914 0.98 0 0.00 0.00 0.00 0.02
#> TCGA.CM.6675.01 6 0.2260 0.000 0.14 0 0.00 0.00 0.00 0.86
#> TCGA.CK.6746.01 2 0.0000 1.000 0.00 1 0.00 0.00 0.00 0.00
#> TCGA.D5.6538.01 4 0.0000 1.000 0.00 0 0.00 1.00 0.00 0.00
#> TCGA.CK.4952.01 3 0.0000 0.933 0.00 0 1.00 0.00 0.00 0.00
#> TCGA.CK.5913.01 2 0.0000 1.000 0.00 1 0.00 0.00 0.00 0.00
#> TCGA.G4.6320.01 1 0.0937 0.906 0.96 0 0.00 0.00 0.00 0.04
#> TCGA.A6.5659.01 4 0.0000 1.000 0.00 0 0.00 1.00 0.00 0.00
cbind(get_classes(res, k = 7), get_membership(res, k = 7))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7
#> TCGA.A6.2686.01 2 0.0000 0.982 0.00 1.00 0.00 0.00 0 0.00 0.00
#> TCGA.DM.A0XD.01 1 0.0863 0.836 0.96 0.00 0.00 0.00 0 0.00 0.04
#> TCGA.D5.7000.01 1 0.2945 0.804 0.74 0.00 0.00 0.00 0 0.00 0.26
#> TCGA.CK.6751.01 1 0.2708 0.820 0.78 0.00 0.00 0.00 0 0.00 0.22
#> TCGA.DM.A1DA.01 1 0.4569 0.682 0.64 0.00 0.00 0.06 0 0.02 0.28
#> TCGA.AZ.4614.01 5 0.0000 0.000 0.00 0.00 0.00 0.00 1 0.00 0.00
#> TCGA.A6.3809.01 2 0.0000 0.982 0.00 1.00 0.00 0.00 0 0.00 0.00
#> TCGA.G4.6322.01 3 0.0000 0.000 0.00 0.00 1.00 0.00 0 0.00 0.00
#> TCGA.D5.6531.01 1 0.0504 0.832 0.98 0.00 0.00 0.00 0 0.02 0.00
#> TCGA.CM.6675.01 6 0.0000 0.000 0.00 0.00 0.00 0.00 0 1.00 0.00
#> TCGA.CK.6746.01 2 0.1166 0.944 0.00 0.94 0.00 0.00 0 0.00 0.06
#> TCGA.D5.6538.01 4 0.0000 1.000 0.00 0.00 0.00 1.00 0 0.00 0.00
#> TCGA.CK.4952.01 7 0.3525 0.000 0.00 0.00 0.44 0.00 0 0.00 0.56
#> TCGA.CK.5913.01 2 0.0000 0.982 0.00 1.00 0.00 0.00 0 0.00 0.00
#> TCGA.G4.6320.01 1 0.0504 0.832 0.98 0.00 0.00 0.00 0 0.02 0.00
#> TCGA.A6.5659.01 4 0.0000 1.000 0.00 0.00 0.00 1.00 0 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.A6.2686.01 2 0.0000 0.938 0.00 1.0 0.00 0.00 0 0.00 0.00 0.00
#> TCGA.DM.A0XD.01 1 0.3193 0.588 0.62 0.0 0.00 0.00 0 0.00 0.00 0.38
#> TCGA.D5.7000.01 1 0.0000 0.461 1.00 0.0 0.00 0.00 0 0.00 0.00 0.00
#> TCGA.CK.6751.01 1 0.0000 0.461 1.00 0.0 0.00 0.00 0 0.00 0.00 0.00
#> TCGA.DM.A1DA.01 8 0.4028 0.000 0.28 0.0 0.00 0.02 0 0.00 0.04 0.66
#> TCGA.AZ.4614.01 5 0.0000 0.000 0.00 0.0 0.00 0.00 1 0.00 0.00 0.00
#> TCGA.A6.3809.01 2 0.0000 0.938 0.00 1.0 0.00 0.00 0 0.00 0.00 0.00
#> TCGA.G4.6322.01 3 0.0000 0.000 0.00 0.0 1.00 0.00 0 0.00 0.00 0.00
#> TCGA.D5.6531.01 1 0.3329 0.531 0.52 0.0 0.00 0.00 0 0.00 0.00 0.48
#> TCGA.CM.6675.01 6 0.0471 0.000 0.00 0.0 0.00 0.00 0 0.98 0.00 0.02
#> TCGA.CK.6746.01 2 0.3178 0.798 0.00 0.8 0.00 0.00 0 0.02 0.04 0.14
#> TCGA.D5.6538.01 4 0.0000 1.000 0.00 0.0 0.00 1.00 0 0.00 0.00 0.00
#> TCGA.CK.4952.01 7 0.1341 0.000 0.00 0.0 0.08 0.00 0 0.00 0.92 0.00
#> TCGA.CK.5913.01 2 0.0000 0.938 0.00 1.0 0.00 0.00 0 0.00 0.00 0.00
#> TCGA.G4.6320.01 1 0.3299 0.569 0.56 0.0 0.00 0.00 0 0.00 0.00 0.44
#> TCGA.A6.5659.01 4 0.0000 1.000 0.00 0.0 0.00 1.00 0 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: Node012. Child nodes: Node01111 , Node01112-leaf , Node01113-leaf , Node01114-leaf , Node01121-leaf , Node01122-leaf , Node01123-leaf , Node01124-leaf , Node01211-leaf , Node01212-leaf , Node01213-leaf , Node01221-leaf , Node01222-leaf , Node01223-leaf , Node01224-leaf , Node02121-leaf , Node02122-leaf , Node02123-leaf , Node04221-leaf , Node04222-leaf , Node04223-leaf .
The object with results only for a single top-value method and a single partitioning method can be extracted as:
res = res_rh["0122"]
A summary of res and all the functions that can be applied to it:
res
#> A 'ConsensusPartition' object with k = 2, 3, 4, 5, 6, 7, 8.
#> On a matrix with 30000 rows and 25 columns.
#> Top rows (1000) are extracted by 'ATC' method.
#> Subgroups are detected by '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 0.52048 0.480 0.480
#> 3 3 1.000 0.978 0.989 0.24604 0.840 0.676
#> 4 4 1.000 0.997 0.998 0.03893 0.980 0.942
#> 5 5 0.957 0.891 0.982 0.00993 0.997 0.990
#> 6 6 0.933 0.812 0.930 0.02990 1.000 1.000
#> 7 7 0.797 0.655 0.894 0.04438 0.970 0.907
#> 8 8 0.807 0.628 0.880 0.04002 0.973 0.910
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.D5.6540.01 2 0 1 0 1
#> TCGA.G4.6588.01 1 0 1 1 0
#> TCGA.AZ.6606.01 2 0 1 0 1
#> TCGA.F4.6570.01 1 0 1 1 0
#> TCGA.G4.6299.01 2 0 1 0 1
#> TCGA.A6.4105.01 2 0 1 0 1
#> TCGA.DT.5265.01 2 0 1 0 1
#> TCGA.CM.6171.01 1 0 1 1 0
#> TCGA.AD.A5EJ.01 1 0 1 1 0
#> TCGA.CK.5916.01 1 0 1 1 0
#> TCGA.CM.5861.01 1 0 1 1 0
#> TCGA.G4.6586.01 1 0 1 1 0
#> TCGA.AZ.6598.01 2 0 1 0 1
#> TCGA.F4.6461.01 1 0 1 1 0
#> TCGA.AD.6889.01 2 0 1 0 1
#> TCGA.AA.3663.01 2 0 1 0 1
#> TCGA.CA.5254.01 2 0 1 0 1
#> TCGA.A6.4107.01 1 0 1 1 0
#> TCGA.A6.5665.01 1 0 1 1 0
#> TCGA.QG.A5Z2.01 2 0 1 0 1
#> TCGA.A6.6653.01 2 0 1 0 1
#> TCGA.A6.5661.01 1 0 1 1 0
#> TCGA.A6.2672.01 1 0 1 1 0
#> TCGA.AA.3492.01 1 0 1 1 0
#> TCGA.DM.A1HB.01 2 0 1 0 1
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.D5.6540.01 2 0.0000 1.000 0.0 1.00 0.00
#> TCGA.G4.6588.01 1 0.0000 1.000 1.0 0.00 0.00
#> TCGA.AZ.6606.01 3 0.0892 0.922 0.0 0.02 0.98
#> TCGA.F4.6570.01 1 0.0000 1.000 1.0 0.00 0.00
#> TCGA.G4.6299.01 2 0.0000 1.000 0.0 1.00 0.00
#> TCGA.A6.4105.01 3 0.0000 0.925 0.0 0.00 1.00
#> TCGA.DT.5265.01 3 0.4002 0.807 0.0 0.16 0.84
#> TCGA.CM.6171.01 1 0.0000 1.000 1.0 0.00 0.00
#> TCGA.AD.A5EJ.01 1 0.0000 1.000 1.0 0.00 0.00
#> TCGA.CK.5916.01 1 0.0000 1.000 1.0 0.00 0.00
#> TCGA.CM.5861.01 1 0.0000 1.000 1.0 0.00 0.00
#> TCGA.G4.6586.01 1 0.0000 1.000 1.0 0.00 0.00
#> TCGA.AZ.6598.01 2 0.0000 1.000 0.0 1.00 0.00
#> TCGA.F4.6461.01 1 0.0000 1.000 1.0 0.00 0.00
#> TCGA.AD.6889.01 2 0.0000 1.000 0.0 1.00 0.00
#> TCGA.AA.3663.01 2 0.0000 1.000 0.0 1.00 0.00
#> TCGA.CA.5254.01 3 0.0000 0.925 0.0 0.00 1.00
#> TCGA.A6.4107.01 3 0.2959 0.860 0.1 0.00 0.90
#> TCGA.A6.5665.01 1 0.0000 1.000 1.0 0.00 0.00
#> TCGA.QG.A5Z2.01 2 0.0000 1.000 0.0 1.00 0.00
#> TCGA.A6.6653.01 2 0.0000 1.000 0.0 1.00 0.00
#> TCGA.A6.5661.01 1 0.0000 1.000 1.0 0.00 0.00
#> TCGA.A6.2672.01 1 0.0000 1.000 1.0 0.00 0.00
#> TCGA.AA.3492.01 1 0.0000 1.000 1.0 0.00 0.00
#> TCGA.DM.A1HB.01 2 0.0000 1.000 0.0 1.00 0.00
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> TCGA.D5.6540.01 2 0.0000 0.997 0 1.00 0.00 0.00
#> TCGA.G4.6588.01 1 0.0000 1.000 1 0.00 0.00 0.00
#> TCGA.AZ.6606.01 3 0.0000 1.000 0 0.00 1.00 0.00
#> TCGA.F4.6570.01 1 0.0000 1.000 1 0.00 0.00 0.00
#> TCGA.G4.6299.01 2 0.0707 0.979 0 0.98 0.02 0.00
#> TCGA.A6.4105.01 3 0.0000 1.000 0 0.00 1.00 0.00
#> TCGA.DT.5265.01 3 0.0000 1.000 0 0.00 1.00 0.00
#> TCGA.CM.6171.01 1 0.0000 1.000 1 0.00 0.00 0.00
#> TCGA.AD.A5EJ.01 1 0.0000 1.000 1 0.00 0.00 0.00
#> TCGA.CK.5916.01 1 0.0000 1.000 1 0.00 0.00 0.00
#> TCGA.CM.5861.01 1 0.0000 1.000 1 0.00 0.00 0.00
#> TCGA.G4.6586.01 1 0.0000 1.000 1 0.00 0.00 0.00
#> TCGA.AZ.6598.01 2 0.0000 0.997 0 1.00 0.00 0.00
#> TCGA.F4.6461.01 1 0.0000 1.000 1 0.00 0.00 0.00
#> TCGA.AD.6889.01 2 0.0000 0.997 0 1.00 0.00 0.00
#> TCGA.AA.3663.01 2 0.0000 0.997 0 1.00 0.00 0.00
#> TCGA.CA.5254.01 4 0.0000 0.980 0 0.00 0.00 1.00
#> TCGA.A6.4107.01 4 0.0707 0.980 0 0.00 0.02 0.98
#> TCGA.A6.5665.01 1 0.0000 1.000 1 0.00 0.00 0.00
#> TCGA.QG.A5Z2.01 2 0.0000 0.997 0 1.00 0.00 0.00
#> TCGA.A6.6653.01 2 0.0000 0.997 0 1.00 0.00 0.00
#> TCGA.A6.5661.01 1 0.0000 1.000 1 0.00 0.00 0.00
#> TCGA.A6.2672.01 1 0.0000 1.000 1 0.00 0.00 0.00
#> TCGA.AA.3492.01 1 0.0000 1.000 1 0.00 0.00 0.00
#> TCGA.DM.A1HB.01 2 0.0000 0.997 0 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.D5.6540.01 2 0.0000 0.971 0.00 1.00 0.00 0.00 0.00
#> TCGA.G4.6588.01 1 0.0000 0.998 1.00 0.00 0.00 0.00 0.00
#> TCGA.AZ.6606.01 3 0.0000 0.934 0.00 0.00 1.00 0.00 0.00
#> TCGA.F4.6570.01 1 0.0000 0.998 1.00 0.00 0.00 0.00 0.00
#> TCGA.G4.6299.01 2 0.3627 0.815 0.00 0.84 0.10 0.02 0.04
#> TCGA.A6.4105.01 3 0.0609 0.928 0.00 0.00 0.98 0.00 0.02
#> TCGA.DT.5265.01 3 0.2438 0.881 0.00 0.04 0.90 0.00 0.06
#> TCGA.CM.6171.01 1 0.0000 0.998 1.00 0.00 0.00 0.00 0.00
#> TCGA.AD.A5EJ.01 1 0.0000 0.998 1.00 0.00 0.00 0.00 0.00
#> TCGA.CK.5916.01 1 0.0000 0.998 1.00 0.00 0.00 0.00 0.00
#> TCGA.CM.5861.01 1 0.0000 0.998 1.00 0.00 0.00 0.00 0.00
#> TCGA.G4.6586.01 1 0.0000 0.998 1.00 0.00 0.00 0.00 0.00
#> TCGA.AZ.6598.01 2 0.0000 0.971 0.00 1.00 0.00 0.00 0.00
#> TCGA.F4.6461.01 1 0.0609 0.980 0.98 0.00 0.00 0.00 0.02
#> TCGA.AD.6889.01 2 0.0000 0.971 0.00 1.00 0.00 0.00 0.00
#> TCGA.AA.3663.01 2 0.1043 0.944 0.00 0.96 0.00 0.00 0.04
#> TCGA.CA.5254.01 4 0.0000 0.000 0.00 0.00 0.00 1.00 0.00
#> TCGA.A6.4107.01 5 0.2280 0.000 0.00 0.00 0.00 0.12 0.88
#> TCGA.A6.5665.01 1 0.0000 0.998 1.00 0.00 0.00 0.00 0.00
#> TCGA.QG.A5Z2.01 2 0.0000 0.971 0.00 1.00 0.00 0.00 0.00
#> TCGA.A6.6653.01 2 0.0000 0.971 0.00 1.00 0.00 0.00 0.00
#> TCGA.A6.5661.01 1 0.0000 0.998 1.00 0.00 0.00 0.00 0.00
#> TCGA.A6.2672.01 1 0.0000 0.998 1.00 0.00 0.00 0.00 0.00
#> TCGA.AA.3492.01 1 0.0000 0.998 1.00 0.00 0.00 0.00 0.00
#> TCGA.DM.A1HB.01 2 0.0000 0.971 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.D5.6540.01 2 0.0000 0.903 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.G4.6588.01 1 0.0000 0.980 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AZ.6606.01 3 0.0000 0.730 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.F4.6570.01 1 0.0000 0.980 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.G4.6299.01 2 0.3982 0.693 0.00 0.74 0.06 0.00 0.00 0.20
#> TCGA.A6.4105.01 3 0.3460 0.658 0.00 0.00 0.76 0.02 0.00 0.22
#> TCGA.DT.5265.01 3 0.3499 0.606 0.00 0.00 0.68 0.00 0.00 0.32
#> TCGA.CM.6171.01 1 0.0000 0.980 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AD.A5EJ.01 1 0.0937 0.971 0.96 0.00 0.00 0.00 0.00 0.04
#> TCGA.CK.5916.01 1 0.0937 0.971 0.96 0.00 0.00 0.00 0.00 0.04
#> TCGA.CM.5861.01 1 0.0000 0.980 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.G4.6586.01 1 0.0000 0.980 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AZ.6598.01 2 0.0000 0.903 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.F4.6461.01 1 0.1556 0.942 0.92 0.00 0.00 0.00 0.00 0.08
#> TCGA.AD.6889.01 2 0.0000 0.903 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.AA.3663.01 2 0.3706 0.524 0.00 0.62 0.00 0.00 0.00 0.38
#> TCGA.CA.5254.01 4 0.0547 0.000 0.00 0.00 0.00 0.98 0.02 0.00
#> TCGA.A6.4107.01 5 0.0000 0.000 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.A6.5665.01 1 0.0937 0.971 0.96 0.00 0.00 0.00 0.00 0.04
#> TCGA.QG.A5Z2.01 2 0.0547 0.897 0.00 0.98 0.00 0.00 0.00 0.02
#> TCGA.A6.6653.01 2 0.0000 0.903 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.A6.5661.01 1 0.0937 0.971 0.96 0.00 0.00 0.00 0.00 0.04
#> TCGA.A6.2672.01 1 0.0000 0.980 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AA.3492.01 1 0.0000 0.980 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DM.A1HB.01 2 0.0937 0.892 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.D5.6540.01 2 0.0000 0.858 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.G4.6588.01 1 0.0000 0.927 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AZ.6606.01 3 0.3943 -0.174 0.00 0.00 0.56 0.00 0.00 0.42 0.02
#> TCGA.F4.6570.01 1 0.0000 0.927 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.G4.6299.01 2 0.5293 0.200 0.00 0.54 0.00 0.00 0.02 0.32 0.12
#> TCGA.A6.4105.01 3 0.0000 0.328 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DT.5265.01 6 0.2708 0.000 0.00 0.00 0.22 0.00 0.00 0.78 0.00
#> TCGA.CM.6171.01 1 0.0504 0.927 0.98 0.00 0.00 0.00 0.00 0.00 0.02
#> TCGA.AD.A5EJ.01 1 0.2278 0.909 0.88 0.00 0.00 0.00 0.00 0.04 0.08
#> TCGA.CK.5916.01 1 0.2278 0.909 0.88 0.00 0.00 0.00 0.00 0.04 0.08
#> TCGA.CM.5861.01 1 0.1166 0.898 0.94 0.00 0.00 0.00 0.00 0.06 0.00
#> TCGA.G4.6586.01 1 0.1166 0.898 0.94 0.00 0.00 0.00 0.00 0.06 0.00
#> TCGA.AZ.6598.01 2 0.0863 0.861 0.00 0.96 0.00 0.00 0.00 0.00 0.04
#> TCGA.F4.6461.01 1 0.3734 0.830 0.78 0.00 0.00 0.00 0.04 0.04 0.14
#> TCGA.AD.6889.01 2 0.0863 0.861 0.00 0.96 0.00 0.00 0.00 0.00 0.04
#> TCGA.AA.3663.01 7 0.2832 0.000 0.00 0.24 0.00 0.00 0.00 0.00 0.76
#> TCGA.CA.5254.01 4 0.0000 0.000 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.A6.4107.01 5 0.0504 0.000 0.00 0.00 0.00 0.02 0.98 0.00 0.00
#> TCGA.A6.5665.01 1 0.2278 0.909 0.88 0.00 0.00 0.00 0.00 0.04 0.08
#> TCGA.QG.A5Z2.01 2 0.0000 0.858 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.A6.6653.01 2 0.0863 0.861 0.00 0.96 0.00 0.00 0.00 0.00 0.04
#> TCGA.A6.5661.01 1 0.2278 0.909 0.88 0.00 0.00 0.00 0.00 0.04 0.08
#> TCGA.A6.2672.01 1 0.0000 0.927 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AA.3492.01 1 0.0000 0.927 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DM.A1HB.01 2 0.1166 0.816 0.00 0.94 0.00 0.00 0.00 0.00 0.06
cbind(get_classes(res, k = 8), get_membership(res, k = 8))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7 p8
#> TCGA.D5.6540.01 2 0.1887 0.846 0.00 0.90 0.00 0 0 0.00 0.04 0.06
#> TCGA.G4.6588.01 1 0.0000 0.848 1.00 0.00 0.00 0 0 0.00 0.00 0.00
#> TCGA.AZ.6606.01 6 0.4504 0.271 0.00 0.00 0.24 0 0 0.64 0.02 0.10
#> TCGA.F4.6570.01 1 0.0000 0.848 1.00 0.00 0.00 0 0 0.00 0.00 0.00
#> TCGA.G4.6299.01 8 0.3845 0.000 0.00 0.28 0.00 0 0 0.06 0.00 0.66
#> TCGA.A6.4105.01 3 0.4169 0.000 0.00 0.00 0.70 0 0 0.10 0.02 0.18
#> TCGA.DT.5265.01 6 0.1341 0.472 0.00 0.00 0.00 0 0 0.92 0.00 0.08
#> TCGA.CM.6171.01 1 0.0000 0.848 1.00 0.00 0.00 0 0 0.00 0.00 0.00
#> TCGA.AD.A5EJ.01 1 0.2938 0.781 0.70 0.00 0.30 0 0 0.00 0.00 0.00
#> TCGA.CK.5916.01 1 0.2938 0.781 0.70 0.00 0.30 0 0 0.00 0.00 0.00
#> TCGA.CM.5861.01 1 0.0471 0.839 0.98 0.00 0.00 0 0 0.00 0.00 0.02
#> TCGA.G4.6586.01 1 0.0471 0.839 0.98 0.00 0.00 0 0 0.00 0.00 0.02
#> TCGA.AZ.6598.01 2 0.0808 0.883 0.00 0.96 0.00 0 0 0.00 0.04 0.00
#> TCGA.F4.6461.01 1 0.3374 0.765 0.68 0.00 0.30 0 0 0.00 0.02 0.00
#> TCGA.AD.6889.01 2 0.0471 0.894 0.00 0.98 0.00 0 0 0.00 0.02 0.00
#> TCGA.AA.3663.01 7 0.1947 0.000 0.00 0.14 0.00 0 0 0.00 0.86 0.00
#> TCGA.CA.5254.01 4 0.0000 0.000 0.00 0.00 0.00 1 0 0.00 0.00 0.00
#> TCGA.A6.4107.01 5 0.0000 0.000 0.00 0.00 0.00 0 1 0.00 0.00 0.00
#> TCGA.A6.5665.01 1 0.2938 0.781 0.70 0.00 0.30 0 0 0.00 0.00 0.00
#> TCGA.QG.A5Z2.01 2 0.0941 0.881 0.00 0.96 0.00 0 0 0.00 0.02 0.02
#> TCGA.A6.6653.01 2 0.0471 0.894 0.00 0.98 0.00 0 0 0.00 0.02 0.00
#> TCGA.A6.5661.01 1 0.2938 0.781 0.70 0.00 0.30 0 0 0.00 0.00 0.00
#> TCGA.A6.2672.01 1 0.0000 0.848 1.00 0.00 0.00 0 0 0.00 0.00 0.00
#> TCGA.AA.3492.01 1 0.0000 0.848 1.00 0.00 0.00 0 0 0.00 0.00 0.00
#> TCGA.DM.A1HB.01 2 0.3073 0.757 0.00 0.80 0.00 0 0 0.00 0.10 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: Node0. Child nodes: Node011 , Node012 , Node021 , Node022-leaf , Node023-leaf , Node041 , Node042 , Node043 .
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 54 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 0.2579 0.743 0.743
#> 3 3 0.888 0.976 0.984 0.9266 0.748 0.661
#> 4 4 0.555 0.741 0.808 0.1866 0.990 0.979
#> 5 5 0.599 0.508 0.647 0.1808 0.653 0.354
#> 6 6 0.704 0.616 0.773 0.0984 0.822 0.435
#> 7 7 0.795 0.754 0.847 0.0628 0.915 0.633
#> 8 8 0.753 0.660 0.809 0.0379 0.995 0.972
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.AA.3494.11 1 0 1 1 0
#> TCGA.AA.3712.11 1 0 1 1 0
#> TCGA.A6.2681.11 1 0 1 1 0
#> TCGA.A6.2675.11 1 0 1 1 0
#> TCGA.AA.3663.11 1 0 1 1 0
#> TCGA.A6.2671.11 1 0 1 1 0
#> TCGA.A6.2680.11 1 0 1 1 0
#> TCGA.AZ.6598.11 1 0 1 1 0
#> TCGA.G4.6295.11 1 0 1 1 0
#> TCGA.A6.6142.01 2 0 1 0 1
#> TCGA.AG.A020.11 1 0 1 1 0
#> TCGA.G4.6311.11 1 0 1 1 0
#> TCGA.G4.6625.11 1 0 1 1 0
#> TCGA.AG.A01Y.11 1 0 1 1 0
#> TCGA.A6.4107.11 1 0 1 1 0
#> TCGA.AG.A02N.11 1 0 1 1 0
#> TCGA.AY.A8YK.01 2 0 1 0 1
#> TCGA.A6.2685.01 2 0 1 0 1
#> TCGA.5M.AAT6.01 2 0 1 0 1
#> TCGA.A6.2684.11 1 0 1 1 0
#> TCGA.G4.6320.11 1 0 1 1 0
#> TCGA.AZ.6599.11 1 0 1 1 0
#> TCGA.A6.A565.01 1 0 1 1 0
#> TCGA.A6.2679.11 1 0 1 1 0
#> TCGA.AD.6964.01 2 0 1 0 1
#> TCGA.G4.6314.11 1 0 1 1 0
#> TCGA.AG.3725.11 1 0 1 1 0
#> TCGA.A6.5667.11 1 0 1 1 0
#> TCGA.AA.3655.11 1 0 1 1 0
#> TCGA.AZ.5403.01 2 0 1 0 1
#> TCGA.AA.3510.11 1 0 1 1 0
#> TCGA.AG.A036.11 1 0 1 1 0
#> TCGA.CM.6162.01 2 0 1 0 1
#> TCGA.F4.6703.01 2 0 1 0 1
#> TCGA.AA.3488.11 1 0 1 1 0
#> TCGA.A6.2685.11 1 0 1 1 0
#> TCGA.G4.6298.11 1 0 1 1 0
#> TCGA.G4.6322.11 1 0 1 1 0
#> TCGA.AA.3660.11 1 0 1 1 0
#> TCGA.G4.6297.11 1 0 1 1 0
#> TCGA.AZ.6600.11 1 0 1 1 0
#> TCGA.AA.3713.11 1 0 1 1 0
#> TCGA.AA.3697.11 1 0 1 1 0
#> TCGA.AZ.6601.11 1 0 1 1 0
#> TCGA.AA.3509.11 1 0 1 1 0
#> TCGA.G4.6302.11 1 0 1 1 0
#> TCGA.AG.3731.11 1 0 1 1 0
#> TCGA.A6.2686.11 1 0 1 1 0
#> TCGA.AA.3495.11 1 0 1 1 0
#> TCGA.AG.A01W.11 1 0 1 1 0
#> TCGA.AA.3506.11 1 0 1 1 0
#> TCGA.AA.3502.11 1 0 1 1 0
#> TCGA.AA.3492.11 1 0 1 1 0
#> TCGA.A6.2682.11 1 0 1 1 0
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.AA.3494.11 3 0.3340 0.904 0.12 0.00 0.88
#> TCGA.AA.3712.11 1 0.0000 0.996 1.00 0.00 0.00
#> TCGA.A6.2681.11 1 0.0000 0.996 1.00 0.00 0.00
#> TCGA.A6.2675.11 1 0.0000 0.996 1.00 0.00 0.00
#> TCGA.AA.3663.11 1 0.0000 0.996 1.00 0.00 0.00
#> TCGA.A6.2671.11 1 0.0000 0.996 1.00 0.00 0.00
#> TCGA.A6.2680.11 1 0.0000 0.996 1.00 0.00 0.00
#> TCGA.AZ.6598.11 1 0.0000 0.996 1.00 0.00 0.00
#> TCGA.G4.6295.11 3 0.0892 0.910 0.02 0.00 0.98
#> TCGA.A6.6142.01 2 0.0000 0.992 0.00 1.00 0.00
#> TCGA.AG.A020.11 1 0.0000 0.996 1.00 0.00 0.00
#> TCGA.G4.6311.11 1 0.0000 0.996 1.00 0.00 0.00
#> TCGA.G4.6625.11 1 0.0000 0.996 1.00 0.00 0.00
#> TCGA.AG.A01Y.11 1 0.0000 0.996 1.00 0.00 0.00
#> TCGA.A6.4107.11 3 0.3340 0.904 0.12 0.00 0.88
#> TCGA.AG.A02N.11 1 0.0000 0.996 1.00 0.00 0.00
#> TCGA.AY.A8YK.01 2 0.0000 0.992 0.00 1.00 0.00
#> TCGA.A6.2685.01 2 0.0892 0.987 0.00 0.98 0.02
#> TCGA.5M.AAT6.01 2 0.0000 0.992 0.00 1.00 0.00
#> TCGA.A6.2684.11 1 0.0000 0.996 1.00 0.00 0.00
#> TCGA.G4.6320.11 1 0.0000 0.996 1.00 0.00 0.00
#> TCGA.AZ.6599.11 1 0.0000 0.996 1.00 0.00 0.00
#> TCGA.A6.A565.01 3 0.0000 0.881 0.00 0.00 1.00
#> TCGA.A6.2679.11 3 0.0892 0.910 0.02 0.00 0.98
#> TCGA.AD.6964.01 2 0.0000 0.992 0.00 1.00 0.00
#> TCGA.G4.6314.11 1 0.0000 0.996 1.00 0.00 0.00
#> TCGA.AG.3725.11 1 0.0000 0.996 1.00 0.00 0.00
#> TCGA.A6.5667.11 1 0.0000 0.996 1.00 0.00 0.00
#> TCGA.AA.3655.11 1 0.0000 0.996 1.00 0.00 0.00
#> TCGA.AZ.5403.01 2 0.0000 0.992 0.00 1.00 0.00
#> TCGA.AA.3510.11 3 0.2066 0.924 0.06 0.00 0.94
#> TCGA.AG.A036.11 1 0.0000 0.996 1.00 0.00 0.00
#> TCGA.CM.6162.01 2 0.0892 0.987 0.00 0.98 0.02
#> TCGA.F4.6703.01 2 0.1529 0.976 0.00 0.96 0.04
#> TCGA.AA.3488.11 1 0.0000 0.996 1.00 0.00 0.00
#> TCGA.A6.2685.11 1 0.0000 0.996 1.00 0.00 0.00
#> TCGA.G4.6298.11 1 0.0000 0.996 1.00 0.00 0.00
#> TCGA.G4.6322.11 1 0.0000 0.996 1.00 0.00 0.00
#> TCGA.AA.3660.11 1 0.0000 0.996 1.00 0.00 0.00
#> TCGA.G4.6297.11 1 0.0000 0.996 1.00 0.00 0.00
#> TCGA.AZ.6600.11 1 0.0000 0.996 1.00 0.00 0.00
#> TCGA.AA.3713.11 3 0.3340 0.904 0.12 0.00 0.88
#> TCGA.AA.3697.11 3 0.3340 0.904 0.12 0.00 0.88
#> TCGA.AZ.6601.11 1 0.0000 0.996 1.00 0.00 0.00
#> TCGA.AA.3509.11 1 0.0000 0.996 1.00 0.00 0.00
#> TCGA.G4.6302.11 3 0.1529 0.924 0.04 0.00 0.96
#> TCGA.AG.3731.11 1 0.0000 0.996 1.00 0.00 0.00
#> TCGA.A6.2686.11 1 0.0000 0.996 1.00 0.00 0.00
#> TCGA.AA.3495.11 1 0.0000 0.996 1.00 0.00 0.00
#> TCGA.AG.A01W.11 1 0.0000 0.996 1.00 0.00 0.00
#> TCGA.AA.3506.11 1 0.3340 0.851 0.88 0.00 0.12
#> TCGA.AA.3502.11 3 0.1529 0.924 0.04 0.00 0.96
#> TCGA.AA.3492.11 1 0.0000 0.996 1.00 0.00 0.00
#> TCGA.A6.2682.11 1 0.0000 0.996 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.AA.3494.11 3 0.5428 0.791 0.12 0.00 0.74 0.14
#> TCGA.AA.3712.11 1 0.0000 0.824 1.00 0.00 0.00 0.00
#> TCGA.A6.2681.11 1 0.4277 0.808 0.72 0.00 0.28 0.00
#> TCGA.A6.2675.11 1 0.3400 0.708 0.82 0.00 0.18 0.00
#> TCGA.AA.3663.11 1 0.3400 0.708 0.82 0.00 0.18 0.00
#> TCGA.A6.2671.11 1 0.0000 0.824 1.00 0.00 0.00 0.00
#> TCGA.A6.2680.11 1 0.4277 0.808 0.72 0.00 0.28 0.00
#> TCGA.AZ.6598.11 1 0.4522 0.790 0.68 0.00 0.32 0.00
#> TCGA.G4.6295.11 3 0.4948 0.745 0.00 0.00 0.56 0.44
#> TCGA.A6.6142.01 4 0.4948 1.000 0.00 0.44 0.00 0.56
#> TCGA.AG.A020.11 1 0.4134 0.810 0.74 0.00 0.26 0.00
#> TCGA.G4.6311.11 1 0.1211 0.822 0.96 0.00 0.04 0.00
#> TCGA.G4.6625.11 1 0.3801 0.816 0.78 0.00 0.22 0.00
#> TCGA.AG.A01Y.11 1 0.4277 0.808 0.72 0.00 0.28 0.00
#> TCGA.A6.4107.11 3 0.0707 0.582 0.02 0.00 0.98 0.00
#> TCGA.AG.A02N.11 1 0.0000 0.824 1.00 0.00 0.00 0.00
#> TCGA.AY.A8YK.01 4 0.4948 1.000 0.00 0.44 0.00 0.56
#> TCGA.A6.2685.01 2 0.0000 0.600 0.00 1.00 0.00 0.00
#> TCGA.5M.AAT6.01 2 0.4855 -0.467 0.00 0.60 0.00 0.40
#> TCGA.A6.2684.11 1 0.4134 0.810 0.74 0.00 0.26 0.00
#> TCGA.G4.6320.11 1 0.0000 0.824 1.00 0.00 0.00 0.00
#> TCGA.AZ.6599.11 1 0.0000 0.824 1.00 0.00 0.00 0.00
#> TCGA.A6.A565.01 3 0.4948 0.745 0.00 0.00 0.56 0.44
#> TCGA.A6.2679.11 3 0.4948 0.745 0.00 0.00 0.56 0.44
#> TCGA.AD.6964.01 4 0.4948 1.000 0.00 0.44 0.00 0.56
#> TCGA.G4.6314.11 1 0.4134 0.810 0.74 0.00 0.26 0.00
#> TCGA.AG.3725.11 1 0.4134 0.810 0.74 0.00 0.26 0.00
#> TCGA.A6.5667.11 1 0.3801 0.816 0.78 0.00 0.22 0.00
#> TCGA.AA.3655.11 1 0.0000 0.824 1.00 0.00 0.00 0.00
#> TCGA.AZ.5403.01 2 0.4855 -0.467 0.00 0.60 0.00 0.40
#> TCGA.AA.3510.11 3 0.5428 0.791 0.12 0.00 0.74 0.14
#> TCGA.AG.A036.11 1 0.0000 0.824 1.00 0.00 0.00 0.00
#> TCGA.CM.6162.01 2 0.0000 0.600 0.00 1.00 0.00 0.00
#> TCGA.F4.6703.01 2 0.0000 0.600 0.00 1.00 0.00 0.00
#> TCGA.AA.3488.11 1 0.2647 0.762 0.88 0.00 0.12 0.00
#> TCGA.A6.2685.11 1 0.4134 0.810 0.74 0.00 0.26 0.00
#> TCGA.G4.6298.11 1 0.0000 0.824 1.00 0.00 0.00 0.00
#> TCGA.G4.6322.11 1 0.0000 0.824 1.00 0.00 0.00 0.00
#> TCGA.AA.3660.11 1 0.4134 0.810 0.74 0.00 0.26 0.00
#> TCGA.G4.6297.11 1 0.4522 0.790 0.68 0.00 0.32 0.00
#> TCGA.AZ.6600.11 1 0.0000 0.824 1.00 0.00 0.00 0.00
#> TCGA.AA.3713.11 3 0.5428 0.791 0.12 0.00 0.74 0.14
#> TCGA.AA.3697.11 3 0.5428 0.791 0.12 0.00 0.74 0.14
#> TCGA.AZ.6601.11 1 0.0000 0.824 1.00 0.00 0.00 0.00
#> TCGA.AA.3509.11 1 0.4948 0.691 0.56 0.00 0.44 0.00
#> TCGA.G4.6302.11 3 0.4406 0.793 0.00 0.00 0.70 0.30
#> TCGA.AG.3731.11 1 0.3400 0.708 0.82 0.00 0.18 0.00
#> TCGA.A6.2686.11 1 0.4277 0.808 0.72 0.00 0.28 0.00
#> TCGA.AA.3495.11 1 0.0707 0.821 0.98 0.00 0.02 0.00
#> TCGA.AG.A01W.11 1 0.4948 0.691 0.56 0.00 0.44 0.00
#> TCGA.AA.3506.11 1 0.4134 0.656 0.74 0.00 0.26 0.00
#> TCGA.AA.3502.11 3 0.4522 0.787 0.00 0.00 0.68 0.32
#> TCGA.AA.3492.11 1 0.4277 0.808 0.72 0.00 0.28 0.00
#> TCGA.A6.2682.11 1 0.0000 0.824 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.AA.3494.11 3 0.2616 0.7107 0.02 0.00 0.88 0.00 0.10
#> TCGA.AA.3712.11 5 0.4302 0.4609 0.48 0.00 0.00 0.00 0.52
#> TCGA.A6.2681.11 1 0.0000 0.7522 1.00 0.00 0.00 0.00 0.00
#> TCGA.A6.2675.11 3 0.5297 0.5146 0.06 0.00 0.58 0.00 0.36
#> TCGA.AA.3663.11 3 0.4990 0.5483 0.04 0.00 0.60 0.00 0.36
#> TCGA.A6.2671.11 5 0.4302 0.4609 0.48 0.00 0.00 0.00 0.52
#> TCGA.A6.2680.11 1 0.0000 0.7522 1.00 0.00 0.00 0.00 0.00
#> TCGA.AZ.6598.11 1 0.3274 0.4674 0.78 0.00 0.22 0.00 0.00
#> TCGA.G4.6295.11 5 0.6541 -0.3060 0.00 0.26 0.26 0.00 0.48
#> TCGA.A6.6142.01 4 0.0000 0.8492 0.00 0.00 0.00 1.00 0.00
#> TCGA.AG.A020.11 1 0.0000 0.7522 1.00 0.00 0.00 0.00 0.00
#> TCGA.G4.6311.11 1 0.4675 -0.2037 0.60 0.00 0.02 0.00 0.38
#> TCGA.G4.6625.11 1 0.2732 0.5853 0.84 0.00 0.00 0.00 0.16
#> TCGA.AG.A01Y.11 1 0.0000 0.7522 1.00 0.00 0.00 0.00 0.00
#> TCGA.A6.4107.11 3 0.3424 0.6077 0.24 0.00 0.76 0.00 0.00
#> TCGA.AG.A02N.11 5 0.4302 0.4609 0.48 0.00 0.00 0.00 0.52
#> TCGA.AY.A8YK.01 4 0.0000 0.8492 0.00 0.00 0.00 1.00 0.00
#> TCGA.A6.2685.01 2 0.3561 1.0000 0.00 0.74 0.00 0.26 0.00
#> TCGA.5M.AAT6.01 4 0.3109 0.7222 0.00 0.20 0.00 0.80 0.00
#> TCGA.A6.2684.11 1 0.0000 0.7522 1.00 0.00 0.00 0.00 0.00
#> TCGA.G4.6320.11 1 0.4302 -0.4279 0.52 0.00 0.00 0.00 0.48
#> TCGA.AZ.6599.11 5 0.4302 0.4609 0.48 0.00 0.00 0.00 0.52
#> TCGA.A6.A565.01 5 0.6541 -0.3060 0.00 0.26 0.26 0.00 0.48
#> TCGA.A6.2679.11 5 0.6541 -0.3060 0.00 0.26 0.26 0.00 0.48
#> TCGA.AD.6964.01 4 0.0000 0.8492 0.00 0.00 0.00 1.00 0.00
#> TCGA.G4.6314.11 1 0.0000 0.7522 1.00 0.00 0.00 0.00 0.00
#> TCGA.AG.3725.11 1 0.0000 0.7522 1.00 0.00 0.00 0.00 0.00
#> TCGA.A6.5667.11 1 0.2516 0.6119 0.86 0.00 0.00 0.00 0.14
#> TCGA.AA.3655.11 5 0.4302 0.4609 0.48 0.00 0.00 0.00 0.52
#> TCGA.AZ.5403.01 4 0.3109 0.7222 0.00 0.20 0.00 0.80 0.00
#> TCGA.AA.3510.11 3 0.2331 0.7011 0.02 0.00 0.90 0.00 0.08
#> TCGA.AG.A036.11 5 0.4302 0.4609 0.48 0.00 0.00 0.00 0.52
#> TCGA.CM.6162.01 2 0.3561 1.0000 0.00 0.74 0.00 0.26 0.00
#> TCGA.F4.6703.01 2 0.3561 1.0000 0.00 0.74 0.00 0.26 0.00
#> TCGA.AA.3488.11 5 0.6697 -0.0523 0.24 0.00 0.38 0.00 0.38
#> TCGA.A6.2685.11 1 0.0000 0.7522 1.00 0.00 0.00 0.00 0.00
#> TCGA.G4.6298.11 5 0.4302 0.4609 0.48 0.00 0.00 0.00 0.52
#> TCGA.G4.6322.11 5 0.4302 0.4609 0.48 0.00 0.00 0.00 0.52
#> TCGA.AA.3660.11 1 0.0000 0.7522 1.00 0.00 0.00 0.00 0.00
#> TCGA.G4.6297.11 1 0.2732 0.5674 0.84 0.00 0.16 0.00 0.00
#> TCGA.AZ.6600.11 5 0.4302 0.4609 0.48 0.00 0.00 0.00 0.52
#> TCGA.AA.3713.11 3 0.2616 0.7107 0.02 0.00 0.88 0.00 0.10
#> TCGA.AA.3697.11 3 0.2616 0.7107 0.02 0.00 0.88 0.00 0.10
#> TCGA.AZ.6601.11 5 0.4302 0.4609 0.48 0.00 0.00 0.00 0.52
#> TCGA.AA.3509.11 3 0.4227 0.4672 0.42 0.00 0.58 0.00 0.00
#> TCGA.G4.6302.11 3 0.3878 0.5363 0.04 0.12 0.82 0.00 0.02
#> TCGA.AG.3731.11 3 0.4990 0.5483 0.04 0.00 0.60 0.00 0.36
#> TCGA.A6.2686.11 1 0.0000 0.7522 1.00 0.00 0.00 0.00 0.00
#> TCGA.AA.3495.11 1 0.5689 -0.3840 0.48 0.00 0.08 0.00 0.44
#> TCGA.AG.A01W.11 3 0.4227 0.4672 0.42 0.00 0.58 0.00 0.00
#> TCGA.AA.3506.11 3 0.3852 0.6824 0.02 0.00 0.76 0.00 0.22
#> TCGA.AA.3502.11 3 0.2873 0.5290 0.00 0.12 0.86 0.00 0.02
#> TCGA.AA.3492.11 1 0.0609 0.7340 0.98 0.00 0.02 0.00 0.00
#> TCGA.A6.2682.11 1 0.4302 -0.4279 0.52 0.00 0.00 0.00 0.48
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> TCGA.AA.3494.11 3 0.4246 0.8962 0.02 0.00 0.58 0.00 0.00 0.40
#> TCGA.AA.3712.11 5 0.0000 0.8310 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.A6.2681.11 1 0.1814 0.8755 0.90 0.00 0.00 0.00 0.10 0.00
#> TCGA.A6.2675.11 6 0.4646 0.5170 0.04 0.00 0.00 0.00 0.46 0.50
#> TCGA.AA.3663.11 6 0.4646 0.5170 0.04 0.00 0.00 0.00 0.46 0.50
#> TCGA.A6.2671.11 5 0.0000 0.8310 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.A6.2680.11 1 0.2048 0.8794 0.88 0.00 0.00 0.00 0.12 0.00
#> TCGA.AZ.6598.11 1 0.2190 0.8452 0.90 0.00 0.00 0.00 0.06 0.04
#> TCGA.G4.6295.11 4 0.4337 0.2377 0.00 0.00 0.02 0.50 0.00 0.48
#> TCGA.A6.6142.01 4 0.6296 0.0732 0.02 0.20 0.34 0.44 0.00 0.00
#> TCGA.AG.A020.11 1 0.2581 0.8753 0.86 0.00 0.00 0.00 0.12 0.02
#> TCGA.G4.6311.11 5 0.4172 0.3789 0.28 0.00 0.00 0.00 0.68 0.04
#> TCGA.G4.6625.11 5 0.3828 -0.1403 0.44 0.00 0.00 0.00 0.56 0.00
#> TCGA.AG.A01Y.11 1 0.2581 0.8753 0.86 0.00 0.00 0.00 0.12 0.02
#> TCGA.A6.4107.11 3 0.4246 0.8962 0.02 0.00 0.58 0.00 0.00 0.40
#> TCGA.AG.A02N.11 5 0.0000 0.8310 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.AY.A8YK.01 4 0.6974 0.0623 0.08 0.20 0.30 0.42 0.00 0.00
#> TCGA.A6.2685.01 2 0.0000 0.6510 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.5M.AAT6.01 2 0.5921 0.2553 0.00 0.46 0.24 0.30 0.00 0.00
#> TCGA.A6.2684.11 1 0.2048 0.8794 0.88 0.00 0.00 0.00 0.12 0.00
#> TCGA.G4.6320.11 5 0.0937 0.8083 0.00 0.00 0.00 0.00 0.96 0.04
#> TCGA.AZ.6599.11 5 0.0000 0.8310 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.A6.A565.01 6 0.3869 -0.5347 0.00 0.00 0.00 0.50 0.00 0.50
#> TCGA.A6.2679.11 4 0.4337 0.2377 0.00 0.00 0.02 0.50 0.00 0.48
#> TCGA.AD.6964.01 4 0.5865 0.0606 0.00 0.20 0.36 0.44 0.00 0.00
#> TCGA.G4.6314.11 1 0.2048 0.8794 0.88 0.00 0.00 0.00 0.12 0.00
#> TCGA.AG.3725.11 1 0.2581 0.8753 0.86 0.00 0.00 0.00 0.12 0.02
#> TCGA.A6.5667.11 1 0.3851 0.3489 0.54 0.00 0.00 0.00 0.46 0.00
#> TCGA.AA.3655.11 5 0.0000 0.8310 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.AZ.5403.01 2 0.5921 0.2553 0.00 0.46 0.24 0.30 0.00 0.00
#> TCGA.AA.3510.11 3 0.4246 0.8962 0.02 0.00 0.58 0.00 0.00 0.40
#> TCGA.AG.A036.11 5 0.0000 0.8310 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.CM.6162.01 2 0.0000 0.6510 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.F4.6703.01 2 0.0547 0.6418 0.00 0.98 0.00 0.00 0.00 0.02
#> TCGA.AA.3488.11 5 0.4632 -0.4914 0.04 0.00 0.00 0.00 0.52 0.44
#> TCGA.A6.2685.11 1 0.2048 0.8794 0.88 0.00 0.00 0.00 0.12 0.00
#> TCGA.G4.6298.11 5 0.0000 0.8310 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.G4.6322.11 5 0.0000 0.8310 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.AA.3660.11 1 0.2048 0.8794 0.88 0.00 0.00 0.00 0.12 0.00
#> TCGA.G4.6297.11 1 0.2190 0.8452 0.90 0.00 0.00 0.00 0.06 0.04
#> TCGA.AZ.6600.11 5 0.0000 0.8310 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.AA.3713.11 3 0.4246 0.8962 0.02 0.00 0.58 0.00 0.00 0.40
#> TCGA.AA.3697.11 3 0.3797 0.8813 0.00 0.00 0.58 0.00 0.00 0.42
#> TCGA.AZ.6601.11 5 0.0937 0.8083 0.00 0.00 0.00 0.00 0.96 0.04
#> TCGA.AA.3509.11 1 0.4328 0.2418 0.52 0.00 0.00 0.00 0.02 0.46
#> TCGA.G4.6302.11 3 0.6224 0.4801 0.20 0.00 0.58 0.14 0.00 0.08
#> TCGA.AG.3731.11 6 0.4646 0.5170 0.04 0.00 0.00 0.00 0.46 0.50
#> TCGA.A6.2686.11 1 0.1814 0.8755 0.90 0.00 0.00 0.00 0.10 0.00
#> TCGA.AA.3495.11 5 0.2728 0.6777 0.04 0.00 0.00 0.00 0.86 0.10
#> TCGA.AG.A01W.11 1 0.4328 0.2418 0.52 0.00 0.00 0.00 0.02 0.46
#> TCGA.AA.3506.11 3 0.3851 0.8438 0.00 0.00 0.54 0.00 0.00 0.46
#> TCGA.AA.3502.11 3 0.5363 0.8314 0.02 0.00 0.58 0.08 0.00 0.32
#> TCGA.AA.3492.11 1 0.1814 0.8755 0.90 0.00 0.00 0.00 0.10 0.00
#> TCGA.A6.2682.11 5 0.0937 0.8083 0.00 0.00 0.00 0.00 0.96 0.04
cbind(get_classes(res, k = 7), get_membership(res, k = 7))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7
#> TCGA.AA.3494.11 3 0.0504 0.8496 0.00 0.00 0.98 0.00 0.00 0.02 0
#> TCGA.AA.3712.11 5 0.0000 0.8226 0.00 0.00 0.00 0.00 1.00 0.00 0
#> TCGA.A6.2681.11 1 0.1860 0.9006 0.92 0.00 0.00 0.02 0.02 0.04 0
#> TCGA.A6.2675.11 6 0.4993 0.7017 0.02 0.00 0.12 0.00 0.24 0.62 0
#> TCGA.AA.3663.11 6 0.5152 0.7003 0.02 0.00 0.14 0.00 0.24 0.60 0
#> TCGA.A6.2671.11 5 0.0000 0.8226 0.00 0.00 0.00 0.00 1.00 0.00 0
#> TCGA.A6.2680.11 1 0.2512 0.8840 0.86 0.00 0.00 0.04 0.00 0.10 0
#> TCGA.AZ.6598.11 1 0.2159 0.8961 0.90 0.00 0.00 0.02 0.02 0.06 0
#> TCGA.G4.6295.11 7 0.0000 1.0000 0.00 0.00 0.00 0.00 0.00 0.00 1
#> TCGA.A6.6142.01 4 0.2572 0.8025 0.00 0.20 0.00 0.80 0.00 0.00 0
#> TCGA.AG.A020.11 1 0.3208 0.8499 0.82 0.00 0.00 0.04 0.02 0.12 0
#> TCGA.G4.6311.11 5 0.5556 0.0337 0.40 0.00 0.00 0.02 0.44 0.14 0
#> TCGA.G4.6625.11 5 0.3745 0.4647 0.26 0.00 0.00 0.00 0.70 0.04 0
#> TCGA.AG.A01Y.11 1 0.3396 0.8452 0.80 0.00 0.00 0.04 0.02 0.14 0
#> TCGA.A6.4107.11 3 0.1363 0.8182 0.02 0.00 0.94 0.00 0.00 0.04 0
#> TCGA.AG.A02N.11 5 0.0000 0.8226 0.00 0.00 0.00 0.00 1.00 0.00 0
#> TCGA.AY.A8YK.01 4 0.2572 0.8025 0.00 0.20 0.00 0.80 0.00 0.00 0
#> TCGA.A6.2685.01 2 0.0000 0.9748 0.00 1.00 0.00 0.00 0.00 0.00 0
#> TCGA.5M.AAT6.01 4 0.3558 0.6044 0.00 0.48 0.00 0.52 0.00 0.00 0
#> TCGA.A6.2684.11 1 0.1006 0.9032 0.96 0.00 0.00 0.02 0.02 0.00 0
#> TCGA.G4.6320.11 5 0.2512 0.7196 0.04 0.00 0.00 0.00 0.86 0.10 0
#> TCGA.AZ.6599.11 5 0.0000 0.8226 0.00 0.00 0.00 0.00 1.00 0.00 0
#> TCGA.A6.A565.01 7 0.0000 1.0000 0.00 0.00 0.00 0.00 0.00 0.00 1
#> TCGA.A6.2679.11 7 0.0000 1.0000 0.00 0.00 0.00 0.00 0.00 0.00 1
#> TCGA.AD.6964.01 4 0.2572 0.8025 0.00 0.20 0.00 0.80 0.00 0.00 0
#> TCGA.G4.6314.11 1 0.1006 0.9032 0.96 0.00 0.00 0.02 0.02 0.00 0
#> TCGA.AG.3725.11 1 0.3208 0.8499 0.82 0.00 0.00 0.04 0.02 0.12 0
#> TCGA.A6.5667.11 5 0.4923 0.0281 0.42 0.00 0.00 0.02 0.50 0.06 0
#> TCGA.AA.3655.11 5 0.0000 0.8226 0.00 0.00 0.00 0.00 1.00 0.00 0
#> TCGA.AZ.5403.01 4 0.3558 0.6044 0.00 0.48 0.00 0.52 0.00 0.00 0
#> TCGA.AA.3510.11 3 0.0000 0.8518 0.00 0.00 1.00 0.00 0.00 0.00 0
#> TCGA.AG.A036.11 5 0.0000 0.8226 0.00 0.00 0.00 0.00 1.00 0.00 0
#> TCGA.CM.6162.01 2 0.0000 0.9748 0.00 1.00 0.00 0.00 0.00 0.00 0
#> TCGA.F4.6703.01 2 0.0863 0.9496 0.00 0.96 0.00 0.00 0.00 0.04 0
#> TCGA.AA.3488.11 6 0.4718 0.6455 0.02 0.00 0.06 0.00 0.32 0.60 0
#> TCGA.A6.2685.11 1 0.2159 0.8933 0.90 0.00 0.00 0.02 0.02 0.06 0
#> TCGA.G4.6298.11 5 0.0000 0.8226 0.00 0.00 0.00 0.00 1.00 0.00 0
#> TCGA.G4.6322.11 5 0.0000 0.8226 0.00 0.00 0.00 0.00 1.00 0.00 0
#> TCGA.AA.3660.11 1 0.2159 0.8933 0.90 0.00 0.00 0.02 0.02 0.06 0
#> TCGA.G4.6297.11 1 0.2159 0.8961 0.90 0.00 0.00 0.02 0.02 0.06 0
#> TCGA.AZ.6600.11 5 0.0000 0.8226 0.00 0.00 0.00 0.00 1.00 0.00 0
#> TCGA.AA.3713.11 3 0.0000 0.8518 0.00 0.00 1.00 0.00 0.00 0.00 0
#> TCGA.AA.3697.11 3 0.0504 0.8496 0.00 0.00 0.98 0.00 0.00 0.02 0
#> TCGA.AZ.6601.11 5 0.1671 0.7440 0.00 0.00 0.00 0.00 0.90 0.10 0
#> TCGA.AA.3509.11 6 0.5383 0.3507 0.30 0.00 0.14 0.02 0.00 0.54 0
#> TCGA.G4.6302.11 3 0.5504 0.4706 0.04 0.00 0.58 0.16 0.00 0.22 0
#> TCGA.AG.3731.11 6 0.5152 0.7003 0.02 0.00 0.14 0.00 0.24 0.60 0
#> TCGA.A6.2686.11 1 0.1860 0.9006 0.92 0.00 0.00 0.02 0.02 0.04 0
#> TCGA.AA.3495.11 6 0.3968 0.4150 0.02 0.00 0.00 0.00 0.44 0.54 0
#> TCGA.AG.A01W.11 6 0.5383 0.3507 0.30 0.00 0.14 0.02 0.00 0.54 0
#> TCGA.AA.3506.11 3 0.3525 0.1554 0.00 0.00 0.56 0.00 0.00 0.44 0
#> TCGA.AA.3502.11 3 0.0000 0.8518 0.00 0.00 1.00 0.00 0.00 0.00 0
#> TCGA.AA.3492.11 1 0.1664 0.9006 0.92 0.00 0.00 0.00 0.02 0.06 0
#> TCGA.A6.2682.11 5 0.2512 0.7196 0.04 0.00 0.00 0.00 0.86 0.10 0
cbind(get_classes(res, k = 8), get_membership(res, k = 8))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7 p8
#> TCGA.AA.3494.11 3 0.0471 0.7439 0.00 0.00 0.98 0.00 0.00 0.02 0.00 0.00
#> TCGA.AA.3712.11 5 0.0000 0.7909 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.A6.2681.11 1 0.3095 0.7161 0.74 0.00 0.00 0.00 0.02 0.00 0.00 0.24
#> TCGA.A6.2675.11 6 0.2407 0.7199 0.00 0.00 0.08 0.00 0.06 0.86 0.00 0.00
#> TCGA.AA.3663.11 6 0.2862 0.7411 0.00 0.00 0.08 0.00 0.10 0.82 0.00 0.00
#> TCGA.A6.2671.11 5 0.0000 0.7909 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.A6.2680.11 1 0.2404 0.7334 0.84 0.00 0.00 0.00 0.02 0.00 0.00 0.14
#> TCGA.AZ.6598.11 1 0.4383 0.6042 0.52 0.00 0.00 0.00 0.02 0.04 0.00 0.42
#> TCGA.G4.6295.11 7 0.0471 0.9617 0.00 0.00 0.02 0.00 0.00 0.00 0.98 0.00
#> TCGA.A6.6142.01 4 0.0471 0.7648 0.00 0.00 0.00 0.98 0.00 0.02 0.00 0.00
#> TCGA.AG.A020.11 1 0.4211 0.5754 0.70 0.00 0.00 0.00 0.02 0.16 0.00 0.12
#> TCGA.G4.6311.11 5 0.7397 -0.0198 0.24 0.08 0.00 0.00 0.26 0.16 0.00 0.26
#> TCGA.G4.6625.11 5 0.3083 0.4676 0.34 0.00 0.00 0.00 0.66 0.00 0.00 0.00
#> TCGA.AG.A01Y.11 1 0.4770 0.5097 0.62 0.00 0.00 0.00 0.02 0.18 0.00 0.18
#> TCGA.A6.4107.11 3 0.2852 0.3417 0.00 0.00 0.72 0.00 0.00 0.00 0.00 0.28
#> TCGA.AG.A02N.11 5 0.0000 0.7909 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.AY.A8YK.01 4 0.0941 0.7568 0.00 0.00 0.00 0.96 0.00 0.02 0.00 0.02
#> TCGA.A6.2685.01 2 0.2114 0.9752 0.00 0.84 0.00 0.16 0.00 0.00 0.00 0.00
#> TCGA.5M.AAT6.01 4 0.3015 0.5313 0.00 0.32 0.00 0.68 0.00 0.00 0.00 0.00
#> TCGA.A6.2684.11 1 0.2025 0.7466 0.88 0.00 0.00 0.00 0.02 0.00 0.00 0.10
#> TCGA.G4.6320.11 5 0.5534 0.5309 0.04 0.08 0.00 0.00 0.62 0.16 0.00 0.10
#> TCGA.AZ.6599.11 5 0.0000 0.7909 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.A6.A565.01 7 0.1275 0.9235 0.00 0.00 0.00 0.00 0.00 0.04 0.94 0.02
#> TCGA.A6.2679.11 7 0.0471 0.9617 0.00 0.00 0.02 0.00 0.00 0.00 0.98 0.00
#> TCGA.AD.6964.01 4 0.0000 0.7655 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.G4.6314.11 1 0.2025 0.7466 0.88 0.00 0.00 0.00 0.02 0.00 0.00 0.10
#> TCGA.AG.3725.11 1 0.4211 0.5754 0.70 0.00 0.00 0.00 0.02 0.16 0.00 0.12
#> TCGA.A6.5667.11 5 0.3329 0.1493 0.48 0.00 0.00 0.00 0.52 0.00 0.00 0.00
#> TCGA.AA.3655.11 5 0.0000 0.7909 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.AZ.5403.01 4 0.3015 0.5313 0.00 0.32 0.00 0.68 0.00 0.00 0.00 0.00
#> TCGA.AA.3510.11 3 0.0471 0.7439 0.00 0.00 0.98 0.00 0.00 0.02 0.00 0.00
#> TCGA.AG.A036.11 5 0.0000 0.7909 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.CM.6162.01 2 0.2114 0.9752 0.00 0.84 0.00 0.16 0.00 0.00 0.00 0.00
#> TCGA.F4.6703.01 2 0.3021 0.9504 0.02 0.80 0.00 0.16 0.00 0.02 0.00 0.00
#> TCGA.AA.3488.11 6 0.3941 0.6955 0.00 0.04 0.04 0.00 0.14 0.76 0.00 0.02
#> TCGA.A6.2685.11 1 0.0471 0.7343 0.98 0.00 0.00 0.00 0.02 0.00 0.00 0.00
#> TCGA.G4.6298.11 5 0.1607 0.7593 0.00 0.04 0.00 0.00 0.92 0.00 0.00 0.04
#> TCGA.G4.6322.11 5 0.0000 0.7909 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.AA.3660.11 1 0.0471 0.7343 0.98 0.00 0.00 0.00 0.02 0.00 0.00 0.00
#> TCGA.G4.6297.11 1 0.4383 0.6042 0.52 0.00 0.00 0.00 0.02 0.04 0.00 0.42
#> TCGA.AZ.6600.11 5 0.0000 0.7909 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.AA.3713.11 3 0.0471 0.7439 0.00 0.00 0.98 0.00 0.00 0.02 0.00 0.00
#> TCGA.AA.3697.11 3 0.0471 0.7439 0.00 0.00 0.98 0.00 0.00 0.02 0.00 0.00
#> TCGA.AZ.6601.11 5 0.3675 0.6340 0.00 0.08 0.00 0.00 0.76 0.14 0.00 0.02
#> TCGA.AA.3509.11 6 0.5584 0.4924 0.16 0.00 0.08 0.00 0.00 0.54 0.00 0.22
#> TCGA.G4.6302.11 8 0.5673 0.0000 0.00 0.08 0.36 0.00 0.00 0.04 0.04 0.48
#> TCGA.AG.3731.11 6 0.2862 0.7411 0.00 0.00 0.08 0.00 0.10 0.82 0.00 0.00
#> TCGA.A6.2686.11 1 0.3095 0.7161 0.74 0.00 0.00 0.00 0.02 0.00 0.00 0.24
#> TCGA.AA.3495.11 6 0.4097 0.5831 0.00 0.08 0.00 0.00 0.20 0.70 0.00 0.02
#> TCGA.AG.A01W.11 6 0.5584 0.4924 0.16 0.00 0.08 0.00 0.00 0.54 0.00 0.22
#> TCGA.AA.3506.11 3 0.3737 0.0285 0.00 0.00 0.50 0.00 0.00 0.48 0.00 0.02
#> TCGA.AA.3502.11 3 0.0471 0.6825 0.00 0.00 0.98 0.00 0.00 0.00 0.02 0.00
#> TCGA.AA.3492.11 1 0.3514 0.6940 0.64 0.00 0.00 0.00 0.02 0.00 0.00 0.34
#> TCGA.A6.2682.11 5 0.5534 0.5309 0.04 0.08 0.00 0.00 0.62 0.16 0.00 0.10
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
consensus_heatmap(res, k = 7)
consensus_heatmap(res, k = 8)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
membership_heatmap(res, k = 7)
membership_heatmap(res, k = 8)
As soon as the classes for columns are determined, the signatures that are significantly different between subgroups can be looked for. Following are the heatmaps for signatures.
get_signatures(res, k = 2)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
get_signatures(res, k = 7)
get_signatures(res, k = 8)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. To get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows (which is done by automatically selecting number of clusters).If there are too many signatures, top_signatures = ... can be set to only show the
signatures with the highest FDRs:
# code only for demonstration
# e.g. to show the top 500 most significant rows
tb = get_signature(res, k = ..., top_signatures = 500)
If the signatures are defined as these which are uniquely high in current group, diff_method argument
can be set to "uniquely_high_in_one_group":
# code only for demonstration
tb = get_signature(res, k = ..., diff_method = "uniquely_high_in_one_group")
UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
dimension_reduction(res, k = 7, method = "UMAP")
dimension_reduction(res, k = 8, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
If matrix rows can be associated to genes, consider to use functional_enrichment(res,
...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.
Parent node: Node02. Child nodes: Node0111 , Node0112 , Node0121 , Node0122 , Node0211-leaf , Node0212 , Node0411-leaf , Node0412-leaf , Node0413-leaf , Node0414-leaf , Node0421-leaf , Node0422 , Node0423-leaf , Node0431-leaf , Node0432-leaf , Node0433-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 36 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 0.5132 0.487 0.487
#> 3 3 0.733 0.787 0.833 0.2306 0.889 0.772
#> 4 4 0.629 0.758 0.789 0.1154 0.889 0.705
#> 5 5 0.594 0.600 0.761 0.0853 0.922 0.726
#> 6 6 0.654 0.504 0.737 0.0578 0.908 0.635
#> 7 7 0.747 0.609 0.747 0.0334 0.903 0.551
#> 8 8 0.770 0.619 0.718 0.0331 0.962 0.765
suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:
suggest_best_k(res)
#> [1] 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.AA.3712.11 1 0 1 1 0
#> TCGA.A6.2681.11 2 0 1 0 1
#> TCGA.A6.2675.11 1 0 1 1 0
#> TCGA.AA.3663.11 1 0 1 1 0
#> TCGA.A6.2671.11 1 0 1 1 0
#> TCGA.A6.2680.11 2 0 1 0 1
#> TCGA.AZ.6598.11 2 0 1 0 1
#> TCGA.AG.A020.11 2 0 1 0 1
#> TCGA.G4.6311.11 1 0 1 1 0
#> TCGA.G4.6625.11 2 0 1 0 1
#> TCGA.AG.A01Y.11 2 0 1 0 1
#> TCGA.AG.A02N.11 1 0 1 1 0
#> TCGA.A6.2684.11 2 0 1 0 1
#> TCGA.G4.6320.11 1 0 1 1 0
#> TCGA.AZ.6599.11 1 0 1 1 0
#> TCGA.G4.6314.11 2 0 1 0 1
#> TCGA.AG.3725.11 2 0 1 0 1
#> TCGA.A6.5667.11 2 0 1 0 1
#> TCGA.AA.3655.11 1 0 1 1 0
#> TCGA.AG.A036.11 1 0 1 1 0
#> TCGA.AA.3488.11 1 0 1 1 0
#> TCGA.A6.2685.11 2 0 1 0 1
#> TCGA.G4.6298.11 1 0 1 1 0
#> TCGA.G4.6322.11 1 0 1 1 0
#> TCGA.AA.3660.11 2 0 1 0 1
#> TCGA.G4.6297.11 2 0 1 0 1
#> TCGA.AZ.6600.11 1 0 1 1 0
#> TCGA.AZ.6601.11 1 0 1 1 0
#> TCGA.AA.3509.11 2 0 1 0 1
#> TCGA.AG.3731.11 1 0 1 1 0
#> TCGA.A6.2686.11 2 0 1 0 1
#> TCGA.AA.3495.11 1 0 1 1 0
#> TCGA.AG.A01W.11 2 0 1 0 1
#> TCGA.AA.3506.11 1 0 1 1 0
#> TCGA.AA.3492.11 2 0 1 0 1
#> TCGA.A6.2682.11 1 0 1 1 0
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.AA.3712.11 1 0.000 0.880 1.00 0.00 0.00
#> TCGA.A6.2681.11 2 0.619 0.765 0.00 0.58 0.42
#> TCGA.A6.2675.11 1 0.000 0.880 1.00 0.00 0.00
#> TCGA.AA.3663.11 1 0.296 0.732 0.90 0.00 0.10
#> TCGA.A6.2671.11 1 0.000 0.880 1.00 0.00 0.00
#> TCGA.A6.2680.11 2 0.369 0.818 0.00 0.86 0.14
#> TCGA.AZ.6598.11 2 0.613 0.773 0.00 0.60 0.40
#> TCGA.AG.A020.11 2 0.000 0.834 0.00 1.00 0.00
#> TCGA.G4.6311.11 3 0.619 0.969 0.42 0.00 0.58
#> TCGA.G4.6625.11 2 0.000 0.834 0.00 1.00 0.00
#> TCGA.AG.A01Y.11 2 0.000 0.834 0.00 1.00 0.00
#> TCGA.AG.A02N.11 1 0.000 0.880 1.00 0.00 0.00
#> TCGA.A6.2684.11 2 0.619 0.765 0.00 0.58 0.42
#> TCGA.G4.6320.11 3 0.619 0.969 0.42 0.00 0.58
#> TCGA.AZ.6599.11 1 0.207 0.805 0.94 0.00 0.06
#> TCGA.G4.6314.11 2 0.619 0.765 0.00 0.58 0.42
#> TCGA.AG.3725.11 2 0.000 0.834 0.00 1.00 0.00
#> TCGA.A6.5667.11 2 0.000 0.834 0.00 1.00 0.00
#> TCGA.AA.3655.11 1 0.000 0.880 1.00 0.00 0.00
#> TCGA.AG.A036.11 1 0.000 0.880 1.00 0.00 0.00
#> TCGA.AA.3488.11 1 0.000 0.880 1.00 0.00 0.00
#> TCGA.A6.2685.11 2 0.000 0.834 0.00 1.00 0.00
#> TCGA.G4.6298.11 3 0.619 0.969 0.42 0.00 0.58
#> TCGA.G4.6322.11 1 0.000 0.880 1.00 0.00 0.00
#> TCGA.AA.3660.11 2 0.000 0.834 0.00 1.00 0.00
#> TCGA.G4.6297.11 2 0.613 0.773 0.00 0.60 0.40
#> TCGA.AZ.6600.11 3 0.619 0.969 0.42 0.00 0.58
#> TCGA.AZ.6601.11 1 0.000 0.880 1.00 0.00 0.00
#> TCGA.AA.3509.11 2 0.000 0.834 0.00 1.00 0.00
#> TCGA.AG.3731.11 1 0.000 0.880 1.00 0.00 0.00
#> TCGA.A6.2686.11 2 0.619 0.765 0.00 0.58 0.42
#> TCGA.AA.3495.11 3 0.630 0.859 0.48 0.00 0.52
#> TCGA.AG.A01W.11 2 0.000 0.834 0.00 1.00 0.00
#> TCGA.AA.3506.11 1 0.583 -0.229 0.66 0.00 0.34
#> TCGA.AA.3492.11 2 0.613 0.773 0.00 0.60 0.40
#> TCGA.A6.2682.11 1 0.583 -0.229 0.66 0.00 0.34
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> TCGA.AA.3712.11 1 0.1211 0.736 0.96 0.00 0.04 0.00
#> TCGA.A6.2681.11 4 0.4713 0.948 0.00 0.36 0.00 0.64
#> TCGA.A6.2675.11 1 0.3606 0.743 0.84 0.00 0.02 0.14
#> TCGA.AA.3663.11 1 0.5594 0.532 0.72 0.00 0.10 0.18
#> TCGA.A6.2671.11 1 0.3975 0.703 0.76 0.00 0.00 0.24
#> TCGA.A6.2680.11 2 0.6686 0.127 0.00 0.62 0.20 0.18
#> TCGA.AZ.6598.11 4 0.6453 0.932 0.00 0.36 0.08 0.56
#> TCGA.AG.A020.11 2 0.0707 0.907 0.00 0.98 0.02 0.00
#> TCGA.G4.6311.11 3 0.4134 0.923 0.26 0.00 0.74 0.00
#> TCGA.G4.6625.11 2 0.0000 0.913 0.00 1.00 0.00 0.00
#> TCGA.AG.A01Y.11 2 0.0000 0.913 0.00 1.00 0.00 0.00
#> TCGA.AG.A02N.11 1 0.1411 0.739 0.96 0.00 0.02 0.02
#> TCGA.A6.2684.11 4 0.4713 0.948 0.00 0.36 0.00 0.64
#> TCGA.G4.6320.11 3 0.4134 0.923 0.26 0.00 0.74 0.00
#> TCGA.AZ.6599.11 1 0.5327 0.669 0.72 0.00 0.06 0.22
#> TCGA.G4.6314.11 4 0.5355 0.939 0.00 0.36 0.02 0.62
#> TCGA.AG.3725.11 2 0.0707 0.907 0.00 0.98 0.02 0.00
#> TCGA.A6.5667.11 2 0.0000 0.913 0.00 1.00 0.00 0.00
#> TCGA.AA.3655.11 1 0.2921 0.738 0.86 0.00 0.00 0.14
#> TCGA.AG.A036.11 1 0.3172 0.737 0.84 0.00 0.00 0.16
#> TCGA.AA.3488.11 1 0.3172 0.737 0.84 0.00 0.00 0.16
#> TCGA.A6.2685.11 2 0.2921 0.774 0.00 0.86 0.14 0.00
#> TCGA.G4.6298.11 3 0.4797 0.915 0.26 0.00 0.72 0.02
#> TCGA.G4.6322.11 1 0.1913 0.733 0.94 0.00 0.02 0.04
#> TCGA.AA.3660.11 2 0.0000 0.913 0.00 1.00 0.00 0.00
#> TCGA.G4.6297.11 4 0.6453 0.932 0.00 0.36 0.08 0.56
#> TCGA.AZ.6600.11 3 0.5256 0.916 0.26 0.00 0.70 0.04
#> TCGA.AZ.6601.11 1 0.1211 0.736 0.96 0.00 0.04 0.00
#> TCGA.AA.3509.11 2 0.0000 0.913 0.00 1.00 0.00 0.00
#> TCGA.AG.3731.11 1 0.1211 0.736 0.96 0.00 0.04 0.00
#> TCGA.A6.2686.11 4 0.4713 0.948 0.00 0.36 0.00 0.64
#> TCGA.AA.3495.11 3 0.7121 0.710 0.30 0.00 0.54 0.16
#> TCGA.AG.A01W.11 2 0.0707 0.907 0.00 0.98 0.02 0.00
#> TCGA.AA.3506.11 1 0.7805 -0.172 0.42 0.00 0.30 0.28
#> TCGA.AA.3492.11 4 0.6714 0.925 0.00 0.36 0.10 0.54
#> TCGA.A6.2682.11 1 0.7785 -0.212 0.42 0.00 0.32 0.26
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> TCGA.AA.3712.11 1 0.2675 0.719 0.90 0.00 0.04 0.04 0.02
#> TCGA.A6.2681.11 4 0.5546 0.927 0.00 0.20 0.02 0.68 0.10
#> TCGA.A6.2675.11 1 0.4458 0.748 0.76 0.00 0.00 0.12 0.12
#> TCGA.AA.3663.11 3 0.4798 0.172 0.44 0.00 0.54 0.02 0.00
#> TCGA.A6.2671.11 1 0.7179 0.560 0.56 0.00 0.20 0.12 0.12
#> TCGA.A6.2680.11 2 0.6359 0.259 0.00 0.52 0.00 0.26 0.22
#> TCGA.AZ.6598.11 4 0.3690 0.912 0.00 0.20 0.02 0.78 0.00
#> TCGA.AG.A020.11 2 0.1216 0.894 0.00 0.96 0.02 0.00 0.02
#> TCGA.G4.6311.11 3 0.5579 -0.490 0.10 0.00 0.60 0.00 0.30
#> TCGA.G4.6625.11 2 0.0609 0.897 0.00 0.98 0.02 0.00 0.00
#> TCGA.AG.A01Y.11 2 0.0609 0.898 0.00 0.98 0.00 0.00 0.02
#> TCGA.AG.A02N.11 1 0.2331 0.762 0.90 0.00 0.00 0.02 0.08
#> TCGA.A6.2684.11 4 0.5210 0.928 0.00 0.20 0.00 0.68 0.12
#> TCGA.G4.6320.11 3 0.5487 -0.437 0.10 0.00 0.62 0.00 0.28
#> TCGA.AZ.6599.11 1 0.5589 0.425 0.64 0.00 0.28 0.04 0.04
#> TCGA.G4.6314.11 4 0.5935 0.920 0.00 0.20 0.04 0.66 0.10
#> TCGA.AG.3725.11 2 0.0609 0.895 0.00 0.98 0.02 0.00 0.00
#> TCGA.A6.5667.11 2 0.1043 0.896 0.00 0.96 0.00 0.00 0.04
#> TCGA.AA.3655.11 1 0.4216 0.752 0.78 0.00 0.00 0.10 0.12
#> TCGA.AG.A036.11 1 0.4676 0.736 0.74 0.00 0.00 0.14 0.12
#> TCGA.AA.3488.11 1 0.4890 0.744 0.72 0.00 0.00 0.14 0.14
#> TCGA.A6.2685.11 2 0.3274 0.767 0.00 0.78 0.00 0.00 0.22
#> TCGA.G4.6298.11 5 0.5895 0.000 0.10 0.00 0.44 0.00 0.46
#> TCGA.G4.6322.11 1 0.3037 0.695 0.86 0.00 0.10 0.04 0.00
#> TCGA.AA.3660.11 2 0.2012 0.891 0.00 0.92 0.02 0.00 0.06
#> TCGA.G4.6297.11 4 0.3690 0.912 0.00 0.20 0.02 0.78 0.00
#> TCGA.AZ.6600.11 3 0.5884 -0.901 0.10 0.00 0.48 0.00 0.42
#> TCGA.AZ.6601.11 1 0.2249 0.729 0.92 0.00 0.04 0.02 0.02
#> TCGA.AA.3509.11 2 0.1216 0.894 0.00 0.96 0.02 0.00 0.02
#> TCGA.AG.3731.11 1 0.2077 0.723 0.92 0.00 0.04 0.04 0.00
#> TCGA.A6.2686.11 4 0.5210 0.928 0.00 0.20 0.00 0.68 0.12
#> TCGA.AA.3495.11 3 0.3106 0.294 0.14 0.00 0.84 0.00 0.02
#> TCGA.AG.A01W.11 2 0.1216 0.894 0.00 0.96 0.02 0.00 0.02
#> TCGA.AA.3506.11 3 0.4728 0.367 0.24 0.00 0.70 0.00 0.06
#> TCGA.AA.3492.11 4 0.3690 0.912 0.00 0.20 0.02 0.78 0.00
#> TCGA.A6.2682.11 3 0.4132 0.388 0.26 0.00 0.72 0.00 0.02
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> TCGA.AA.3712.11 1 0.0547 0.5591 0.98 0.00 0.00 0.02 0.00 0.00
#> TCGA.A6.2681.11 4 0.1814 0.8093 0.00 0.10 0.00 0.90 0.00 0.00
#> TCGA.A6.2675.11 1 0.5708 0.1956 0.50 0.00 0.00 0.02 0.38 0.10
#> TCGA.AA.3663.11 1 0.6489 -0.1208 0.52 0.00 0.04 0.02 0.30 0.12
#> TCGA.A6.2671.11 5 0.3647 -0.1652 0.36 0.00 0.00 0.00 0.64 0.00
#> TCGA.A6.2680.11 6 0.5195 0.0000 0.00 0.36 0.00 0.10 0.00 0.54
#> TCGA.AZ.6598.11 4 0.6138 0.7155 0.00 0.10 0.00 0.60 0.12 0.18
#> TCGA.AG.A020.11 2 0.1480 0.8524 0.00 0.94 0.00 0.00 0.04 0.02
#> TCGA.G4.6311.11 3 0.5064 0.7211 0.04 0.00 0.70 0.02 0.04 0.20
#> TCGA.G4.6625.11 2 0.0000 0.8630 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.AG.A01Y.11 2 0.1092 0.8565 0.00 0.96 0.00 0.00 0.02 0.02
#> TCGA.AG.A02N.11 1 0.3076 0.4516 0.76 0.00 0.00 0.00 0.24 0.00
#> TCGA.A6.2684.11 4 0.1814 0.8093 0.00 0.10 0.00 0.90 0.00 0.00
#> TCGA.G4.6320.11 3 0.5487 0.7078 0.04 0.00 0.66 0.02 0.06 0.22
#> TCGA.AZ.6599.11 1 0.6036 0.1521 0.58 0.00 0.04 0.02 0.28 0.08
#> TCGA.G4.6314.11 4 0.1814 0.8093 0.00 0.10 0.00 0.90 0.00 0.00
#> TCGA.AG.3725.11 2 0.0547 0.8575 0.00 0.98 0.00 0.00 0.00 0.02
#> TCGA.A6.5667.11 2 0.2403 0.8096 0.00 0.90 0.02 0.00 0.04 0.04
#> TCGA.AA.3655.11 1 0.3828 0.2395 0.56 0.00 0.00 0.00 0.44 0.00
#> TCGA.AG.A036.11 5 0.4328 -0.3546 0.46 0.00 0.00 0.00 0.52 0.02
#> TCGA.AA.3488.11 1 0.4310 0.1874 0.54 0.00 0.00 0.00 0.44 0.02
#> TCGA.A6.2685.11 2 0.4144 -0.0144 0.00 0.62 0.00 0.00 0.02 0.36
#> TCGA.G4.6298.11 3 0.0547 0.6931 0.02 0.00 0.98 0.00 0.00 0.00
#> TCGA.G4.6322.11 1 0.1480 0.5420 0.94 0.00 0.00 0.02 0.04 0.00
#> TCGA.AA.3660.11 2 0.2190 0.8398 0.00 0.90 0.00 0.00 0.06 0.04
#> TCGA.G4.6297.11 4 0.6138 0.7155 0.00 0.10 0.00 0.60 0.12 0.18
#> TCGA.AZ.6600.11 3 0.1092 0.6941 0.02 0.00 0.96 0.00 0.00 0.02
#> TCGA.AZ.6601.11 1 0.0000 0.5619 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AA.3509.11 2 0.0547 0.8615 0.00 0.98 0.00 0.00 0.00 0.02
#> TCGA.AG.3731.11 1 0.0547 0.5604 0.98 0.00 0.00 0.02 0.00 0.00
#> TCGA.A6.2686.11 4 0.1814 0.8093 0.00 0.10 0.00 0.90 0.00 0.00
#> TCGA.AA.3495.11 3 0.7000 0.2701 0.06 0.00 0.36 0.00 0.28 0.30
#> TCGA.AG.A01W.11 2 0.1480 0.8524 0.00 0.94 0.00 0.00 0.04 0.02
#> TCGA.AA.3506.11 5 0.7371 0.0687 0.10 0.00 0.20 0.02 0.46 0.22
#> TCGA.AA.3492.11 4 0.6138 0.7155 0.00 0.10 0.00 0.60 0.12 0.18
#> TCGA.A6.2682.11 5 0.7941 0.0281 0.22 0.00 0.20 0.02 0.36 0.20
cbind(get_classes(res, k = 7), get_membership(res, k = 7))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7
#> TCGA.AA.3712.11 7 0.3985 0.875 0.46 0.00 0.00 0.00 0.00 0.02 0.52
#> TCGA.A6.2681.11 4 0.1166 0.838 0.00 0.06 0.00 0.94 0.00 0.00 0.00
#> TCGA.A6.2675.11 1 0.4181 0.346 0.74 0.00 0.00 0.00 0.04 0.16 0.06
#> TCGA.AA.3663.11 5 0.4931 0.623 0.08 0.00 0.08 0.00 0.68 0.00 0.16
#> TCGA.A6.2671.11 1 0.3780 0.372 0.72 0.00 0.00 0.00 0.24 0.02 0.02
#> TCGA.A6.2680.11 6 0.4146 0.763 0.00 0.24 0.00 0.08 0.00 0.68 0.00
#> TCGA.AZ.6598.11 4 0.5519 0.778 0.00 0.06 0.00 0.64 0.06 0.04 0.20
#> TCGA.AG.A020.11 2 0.2769 0.787 0.00 0.86 0.00 0.00 0.04 0.02 0.08
#> TCGA.G4.6311.11 3 0.6428 0.649 0.02 0.00 0.60 0.06 0.16 0.08 0.08
#> TCGA.G4.6625.11 2 0.2509 0.787 0.00 0.88 0.00 0.00 0.04 0.06 0.02
#> TCGA.AG.A01Y.11 2 0.1860 0.802 0.00 0.92 0.00 0.00 0.04 0.02 0.02
#> TCGA.AG.A02N.11 1 0.3943 -0.615 0.56 0.00 0.00 0.00 0.00 0.02 0.42
#> TCGA.A6.2684.11 4 0.1166 0.838 0.00 0.06 0.00 0.94 0.00 0.00 0.00
#> TCGA.G4.6320.11 3 0.6428 0.649 0.02 0.00 0.60 0.06 0.16 0.08 0.08
#> TCGA.AZ.6599.11 1 0.6454 0.111 0.42 0.00 0.00 0.00 0.22 0.08 0.28
#> TCGA.G4.6314.11 4 0.1664 0.835 0.00 0.06 0.00 0.92 0.02 0.00 0.00
#> TCGA.AG.3725.11 2 0.1860 0.793 0.00 0.92 0.00 0.00 0.02 0.02 0.04
#> TCGA.A6.5667.11 2 0.3635 0.783 0.00 0.82 0.02 0.00 0.06 0.04 0.06
#> TCGA.AA.3655.11 1 0.1928 0.376 0.90 0.00 0.00 0.00 0.00 0.02 0.08
#> TCGA.AG.A036.11 1 0.0504 0.433 0.98 0.00 0.00 0.00 0.02 0.00 0.00
#> TCGA.AA.3488.11 1 0.2421 0.395 0.88 0.00 0.00 0.00 0.02 0.02 0.08
#> TCGA.A6.2685.11 6 0.3358 0.716 0.00 0.36 0.00 0.00 0.00 0.64 0.00
#> TCGA.G4.6298.11 3 0.0504 0.689 0.02 0.00 0.98 0.00 0.00 0.00 0.00
#> TCGA.G4.6322.11 1 0.5293 -0.704 0.46 0.00 0.00 0.00 0.10 0.02 0.42
#> TCGA.AA.3660.11 2 0.3744 0.771 0.00 0.78 0.00 0.00 0.12 0.08 0.02
#> TCGA.G4.6297.11 4 0.5519 0.778 0.00 0.06 0.00 0.64 0.06 0.04 0.20
#> TCGA.AZ.6600.11 3 0.1006 0.681 0.02 0.00 0.96 0.00 0.02 0.00 0.00
#> TCGA.AZ.6601.11 7 0.3985 0.880 0.46 0.00 0.00 0.00 0.02 0.00 0.52
#> TCGA.AA.3509.11 2 0.2804 0.783 0.00 0.86 0.00 0.00 0.06 0.06 0.02
#> TCGA.AG.3731.11 7 0.3525 0.906 0.44 0.00 0.00 0.00 0.00 0.00 0.56
#> TCGA.A6.2686.11 4 0.1166 0.838 0.00 0.06 0.00 0.94 0.00 0.00 0.00
#> TCGA.AA.3495.11 5 0.6394 0.382 0.06 0.00 0.28 0.04 0.54 0.04 0.04
#> TCGA.AG.A01W.11 2 0.2769 0.787 0.00 0.86 0.00 0.00 0.04 0.02 0.08
#> TCGA.AA.3506.11 5 0.4939 0.702 0.20 0.00 0.14 0.00 0.64 0.02 0.00
#> TCGA.AA.3492.11 4 0.5632 0.764 0.00 0.06 0.00 0.62 0.06 0.04 0.22
#> TCGA.A6.2682.11 5 0.4514 0.729 0.14 0.00 0.14 0.00 0.70 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.AA.3712.11 7 0.0000 0.7275 0.00 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.A6.2681.11 4 0.0471 0.7391 0.02 0.00 0.00 0.98 0.00 0.00 0.00 0.00
#> TCGA.A6.2675.11 1 0.5983 0.4925 0.46 0.14 0.00 0.00 0.06 0.02 0.32 0.00
#> TCGA.AA.3663.11 5 0.5332 0.4049 0.00 0.08 0.08 0.00 0.52 0.00 0.32 0.00
#> TCGA.A6.2671.11 1 0.4992 0.6305 0.58 0.02 0.00 0.00 0.20 0.00 0.20 0.00
#> TCGA.A6.2680.11 6 0.2348 0.7392 0.00 0.02 0.00 0.04 0.00 0.88 0.00 0.06
#> TCGA.AZ.6598.11 4 0.6204 0.6625 0.08 0.16 0.00 0.54 0.06 0.16 0.00 0.00
#> TCGA.AG.A020.11 8 0.0000 0.6886 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.G4.6311.11 3 0.4890 0.4842 0.02 0.06 0.56 0.00 0.34 0.02 0.00 0.00
#> TCGA.G4.6625.11 8 0.3907 0.7338 0.00 0.38 0.00 0.00 0.04 0.00 0.00 0.58
#> TCGA.AG.A01Y.11 8 0.3570 0.7336 0.02 0.36 0.00 0.00 0.00 0.00 0.00 0.62
#> TCGA.AG.A02N.11 7 0.3021 0.5021 0.16 0.02 0.00 0.00 0.02 0.00 0.80 0.00
#> TCGA.A6.2684.11 4 0.0000 0.7401 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.G4.6320.11 3 0.4940 0.4885 0.02 0.04 0.56 0.00 0.34 0.04 0.00 0.00
#> TCGA.AZ.6599.11 7 0.5584 -0.0273 0.16 0.08 0.00 0.00 0.22 0.00 0.54 0.00
#> TCGA.G4.6314.11 4 0.2807 0.6968 0.10 0.02 0.00 0.84 0.04 0.00 0.00 0.00
#> TCGA.AG.3725.11 8 0.2406 0.7113 0.00 0.20 0.00 0.00 0.00 0.00 0.00 0.80
#> TCGA.A6.5667.11 8 0.5747 0.6131 0.10 0.24 0.00 0.00 0.04 0.06 0.00 0.56
#> TCGA.AA.3655.11 1 0.3729 0.4735 0.52 0.00 0.00 0.00 0.02 0.00 0.46 0.00
#> TCGA.AG.A036.11 1 0.3922 0.7215 0.64 0.00 0.00 0.00 0.06 0.00 0.30 0.00
#> TCGA.AA.3488.11 1 0.4621 0.7114 0.58 0.02 0.00 0.00 0.08 0.00 0.32 0.00
#> TCGA.A6.2685.11 6 0.3431 0.6856 0.00 0.06 0.00 0.00 0.00 0.74 0.00 0.20
#> TCGA.G4.6298.11 3 0.0000 0.6049 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.G4.6322.11 7 0.3421 0.5882 0.04 0.08 0.00 0.00 0.08 0.00 0.80 0.00
#> TCGA.AA.3660.11 8 0.3374 0.6976 0.00 0.30 0.00 0.00 0.02 0.00 0.00 0.68
#> TCGA.G4.6297.11 4 0.6277 0.6633 0.08 0.14 0.00 0.54 0.08 0.16 0.00 0.00
#> TCGA.AZ.6600.11 3 0.0941 0.5937 0.00 0.02 0.96 0.00 0.02 0.00 0.00 0.00
#> TCGA.AZ.6601.11 7 0.0941 0.7149 0.02 0.00 0.00 0.00 0.02 0.00 0.96 0.00
#> TCGA.AA.3509.11 8 0.3658 0.7305 0.00 0.40 0.00 0.00 0.02 0.00 0.00 0.58
#> TCGA.AG.3731.11 7 0.0000 0.7275 0.00 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.A6.2686.11 4 0.0000 0.7401 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.AA.3495.11 5 0.4375 0.2962 0.02 0.04 0.26 0.00 0.66 0.02 0.00 0.00
#> TCGA.AG.A01W.11 8 0.0471 0.6904 0.00 0.00 0.00 0.00 0.02 0.00 0.00 0.98
#> TCGA.AA.3506.11 5 0.4643 0.5979 0.12 0.04 0.12 0.00 0.70 0.00 0.02 0.00
#> TCGA.AA.3492.11 4 0.6204 0.6625 0.08 0.16 0.00 0.54 0.06 0.16 0.00 0.00
#> TCGA.A6.2682.11 5 0.4767 0.6241 0.06 0.06 0.14 0.00 0.70 0.00 0.04 0.00
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
consensus_heatmap(res, k = 7)
consensus_heatmap(res, k = 8)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
membership_heatmap(res, k = 7)
membership_heatmap(res, k = 8)
As soon as the classes for columns are determined, the signatures that are significantly different between subgroups can be looked for. Following are the heatmaps for signatures.
get_signatures(res, k = 2)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
get_signatures(res, k = 7)
get_signatures(res, k = 8)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. To get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows (which is done by automatically selecting number of clusters).If there are too many signatures, top_signatures = ... can be set to only show the
signatures with the highest FDRs:
# code only for demonstration
# e.g. to show the top 500 most significant rows
tb = get_signature(res, k = ..., top_signatures = 500)
If the signatures are defined as these which are uniquely high in current group, diff_method argument
can be set to "uniquely_high_in_one_group":
# code only for demonstration
tb = get_signature(res, k = ..., diff_method = "uniquely_high_in_one_group")
UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
dimension_reduction(res, k = 7, method = "UMAP")
dimension_reduction(res, k = 8, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
If matrix rows can be associated to genes, consider to use functional_enrichment(res,
...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.
Parent node: Node021. Child nodes: Node01111 , Node01112-leaf , Node01113-leaf , Node01114-leaf , Node01121-leaf , Node01122-leaf , Node01123-leaf , Node01124-leaf , Node01211-leaf , Node01212-leaf , Node01213-leaf , Node01221-leaf , Node01222-leaf , Node01223-leaf , Node01224-leaf , Node02121-leaf , Node02122-leaf , Node02123-leaf , Node04221-leaf , Node04222-leaf , Node04223-leaf .
The object with results only for a single top-value method and a single partitioning method can be extracted as:
res = res_rh["0212"]
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 '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 0.4858 0.515 0.515
#> 3 3 0.735 0.976 0.944 0.3752 0.794 0.600
#> 4 4 0.860 0.891 0.894 0.1283 0.941 0.810
#> 5 5 0.787 0.879 0.867 0.0665 0.926 0.706
#> 6 6 0.846 0.586 0.800 0.0494 0.919 0.607
#> 7 7 0.809 0.747 0.814 0.0340 0.941 0.652
#> 8 8 0.868 0.679 0.834 0.0243 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] 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.A6.2681.11 1 0 1 1 0
#> TCGA.A6.2680.11 1 0 1 1 0
#> TCGA.AZ.6598.11 2 0 1 0 1
#> TCGA.AG.A020.11 2 0 1 0 1
#> TCGA.G4.6625.11 2 0 1 0 1
#> TCGA.AG.A01Y.11 2 0 1 0 1
#> TCGA.A6.2684.11 1 0 1 1 0
#> TCGA.G4.6314.11 1 0 1 1 0
#> TCGA.AG.3725.11 2 0 1 0 1
#> TCGA.A6.5667.11 2 0 1 0 1
#> TCGA.A6.2685.11 2 0 1 0 1
#> TCGA.AA.3660.11 2 0 1 0 1
#> TCGA.G4.6297.11 2 0 1 0 1
#> TCGA.AA.3509.11 2 0 1 0 1
#> TCGA.A6.2686.11 1 0 1 1 0
#> TCGA.AG.A01W.11 2 0 1 0 1
#> TCGA.AA.3492.11 1 0 1 1 0
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.A6.2681.11 1 0.0 0.949 1.00 0.00 0.00
#> TCGA.A6.2680.11 1 0.4 0.895 0.84 0.00 0.16
#> TCGA.AZ.6598.11 2 0.0 1.000 0.00 1.00 0.00
#> TCGA.AG.A020.11 3 0.4 1.000 0.00 0.16 0.84
#> TCGA.G4.6625.11 2 0.0 1.000 0.00 1.00 0.00
#> TCGA.AG.A01Y.11 3 0.4 1.000 0.00 0.16 0.84
#> TCGA.A6.2684.11 1 0.0 0.949 1.00 0.00 0.00
#> TCGA.G4.6314.11 1 0.0 0.949 1.00 0.00 0.00
#> TCGA.AG.3725.11 2 0.0 1.000 0.00 1.00 0.00
#> TCGA.A6.5667.11 2 0.0 1.000 0.00 1.00 0.00
#> TCGA.A6.2685.11 2 0.0 1.000 0.00 1.00 0.00
#> TCGA.AA.3660.11 2 0.0 1.000 0.00 1.00 0.00
#> TCGA.G4.6297.11 2 0.0 1.000 0.00 1.00 0.00
#> TCGA.AA.3509.11 3 0.4 1.000 0.00 0.16 0.84
#> TCGA.A6.2686.11 1 0.0 0.949 1.00 0.00 0.00
#> TCGA.AG.A01W.11 3 0.4 1.000 0.00 0.16 0.84
#> TCGA.AA.3492.11 1 0.4 0.895 0.84 0.00 0.16
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> TCGA.A6.2681.11 1 0.491 1.000 0.58 0.00 0 0.42
#> TCGA.A6.2680.11 4 0.000 0.781 0.00 0.00 0 1.00
#> TCGA.AZ.6598.11 2 0.491 0.634 0.42 0.58 0 0.00
#> TCGA.AG.A020.11 3 0.000 1.000 0.00 0.00 1 0.00
#> TCGA.G4.6625.11 2 0.000 0.872 0.00 1.00 0 0.00
#> TCGA.AG.A01Y.11 3 0.000 1.000 0.00 0.00 1 0.00
#> TCGA.A6.2684.11 1 0.491 1.000 0.58 0.00 0 0.42
#> TCGA.G4.6314.11 1 0.491 1.000 0.58 0.00 0 0.42
#> TCGA.AG.3725.11 2 0.000 0.872 0.00 1.00 0 0.00
#> TCGA.A6.5667.11 2 0.000 0.872 0.00 1.00 0 0.00
#> TCGA.A6.2685.11 2 0.000 0.872 0.00 1.00 0 0.00
#> TCGA.AA.3660.11 2 0.000 0.872 0.00 1.00 0 0.00
#> TCGA.G4.6297.11 2 0.491 0.634 0.42 0.58 0 0.00
#> TCGA.AA.3509.11 3 0.000 1.000 0.00 0.00 1 0.00
#> TCGA.A6.2686.11 1 0.491 1.000 0.58 0.00 0 0.42
#> TCGA.AG.A01W.11 3 0.000 1.000 0.00 0.00 1 0.00
#> TCGA.AA.3492.11 4 0.265 0.739 0.12 0.00 0 0.88
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> TCGA.A6.2681.11 1 0.4227 1.000 0.58 0.00 0.00 0.42 0.00
#> TCGA.A6.2680.11 4 0.0000 0.647 0.00 0.00 0.00 1.00 0.00
#> TCGA.AZ.6598.11 5 0.2280 1.000 0.00 0.12 0.00 0.00 0.88
#> TCGA.AG.A020.11 3 0.3561 0.846 0.26 0.00 0.74 0.00 0.00
#> TCGA.G4.6625.11 2 0.2516 0.858 0.14 0.86 0.00 0.00 0.00
#> TCGA.AG.A01Y.11 3 0.0000 0.846 0.00 0.00 1.00 0.00 0.00
#> TCGA.A6.2684.11 1 0.4227 1.000 0.58 0.00 0.00 0.42 0.00
#> TCGA.G4.6314.11 1 0.4227 1.000 0.58 0.00 0.00 0.42 0.00
#> TCGA.AG.3725.11 2 0.3274 0.801 0.22 0.78 0.00 0.00 0.00
#> TCGA.A6.5667.11 2 0.0000 0.902 0.00 1.00 0.00 0.00 0.00
#> TCGA.A6.2685.11 2 0.0609 0.901 0.02 0.98 0.00 0.00 0.00
#> TCGA.AA.3660.11 2 0.0609 0.901 0.02 0.98 0.00 0.00 0.00
#> TCGA.G4.6297.11 5 0.2280 1.000 0.00 0.12 0.00 0.00 0.88
#> TCGA.AA.3509.11 3 0.0000 0.846 0.00 0.00 1.00 0.00 0.00
#> TCGA.A6.2686.11 1 0.4227 1.000 0.58 0.00 0.00 0.42 0.00
#> TCGA.AG.A01W.11 3 0.3561 0.846 0.26 0.00 0.74 0.00 0.00
#> TCGA.AA.3492.11 4 0.4676 0.553 0.14 0.00 0.00 0.74 0.12
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> TCGA.A6.2681.11 1 0.0000 0.756 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.A6.2680.11 4 0.3578 0.000 0.34 0.00 0.00 0.66 0.00 0.00
#> TCGA.AZ.6598.11 5 0.0547 1.000 0.00 0.02 0.00 0.00 0.98 0.00
#> TCGA.AG.A020.11 3 0.5422 0.767 0.00 0.02 0.62 0.24 0.00 0.12
#> TCGA.G4.6625.11 2 0.0547 0.572 0.00 0.98 0.00 0.00 0.00 0.02
#> TCGA.AG.A01Y.11 3 0.0000 0.767 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.A6.2684.11 1 0.0547 0.756 0.98 0.00 0.00 0.00 0.02 0.00
#> TCGA.G4.6314.11 1 0.0000 0.756 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AG.3725.11 2 0.0000 0.570 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.A6.5667.11 2 0.5285 -0.602 0.00 0.48 0.00 0.10 0.00 0.42
#> TCGA.A6.2685.11 6 0.3647 1.000 0.00 0.36 0.00 0.00 0.00 0.64
#> TCGA.AA.3660.11 6 0.3647 1.000 0.00 0.36 0.00 0.00 0.00 0.64
#> TCGA.G4.6297.11 5 0.0547 1.000 0.00 0.02 0.00 0.00 0.98 0.00
#> TCGA.AA.3509.11 3 0.0000 0.767 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.A6.2686.11 1 0.0547 0.756 0.98 0.00 0.00 0.00 0.02 0.00
#> TCGA.AG.A01W.11 3 0.5422 0.767 0.00 0.02 0.62 0.24 0.00 0.12
#> TCGA.AA.3492.11 1 0.6010 -0.679 0.40 0.00 0.00 0.36 0.00 0.24
cbind(get_classes(res, k = 7), get_membership(res, k = 7))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7
#> TCGA.A6.2681.11 1 0.1671 0.913 0.90 0.10 0.00 0.00 0.00 0.00 0.00
#> TCGA.A6.2680.11 4 0.1886 0.000 0.12 0.00 0.00 0.88 0.00 0.00 0.00
#> TCGA.AZ.6598.11 5 0.0504 1.000 0.00 0.00 0.00 0.00 0.98 0.02 0.00
#> TCGA.AG.A020.11 3 0.0000 0.737 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.G4.6625.11 2 0.2708 0.845 0.00 0.78 0.00 0.00 0.00 0.22 0.00
#> TCGA.AG.A01Y.11 3 0.3413 0.737 0.00 0.00 0.62 0.00 0.00 0.00 0.38
#> TCGA.A6.2684.11 1 0.0504 0.907 0.98 0.02 0.00 0.00 0.00 0.00 0.00
#> TCGA.G4.6314.11 1 0.1671 0.913 0.90 0.10 0.00 0.00 0.00 0.00 0.00
#> TCGA.AG.3725.11 2 0.4696 0.853 0.00 0.70 0.06 0.08 0.00 0.16 0.00
#> TCGA.A6.5667.11 6 0.3863 0.694 0.00 0.04 0.00 0.02 0.00 0.74 0.20
#> TCGA.A6.2685.11 6 0.0000 0.861 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.AA.3660.11 6 0.0000 0.861 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.G4.6297.11 5 0.0504 1.000 0.00 0.00 0.00 0.00 0.98 0.02 0.00
#> TCGA.AA.3509.11 3 0.3459 0.733 0.00 0.00 0.60 0.00 0.00 0.00 0.40
#> TCGA.A6.2686.11 1 0.0504 0.907 0.98 0.00 0.00 0.00 0.02 0.00 0.00
#> TCGA.AG.A01W.11 3 0.0504 0.733 0.00 0.00 0.98 0.02 0.00 0.00 0.00
#> TCGA.AA.3492.11 7 0.6527 0.000 0.18 0.10 0.00 0.32 0.00 0.00 0.40
cbind(get_classes(res, k = 8), get_membership(res, k = 8))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7 p8
#> TCGA.A6.2681.11 1 0.0000 0.742 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.A6.2680.11 8 0.3036 0.000 0.04 0.00 0.00 0.00 0.00 0.00 0.18 0.78
#> TCGA.AZ.6598.11 5 0.1804 0.934 0.00 0.00 0.00 0.08 0.90 0.02 0.00 0.00
#> TCGA.AG.A020.11 3 0.3570 0.699 0.00 0.02 0.62 0.36 0.00 0.00 0.00 0.00
#> TCGA.G4.6625.11 2 0.2114 0.907 0.00 0.84 0.00 0.00 0.00 0.16 0.00 0.00
#> TCGA.AG.A01Y.11 3 0.0000 0.699 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.A6.2684.11 1 0.3922 0.736 0.64 0.06 0.00 0.30 0.00 0.00 0.00 0.00
#> TCGA.G4.6314.11 1 0.0941 0.742 0.96 0.02 0.00 0.00 0.02 0.00 0.00 0.00
#> TCGA.AG.3725.11 2 0.3444 0.909 0.00 0.78 0.00 0.06 0.00 0.14 0.02 0.00
#> TCGA.A6.5667.11 6 0.5407 0.537 0.00 0.08 0.00 0.12 0.00 0.62 0.02 0.16
#> TCGA.A6.2685.11 6 0.0000 0.803 0.00 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.AA.3660.11 6 0.0000 0.803 0.00 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.G4.6297.11 5 0.0471 0.934 0.00 0.00 0.00 0.00 0.98 0.02 0.00 0.00
#> TCGA.AA.3509.11 3 0.1557 0.680 0.00 0.00 0.92 0.00 0.00 0.00 0.02 0.06
#> TCGA.A6.2686.11 1 0.4244 0.736 0.64 0.12 0.00 0.24 0.00 0.00 0.00 0.00
#> TCGA.AG.A01W.11 3 0.3714 0.680 0.00 0.02 0.54 0.44 0.00 0.00 0.00 0.00
#> TCGA.AA.3492.11 7 0.1091 0.000 0.06 0.00 0.00 0.00 0.00 0.00 0.94 0.00
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
consensus_heatmap(res, k = 7)
consensus_heatmap(res, k = 8)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
membership_heatmap(res, k = 7)
membership_heatmap(res, k = 8)
As soon as the classes for columns are determined, the signatures that are significantly different between subgroups can be looked for. Following are the heatmaps for signatures.
get_signatures(res, k = 2)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
get_signatures(res, k = 7)
get_signatures(res, k = 8)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. To get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows (which is done by automatically selecting number of clusters).If there are too many signatures, top_signatures = ... can be set to only show the
signatures with the highest FDRs:
# code only for demonstration
# e.g. to show the top 500 most significant rows
tb = get_signature(res, k = ..., top_signatures = 500)
If the signatures are defined as these which are uniquely high in current group, diff_method argument
can be set to "uniquely_high_in_one_group":
# code only for demonstration
tb = get_signature(res, k = ..., diff_method = "uniquely_high_in_one_group")
UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
dimension_reduction(res, k = 7, method = "UMAP")
dimension_reduction(res, k = 8, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
If matrix rows can be associated to genes, consider to use functional_enrichment(res,
...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.
Parent node: Node0. Child nodes: Node011 , Node012 , Node021 , Node022-leaf , Node023-leaf , Node041 , Node042 , Node043 .
The object with results only for a single top-value method and a single partitioning method can be extracted as:
res = res_rh["04"]
A summary of res and all the functions that can be applied to it:
res
#> A 'ConsensusPartition' object with k = 2, 3, 4, 5, 6, 7, 8.
#> On a matrix with 30000 rows and 82 columns.
#> Top rows (1000) are extracted by 'ATC' method.
#> Subgroups are detected by 'kmeans' method.
#> Performed in total 350 partitions by row resampling.
#> Best k for subgroups seems to be 3.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_partitions"
#> [7] "compare_signatures" "consensus_heatmap" "dimension_reduction"
#> [10] "functional_enrichment" "get_anno_col" "get_anno"
#> [13] "get_classes" "get_consensus" "get_matrix"
#> [16] "get_membership" "get_param" "get_signatures"
#> [19] "get_stats" "is_best_k" "is_stable_k"
#> [22] "membership_heatmap" "ncol" "nrow"
#> [25] "plot_ecdf" "predict_classes" "rownames"
#> [28] "select_partition_number" "show" "suggest_best_k"
#> [31] "test_to_known_factors" "top_rows_heatmap"
collect_plots() function collects all the plots made from res for all k (number of subgroups)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
The plots are:
k and the heatmap of
predicted classes for each k.k.k.k.All the plots in panels can be made by individual functions and they are plotted later in this section.
select_partition_number() produces several plots showing different
statistics for choosing “optimized” k. There are following statistics:
k;k, the area increased is defined as \(A_k - A_{k-1}\).The detailed explanations of these statistics can be found in the cola vignette.
Generally speaking, higher 1-PAC score, higher mean silhouette score or higher
concordance corresponds to better partition. Rand index and Jaccard index
measure how similar the current partition is compared to partition with k-1.
If they are too similar, we won't accept k is better than k-1.
select_partition_number(res)
The numeric values for all these statistics can be obtained by get_stats().
get_stats(res)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> 2 2 1.000 0.986 0.992 0.4961 0.505 0.505
#> 3 3 1.000 0.959 0.982 0.3216 0.773 0.580
#> 4 4 0.771 0.684 0.770 0.1227 0.877 0.664
#> 5 5 0.737 0.673 0.836 0.0705 0.860 0.542
#> 6 6 0.747 0.721 0.830 0.0419 0.900 0.583
#> 7 7 0.788 0.715 0.826 0.0271 0.947 0.717
#> 8 8 0.814 0.681 0.814 0.0195 0.978 0.861
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.F5.6464.01 1 0.000 1.000 1.00 0.00
#> TCGA.AZ.4308.01 2 0.000 0.985 0.00 1.00
#> TCGA.D5.5541.01 2 0.000 0.985 0.00 1.00
#> TCGA.F5.6812.01 1 0.000 1.000 1.00 0.00
#> TCGA.A6.6648.01 2 0.000 0.985 0.00 1.00
#> TCGA.F4.6805.01 1 0.000 1.000 1.00 0.00
#> TCGA.AF.A56K.01 2 0.000 0.985 0.00 1.00
#> TCGA.G4.6627.01 1 0.000 1.000 1.00 0.00
#> TCGA.D5.6929.01 2 0.000 0.985 0.00 1.00
#> TCGA.DC.6157.01 2 0.000 0.985 0.00 1.00
#> TCGA.AF.6655.01 2 0.402 0.930 0.08 0.92
#> TCGA.CM.6164.01 2 0.327 0.950 0.06 0.94
#> TCGA.AF.2687.01 2 0.000 0.985 0.00 1.00
#> TCGA.F4.6704.01 2 0.000 0.985 0.00 1.00
#> TCGA.A6.A567.01 2 0.000 0.985 0.00 1.00
#> TCGA.AG.3732.01 2 0.000 0.985 0.00 1.00
#> TCGA.EI.6885.01 2 0.000 0.985 0.00 1.00
#> TCGA.DC.4749.01 2 0.000 0.985 0.00 1.00
#> TCGA.5M.AAT5.01 2 0.000 0.985 0.00 1.00
#> TCGA.DC.6160.01 2 0.327 0.950 0.06 0.94
#> TCGA.D5.6534.01 1 0.000 1.000 1.00 0.00
#> TCGA.F5.6863.01 1 0.000 1.000 1.00 0.00
#> TCGA.G4.6317.02 2 0.000 0.985 0.00 1.00
#> TCGA.CK.4948.01 2 0.000 0.985 0.00 1.00
#> TCGA.A6.6651.01 1 0.000 1.000 1.00 0.00
#> TCGA.G4.6309.01 2 0.000 0.985 0.00 1.00
#> TCGA.AF.2693.01 1 0.000 1.000 1.00 0.00
#> TCGA.CM.5868.01 2 0.000 0.985 0.00 1.00
#> TCGA.AF.4110.01 1 0.000 1.000 1.00 0.00
#> TCGA.AZ.4313.01 2 0.327 0.950 0.06 0.94
#> TCGA.A6.2675.01 2 0.327 0.950 0.06 0.94
#> TCGA.AA.3494.01 2 0.000 0.985 0.00 1.00
#> TCGA.G4.6307.01 2 0.000 0.985 0.00 1.00
#> TCGA.CI.6624.01 2 0.327 0.950 0.06 0.94
#> TCGA.F5.6810.01 2 0.000 0.985 0.00 1.00
#> TCGA.CM.6167.01 1 0.000 1.000 1.00 0.00
#> TCGA.CM.4752.01 2 0.000 0.985 0.00 1.00
#> TCGA.A6.6781.01 1 0.000 1.000 1.00 0.00
#> TCGA.DM.A0XF.01 2 0.327 0.950 0.06 0.94
#> TCGA.G4.6295.01 2 0.000 0.985 0.00 1.00
#> TCGA.AZ.6605.01 1 0.000 1.000 1.00 0.00
#> TCGA.G5.6572.01 1 0.000 1.000 1.00 0.00
#> TCGA.DM.A280.01 1 0.000 1.000 1.00 0.00
#> TCGA.AA.3489.01 1 0.000 1.000 1.00 0.00
#> TCGA.AG.A01Y.01 2 0.000 0.985 0.00 1.00
#> TCGA.AZ.6603.01 2 0.000 0.985 0.00 1.00
#> TCGA.G4.6302.01 1 0.000 1.000 1.00 0.00
#> TCGA.G5.6235.01 1 0.000 1.000 1.00 0.00
#> TCGA.CI.6621.01 1 0.000 1.000 1.00 0.00
#> TCGA.F4.6857.01 1 0.000 1.000 1.00 0.00
#> TCGA.AZ.4323.01 1 0.000 1.000 1.00 0.00
#> TCGA.AF.6672.01 2 0.000 0.985 0.00 1.00
#> TCGA.AD.6963.01 1 0.000 1.000 1.00 0.00
#> TCGA.D5.6928.01 1 0.000 1.000 1.00 0.00
#> TCGA.A6.3810.01 2 0.327 0.950 0.06 0.94
#> TCGA.D5.6923.01 1 0.000 1.000 1.00 0.00
#> TCGA.AF.2690.01 1 0.000 1.000 1.00 0.00
#> TCGA.NH.A8F7.01 2 0.000 0.985 0.00 1.00
#> TCGA.G5.6572.02 1 0.000 1.000 1.00 0.00
#> TCGA.DY.A0XA.01 2 0.000 0.985 0.00 1.00
#> TCGA.DM.A28E.01 2 0.000 0.985 0.00 1.00
#> TCGA.CI.6623.01 2 0.327 0.950 0.06 0.94
#> TCGA.AU.3779.01 1 0.000 1.000 1.00 0.00
#> TCGA.AH.6547.01 1 0.000 1.000 1.00 0.00
#> TCGA.CA.5797.01 2 0.000 0.985 0.00 1.00
#> TCGA.F4.6460.01 1 0.000 1.000 1.00 0.00
#> TCGA.F5.6702.01 2 0.327 0.950 0.06 0.94
#> TCGA.D5.6927.01 1 0.000 1.000 1.00 0.00
#> TCGA.G4.6304.01 1 0.000 1.000 1.00 0.00
#> TCGA.EI.6513.01 2 0.000 0.985 0.00 1.00
#> TCGA.D5.6539.01 1 0.000 1.000 1.00 0.00
#> TCGA.BM.6198.01 1 0.000 1.000 1.00 0.00
#> TCGA.CM.6674.01 1 0.000 1.000 1.00 0.00
#> TCGA.CM.4743.01 1 0.000 1.000 1.00 0.00
#> TCGA.F5.6465.01 2 0.000 0.985 0.00 1.00
#> TCGA.CM.5344.01 2 0.000 0.985 0.00 1.00
#> TCGA.AZ.4681.01 2 0.000 0.985 0.00 1.00
#> TCGA.A6.6140.01 2 0.327 0.950 0.06 0.94
#> TCGA.DM.A1D0.01 2 0.000 0.985 0.00 1.00
#> TCGA.EI.6509.01 2 0.000 0.985 0.00 1.00
#> TCGA.CI.6619.01 2 0.000 0.985 0.00 1.00
#> TCGA.WS.AB45.01 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.F5.6464.01 1 0.000 1.000 1 0.00 0.00
#> TCGA.AZ.4308.01 2 0.000 0.955 0 1.00 0.00
#> TCGA.D5.5541.01 2 0.571 0.573 0 0.68 0.32
#> TCGA.F5.6812.01 1 0.000 1.000 1 0.00 0.00
#> TCGA.A6.6648.01 2 0.000 0.955 0 1.00 0.00
#> TCGA.F4.6805.01 1 0.000 1.000 1 0.00 0.00
#> TCGA.AF.A56K.01 2 0.000 0.955 0 1.00 0.00
#> TCGA.G4.6627.01 1 0.000 1.000 1 0.00 0.00
#> TCGA.D5.6929.01 2 0.583 0.536 0 0.66 0.34
#> TCGA.DC.6157.01 3 0.000 0.996 0 0.00 1.00
#> TCGA.AF.6655.01 2 0.000 0.955 0 1.00 0.00
#> TCGA.CM.6164.01 2 0.000 0.955 0 1.00 0.00
#> TCGA.AF.2687.01 2 0.583 0.536 0 0.66 0.34
#> TCGA.F4.6704.01 2 0.000 0.955 0 1.00 0.00
#> TCGA.A6.A567.01 3 0.000 0.996 0 0.00 1.00
#> TCGA.AG.3732.01 2 0.000 0.955 0 1.00 0.00
#> TCGA.EI.6885.01 3 0.000 0.996 0 0.00 1.00
#> TCGA.DC.4749.01 2 0.000 0.955 0 1.00 0.00
#> TCGA.5M.AAT5.01 3 0.000 0.996 0 0.00 1.00
#> TCGA.DC.6160.01 2 0.000 0.955 0 1.00 0.00
#> TCGA.D5.6534.01 1 0.000 1.000 1 0.00 0.00
#> TCGA.F5.6863.01 2 0.000 0.955 0 1.00 0.00
#> TCGA.G4.6317.02 3 0.000 0.996 0 0.00 1.00
#> TCGA.CK.4948.01 3 0.207 0.931 0 0.06 0.94
#> TCGA.A6.6651.01 1 0.000 1.000 1 0.00 0.00
#> TCGA.G4.6309.01 2 0.000 0.955 0 1.00 0.00
#> TCGA.AF.2693.01 1 0.000 1.000 1 0.00 0.00
#> TCGA.CM.5868.01 2 0.296 0.866 0 0.90 0.10
#> TCGA.AF.4110.01 1 0.000 1.000 1 0.00 0.00
#> TCGA.AZ.4313.01 2 0.000 0.955 0 1.00 0.00
#> TCGA.A6.2675.01 2 0.000 0.955 0 1.00 0.00
#> TCGA.AA.3494.01 3 0.000 0.996 0 0.00 1.00
#> TCGA.G4.6307.01 3 0.000 0.996 0 0.00 1.00
#> TCGA.CI.6624.01 2 0.000 0.955 0 1.00 0.00
#> TCGA.F5.6810.01 3 0.000 0.996 0 0.00 1.00
#> TCGA.CM.6167.01 1 0.000 1.000 1 0.00 0.00
#> TCGA.CM.4752.01 2 0.583 0.536 0 0.66 0.34
#> TCGA.A6.6781.01 1 0.000 1.000 1 0.00 0.00
#> TCGA.DM.A0XF.01 2 0.000 0.955 0 1.00 0.00
#> TCGA.G4.6295.01 3 0.000 0.996 0 0.00 1.00
#> TCGA.AZ.6605.01 1 0.000 1.000 1 0.00 0.00
#> TCGA.G5.6572.01 1 0.000 1.000 1 0.00 0.00
#> TCGA.DM.A280.01 1 0.000 1.000 1 0.00 0.00
#> TCGA.AA.3489.01 1 0.000 1.000 1 0.00 0.00
#> TCGA.AG.A01Y.01 3 0.000 0.996 0 0.00 1.00
#> TCGA.AZ.6603.01 3 0.000 0.996 0 0.00 1.00
#> TCGA.G4.6302.01 1 0.000 1.000 1 0.00 0.00
#> TCGA.G5.6235.01 1 0.000 1.000 1 0.00 0.00
#> TCGA.CI.6621.01 1 0.000 1.000 1 0.00 0.00
#> TCGA.F4.6857.01 1 0.000 1.000 1 0.00 0.00
#> TCGA.AZ.4323.01 1 0.000 1.000 1 0.00 0.00
#> TCGA.AF.6672.01 3 0.000 0.996 0 0.00 1.00
#> TCGA.AD.6963.01 2 0.000 0.955 0 1.00 0.00
#> TCGA.D5.6928.01 1 0.000 1.000 1 0.00 0.00
#> TCGA.A6.3810.01 2 0.000 0.955 0 1.00 0.00
#> TCGA.D5.6923.01 1 0.000 1.000 1 0.00 0.00
#> TCGA.AF.2690.01 1 0.000 1.000 1 0.00 0.00
#> TCGA.NH.A8F7.01 3 0.000 0.996 0 0.00 1.00
#> TCGA.G5.6572.02 1 0.000 1.000 1 0.00 0.00
#> TCGA.DY.A0XA.01 2 0.000 0.955 0 1.00 0.00
#> TCGA.DM.A28E.01 2 0.000 0.955 0 1.00 0.00
#> TCGA.CI.6623.01 2 0.000 0.955 0 1.00 0.00
#> TCGA.AU.3779.01 2 0.000 0.955 0 1.00 0.00
#> TCGA.AH.6547.01 1 0.000 1.000 1 0.00 0.00
#> TCGA.CA.5797.01 3 0.000 0.996 0 0.00 1.00
#> TCGA.F4.6460.01 2 0.000 0.955 0 1.00 0.00
#> TCGA.F5.6702.01 2 0.000 0.955 0 1.00 0.00
#> TCGA.D5.6927.01 1 0.000 1.000 1 0.00 0.00
#> TCGA.G4.6304.01 1 0.000 1.000 1 0.00 0.00
#> TCGA.EI.6513.01 3 0.000 0.996 0 0.00 1.00
#> TCGA.D5.6539.01 1 0.000 1.000 1 0.00 0.00
#> TCGA.BM.6198.01 1 0.000 1.000 1 0.00 0.00
#> TCGA.CM.6674.01 1 0.000 1.000 1 0.00 0.00
#> TCGA.CM.4743.01 1 0.000 1.000 1 0.00 0.00
#> TCGA.F5.6465.01 2 0.000 0.955 0 1.00 0.00
#> TCGA.CM.5344.01 2 0.000 0.955 0 1.00 0.00
#> TCGA.AZ.4681.01 3 0.000 0.996 0 0.00 1.00
#> TCGA.A6.6140.01 2 0.000 0.955 0 1.00 0.00
#> TCGA.DM.A1D0.01 2 0.000 0.955 0 1.00 0.00
#> TCGA.EI.6509.01 2 0.000 0.955 0 1.00 0.00
#> TCGA.CI.6619.01 2 0.000 0.955 0 1.00 0.00
#> TCGA.WS.AB45.01 1 0.000 1.000 1 0.00 0.00
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> TCGA.F5.6464.01 1 0.4994 0.4439 0.52 0.00 0.00 0.48
#> TCGA.AZ.4308.01 2 0.0000 0.7614 0.00 1.00 0.00 0.00
#> TCGA.D5.5541.01 2 0.0000 0.7614 0.00 1.00 0.00 0.00
#> TCGA.F5.6812.01 1 0.4713 0.6479 0.64 0.00 0.00 0.36
#> TCGA.A6.6648.01 2 0.2647 0.7161 0.00 0.88 0.00 0.12
#> TCGA.F4.6805.01 1 0.0000 0.8929 1.00 0.00 0.00 0.00
#> TCGA.AF.A56K.01 2 0.0000 0.7614 0.00 1.00 0.00 0.00
#> TCGA.G4.6627.01 1 0.0000 0.8929 1.00 0.00 0.00 0.00
#> TCGA.D5.6929.01 2 0.0000 0.7614 0.00 1.00 0.00 0.00
#> TCGA.DC.6157.01 3 0.1637 0.9287 0.00 0.06 0.94 0.00
#> TCGA.AF.6655.01 4 0.4624 0.4247 0.00 0.34 0.00 0.66
#> TCGA.CM.6164.01 2 0.4977 -0.0775 0.00 0.54 0.00 0.46
#> TCGA.AF.2687.01 2 0.0000 0.7614 0.00 1.00 0.00 0.00
#> TCGA.F4.6704.01 2 0.1637 0.7417 0.00 0.94 0.00 0.06
#> TCGA.A6.A567.01 3 0.0000 0.9484 0.00 0.00 1.00 0.00
#> TCGA.AG.3732.01 2 0.3801 0.6496 0.00 0.78 0.00 0.22
#> TCGA.EI.6885.01 3 0.2345 0.9001 0.00 0.10 0.90 0.00
#> TCGA.DC.4749.01 2 0.3172 0.6987 0.00 0.84 0.00 0.16
#> TCGA.5M.AAT5.01 3 0.0000 0.9484 0.00 0.00 1.00 0.00
#> TCGA.DC.6160.01 4 0.4790 0.3523 0.00 0.38 0.00 0.62
#> TCGA.D5.6534.01 1 0.0000 0.8929 1.00 0.00 0.00 0.00
#> TCGA.F5.6863.01 4 0.0707 0.5510 0.00 0.02 0.00 0.98
#> TCGA.G4.6317.02 3 0.0000 0.9484 0.00 0.00 1.00 0.00
#> TCGA.CK.4948.01 2 0.1637 0.6996 0.00 0.94 0.06 0.00
#> TCGA.A6.6651.01 1 0.4855 0.5940 0.60 0.00 0.00 0.40
#> TCGA.G4.6309.01 2 0.3172 0.6987 0.00 0.84 0.00 0.16
#> TCGA.AF.2693.01 4 0.4277 0.1905 0.28 0.00 0.00 0.72
#> TCGA.CM.5868.01 2 0.0000 0.7614 0.00 1.00 0.00 0.00
#> TCGA.AF.4110.01 1 0.4855 0.5940 0.60 0.00 0.00 0.40
#> TCGA.AZ.4313.01 2 0.4977 -0.0775 0.00 0.54 0.00 0.46
#> TCGA.A6.2675.01 4 0.4977 0.1970 0.00 0.46 0.00 0.54
#> TCGA.AA.3494.01 3 0.0000 0.9484 0.00 0.00 1.00 0.00
#> TCGA.G4.6307.01 3 0.1637 0.9287 0.00 0.06 0.94 0.00
#> TCGA.CI.6624.01 2 0.4948 -0.0303 0.00 0.56 0.00 0.44
#> TCGA.F5.6810.01 3 0.0000 0.9484 0.00 0.00 1.00 0.00
#> TCGA.CM.6167.01 1 0.0000 0.8929 1.00 0.00 0.00 0.00
#> TCGA.CM.4752.01 2 0.0000 0.7614 0.00 1.00 0.00 0.00
#> TCGA.A6.6781.01 1 0.0000 0.8929 1.00 0.00 0.00 0.00
#> TCGA.DM.A0XF.01 4 0.4977 0.1970 0.00 0.46 0.00 0.54
#> TCGA.G4.6295.01 3 0.0000 0.9484 0.00 0.00 1.00 0.00
#> TCGA.AZ.6605.01 1 0.4522 0.6872 0.68 0.00 0.00 0.32
#> TCGA.G5.6572.01 1 0.0000 0.8929 1.00 0.00 0.00 0.00
#> TCGA.DM.A280.01 1 0.2011 0.8595 0.92 0.00 0.00 0.08
#> TCGA.AA.3489.01 1 0.0000 0.8929 1.00 0.00 0.00 0.00
#> TCGA.AG.A01Y.01 3 0.5535 0.4099 0.00 0.42 0.56 0.02
#> TCGA.AZ.6603.01 3 0.1637 0.9287 0.00 0.06 0.94 0.00
#> TCGA.G4.6302.01 1 0.0000 0.8929 1.00 0.00 0.00 0.00
#> TCGA.G5.6235.01 4 0.4406 0.1597 0.30 0.00 0.00 0.70
#> TCGA.CI.6621.01 1 0.0000 0.8929 1.00 0.00 0.00 0.00
#> TCGA.F4.6857.01 1 0.2011 0.8595 0.92 0.00 0.00 0.08
#> TCGA.AZ.4323.01 1 0.0000 0.8929 1.00 0.00 0.00 0.00
#> TCGA.AF.6672.01 3 0.0000 0.9484 0.00 0.00 1.00 0.00
#> TCGA.AD.6963.01 4 0.4948 0.2781 0.00 0.44 0.00 0.56
#> TCGA.D5.6928.01 1 0.2011 0.8595 0.92 0.00 0.00 0.08
#> TCGA.A6.3810.01 4 0.4277 0.4766 0.00 0.28 0.00 0.72
#> TCGA.D5.6923.01 4 0.2647 0.5088 0.12 0.00 0.00 0.88
#> TCGA.AF.2690.01 1 0.4713 0.6479 0.64 0.00 0.00 0.36
#> TCGA.NH.A8F7.01 3 0.1637 0.9287 0.00 0.06 0.94 0.00
#> TCGA.G5.6572.02 1 0.0000 0.8929 1.00 0.00 0.00 0.00
#> TCGA.DY.A0XA.01 2 0.2921 0.7074 0.00 0.86 0.00 0.14
#> TCGA.DM.A28E.01 2 0.4907 0.2801 0.00 0.58 0.00 0.42
#> TCGA.CI.6623.01 4 0.4907 0.2779 0.00 0.42 0.00 0.58
#> TCGA.AU.3779.01 4 0.0707 0.5510 0.00 0.02 0.00 0.98
#> TCGA.AH.6547.01 1 0.0000 0.8929 1.00 0.00 0.00 0.00
#> TCGA.CA.5797.01 3 0.0000 0.9484 0.00 0.00 1.00 0.00
#> TCGA.F4.6460.01 4 0.1211 0.5519 0.00 0.04 0.00 0.96
#> TCGA.F5.6702.01 2 0.4948 -0.0303 0.00 0.56 0.00 0.44
#> TCGA.D5.6927.01 1 0.0000 0.8929 1.00 0.00 0.00 0.00
#> TCGA.G4.6304.01 1 0.0000 0.8929 1.00 0.00 0.00 0.00
#> TCGA.EI.6513.01 3 0.0000 0.9484 0.00 0.00 1.00 0.00
#> TCGA.D5.6539.01 1 0.0000 0.8929 1.00 0.00 0.00 0.00
#> TCGA.BM.6198.01 1 0.4624 0.6685 0.66 0.00 0.00 0.34
#> TCGA.CM.6674.01 1 0.0000 0.8929 1.00 0.00 0.00 0.00
#> TCGA.CM.4743.01 1 0.0000 0.8929 1.00 0.00 0.00 0.00
#> TCGA.F5.6465.01 2 0.0000 0.7614 0.00 1.00 0.00 0.00
#> TCGA.CM.5344.01 2 0.0000 0.7614 0.00 1.00 0.00 0.00
#> TCGA.AZ.4681.01 3 0.0000 0.9484 0.00 0.00 1.00 0.00
#> TCGA.A6.6140.01 4 0.4624 0.4247 0.00 0.34 0.00 0.66
#> TCGA.DM.A1D0.01 2 0.4948 0.2170 0.00 0.56 0.00 0.44
#> TCGA.EI.6509.01 2 0.3172 0.6987 0.00 0.84 0.00 0.16
#> TCGA.CI.6619.01 2 0.1637 0.7417 0.00 0.94 0.00 0.06
#> TCGA.WS.AB45.01 1 0.0000 0.8929 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.F5.6464.01 4 0.1732 0.692 0.08 0.00 0.00 0.92 0.00
#> TCGA.AZ.4308.01 2 0.2020 0.614 0.00 0.90 0.00 0.00 0.10
#> TCGA.D5.5541.01 2 0.1216 0.625 0.00 0.96 0.00 0.02 0.02
#> TCGA.F5.6812.01 4 0.3424 0.605 0.24 0.00 0.00 0.76 0.00
#> TCGA.A6.6648.01 2 0.4644 0.537 0.00 0.68 0.00 0.04 0.28
#> TCGA.F4.6805.01 1 0.1043 0.894 0.96 0.00 0.00 0.00 0.04
#> TCGA.AF.A56K.01 2 0.0609 0.641 0.00 0.98 0.00 0.00 0.02
#> TCGA.G4.6627.01 1 0.0000 0.902 1.00 0.00 0.00 0.00 0.00
#> TCGA.D5.6929.01 2 0.0000 0.657 0.00 1.00 0.00 0.00 0.00
#> TCGA.DC.6157.01 3 0.3463 0.863 0.00 0.12 0.84 0.02 0.02
#> TCGA.AF.6655.01 2 0.6632 0.225 0.00 0.40 0.00 0.22 0.38
#> TCGA.CM.6164.01 2 0.6033 0.537 0.00 0.58 0.00 0.20 0.22
#> TCGA.AF.2687.01 2 0.0000 0.657 0.00 1.00 0.00 0.00 0.00
#> TCGA.F4.6704.01 2 0.2616 0.653 0.00 0.88 0.00 0.02 0.10
#> TCGA.A6.A567.01 3 0.2616 0.879 0.00 0.10 0.88 0.02 0.00
#> TCGA.AG.3732.01 2 0.4287 0.177 0.00 0.54 0.00 0.00 0.46
#> TCGA.EI.6885.01 3 0.3999 0.767 0.00 0.24 0.74 0.02 0.00
#> TCGA.DC.4749.01 5 0.3274 0.727 0.00 0.22 0.00 0.00 0.78
#> TCGA.5M.AAT5.01 3 0.0000 0.907 0.00 0.00 1.00 0.00 0.00
#> TCGA.DC.6160.01 5 0.6548 -0.298 0.00 0.38 0.00 0.20 0.42
#> TCGA.D5.6534.01 1 0.1043 0.889 0.96 0.00 0.00 0.00 0.04
#> TCGA.F5.6863.01 4 0.3983 0.312 0.00 0.00 0.00 0.66 0.34
#> TCGA.G4.6317.02 3 0.0000 0.907 0.00 0.00 1.00 0.00 0.00
#> TCGA.CK.4948.01 2 0.0000 0.657 0.00 1.00 0.00 0.00 0.00
#> TCGA.A6.6651.01 4 0.3037 0.690 0.10 0.00 0.00 0.86 0.04
#> TCGA.G4.6309.01 5 0.3796 0.669 0.00 0.30 0.00 0.00 0.70
#> TCGA.AF.2693.01 4 0.1216 0.667 0.02 0.00 0.00 0.96 0.02
#> TCGA.CM.5868.01 2 0.0000 0.657 0.00 1.00 0.00 0.00 0.00
#> TCGA.AF.4110.01 4 0.3274 0.627 0.22 0.00 0.00 0.78 0.00
#> TCGA.AZ.4313.01 2 0.5904 0.555 0.00 0.60 0.00 0.20 0.20
#> TCGA.A6.2675.01 2 0.6398 0.430 0.00 0.50 0.00 0.20 0.30
#> TCGA.AA.3494.01 3 0.0000 0.907 0.00 0.00 1.00 0.00 0.00
#> TCGA.G4.6307.01 3 0.3463 0.863 0.00 0.12 0.84 0.02 0.02
#> TCGA.CI.6624.01 2 0.5904 0.555 0.00 0.60 0.00 0.20 0.20
#> TCGA.F5.6810.01 3 0.0000 0.907 0.00 0.00 1.00 0.00 0.00
#> TCGA.CM.6167.01 1 0.0609 0.899 0.98 0.00 0.00 0.00 0.02
#> TCGA.CM.4752.01 2 0.0000 0.657 0.00 1.00 0.00 0.00 0.00
#> TCGA.A6.6781.01 1 0.0000 0.902 1.00 0.00 0.00 0.00 0.00
#> TCGA.DM.A0XF.01 2 0.6398 0.430 0.00 0.50 0.00 0.20 0.30
#> TCGA.G4.6295.01 3 0.0000 0.907 0.00 0.00 1.00 0.00 0.00
#> TCGA.AZ.6605.01 4 0.5048 0.263 0.38 0.00 0.00 0.58 0.04
#> TCGA.G5.6572.01 1 0.0609 0.895 0.98 0.00 0.00 0.00 0.02
#> TCGA.DM.A280.01 1 0.4921 0.447 0.62 0.00 0.00 0.34 0.04
#> TCGA.AA.3489.01 1 0.0609 0.899 0.98 0.00 0.00 0.00 0.02
#> TCGA.AG.A01Y.01 3 0.4767 0.508 0.00 0.42 0.56 0.02 0.00
#> TCGA.AZ.6603.01 3 0.3106 0.858 0.00 0.14 0.84 0.02 0.00
#> TCGA.G4.6302.01 1 0.0000 0.902 1.00 0.00 0.00 0.00 0.00
#> TCGA.G5.6235.01 4 0.2012 0.686 0.06 0.00 0.00 0.92 0.02
#> TCGA.CI.6621.01 1 0.0609 0.895 0.98 0.00 0.00 0.00 0.02
#> TCGA.F4.6857.01 1 0.4921 0.447 0.62 0.00 0.00 0.34 0.04
#> TCGA.AZ.4323.01 1 0.0000 0.902 1.00 0.00 0.00 0.00 0.00
#> TCGA.AF.6672.01 3 0.0609 0.904 0.00 0.00 0.98 0.02 0.00
#> TCGA.AD.6963.01 2 0.6157 0.526 0.00 0.56 0.00 0.22 0.22
#> TCGA.D5.6928.01 1 0.4921 0.447 0.62 0.00 0.00 0.34 0.04
#> TCGA.A6.3810.01 4 0.6219 -0.138 0.00 0.14 0.00 0.44 0.42
#> TCGA.D5.6923.01 4 0.0609 0.650 0.00 0.00 0.00 0.98 0.02
#> TCGA.AF.2690.01 4 0.3424 0.605 0.24 0.00 0.00 0.76 0.00
#> TCGA.NH.A8F7.01 3 0.2610 0.885 0.00 0.06 0.90 0.02 0.02
#> TCGA.G5.6572.02 1 0.0609 0.895 0.98 0.00 0.00 0.00 0.02
#> TCGA.DY.A0XA.01 5 0.4252 0.678 0.00 0.28 0.00 0.02 0.70
#> TCGA.DM.A28E.01 5 0.2331 0.722 0.00 0.08 0.00 0.02 0.90
#> TCGA.CI.6623.01 2 0.6455 0.394 0.00 0.48 0.00 0.20 0.32
#> TCGA.AU.3779.01 4 0.3561 0.440 0.00 0.00 0.00 0.74 0.26
#> TCGA.AH.6547.01 1 0.0000 0.902 1.00 0.00 0.00 0.00 0.00
#> TCGA.CA.5797.01 3 0.0000 0.907 0.00 0.00 1.00 0.00 0.00
#> TCGA.F4.6460.01 4 0.4182 0.207 0.00 0.00 0.00 0.60 0.40
#> TCGA.F5.6702.01 2 0.5904 0.555 0.00 0.60 0.00 0.20 0.20
#> TCGA.D5.6927.01 1 0.0609 0.899 0.98 0.00 0.00 0.00 0.02
#> TCGA.G4.6304.01 1 0.0000 0.902 1.00 0.00 0.00 0.00 0.00
#> TCGA.EI.6513.01 3 0.0000 0.907 0.00 0.00 1.00 0.00 0.00
#> TCGA.D5.6539.01 1 0.4840 0.497 0.64 0.00 0.00 0.32 0.04
#> TCGA.BM.6198.01 4 0.3424 0.605 0.24 0.00 0.00 0.76 0.00
#> TCGA.CM.6674.01 1 0.0609 0.899 0.98 0.00 0.00 0.00 0.02
#> TCGA.CM.4743.01 1 0.0000 0.902 1.00 0.00 0.00 0.00 0.00
#> TCGA.F5.6465.01 2 0.0609 0.658 0.00 0.98 0.00 0.00 0.02
#> TCGA.CM.5344.01 2 0.0000 0.657 0.00 1.00 0.00 0.00 0.00
#> TCGA.AZ.4681.01 3 0.0000 0.907 0.00 0.00 1.00 0.00 0.00
#> TCGA.A6.6140.01 5 0.2438 0.708 0.00 0.06 0.00 0.04 0.90
#> TCGA.DM.A1D0.01 5 0.2438 0.708 0.00 0.06 0.00 0.04 0.90
#> TCGA.EI.6509.01 5 0.3561 0.709 0.00 0.26 0.00 0.00 0.74
#> TCGA.CI.6619.01 2 0.2020 0.656 0.00 0.90 0.00 0.00 0.10
#> TCGA.WS.AB45.01 1 0.0000 0.902 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.F5.6464.01 4 0.2581 0.789 0.02 0.00 0.00 0.86 0.00 0.12
#> TCGA.AZ.4308.01 2 0.3198 0.583 0.00 0.74 0.00 0.00 0.26 0.00
#> TCGA.D5.5541.01 2 0.2350 0.754 0.00 0.88 0.00 0.02 0.10 0.00
#> TCGA.F5.6812.01 4 0.2631 0.803 0.18 0.00 0.00 0.82 0.00 0.00
#> TCGA.A6.6648.01 6 0.5432 0.474 0.00 0.40 0.00 0.00 0.12 0.48
#> TCGA.F4.6805.01 1 0.0000 0.886 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AF.A56K.01 2 0.1814 0.768 0.00 0.90 0.00 0.00 0.10 0.00
#> TCGA.G4.6627.01 1 0.0000 0.886 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D5.6929.01 2 0.0000 0.818 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DC.6157.01 3 0.5190 0.755 0.00 0.18 0.68 0.10 0.04 0.00
#> TCGA.AF.6655.01 6 0.4238 0.730 0.00 0.16 0.00 0.04 0.04 0.76
#> TCGA.CM.6164.01 6 0.4172 0.749 0.00 0.28 0.00 0.00 0.04 0.68
#> TCGA.AF.2687.01 2 0.0000 0.818 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.F4.6704.01 2 0.3499 0.216 0.00 0.68 0.00 0.00 0.00 0.32
#> TCGA.A6.A567.01 3 0.4195 0.770 0.00 0.20 0.74 0.04 0.02 0.00
#> TCGA.AG.3732.01 5 0.5150 0.538 0.00 0.16 0.00 0.00 0.62 0.22
#> TCGA.EI.6885.01 2 0.4971 0.122 0.00 0.58 0.36 0.04 0.02 0.00
#> TCGA.DC.4749.01 5 0.2728 0.838 0.00 0.10 0.00 0.00 0.86 0.04
#> TCGA.5M.AAT5.01 3 0.0000 0.879 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.DC.6160.01 6 0.3697 0.647 0.00 0.06 0.00 0.04 0.08 0.82
#> TCGA.D5.6534.01 1 0.3045 0.767 0.86 0.00 0.00 0.02 0.06 0.06
#> TCGA.F5.6863.01 6 0.4938 0.317 0.00 0.00 0.00 0.34 0.08 0.58
#> TCGA.G4.6317.02 3 0.0000 0.879 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.CK.4948.01 2 0.0000 0.818 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.A6.6651.01 4 0.5256 0.775 0.08 0.00 0.00 0.68 0.06 0.18
#> TCGA.G4.6309.01 5 0.3045 0.839 0.00 0.10 0.00 0.00 0.84 0.06
#> TCGA.AF.2693.01 4 0.2454 0.757 0.00 0.00 0.00 0.84 0.00 0.16
#> TCGA.CM.5868.01 2 0.0000 0.818 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.AF.4110.01 4 0.2794 0.819 0.08 0.00 0.00 0.86 0.00 0.06
#> TCGA.AZ.4313.01 6 0.3409 0.737 0.00 0.30 0.00 0.00 0.00 0.70
#> TCGA.A6.2675.01 6 0.4067 0.757 0.00 0.26 0.00 0.00 0.04 0.70
#> TCGA.AA.3494.01 3 0.1092 0.874 0.00 0.00 0.96 0.02 0.02 0.00
#> TCGA.G4.6307.01 3 0.5190 0.755 0.00 0.18 0.68 0.10 0.04 0.00
#> TCGA.CI.6624.01 6 0.3499 0.720 0.00 0.32 0.00 0.00 0.00 0.68
#> TCGA.F5.6810.01 3 0.0000 0.879 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.CM.6167.01 1 0.0000 0.886 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CM.4752.01 2 0.0000 0.818 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.A6.6781.01 1 0.0000 0.886 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DM.A0XF.01 6 0.4067 0.757 0.00 0.26 0.00 0.00 0.04 0.70
#> TCGA.G4.6295.01 3 0.0000 0.879 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.AZ.6605.01 4 0.3678 0.792 0.18 0.00 0.00 0.78 0.02 0.02
#> TCGA.G5.6572.01 1 0.0937 0.863 0.96 0.00 0.00 0.00 0.04 0.00
#> TCGA.DM.A280.01 1 0.6119 -0.197 0.44 0.00 0.00 0.42 0.06 0.08
#> TCGA.AA.3489.01 1 0.0000 0.886 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AG.A01Y.01 2 0.4844 0.470 0.00 0.70 0.22 0.04 0.02 0.02
#> TCGA.AZ.6603.01 3 0.5190 0.755 0.00 0.18 0.68 0.10 0.04 0.00
#> TCGA.G4.6302.01 1 0.0000 0.886 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.G5.6235.01 4 0.3982 0.742 0.00 0.00 0.00 0.74 0.06 0.20
#> TCGA.CI.6621.01 1 0.0937 0.863 0.96 0.00 0.00 0.00 0.04 0.00
#> TCGA.F4.6857.01 1 0.6119 -0.197 0.44 0.00 0.00 0.42 0.06 0.08
#> TCGA.AZ.4323.01 1 0.0000 0.886 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AF.6672.01 3 0.2020 0.866 0.00 0.02 0.92 0.04 0.02 0.00
#> TCGA.AD.6963.01 6 0.4247 0.721 0.00 0.24 0.00 0.00 0.06 0.70
#> TCGA.D5.6928.01 1 0.6119 -0.197 0.44 0.00 0.00 0.42 0.06 0.08
#> TCGA.A6.3810.01 6 0.3697 0.631 0.00 0.04 0.00 0.06 0.08 0.82
#> TCGA.D5.6923.01 4 0.2454 0.757 0.00 0.00 0.00 0.84 0.00 0.16
#> TCGA.AF.2690.01 4 0.2454 0.815 0.16 0.00 0.00 0.84 0.00 0.00
#> TCGA.NH.A8F7.01 3 0.4860 0.786 0.00 0.14 0.72 0.10 0.04 0.00
#> TCGA.G5.6572.02 1 0.0000 0.886 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DY.A0XA.01 5 0.3258 0.836 0.00 0.10 0.00 0.02 0.84 0.04
#> TCGA.DM.A28E.01 5 0.3351 0.793 0.00 0.00 0.00 0.04 0.80 0.16
#> TCGA.CI.6623.01 6 0.4247 0.750 0.00 0.24 0.00 0.00 0.06 0.70
#> TCGA.AU.3779.01 6 0.4246 0.205 0.00 0.00 0.00 0.40 0.02 0.58
#> TCGA.AH.6547.01 1 0.0000 0.886 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CA.5797.01 3 0.0000 0.879 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.F4.6460.01 6 0.3321 0.590 0.00 0.00 0.00 0.10 0.08 0.82
#> TCGA.F5.6702.01 6 0.3499 0.720 0.00 0.32 0.00 0.00 0.00 0.68
#> TCGA.D5.6927.01 1 0.0000 0.886 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.G4.6304.01 1 0.0000 0.886 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EI.6513.01 3 0.0000 0.879 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.D5.6539.01 4 0.4246 0.389 0.40 0.00 0.00 0.58 0.02 0.00
#> TCGA.BM.6198.01 4 0.3156 0.799 0.18 0.00 0.00 0.80 0.02 0.00
#> TCGA.CM.6674.01 1 0.0000 0.886 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CM.4743.01 1 0.0000 0.886 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.F5.6465.01 2 0.0547 0.802 0.00 0.98 0.00 0.00 0.00 0.02
#> TCGA.CM.5344.01 2 0.0000 0.818 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.AZ.4681.01 3 0.0000 0.879 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.A6.6140.01 5 0.4613 0.672 0.00 0.00 0.00 0.08 0.66 0.26
#> TCGA.DM.A1D0.01 5 0.3821 0.763 0.00 0.00 0.00 0.04 0.74 0.22
#> TCGA.EI.6509.01 5 0.3045 0.839 0.00 0.10 0.00 0.00 0.84 0.06
#> TCGA.CI.6619.01 2 0.2454 0.609 0.00 0.84 0.00 0.00 0.00 0.16
#> TCGA.WS.AB45.01 1 0.0000 0.886 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.F5.6464.01 4 0.2803 0.6612 0.00 0.00 0.00 0.84 0.00 0.06 0.10
#> TCGA.AZ.4308.01 2 0.4714 0.5706 0.00 0.60 0.00 0.00 0.28 0.12 0.00
#> TCGA.D5.5541.01 2 0.2512 0.8251 0.00 0.86 0.00 0.00 0.04 0.10 0.00
#> TCGA.F5.6812.01 4 0.2803 0.7047 0.06 0.00 0.00 0.84 0.00 0.00 0.10
#> TCGA.A6.6648.01 6 0.3000 0.7394 0.00 0.10 0.00 0.00 0.04 0.84 0.02
#> TCGA.F4.6805.01 1 0.0000 0.9467 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AF.A56K.01 2 0.3670 0.7658 0.00 0.76 0.00 0.00 0.14 0.10 0.00
#> TCGA.G4.6627.01 1 0.0000 0.9467 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D5.6929.01 2 0.2422 0.8641 0.00 0.82 0.00 0.00 0.00 0.18 0.00
#> TCGA.DC.6157.01 3 0.6065 0.6405 0.00 0.22 0.56 0.02 0.06 0.00 0.14
#> TCGA.AF.6655.01 6 0.1928 0.7759 0.00 0.00 0.00 0.00 0.02 0.90 0.08
#> TCGA.CM.6164.01 6 0.0504 0.8100 0.00 0.00 0.00 0.00 0.00 0.98 0.02
#> TCGA.AF.2687.01 2 0.2422 0.8641 0.00 0.82 0.00 0.00 0.00 0.18 0.00
#> TCGA.F4.6704.01 6 0.1671 0.7437 0.00 0.10 0.00 0.00 0.00 0.90 0.00
#> TCGA.A6.A567.01 3 0.4623 0.6238 0.00 0.28 0.64 0.04 0.00 0.00 0.04
#> TCGA.AG.3732.01 5 0.4003 0.4027 0.00 0.04 0.00 0.00 0.64 0.32 0.00
#> TCGA.EI.6885.01 2 0.4318 0.4822 0.00 0.70 0.22 0.04 0.00 0.00 0.04
#> TCGA.DC.4749.01 5 0.1928 0.7935 0.00 0.08 0.00 0.00 0.90 0.00 0.02
#> TCGA.5M.AAT5.01 3 0.0000 0.8249 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DC.6160.01 6 0.3909 0.3641 0.00 0.00 0.00 0.00 0.02 0.58 0.40
#> TCGA.D5.6534.01 1 0.5254 0.5254 0.66 0.06 0.00 0.20 0.04 0.00 0.04
#> TCGA.F5.6863.01 7 0.4146 0.4974 0.00 0.00 0.00 0.24 0.00 0.08 0.68
#> TCGA.G4.6317.02 3 0.0000 0.8249 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.CK.4948.01 2 0.2422 0.8641 0.00 0.82 0.00 0.00 0.00 0.18 0.00
#> TCGA.A6.6651.01 4 0.4225 0.6058 0.00 0.06 0.00 0.78 0.04 0.08 0.04
#> TCGA.G4.6309.01 5 0.1928 0.7866 0.00 0.08 0.00 0.00 0.90 0.02 0.00
#> TCGA.AF.2693.01 4 0.3667 0.5736 0.00 0.00 0.00 0.74 0.00 0.06 0.20
#> TCGA.CM.5868.01 2 0.2422 0.8641 0.00 0.82 0.00 0.00 0.00 0.18 0.00
#> TCGA.AF.4110.01 4 0.3396 0.6744 0.04 0.00 0.00 0.80 0.00 0.02 0.14
#> TCGA.AZ.4313.01 6 0.0000 0.8100 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.A6.2675.01 6 0.1363 0.8054 0.00 0.00 0.00 0.00 0.02 0.94 0.04
#> TCGA.AA.3494.01 3 0.1860 0.8128 0.00 0.02 0.92 0.02 0.00 0.00 0.04
#> TCGA.G4.6307.01 3 0.6065 0.6405 0.00 0.22 0.56 0.02 0.06 0.00 0.14
#> TCGA.CI.6624.01 6 0.0000 0.8100 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.F5.6810.01 3 0.0000 0.8249 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.CM.6167.01 1 0.2421 0.8518 0.88 0.02 0.00 0.08 0.02 0.00 0.00
#> TCGA.CM.4752.01 2 0.2422 0.8641 0.00 0.82 0.00 0.00 0.00 0.18 0.00
#> TCGA.A6.6781.01 1 0.0000 0.9467 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DM.A0XF.01 6 0.1363 0.8054 0.00 0.00 0.00 0.00 0.02 0.94 0.04
#> TCGA.G4.6295.01 3 0.0000 0.8249 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.AZ.6605.01 4 0.1664 0.6927 0.06 0.02 0.00 0.92 0.00 0.00 0.00
#> TCGA.G5.6572.01 1 0.2509 0.8730 0.88 0.04 0.00 0.00 0.02 0.00 0.06
#> TCGA.DM.A280.01 4 0.6159 0.4710 0.30 0.06 0.00 0.54 0.04 0.02 0.04
#> TCGA.AA.3489.01 1 0.1363 0.9051 0.94 0.00 0.00 0.04 0.02 0.00 0.00
#> TCGA.AG.A01Y.01 2 0.5162 0.5596 0.00 0.68 0.16 0.06 0.02 0.00 0.08
#> TCGA.AZ.6603.01 3 0.6065 0.6405 0.00 0.22 0.56 0.02 0.06 0.00 0.14
#> TCGA.G4.6302.01 1 0.0000 0.9467 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.G5.6235.01 4 0.2421 0.6564 0.00 0.02 0.00 0.88 0.02 0.08 0.00
#> TCGA.CI.6621.01 1 0.2159 0.8870 0.90 0.02 0.00 0.00 0.02 0.00 0.06
#> TCGA.F4.6857.01 4 0.6259 0.3930 0.34 0.06 0.00 0.50 0.04 0.02 0.04
#> TCGA.AZ.4323.01 1 0.0000 0.9467 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AF.6672.01 3 0.2857 0.7984 0.00 0.04 0.86 0.04 0.00 0.00 0.06
#> TCGA.AD.6963.01 6 0.0000 0.8100 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.D5.6928.01 4 0.6259 0.3930 0.34 0.06 0.00 0.50 0.04 0.02 0.04
#> TCGA.A6.3810.01 6 0.3909 0.3641 0.00 0.00 0.00 0.00 0.02 0.58 0.40
#> TCGA.D5.6923.01 4 0.3667 0.5736 0.00 0.00 0.00 0.74 0.00 0.06 0.20
#> TCGA.AF.2690.01 4 0.2803 0.7047 0.06 0.00 0.00 0.84 0.00 0.00 0.10
#> TCGA.NH.A8F7.01 3 0.5962 0.6600 0.00 0.20 0.58 0.02 0.06 0.00 0.14
#> TCGA.G5.6572.02 1 0.1860 0.8990 0.92 0.02 0.00 0.00 0.02 0.00 0.04
#> TCGA.DY.A0XA.01 5 0.2163 0.7749 0.00 0.10 0.00 0.00 0.88 0.00 0.02
#> TCGA.DM.A28E.01 5 0.3519 0.4780 0.00 0.04 0.00 0.00 0.74 0.00 0.22
#> TCGA.CI.6623.01 6 0.1363 0.8054 0.00 0.00 0.00 0.00 0.02 0.94 0.04
#> TCGA.AU.3779.01 7 0.4615 0.4022 0.00 0.00 0.00 0.30 0.00 0.10 0.60
#> TCGA.AH.6547.01 1 0.0000 0.9467 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CA.5797.01 3 0.0000 0.8249 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.F4.6460.01 6 0.4283 0.0907 0.00 0.00 0.00 0.04 0.00 0.48 0.48
#> TCGA.F5.6702.01 6 0.0000 0.8100 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.D5.6927.01 1 0.0000 0.9467 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.G4.6304.01 1 0.0000 0.9467 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EI.6513.01 3 0.0000 0.8249 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.D5.6539.01 4 0.2945 0.5968 0.26 0.00 0.00 0.74 0.00 0.00 0.00
#> TCGA.BM.6198.01 4 0.2803 0.7047 0.06 0.00 0.00 0.84 0.00 0.00 0.10
#> TCGA.CM.6674.01 1 0.0000 0.9467 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CM.4743.01 1 0.0000 0.9467 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.F5.6465.01 2 0.2708 0.8291 0.00 0.78 0.00 0.00 0.00 0.22 0.00
#> TCGA.CM.5344.01 2 0.2422 0.8641 0.00 0.82 0.00 0.00 0.00 0.18 0.00
#> TCGA.AZ.4681.01 3 0.0000 0.8249 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.A6.6140.01 7 0.3459 0.2602 0.00 0.00 0.00 0.00 0.40 0.00 0.60
#> TCGA.DM.A1D0.01 7 0.3994 0.0542 0.00 0.02 0.00 0.00 0.48 0.00 0.50
#> TCGA.EI.6509.01 5 0.1928 0.7935 0.00 0.08 0.00 0.00 0.90 0.00 0.02
#> TCGA.CI.6619.01 6 0.3294 0.2740 0.00 0.34 0.00 0.00 0.00 0.66 0.00
#> TCGA.WS.AB45.01 1 0.0000 0.9467 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.F5.6464.01 4 0.1275 0.738 0.02 0.00 0.00 0.94 0.00 0.04 0.00 0.00
#> TCGA.AZ.4308.01 2 0.3299 0.303 0.00 0.56 0.00 0.00 0.44 0.00 0.00 0.00
#> TCGA.D5.5541.01 2 0.2025 0.755 0.00 0.88 0.00 0.00 0.10 0.00 0.00 0.02
#> TCGA.F5.6812.01 4 0.1091 0.756 0.06 0.00 0.00 0.94 0.00 0.00 0.00 0.00
#> TCGA.A6.6648.01 6 0.2623 0.711 0.00 0.10 0.00 0.00 0.06 0.84 0.00 0.00
#> TCGA.F4.6805.01 1 0.0471 0.915 0.98 0.00 0.00 0.00 0.00 0.00 0.02 0.00
#> TCGA.AF.A56K.01 2 0.2650 0.667 0.00 0.76 0.00 0.00 0.24 0.00 0.00 0.00
#> TCGA.G4.6627.01 1 0.0000 0.918 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D5.6929.01 2 0.0808 0.785 0.00 0.96 0.00 0.00 0.00 0.04 0.00 0.00
#> TCGA.DC.6157.01 8 0.5898 0.943 0.00 0.16 0.34 0.00 0.08 0.00 0.00 0.42
#> TCGA.AF.6655.01 6 0.0471 0.774 0.00 0.00 0.00 0.00 0.00 0.98 0.02 0.00
#> TCGA.CM.6164.01 6 0.0808 0.801 0.00 0.04 0.00 0.00 0.00 0.96 0.00 0.00
#> TCGA.AF.2687.01 2 0.1275 0.785 0.00 0.94 0.00 0.02 0.00 0.04 0.00 0.00
#> TCGA.F4.6704.01 6 0.2650 0.629 0.00 0.24 0.00 0.00 0.00 0.76 0.00 0.00
#> TCGA.A6.A567.01 2 0.5734 -0.368 0.00 0.42 0.40 0.02 0.00 0.00 0.04 0.12
#> TCGA.AG.3732.01 5 0.2856 0.604 0.00 0.02 0.00 0.00 0.78 0.20 0.00 0.00
#> TCGA.EI.6885.01 2 0.4464 0.560 0.00 0.72 0.10 0.02 0.00 0.00 0.04 0.12
#> TCGA.DC.4749.01 5 0.1275 0.827 0.00 0.02 0.00 0.00 0.94 0.00 0.04 0.00
#> TCGA.5M.AAT5.01 3 0.0471 0.805 0.00 0.00 0.98 0.02 0.00 0.00 0.00 0.00
#> TCGA.DC.6160.01 6 0.3142 0.133 0.00 0.00 0.00 0.00 0.00 0.64 0.36 0.00
#> TCGA.D5.6534.01 1 0.5870 0.190 0.50 0.00 0.00 0.20 0.00 0.00 0.10 0.20
#> TCGA.F5.6863.01 7 0.4458 0.603 0.00 0.00 0.00 0.18 0.00 0.20 0.62 0.00
#> TCGA.G4.6317.02 3 0.0471 0.805 0.00 0.00 0.98 0.02 0.00 0.00 0.00 0.00
#> TCGA.CK.4948.01 2 0.1275 0.785 0.00 0.94 0.00 0.02 0.00 0.04 0.00 0.00
#> TCGA.A6.6651.01 4 0.4946 0.637 0.00 0.00 0.00 0.62 0.00 0.06 0.10 0.22
#> TCGA.G4.6309.01 5 0.0471 0.825 0.00 0.02 0.00 0.00 0.98 0.00 0.00 0.00
#> TCGA.AF.2693.01 4 0.4096 0.595 0.02 0.00 0.00 0.74 0.00 0.04 0.16 0.04
#> TCGA.CM.5868.01 2 0.1607 0.786 0.00 0.92 0.00 0.00 0.04 0.04 0.00 0.00
#> TCGA.AF.4110.01 4 0.3369 0.696 0.04 0.00 0.00 0.82 0.00 0.02 0.08 0.04
#> TCGA.AZ.4313.01 6 0.1275 0.802 0.00 0.04 0.00 0.00 0.00 0.94 0.00 0.02
#> TCGA.A6.2675.01 6 0.0000 0.792 0.00 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.AA.3494.01 3 0.2569 0.598 0.00 0.00 0.82 0.02 0.00 0.00 0.00 0.16
#> TCGA.G4.6307.01 8 0.5816 0.971 0.00 0.14 0.36 0.00 0.08 0.00 0.00 0.42
#> TCGA.CI.6624.01 6 0.1275 0.802 0.00 0.04 0.00 0.00 0.00 0.94 0.00 0.02
#> TCGA.F5.6810.01 3 0.0000 0.808 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CM.6167.01 1 0.1557 0.883 0.92 0.00 0.00 0.00 0.00 0.00 0.06 0.02
#> TCGA.CM.4752.01 2 0.1275 0.785 0.00 0.94 0.00 0.02 0.00 0.04 0.00 0.00
#> TCGA.A6.6781.01 1 0.0941 0.919 0.96 0.02 0.00 0.00 0.00 0.00 0.00 0.02
#> TCGA.DM.A0XF.01 6 0.0000 0.792 0.00 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.G4.6295.01 3 0.0000 0.808 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AZ.6605.01 4 0.2864 0.751 0.08 0.00 0.00 0.84 0.00 0.00 0.06 0.02
#> TCGA.G5.6572.01 1 0.2648 0.826 0.84 0.00 0.00 0.00 0.00 0.00 0.08 0.08
#> TCGA.DM.A280.01 4 0.5633 0.619 0.14 0.00 0.00 0.54 0.00 0.00 0.10 0.22
#> TCGA.AA.3489.01 1 0.2020 0.866 0.90 0.00 0.00 0.02 0.00 0.00 0.06 0.02
#> TCGA.AG.A01Y.01 2 0.4160 0.631 0.00 0.76 0.04 0.04 0.00 0.00 0.06 0.10
#> TCGA.AZ.6603.01 8 0.5816 0.971 0.00 0.14 0.36 0.00 0.08 0.00 0.00 0.42
#> TCGA.G4.6302.01 1 0.0941 0.919 0.96 0.02 0.00 0.00 0.00 0.00 0.00 0.02
#> TCGA.G5.6235.01 4 0.3444 0.705 0.00 0.00 0.00 0.78 0.00 0.06 0.02 0.14
#> TCGA.CI.6621.01 1 0.2407 0.842 0.86 0.00 0.00 0.00 0.00 0.00 0.06 0.08
#> TCGA.F4.6857.01 4 0.5633 0.619 0.14 0.00 0.00 0.54 0.00 0.00 0.10 0.22
#> TCGA.AZ.4323.01 1 0.0941 0.919 0.96 0.02 0.00 0.00 0.00 0.00 0.00 0.02
#> TCGA.AF.6672.01 3 0.4713 0.229 0.00 0.08 0.68 0.02 0.00 0.00 0.04 0.18
#> TCGA.AD.6963.01 6 0.1275 0.802 0.00 0.04 0.00 0.00 0.00 0.94 0.00 0.02
#> TCGA.D5.6928.01 4 0.5633 0.619 0.14 0.00 0.00 0.54 0.00 0.00 0.10 0.22
#> TCGA.A6.3810.01 6 0.3142 0.133 0.00 0.00 0.00 0.00 0.00 0.64 0.36 0.00
#> TCGA.D5.6923.01 4 0.3913 0.565 0.00 0.00 0.00 0.74 0.00 0.06 0.16 0.04
#> TCGA.AF.2690.01 4 0.1091 0.756 0.06 0.00 0.00 0.94 0.00 0.00 0.00 0.00
#> TCGA.NH.A8F7.01 3 0.5273 -0.768 0.00 0.06 0.44 0.00 0.08 0.00 0.00 0.42
#> TCGA.G5.6572.02 1 0.1741 0.902 0.92 0.02 0.00 0.00 0.00 0.00 0.02 0.04
#> TCGA.DY.A0XA.01 5 0.1275 0.807 0.00 0.02 0.00 0.00 0.94 0.00 0.00 0.04
#> TCGA.DM.A28E.01 5 0.4651 0.439 0.00 0.00 0.00 0.00 0.58 0.00 0.24 0.18
#> TCGA.CI.6623.01 6 0.0000 0.792 0.00 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.AU.3779.01 7 0.5535 0.526 0.00 0.00 0.00 0.24 0.00 0.22 0.50 0.04
#> TCGA.AH.6547.01 1 0.0000 0.918 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CA.5797.01 3 0.0000 0.808 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.F4.6460.01 7 0.3333 0.146 0.00 0.00 0.00 0.00 0.00 0.50 0.50 0.00
#> TCGA.F5.6702.01 6 0.1275 0.802 0.00 0.04 0.00 0.00 0.00 0.94 0.00 0.02
#> TCGA.D5.6927.01 1 0.0471 0.915 0.98 0.00 0.00 0.00 0.00 0.00 0.02 0.00
#> TCGA.G4.6304.01 1 0.0941 0.919 0.96 0.02 0.00 0.00 0.00 0.00 0.00 0.02
#> TCGA.EI.6513.01 3 0.0000 0.808 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D5.6539.01 4 0.4309 0.651 0.18 0.00 0.00 0.70 0.00 0.00 0.06 0.06
#> TCGA.BM.6198.01 4 0.2407 0.736 0.06 0.00 0.00 0.86 0.00 0.00 0.00 0.08
#> TCGA.CM.6674.01 1 0.0471 0.915 0.98 0.00 0.00 0.00 0.00 0.00 0.02 0.00
#> TCGA.CM.4743.01 1 0.0941 0.919 0.96 0.02 0.00 0.00 0.00 0.00 0.00 0.02
#> TCGA.F5.6465.01 2 0.2862 0.735 0.00 0.82 0.00 0.00 0.10 0.08 0.00 0.00
#> TCGA.CM.5344.01 2 0.1607 0.786 0.00 0.92 0.00 0.00 0.04 0.04 0.00 0.00
#> TCGA.AZ.4681.01 3 0.0471 0.805 0.00 0.00 0.98 0.02 0.00 0.00 0.00 0.00
#> TCGA.A6.6140.01 7 0.3757 0.390 0.00 0.00 0.00 0.00 0.26 0.06 0.68 0.00
#> TCGA.DM.A1D0.01 7 0.4522 0.169 0.00 0.00 0.00 0.00 0.34 0.04 0.58 0.04
#> TCGA.EI.6509.01 5 0.1275 0.827 0.00 0.02 0.00 0.00 0.94 0.00 0.04 0.00
#> TCGA.CI.6619.01 6 0.3299 0.266 0.00 0.44 0.00 0.00 0.00 0.56 0.00 0.00
#> TCGA.WS.AB45.01 1 0.0941 0.919 0.96 0.02 0.00 0.00 0.00 0.00 0.00 0.02
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
consensus_heatmap(res, k = 7)
consensus_heatmap(res, k = 8)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
membership_heatmap(res, k = 7)
membership_heatmap(res, k = 8)
As soon as the classes for columns are determined, the signatures that are significantly different between subgroups can be looked for. Following are the heatmaps for signatures.
get_signatures(res, k = 2)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
get_signatures(res, k = 7)
get_signatures(res, k = 8)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. To get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows (which is done by automatically selecting number of clusters).If there are too many signatures, top_signatures = ... can be set to only show the
signatures with the highest FDRs:
# code only for demonstration
# e.g. to show the top 500 most significant rows
tb = get_signature(res, k = ..., top_signatures = 500)
If the signatures are defined as these which are uniquely high in current group, diff_method argument
can be set to "uniquely_high_in_one_group":
# code only for demonstration
tb = get_signature(res, k = ..., diff_method = "uniquely_high_in_one_group")
UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
dimension_reduction(res, k = 7, method = "UMAP")
dimension_reduction(res, k = 8, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
If matrix rows can be associated to genes, consider to use functional_enrichment(res,
...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.
Parent node: Node04. Child nodes: Node0111 , Node0112 , Node0121 , Node0122 , Node0211-leaf , Node0212 , Node0411-leaf , Node0412-leaf , Node0413-leaf , Node0414-leaf , Node0421-leaf , Node0422 , Node0423-leaf , Node0431-leaf , Node0432-leaf , Node0433-leaf .
The object with results only for a single top-value method and a single partitioning method can be extracted as:
res = res_rh["041"]
A summary of res and all the functions that can be applied to it:
res
#> A 'ConsensusPartition' object with k = 2, 3, 4, 5, 6, 7, 8.
#> On a matrix with 30000 rows and 31 columns.
#> Top rows (1000) are extracted by 'ATC' method.
#> Subgroups are detected by 'skmeans' method.
#> Performed in total 350 partitions by row resampling.
#> Best k for subgroups seems to be 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 0.4522 0.548 0.548
#> 3 3 1.000 0.993 0.997 0.4770 0.682 0.470
#> 4 4 1.000 0.997 0.999 0.1376 0.890 0.679
#> 5 5 0.929 0.910 0.953 0.0255 0.987 0.946
#> 6 6 0.884 0.778 0.919 0.0269 0.981 0.915
#> 7 7 0.869 0.721 0.875 0.0270 0.946 0.750
#> 8 8 0.867 0.636 0.826 0.0151 0.963 0.798
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.F5.6464.01 2 0 1 0 1
#> TCGA.F5.6812.01 1 0 1 1 0
#> TCGA.F4.6805.01 2 0 1 0 1
#> TCGA.G4.6627.01 2 0 1 0 1
#> TCGA.D5.6534.01 2 0 1 0 1
#> TCGA.A6.6651.01 2 0 1 0 1
#> TCGA.AF.2693.01 1 0 1 1 0
#> TCGA.AF.4110.01 1 0 1 1 0
#> TCGA.CM.6167.01 2 0 1 0 1
#> TCGA.A6.6781.01 2 0 1 0 1
#> TCGA.AZ.6605.01 2 0 1 0 1
#> TCGA.G5.6572.01 1 0 1 1 0
#> TCGA.DM.A280.01 2 0 1 0 1
#> TCGA.AA.3489.01 2 0 1 0 1
#> TCGA.G4.6302.01 2 0 1 0 1
#> TCGA.G5.6235.01 1 0 1 1 0
#> TCGA.CI.6621.01 1 0 1 1 0
#> TCGA.F4.6857.01 2 0 1 0 1
#> TCGA.AZ.4323.01 2 0 1 0 1
#> TCGA.D5.6928.01 2 0 1 0 1
#> TCGA.D5.6923.01 1 0 1 1 0
#> TCGA.AF.2690.01 1 0 1 1 0
#> TCGA.G5.6572.02 2 0 1 0 1
#> TCGA.AH.6547.01 2 0 1 0 1
#> TCGA.D5.6927.01 2 0 1 0 1
#> TCGA.G4.6304.01 2 0 1 0 1
#> TCGA.D5.6539.01 1 0 1 1 0
#> TCGA.BM.6198.01 1 0 1 1 0
#> TCGA.CM.6674.01 2 0 1 0 1
#> TCGA.CM.4743.01 2 0 1 0 1
#> TCGA.WS.AB45.01 2 0 1 0 1
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.F5.6464.01 2 0.2537 0.914 0 0.92 0.08
#> TCGA.F5.6812.01 1 0.0000 1.000 1 0.00 0.00
#> TCGA.F4.6805.01 2 0.0000 0.992 0 1.00 0.00
#> TCGA.G4.6627.01 2 0.0000 0.992 0 1.00 0.00
#> TCGA.D5.6534.01 3 0.0000 1.000 0 0.00 1.00
#> TCGA.A6.6651.01 2 0.0000 0.992 0 1.00 0.00
#> TCGA.AF.2693.01 1 0.0000 1.000 1 0.00 0.00
#> TCGA.AF.4110.01 1 0.0000 1.000 1 0.00 0.00
#> TCGA.CM.6167.01 2 0.0000 0.992 0 1.00 0.00
#> TCGA.A6.6781.01 2 0.0892 0.976 0 0.98 0.02
#> TCGA.AZ.6605.01 2 0.0000 0.992 0 1.00 0.00
#> TCGA.G5.6572.01 1 0.0000 1.000 1 0.00 0.00
#> TCGA.DM.A280.01 3 0.0000 1.000 0 0.00 1.00
#> TCGA.AA.3489.01 2 0.0000 0.992 0 1.00 0.00
#> TCGA.G4.6302.01 3 0.0000 1.000 0 0.00 1.00
#> TCGA.G5.6235.01 1 0.0000 1.000 1 0.00 0.00
#> TCGA.CI.6621.01 1 0.0000 1.000 1 0.00 0.00
#> TCGA.F4.6857.01 3 0.0000 1.000 0 0.00 1.00
#> TCGA.AZ.4323.01 3 0.0000 1.000 0 0.00 1.00
#> TCGA.D5.6928.01 3 0.0000 1.000 0 0.00 1.00
#> TCGA.D5.6923.01 1 0.0000 1.000 1 0.00 0.00
#> TCGA.AF.2690.01 2 0.0000 0.992 0 1.00 0.00
#> TCGA.G5.6572.02 2 0.0000 0.992 0 1.00 0.00
#> TCGA.AH.6547.01 2 0.0000 0.992 0 1.00 0.00
#> TCGA.D5.6927.01 2 0.0000 0.992 0 1.00 0.00
#> TCGA.G4.6304.01 3 0.0000 1.000 0 0.00 1.00
#> TCGA.D5.6539.01 1 0.0000 1.000 1 0.00 0.00
#> TCGA.BM.6198.01 2 0.0000 0.992 0 1.00 0.00
#> TCGA.CM.6674.01 2 0.0000 0.992 0 1.00 0.00
#> TCGA.CM.4743.01 3 0.0000 1.000 0 0.00 1.00
#> TCGA.WS.AB45.01 3 0.0000 1.000 0 0.00 1.00
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> TCGA.F5.6464.01 2 0.000 0.996 0 1.00 0 0.00
#> TCGA.F5.6812.01 4 0.000 1.000 0 0.00 0 1.00
#> TCGA.F4.6805.01 2 0.000 0.996 0 1.00 0 0.00
#> TCGA.G4.6627.01 2 0.000 0.996 0 1.00 0 0.00
#> TCGA.D5.6534.01 3 0.000 1.000 0 0.00 1 0.00
#> TCGA.A6.6651.01 2 0.121 0.958 0 0.96 0 0.04
#> TCGA.AF.2693.01 1 0.000 1.000 1 0.00 0 0.00
#> TCGA.AF.4110.01 1 0.000 1.000 1 0.00 0 0.00
#> TCGA.CM.6167.01 2 0.000 0.996 0 1.00 0 0.00
#> TCGA.A6.6781.01 2 0.000 0.996 0 1.00 0 0.00
#> TCGA.AZ.6605.01 4 0.000 1.000 0 0.00 0 1.00
#> TCGA.G5.6572.01 1 0.000 1.000 1 0.00 0 0.00
#> TCGA.DM.A280.01 3 0.000 1.000 0 0.00 1 0.00
#> TCGA.AA.3489.01 2 0.000 0.996 0 1.00 0 0.00
#> TCGA.G4.6302.01 3 0.000 1.000 0 0.00 1 0.00
#> TCGA.G5.6235.01 1 0.000 1.000 1 0.00 0 0.00
#> TCGA.CI.6621.01 1 0.000 1.000 1 0.00 0 0.00
#> TCGA.F4.6857.01 3 0.000 1.000 0 0.00 1 0.00
#> TCGA.AZ.4323.01 3 0.000 1.000 0 0.00 1 0.00
#> TCGA.D5.6928.01 3 0.000 1.000 0 0.00 1 0.00
#> TCGA.D5.6923.01 1 0.000 1.000 1 0.00 0 0.00
#> TCGA.AF.2690.01 4 0.000 1.000 0 0.00 0 1.00
#> TCGA.G5.6572.02 4 0.000 1.000 0 0.00 0 1.00
#> TCGA.AH.6547.01 2 0.000 0.996 0 1.00 0 0.00
#> TCGA.D5.6927.01 2 0.000 0.996 0 1.00 0 0.00
#> TCGA.G4.6304.01 3 0.000 1.000 0 0.00 1 0.00
#> TCGA.D5.6539.01 1 0.000 1.000 1 0.00 0 0.00
#> TCGA.BM.6198.01 4 0.000 1.000 0 0.00 0 1.00
#> TCGA.CM.6674.01 2 0.000 0.996 0 1.00 0 0.00
#> TCGA.CM.4743.01 3 0.000 1.000 0 0.00 1 0.00
#> TCGA.WS.AB45.01 3 0.000 1.000 0 0.00 1 0.00
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> TCGA.F5.6464.01 2 0.3390 0.769 0.00 0.84 0.1 0.00 0.06
#> TCGA.F5.6812.01 4 0.1648 0.931 0.04 0.00 0.0 0.94 0.02
#> TCGA.F4.6805.01 2 0.2012 0.876 0.00 0.92 0.0 0.06 0.02
#> TCGA.G4.6627.01 2 0.1410 0.902 0.00 0.94 0.0 0.00 0.06
#> TCGA.D5.6534.01 3 0.0000 1.000 0.00 0.00 1.0 0.00 0.00
#> TCGA.A6.6651.01 2 0.2616 0.847 0.00 0.88 0.0 0.10 0.02
#> TCGA.AF.2693.01 1 0.0000 0.965 1.00 0.00 0.0 0.00 0.00
#> TCGA.AF.4110.01 1 0.0000 0.965 1.00 0.00 0.0 0.00 0.00
#> TCGA.CM.6167.01 2 0.0609 0.892 0.00 0.98 0.0 0.00 0.02
#> TCGA.A6.6781.01 2 0.2280 0.890 0.00 0.88 0.0 0.00 0.12
#> TCGA.AZ.6605.01 4 0.0000 0.978 0.00 0.00 0.0 1.00 0.00
#> TCGA.G5.6572.01 1 0.2280 0.812 0.88 0.00 0.0 0.00 0.12
#> TCGA.DM.A280.01 3 0.0000 1.000 0.00 0.00 1.0 0.00 0.00
#> TCGA.AA.3489.01 2 0.1732 0.901 0.00 0.92 0.0 0.00 0.08
#> TCGA.G4.6302.01 3 0.0000 1.000 0.00 0.00 1.0 0.00 0.00
#> TCGA.G5.6235.01 1 0.0000 0.965 1.00 0.00 0.0 0.00 0.00
#> TCGA.CI.6621.01 1 0.0000 0.965 1.00 0.00 0.0 0.00 0.00
#> TCGA.F4.6857.01 3 0.0000 1.000 0.00 0.00 1.0 0.00 0.00
#> TCGA.AZ.4323.01 3 0.0000 1.000 0.00 0.00 1.0 0.00 0.00
#> TCGA.D5.6928.01 3 0.0000 1.000 0.00 0.00 1.0 0.00 0.00
#> TCGA.D5.6923.01 1 0.0000 0.965 1.00 0.00 0.0 0.00 0.00
#> TCGA.AF.2690.01 4 0.0609 0.971 0.00 0.00 0.0 0.98 0.02
#> TCGA.G5.6572.02 4 0.0000 0.978 0.00 0.00 0.0 1.00 0.00
#> TCGA.AH.6547.01 2 0.2012 0.876 0.00 0.92 0.0 0.06 0.02
#> TCGA.D5.6927.01 2 0.2020 0.897 0.00 0.90 0.0 0.00 0.10
#> TCGA.G4.6304.01 3 0.0000 1.000 0.00 0.00 1.0 0.00 0.00
#> TCGA.D5.6539.01 5 0.3895 0.000 0.32 0.00 0.0 0.00 0.68
#> TCGA.BM.6198.01 4 0.0000 0.978 0.00 0.00 0.0 1.00 0.00
#> TCGA.CM.6674.01 2 0.2280 0.890 0.00 0.88 0.0 0.00 0.12
#> TCGA.CM.4743.01 3 0.0000 1.000 0.00 0.00 1.0 0.00 0.00
#> TCGA.WS.AB45.01 3 0.0000 1.000 0.00 0.00 1.0 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.F5.6464.01 6 0.3706 0.000 0.00 0.38 0 0.00 0.00 0.62
#> TCGA.F5.6812.01 4 0.3382 0.807 0.04 0.00 0 0.84 0.04 0.08
#> TCGA.F4.6805.01 2 0.4727 0.482 0.00 0.66 0 0.10 0.00 0.24
#> TCGA.G4.6627.01 2 0.0937 0.697 0.00 0.96 0 0.00 0.00 0.04
#> TCGA.D5.6534.01 3 0.0000 1.000 0.00 0.00 1 0.00 0.00 0.00
#> TCGA.A6.6651.01 2 0.5509 0.275 0.00 0.54 0 0.30 0.00 0.16
#> TCGA.AF.2693.01 1 0.0547 0.954 0.98 0.00 0 0.00 0.00 0.02
#> TCGA.AF.4110.01 1 0.0000 0.957 1.00 0.00 0 0.00 0.00 0.00
#> TCGA.CM.6167.01 2 0.2048 0.654 0.00 0.88 0 0.00 0.00 0.12
#> TCGA.A6.6781.01 2 0.0547 0.688 0.00 0.98 0 0.00 0.00 0.02
#> TCGA.AZ.6605.01 4 0.1865 0.845 0.00 0.04 0 0.92 0.00 0.04
#> TCGA.G5.6572.01 1 0.3270 0.816 0.82 0.00 0 0.00 0.06 0.12
#> TCGA.DM.A280.01 3 0.0000 1.000 0.00 0.00 1 0.00 0.00 0.00
#> TCGA.AA.3489.01 2 0.0000 0.703 0.00 1.00 0 0.00 0.00 0.00
#> TCGA.G4.6302.01 3 0.0000 1.000 0.00 0.00 1 0.00 0.00 0.00
#> TCGA.G5.6235.01 1 0.0547 0.954 0.98 0.00 0 0.00 0.00 0.02
#> TCGA.CI.6621.01 1 0.0000 0.957 1.00 0.00 0 0.00 0.00 0.00
#> TCGA.F4.6857.01 3 0.0000 1.000 0.00 0.00 1 0.00 0.00 0.00
#> TCGA.AZ.4323.01 3 0.0000 1.000 0.00 0.00 1 0.00 0.00 0.00
#> TCGA.D5.6928.01 3 0.0000 1.000 0.00 0.00 1 0.00 0.00 0.00
#> TCGA.D5.6923.01 1 0.0000 0.957 1.00 0.00 0 0.00 0.00 0.00
#> TCGA.AF.2690.01 4 0.0000 0.871 0.00 0.00 0 1.00 0.00 0.00
#> TCGA.G5.6572.02 4 0.1480 0.861 0.00 0.02 0 0.94 0.00 0.04
#> TCGA.AH.6547.01 2 0.4926 0.461 0.00 0.64 0 0.12 0.00 0.24
#> TCGA.D5.6927.01 2 0.0000 0.703 0.00 1.00 0 0.00 0.00 0.00
#> TCGA.G4.6304.01 3 0.0000 1.000 0.00 0.00 1 0.00 0.00 0.00
#> TCGA.D5.6539.01 5 0.1267 0.000 0.06 0.00 0 0.00 0.94 0.00
#> TCGA.BM.6198.01 4 0.2981 0.799 0.00 0.00 0 0.82 0.02 0.16
#> TCGA.CM.6674.01 2 0.0547 0.688 0.00 0.98 0 0.00 0.00 0.02
#> TCGA.CM.4743.01 3 0.0000 1.000 0.00 0.00 1 0.00 0.00 0.00
#> TCGA.WS.AB45.01 3 0.0000 1.000 0.00 0.00 1 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.F5.6464.01 6 0.3011 0.000 0.00 0.12 0.00 0.00 0.00 0.82 0.06
#> TCGA.F5.6812.01 4 0.2654 0.585 0.10 0.00 0.00 0.86 0.02 0.00 0.02
#> TCGA.F4.6805.01 7 0.1166 0.680 0.00 0.06 0.00 0.00 0.00 0.00 0.94
#> TCGA.G4.6627.01 2 0.3815 0.812 0.00 0.62 0.00 0.00 0.00 0.02 0.36
#> TCGA.D5.6534.01 3 0.0504 0.979 0.00 0.00 0.98 0.00 0.00 0.02 0.00
#> TCGA.A6.6651.01 7 0.0000 0.683 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.AF.2693.01 1 0.0504 0.887 0.98 0.00 0.00 0.00 0.00 0.02 0.00
#> TCGA.AF.4110.01 1 0.0504 0.896 0.98 0.00 0.00 0.00 0.02 0.00 0.00
#> TCGA.CM.6167.01 2 0.4505 0.685 0.00 0.50 0.00 0.00 0.00 0.06 0.44
#> TCGA.A6.6781.01 2 0.2422 0.797 0.00 0.82 0.00 0.00 0.00 0.00 0.18
#> TCGA.AZ.6605.01 7 0.3546 -0.483 0.00 0.00 0.00 0.46 0.00 0.00 0.54
#> TCGA.G5.6572.01 1 0.6045 0.499 0.60 0.10 0.00 0.08 0.04 0.18 0.00
#> TCGA.DM.A280.01 3 0.0000 0.997 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.AA.3489.01 2 0.3815 0.812 0.00 0.62 0.00 0.00 0.00 0.02 0.36
#> TCGA.G4.6302.01 3 0.0000 0.997 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.G5.6235.01 1 0.1505 0.873 0.94 0.02 0.00 0.00 0.02 0.02 0.00
#> TCGA.CI.6621.01 1 0.0504 0.896 0.98 0.00 0.00 0.00 0.02 0.00 0.00
#> TCGA.F4.6857.01 3 0.0000 0.997 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.AZ.4323.01 3 0.0000 0.997 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.D5.6928.01 3 0.0000 0.997 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.D5.6923.01 1 0.0504 0.896 0.98 0.00 0.00 0.00 0.02 0.00 0.00
#> TCGA.AF.2690.01 4 0.3294 0.580 0.00 0.00 0.00 0.66 0.00 0.00 0.34
#> TCGA.G5.6572.02 4 0.3546 0.393 0.00 0.00 0.00 0.54 0.00 0.00 0.46
#> TCGA.AH.6547.01 7 0.1166 0.680 0.00 0.06 0.00 0.00 0.00 0.00 0.94
#> TCGA.D5.6927.01 2 0.2708 0.816 0.00 0.78 0.00 0.00 0.00 0.00 0.22
#> TCGA.G4.6304.01 3 0.0000 0.997 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.D5.6539.01 5 0.1006 0.000 0.02 0.00 0.00 0.02 0.96 0.00 0.00
#> TCGA.BM.6198.01 4 0.2572 0.620 0.00 0.06 0.00 0.86 0.00 0.00 0.08
#> TCGA.CM.6674.01 2 0.2422 0.797 0.00 0.82 0.00 0.00 0.00 0.00 0.18
#> TCGA.CM.4743.01 3 0.0000 0.997 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.WS.AB45.01 3 0.0000 0.997 0.00 0.00 1.00 0.00 0.00 0.00 0.00
cbind(get_classes(res, k = 8), get_membership(res, k = 8))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7 p8
#> TCGA.F5.6464.01 6 0.0808 0.000 0.00 0.00 0.00 0.00 0.00 0.96 0.04 0.00
#> TCGA.F5.6812.01 4 0.4862 -0.330 0.16 0.00 0.00 0.60 0.02 0.00 0.00 0.22
#> TCGA.F4.6805.01 7 0.5054 0.527 0.00 0.20 0.00 0.36 0.00 0.00 0.44 0.00
#> TCGA.G4.6627.01 2 0.3095 0.670 0.00 0.74 0.00 0.02 0.00 0.00 0.24 0.00
#> TCGA.D5.6534.01 3 0.0471 0.981 0.00 0.00 0.98 0.00 0.00 0.02 0.00 0.00
#> TCGA.A6.6651.01 7 0.5123 0.511 0.00 0.22 0.00 0.36 0.00 0.00 0.42 0.00
#> TCGA.AF.2693.01 1 0.0808 0.903 0.96 0.00 0.00 0.00 0.00 0.00 0.04 0.00
#> TCGA.AF.4110.01 1 0.0000 0.918 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CM.6167.01 2 0.4040 0.434 0.00 0.58 0.00 0.02 0.00 0.02 0.38 0.00
#> TCGA.A6.6781.01 2 0.0941 0.722 0.00 0.96 0.00 0.00 0.02 0.02 0.00 0.00
#> TCGA.AZ.6605.01 4 0.2020 0.536 0.00 0.02 0.00 0.90 0.00 0.00 0.06 0.02
#> TCGA.G5.6572.01 7 0.5210 -0.366 0.18 0.00 0.00 0.00 0.00 0.02 0.52 0.28
#> TCGA.DM.A280.01 3 0.0000 0.995 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AA.3489.01 2 0.2856 0.694 0.00 0.78 0.00 0.02 0.00 0.00 0.20 0.00
#> TCGA.G4.6302.01 3 0.0000 0.995 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.G5.6235.01 1 0.4077 0.726 0.76 0.00 0.00 0.00 0.08 0.02 0.04 0.10
#> TCGA.CI.6621.01 1 0.0471 0.918 0.98 0.00 0.00 0.00 0.00 0.00 0.00 0.02
#> TCGA.F4.6857.01 3 0.0471 0.981 0.00 0.00 0.98 0.00 0.00 0.02 0.00 0.00
#> TCGA.AZ.4323.01 3 0.0000 0.995 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D5.6928.01 3 0.0000 0.995 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D5.6923.01 1 0.0471 0.918 0.98 0.00 0.00 0.00 0.00 0.00 0.00 0.02
#> TCGA.AF.2690.01 4 0.1341 0.482 0.00 0.00 0.00 0.92 0.00 0.00 0.00 0.08
#> TCGA.G5.6572.02 4 0.2165 0.551 0.00 0.00 0.00 0.88 0.00 0.00 0.06 0.06
#> TCGA.AH.6547.01 7 0.5030 0.525 0.00 0.20 0.00 0.34 0.00 0.00 0.46 0.00
#> TCGA.D5.6927.01 2 0.1091 0.723 0.00 0.94 0.00 0.00 0.00 0.00 0.06 0.00
#> TCGA.G4.6304.01 3 0.0000 0.995 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D5.6539.01 5 0.0471 0.000 0.02 0.00 0.00 0.00 0.98 0.00 0.00 0.00
#> TCGA.BM.6198.01 8 0.3299 0.000 0.00 0.00 0.00 0.44 0.00 0.00 0.00 0.56
#> TCGA.CM.6674.01 2 0.0941 0.722 0.00 0.96 0.00 0.00 0.02 0.02 0.00 0.00
#> TCGA.CM.4743.01 3 0.0000 0.995 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.WS.AB45.01 3 0.0000 0.995 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: Node04. Child nodes: Node0111 , Node0112 , Node0121 , Node0122 , Node0211-leaf , Node0212 , Node0411-leaf , Node0412-leaf , Node0413-leaf , Node0414-leaf , Node0421-leaf , Node0422 , Node0423-leaf , Node0431-leaf , Node0432-leaf , Node0433-leaf .
The object with results only for a single top-value method and a single partitioning method can be extracted as:
res = res_rh["042"]
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 34 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 0.5139 0.487 0.487
#> 3 3 1.000 1.000 1.000 0.2668 0.863 0.718
#> 4 4 1.000 1.000 1.000 0.0985 0.929 0.798
#> 5 5 0.829 0.928 0.905 0.0806 0.920 0.719
#> 6 6 0.778 0.681 0.861 0.0426 0.984 0.922
#> 7 7 0.738 0.775 0.863 0.0312 0.968 0.833
#> 8 8 0.790 0.752 0.867 0.0244 0.979 0.870
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.AZ.4308.01 1 0 1 1 0
#> TCGA.D5.5541.01 1 0 1 1 0
#> TCGA.A6.6648.01 1 0 1 1 0
#> TCGA.AF.A56K.01 1 0 1 1 0
#> TCGA.D5.6929.01 2 0 1 0 1
#> TCGA.AF.6655.01 1 0 1 1 0
#> TCGA.CM.6164.01 2 0 1 0 1
#> TCGA.AF.2687.01 1 0 1 1 0
#> TCGA.F4.6704.01 1 0 1 1 0
#> TCGA.AG.3732.01 2 0 1 0 1
#> TCGA.DC.4749.01 1 0 1 1 0
#> TCGA.DC.6160.01 1 0 1 1 0
#> TCGA.F5.6863.01 2 0 1 0 1
#> TCGA.G4.6309.01 2 0 1 0 1
#> TCGA.CM.5868.01 2 0 1 0 1
#> TCGA.AZ.4313.01 2 0 1 0 1
#> TCGA.A6.2675.01 1 0 1 1 0
#> TCGA.CI.6624.01 2 0 1 0 1
#> TCGA.CM.4752.01 1 0 1 1 0
#> TCGA.DM.A0XF.01 2 0 1 0 1
#> TCGA.AD.6963.01 1 0 1 1 0
#> TCGA.A6.3810.01 1 0 1 1 0
#> TCGA.DY.A0XA.01 2 0 1 0 1
#> TCGA.DM.A28E.01 2 0 1 0 1
#> TCGA.CI.6623.01 1 0 1 1 0
#> TCGA.AU.3779.01 2 0 1 0 1
#> TCGA.F4.6460.01 2 0 1 0 1
#> TCGA.F5.6702.01 1 0 1 1 0
#> TCGA.F5.6465.01 2 0 1 0 1
#> TCGA.CM.5344.01 2 0 1 0 1
#> TCGA.A6.6140.01 1 0 1 1 0
#> TCGA.DM.A1D0.01 2 0 1 0 1
#> TCGA.EI.6509.01 1 0 1 1 0
#> TCGA.CI.6619.01 1 0 1 1 0
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.AZ.4308.01 1 0 1 1 0 0
#> TCGA.D5.5541.01 1 0 1 1 0 0
#> TCGA.A6.6648.01 1 0 1 1 0 0
#> TCGA.AF.A56K.01 3 0 1 0 0 1
#> TCGA.D5.6929.01 2 0 1 0 1 0
#> TCGA.AF.6655.01 1 0 1 1 0 0
#> TCGA.CM.6164.01 2 0 1 0 1 0
#> TCGA.AF.2687.01 3 0 1 0 0 1
#> TCGA.F4.6704.01 3 0 1 0 0 1
#> TCGA.AG.3732.01 2 0 1 0 1 0
#> TCGA.DC.4749.01 1 0 1 1 0 0
#> TCGA.DC.6160.01 1 0 1 1 0 0
#> TCGA.F5.6863.01 2 0 1 0 1 0
#> TCGA.G4.6309.01 2 0 1 0 1 0
#> TCGA.CM.5868.01 2 0 1 0 1 0
#> TCGA.AZ.4313.01 2 0 1 0 1 0
#> TCGA.A6.2675.01 1 0 1 1 0 0
#> TCGA.CI.6624.01 2 0 1 0 1 0
#> TCGA.CM.4752.01 3 0 1 0 0 1
#> TCGA.DM.A0XF.01 2 0 1 0 1 0
#> TCGA.AD.6963.01 3 0 1 0 0 1
#> TCGA.A6.3810.01 1 0 1 1 0 0
#> TCGA.DY.A0XA.01 2 0 1 0 1 0
#> TCGA.DM.A28E.01 2 0 1 0 1 0
#> TCGA.CI.6623.01 1 0 1 1 0 0
#> TCGA.AU.3779.01 2 0 1 0 1 0
#> TCGA.F4.6460.01 2 0 1 0 1 0
#> TCGA.F5.6702.01 3 0 1 0 0 1
#> TCGA.F5.6465.01 2 0 1 0 1 0
#> TCGA.CM.5344.01 2 0 1 0 1 0
#> TCGA.A6.6140.01 1 0 1 1 0 0
#> TCGA.DM.A1D0.01 2 0 1 0 1 0
#> TCGA.EI.6509.01 1 0 1 1 0 0
#> TCGA.CI.6619.01 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.AZ.4308.01 4 0 1 0 0 0 1
#> TCGA.D5.5541.01 1 0 1 1 0 0 0
#> TCGA.A6.6648.01 1 0 1 1 0 0 0
#> TCGA.AF.A56K.01 3 0 1 0 0 1 0
#> TCGA.D5.6929.01 4 0 1 0 0 0 1
#> TCGA.AF.6655.01 1 0 1 1 0 0 0
#> TCGA.CM.6164.01 2 0 1 0 1 0 0
#> TCGA.AF.2687.01 3 0 1 0 0 1 0
#> TCGA.F4.6704.01 3 0 1 0 0 1 0
#> TCGA.AG.3732.01 2 0 1 0 1 0 0
#> TCGA.DC.4749.01 1 0 1 1 0 0 0
#> TCGA.DC.6160.01 1 0 1 1 0 0 0
#> TCGA.F5.6863.01 2 0 1 0 1 0 0
#> TCGA.G4.6309.01 2 0 1 0 1 0 0
#> TCGA.CM.5868.01 2 0 1 0 1 0 0
#> TCGA.AZ.4313.01 2 0 1 0 1 0 0
#> TCGA.A6.2675.01 1 0 1 1 0 0 0
#> TCGA.CI.6624.01 2 0 1 0 1 0 0
#> TCGA.CM.4752.01 3 0 1 0 0 1 0
#> TCGA.DM.A0XF.01 2 0 1 0 1 0 0
#> TCGA.AD.6963.01 3 0 1 0 0 1 0
#> TCGA.A6.3810.01 1 0 1 1 0 0 0
#> TCGA.DY.A0XA.01 2 0 1 0 1 0 0
#> TCGA.DM.A28E.01 2 0 1 0 1 0 0
#> TCGA.CI.6623.01 1 0 1 1 0 0 0
#> TCGA.AU.3779.01 2 0 1 0 1 0 0
#> TCGA.F4.6460.01 2 0 1 0 1 0 0
#> TCGA.F5.6702.01 3 0 1 0 0 1 0
#> TCGA.F5.6465.01 2 0 1 0 1 0 0
#> TCGA.CM.5344.01 4 0 1 0 0 0 1
#> TCGA.A6.6140.01 1 0 1 1 0 0 0
#> TCGA.DM.A1D0.01 2 0 1 0 1 0 0
#> TCGA.EI.6509.01 1 0 1 1 0 0 0
#> TCGA.CI.6619.01 3 0 1 0 0 1 0
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> TCGA.AZ.4308.01 4 0.293 0.795 0.00 0.00 0.00 0.82 0.18
#> TCGA.D5.5541.01 1 0.000 0.950 1.00 0.00 0.00 0.00 0.00
#> TCGA.A6.6648.01 1 0.000 0.950 1.00 0.00 0.00 0.00 0.00
#> TCGA.AF.A56K.01 3 0.304 0.867 0.10 0.00 0.86 0.00 0.04
#> TCGA.D5.6929.01 4 0.356 0.660 0.00 0.00 0.00 0.74 0.26
#> TCGA.AF.6655.01 1 0.000 0.950 1.00 0.00 0.00 0.00 0.00
#> TCGA.CM.6164.01 5 0.406 1.000 0.00 0.36 0.00 0.00 0.64
#> TCGA.AF.2687.01 3 0.000 0.963 0.00 0.00 1.00 0.00 0.00
#> TCGA.F4.6704.01 3 0.104 0.952 0.00 0.00 0.96 0.00 0.04
#> TCGA.AG.3732.01 2 0.173 0.872 0.00 0.92 0.00 0.00 0.08
#> TCGA.DC.4749.01 1 0.252 0.906 0.86 0.00 0.00 0.00 0.14
#> TCGA.DC.6160.01 1 0.104 0.946 0.96 0.00 0.00 0.00 0.04
#> TCGA.F5.6863.01 2 0.000 0.947 0.00 1.00 0.00 0.00 0.00
#> TCGA.G4.6309.01 2 0.202 0.840 0.00 0.90 0.00 0.00 0.10
#> TCGA.CM.5868.01 5 0.406 1.000 0.00 0.36 0.00 0.00 0.64
#> TCGA.AZ.4313.01 5 0.406 1.000 0.00 0.36 0.00 0.00 0.64
#> TCGA.A6.2675.01 1 0.000 0.950 1.00 0.00 0.00 0.00 0.00
#> TCGA.CI.6624.01 5 0.406 1.000 0.00 0.36 0.00 0.00 0.64
#> TCGA.CM.4752.01 3 0.000 0.963 0.00 0.00 1.00 0.00 0.00
#> TCGA.DM.A0XF.01 2 0.104 0.922 0.00 0.96 0.00 0.00 0.04
#> TCGA.AD.6963.01 3 0.165 0.944 0.02 0.00 0.94 0.00 0.04
#> TCGA.A6.3810.01 1 0.104 0.946 0.96 0.00 0.00 0.00 0.04
#> TCGA.DY.A0XA.01 2 0.000 0.947 0.00 1.00 0.00 0.00 0.00
#> TCGA.DM.A28E.01 2 0.000 0.947 0.00 1.00 0.00 0.00 0.00
#> TCGA.CI.6623.01 1 0.000 0.950 1.00 0.00 0.00 0.00 0.00
#> TCGA.AU.3779.01 2 0.000 0.947 0.00 1.00 0.00 0.00 0.00
#> TCGA.F4.6460.01 2 0.104 0.922 0.00 0.96 0.00 0.00 0.04
#> TCGA.F5.6702.01 3 0.000 0.963 0.00 0.00 1.00 0.00 0.00
#> TCGA.F5.6465.01 5 0.406 1.000 0.00 0.36 0.00 0.00 0.64
#> TCGA.CM.5344.01 4 0.000 0.818 0.00 0.00 0.00 1.00 0.00
#> TCGA.A6.6140.01 1 0.252 0.906 0.86 0.00 0.00 0.00 0.14
#> TCGA.DM.A1D0.01 2 0.000 0.947 0.00 1.00 0.00 0.00 0.00
#> TCGA.EI.6509.01 1 0.252 0.906 0.86 0.00 0.00 0.00 0.14
#> TCGA.CI.6619.01 3 0.000 0.963 0.00 0.00 1.00 0.00 0.00
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> TCGA.AZ.4308.01 4 0.5324 0.579 0.00 0.00 0.00 0.54 0.12 0.34
#> TCGA.D5.5541.01 1 0.0547 0.669 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.A6.6648.01 1 0.0547 0.669 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.AF.A56K.01 3 0.5813 0.634 0.20 0.00 0.62 0.00 0.06 0.12
#> TCGA.D5.6929.01 4 0.3309 0.522 0.00 0.00 0.00 0.72 0.28 0.00
#> TCGA.AF.6655.01 1 0.0547 0.664 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.CM.6164.01 5 0.2631 0.977 0.00 0.18 0.00 0.00 0.82 0.00
#> TCGA.AF.2687.01 3 0.0547 0.864 0.00 0.00 0.98 0.00 0.00 0.02
#> TCGA.F4.6704.01 3 0.2794 0.825 0.00 0.00 0.86 0.00 0.06 0.08
#> TCGA.AG.3732.01 2 0.1814 0.872 0.00 0.90 0.00 0.00 0.10 0.00
#> TCGA.DC.4749.01 1 0.3864 -0.891 0.52 0.00 0.00 0.00 0.00 0.48
#> TCGA.DC.6160.01 1 0.2260 0.514 0.86 0.00 0.00 0.00 0.00 0.14
#> TCGA.F5.6863.01 2 0.0000 0.939 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.G4.6309.01 2 0.2631 0.768 0.00 0.82 0.00 0.00 0.18 0.00
#> TCGA.CM.5868.01 5 0.2793 0.968 0.00 0.20 0.00 0.00 0.80 0.00
#> TCGA.AZ.4313.01 5 0.2631 0.977 0.00 0.18 0.00 0.00 0.82 0.00
#> TCGA.A6.2675.01 1 0.0547 0.669 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.CI.6624.01 5 0.2631 0.977 0.00 0.18 0.00 0.00 0.82 0.00
#> TCGA.CM.4752.01 3 0.0547 0.864 0.00 0.00 0.98 0.00 0.00 0.02
#> TCGA.DM.A0XF.01 2 0.1267 0.917 0.00 0.94 0.00 0.00 0.06 0.00
#> TCGA.AD.6963.01 3 0.4733 0.763 0.08 0.00 0.74 0.00 0.06 0.12
#> TCGA.A6.3810.01 1 0.1814 0.586 0.90 0.00 0.00 0.00 0.00 0.10
#> TCGA.DY.A0XA.01 2 0.0000 0.939 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DM.A28E.01 2 0.0000 0.939 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.CI.6623.01 1 0.0547 0.669 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.AU.3779.01 2 0.0000 0.939 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.F4.6460.01 2 0.1267 0.913 0.00 0.94 0.00 0.00 0.06 0.00
#> TCGA.F5.6702.01 3 0.0000 0.864 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.F5.6465.01 5 0.2941 0.947 0.00 0.22 0.00 0.00 0.78 0.00
#> TCGA.CM.5344.01 4 0.0547 0.695 0.00 0.00 0.00 0.98 0.02 0.00
#> TCGA.A6.6140.01 1 0.3864 -0.891 0.52 0.00 0.00 0.00 0.00 0.48
#> TCGA.DM.A1D0.01 2 0.0000 0.939 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.EI.6509.01 6 0.3864 0.000 0.48 0.00 0.00 0.00 0.00 0.52
#> TCGA.CI.6619.01 3 0.0547 0.864 0.00 0.00 0.98 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.AZ.4308.01 7 0.0000 0.000 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.D5.5541.01 1 0.1166 0.796 0.94 0.00 0.00 0.00 0.00 0.06 0.00
#> TCGA.A6.6648.01 1 0.1166 0.805 0.94 0.00 0.00 0.00 0.00 0.06 0.00
#> TCGA.AF.A56K.01 3 0.7669 0.307 0.28 0.00 0.34 0.18 0.10 0.10 0.00
#> TCGA.D5.6929.01 4 0.3670 0.687 0.00 0.00 0.00 0.76 0.14 0.00 0.10
#> TCGA.AF.6655.01 1 0.3315 0.768 0.82 0.00 0.00 0.08 0.02 0.08 0.00
#> TCGA.CM.6164.01 5 0.2081 0.962 0.00 0.14 0.00 0.00 0.86 0.00 0.00
#> TCGA.AF.2687.01 3 0.0000 0.751 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.F4.6704.01 3 0.4405 0.666 0.00 0.00 0.74 0.10 0.08 0.08 0.00
#> TCGA.AG.3732.01 2 0.2081 0.837 0.00 0.86 0.00 0.00 0.14 0.00 0.00
#> TCGA.DC.4749.01 6 0.3047 0.862 0.28 0.00 0.00 0.00 0.00 0.72 0.00
#> TCGA.DC.6160.01 1 0.2081 0.723 0.86 0.00 0.00 0.00 0.00 0.14 0.00
#> TCGA.F5.6863.01 2 0.0000 0.916 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.G4.6309.01 2 0.2572 0.764 0.00 0.80 0.00 0.00 0.20 0.00 0.00
#> TCGA.CM.5868.01 5 0.1886 0.970 0.00 0.12 0.00 0.00 0.88 0.00 0.00
#> TCGA.AZ.4313.01 5 0.1886 0.970 0.00 0.12 0.00 0.00 0.88 0.00 0.00
#> TCGA.A6.2675.01 1 0.2769 0.799 0.86 0.00 0.00 0.08 0.04 0.02 0.00
#> TCGA.CI.6624.01 5 0.1886 0.970 0.00 0.12 0.00 0.00 0.88 0.00 0.00
#> TCGA.CM.4752.01 3 0.0000 0.751 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DM.A0XF.01 2 0.1886 0.862 0.00 0.88 0.00 0.00 0.12 0.00 0.00
#> TCGA.AD.6963.01 3 0.7041 0.505 0.12 0.00 0.50 0.18 0.10 0.10 0.00
#> TCGA.A6.3810.01 1 0.2081 0.723 0.86 0.00 0.00 0.00 0.00 0.14 0.00
#> TCGA.DY.A0XA.01 2 0.0000 0.916 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DM.A28E.01 2 0.0000 0.916 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CI.6623.01 1 0.2769 0.799 0.86 0.00 0.00 0.08 0.04 0.02 0.00
#> TCGA.AU.3779.01 2 0.0000 0.916 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.F4.6460.01 2 0.1886 0.854 0.00 0.88 0.00 0.00 0.12 0.00 0.00
#> TCGA.F5.6702.01 3 0.0504 0.750 0.00 0.00 0.98 0.02 0.00 0.00 0.00
#> TCGA.F5.6465.01 5 0.2422 0.918 0.00 0.18 0.00 0.00 0.82 0.00 0.00
#> TCGA.CM.5344.01 4 0.3047 0.644 0.00 0.00 0.00 0.72 0.00 0.00 0.28
#> TCGA.A6.6140.01 6 0.3047 0.862 0.28 0.00 0.00 0.00 0.00 0.72 0.00
#> TCGA.DM.A1D0.01 2 0.0000 0.916 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EI.6509.01 6 0.2376 0.722 0.12 0.00 0.00 0.02 0.00 0.86 0.00
#> TCGA.CI.6619.01 3 0.0000 0.751 0.00 0.00 1.00 0.00 0.00 0.00 0.00
cbind(get_classes(res, k = 8), get_membership(res, k = 8))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7 p8
#> TCGA.AZ.4308.01 7 0.0000 0.000 0.00 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.D5.5541.01 1 0.2818 0.685 0.82 0.00 0.00 0.00 0.00 0.12 0.00 0.06
#> TCGA.A6.6648.01 1 0.2888 0.666 0.80 0.00 0.00 0.00 0.00 0.16 0.00 0.04
#> TCGA.AF.A56K.01 8 0.3263 0.630 0.12 0.00 0.10 0.00 0.00 0.00 0.00 0.78
#> TCGA.D5.6929.01 4 0.0000 0.959 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.AF.6655.01 1 0.2864 0.674 0.84 0.00 0.00 0.00 0.02 0.06 0.00 0.08
#> TCGA.CM.6164.01 5 0.1091 0.955 0.00 0.06 0.00 0.00 0.94 0.00 0.00 0.00
#> TCGA.AF.2687.01 3 0.0000 0.952 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.F4.6704.01 8 0.3272 0.539 0.00 0.00 0.42 0.00 0.00 0.00 0.00 0.58
#> TCGA.AG.3732.01 2 0.2756 0.678 0.00 0.74 0.00 0.00 0.26 0.00 0.00 0.00
#> TCGA.DC.4749.01 6 0.2406 0.742 0.20 0.00 0.00 0.00 0.00 0.80 0.00 0.00
#> TCGA.DC.6160.01 1 0.3142 0.477 0.64 0.00 0.00 0.00 0.00 0.36 0.00 0.00
#> TCGA.F5.6863.01 2 0.0000 0.848 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.G4.6309.01 2 0.3015 0.590 0.00 0.68 0.00 0.00 0.32 0.00 0.00 0.00
#> TCGA.CM.5868.01 5 0.0808 0.963 0.00 0.04 0.00 0.00 0.96 0.00 0.00 0.00
#> TCGA.AZ.4313.01 5 0.0808 0.963 0.00 0.04 0.00 0.00 0.96 0.00 0.00 0.00
#> TCGA.A6.2675.01 1 0.2859 0.657 0.82 0.00 0.00 0.00 0.02 0.02 0.00 0.14
#> TCGA.CI.6624.01 5 0.0808 0.963 0.00 0.04 0.00 0.00 0.96 0.00 0.00 0.00
#> TCGA.CM.4752.01 3 0.0471 0.950 0.00 0.00 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.DM.A0XF.01 2 0.2852 0.666 0.00 0.72 0.00 0.00 0.28 0.00 0.00 0.00
#> TCGA.AD.6963.01 8 0.3198 0.731 0.02 0.00 0.26 0.00 0.00 0.00 0.00 0.72
#> TCGA.A6.3810.01 1 0.3015 0.546 0.68 0.00 0.00 0.00 0.00 0.32 0.00 0.00
#> TCGA.DY.A0XA.01 2 0.0000 0.848 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DM.A28E.01 2 0.0000 0.848 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CI.6623.01 1 0.2888 0.633 0.80 0.00 0.00 0.00 0.04 0.00 0.00 0.16
#> TCGA.AU.3779.01 2 0.0000 0.848 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.F4.6460.01 2 0.2404 0.768 0.00 0.84 0.00 0.02 0.14 0.00 0.00 0.00
#> TCGA.F5.6702.01 3 0.1341 0.886 0.00 0.00 0.92 0.00 0.00 0.00 0.00 0.08
#> TCGA.F5.6465.01 5 0.1765 0.888 0.00 0.12 0.00 0.00 0.88 0.00 0.00 0.00
#> TCGA.CM.5344.01 4 0.0808 0.958 0.00 0.00 0.00 0.96 0.00 0.00 0.04 0.00
#> TCGA.A6.6140.01 6 0.2534 0.721 0.22 0.00 0.00 0.00 0.00 0.78 0.00 0.00
#> TCGA.DM.A1D0.01 2 0.0000 0.848 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EI.6509.01 6 0.1765 0.540 0.00 0.00 0.00 0.00 0.00 0.88 0.00 0.12
#> TCGA.CI.6619.01 3 0.0000 0.952 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: Node042. Child nodes: Node01111 , Node01112-leaf , Node01113-leaf , Node01114-leaf , Node01121-leaf , Node01122-leaf , Node01123-leaf , Node01124-leaf , Node01211-leaf , Node01212-leaf , Node01213-leaf , Node01221-leaf , Node01222-leaf , Node01223-leaf , Node01224-leaf , Node02121-leaf , Node02122-leaf , Node02123-leaf , Node04221-leaf , Node04222-leaf , Node04223-leaf .
The object with results only for a single top-value method and a single partitioning method can be extracted as:
res = res_rh["0422"]
A summary of res and all the functions that can be applied to it:
res
#> A 'ConsensusPartition' object with k = 2, 3, 4, 5, 6, 7, 8.
#> On a matrix with 30000 rows and 16 columns.
#> Top rows (1000) are extracted by 'ATC' method.
#> Subgroups are detected by 'kmeans' method.
#> Performed in total 350 partitions by row resampling.
#> Best k for subgroups seems to be 3.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_partitions"
#> [7] "compare_signatures" "consensus_heatmap" "dimension_reduction"
#> [10] "functional_enrichment" "get_anno_col" "get_anno"
#> [13] "get_classes" "get_consensus" "get_matrix"
#> [16] "get_membership" "get_param" "get_signatures"
#> [19] "get_stats" "is_best_k" "is_stable_k"
#> [22] "membership_heatmap" "ncol" "nrow"
#> [25] "plot_ecdf" "predict_classes" "rownames"
#> [28] "select_partition_number" "show" "suggest_best_k"
#> [31] "test_to_known_factors" "top_rows_heatmap"
collect_plots() function collects all the plots made from res for all k (number of subgroups)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
The plots are:
k and the heatmap of
predicted classes for each k.k.k.k.All the plots in panels can be made by individual functions and they are plotted later in this section.
select_partition_number() produces several plots showing different
statistics for choosing “optimized” k. There are following statistics:
k;k, the area increased is defined as \(A_k - A_{k-1}\).The detailed explanations of these statistics can be found in the cola vignette.
Generally speaking, higher 1-PAC score, higher mean silhouette score or higher
concordance corresponds to better partition. Rand index and Jaccard index
measure how similar the current partition is compared to partition with k-1.
If they are too similar, we won't accept k is better than k-1.
select_partition_number(res)
The numeric values for all these statistics can be obtained by get_stats().
get_stats(res)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> 2 2 1.000 1.000 1.000 0.5255 0.475 0.475
#> 3 3 1.000 1.000 1.000 0.2852 0.750 0.524
#> 4 4 0.850 0.829 0.910 0.1173 0.900 0.700
#> 5 5 0.883 0.931 0.906 0.0680 0.933 0.724
#> 6 6 0.817 0.820 0.861 0.0393 1.000 1.000
#> 7 7 0.817 0.733 0.856 0.0370 0.967 0.810
#> 8 8 0.842 0.510 0.749 0.0275 0.975 0.824
suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:
suggest_best_k(res)
#> [1] 3
#> attr(,"optional")
#> [1] 2
There is also optional best \(k\) = 2 that is worth to check.
Following is the table of the partitions (You need to click the show/hide
code output link to see it). The membership matrix (columns with name p*)
is inferred by
clue::cl_consensus()
function with the SE method. Basically the value in the membership matrix
represents the probability to belong to a certain group. The finall subgroup
label for an item is determined with the group with highest probability it
belongs to.
In get_classes() function, the entropy is calculated from the membership
matrix and the silhouette score is calculated from the consensus matrix.
cbind(get_classes(res, k = 2), get_membership(res, k = 2))
#> class entropy silhouette p1 p2
#> TCGA.D5.6929.01 2 0 1 0 1
#> TCGA.CM.6164.01 2 0 1 0 1
#> TCGA.AG.3732.01 2 0 1 0 1
#> TCGA.F5.6863.01 1 0 1 1 0
#> TCGA.G4.6309.01 2 0 1 0 1
#> TCGA.CM.5868.01 2 0 1 0 1
#> TCGA.AZ.4313.01 2 0 1 0 1
#> TCGA.CI.6624.01 2 0 1 0 1
#> TCGA.DM.A0XF.01 1 0 1 1 0
#> TCGA.DY.A0XA.01 1 0 1 1 0
#> TCGA.DM.A28E.01 1 0 1 1 0
#> TCGA.AU.3779.01 1 0 1 1 0
#> TCGA.F4.6460.01 1 0 1 1 0
#> TCGA.F5.6465.01 2 0 1 0 1
#> TCGA.CM.5344.01 2 0 1 0 1
#> TCGA.DM.A1D0.01 1 0 1 1 0
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.D5.6929.01 2 0 1 0 1 0
#> TCGA.CM.6164.01 2 0 1 0 1 0
#> TCGA.AG.3732.01 3 0 1 0 0 1
#> TCGA.F5.6863.01 1 0 1 1 0 0
#> TCGA.G4.6309.01 3 0 1 0 0 1
#> TCGA.CM.5868.01 2 0 1 0 1 0
#> TCGA.AZ.4313.01 3 0 1 0 0 1
#> TCGA.CI.6624.01 2 0 1 0 1 0
#> TCGA.DM.A0XF.01 2 0 1 0 1 0
#> TCGA.DY.A0XA.01 1 0 1 1 0 0
#> TCGA.DM.A28E.01 1 0 1 1 0 0
#> TCGA.AU.3779.01 1 0 1 1 0 0
#> TCGA.F4.6460.01 1 0 1 1 0 0
#> TCGA.F5.6465.01 2 0 1 0 1 0
#> TCGA.CM.5344.01 2 0 1 0 1 0
#> TCGA.DM.A1D0.01 1 0 1 1 0 0
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> TCGA.D5.6929.01 2 0.000 0.739 0.00 1.00 0.00 0.00
#> TCGA.CM.6164.01 2 0.441 0.842 0.00 0.70 0.00 0.30
#> TCGA.AG.3732.01 3 0.000 0.969 0.00 0.00 1.00 0.00
#> TCGA.F5.6863.01 1 0.000 1.000 1.00 0.00 0.00 0.00
#> TCGA.G4.6309.01 3 0.201 0.936 0.00 0.00 0.92 0.08
#> TCGA.CM.5868.01 2 0.441 0.842 0.00 0.70 0.00 0.30
#> TCGA.AZ.4313.01 3 0.000 0.969 0.00 0.00 1.00 0.00
#> TCGA.CI.6624.01 2 0.380 0.835 0.00 0.78 0.00 0.22
#> TCGA.DM.A0XF.01 4 0.201 0.308 0.00 0.08 0.00 0.92
#> TCGA.DY.A0XA.01 1 0.000 1.000 1.00 0.00 0.00 0.00
#> TCGA.DM.A28E.01 1 0.000 1.000 1.00 0.00 0.00 0.00
#> TCGA.AU.3779.01 4 0.479 0.242 0.38 0.00 0.00 0.62
#> TCGA.F4.6460.01 1 0.000 1.000 1.00 0.00 0.00 0.00
#> TCGA.F5.6465.01 2 0.000 0.739 0.00 1.00 0.00 0.00
#> TCGA.CM.5344.01 2 0.441 0.842 0.00 0.70 0.00 0.30
#> TCGA.DM.A1D0.01 1 0.000 1.000 1.00 0.00 0.00 0.00
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> TCGA.D5.6929.01 5 0.4262 1.000 0.00 0.44 0.00 0.00 0.56
#> TCGA.CM.6164.01 2 0.0609 0.969 0.00 0.98 0.00 0.00 0.02
#> TCGA.AG.3732.01 3 0.0000 0.935 0.00 0.00 1.00 0.00 0.00
#> TCGA.F5.6863.01 1 0.0000 0.937 1.00 0.00 0.00 0.00 0.00
#> TCGA.G4.6309.01 3 0.3291 0.866 0.00 0.00 0.84 0.04 0.12
#> TCGA.CM.5868.01 2 0.0609 0.969 0.00 0.98 0.00 0.00 0.02
#> TCGA.AZ.4313.01 3 0.0000 0.935 0.00 0.00 1.00 0.00 0.00
#> TCGA.CI.6624.01 2 0.0609 0.949 0.00 0.98 0.00 0.00 0.02
#> TCGA.DM.A0XF.01 4 0.1043 0.924 0.00 0.04 0.00 0.96 0.00
#> TCGA.DY.A0XA.01 1 0.3684 0.711 0.72 0.00 0.00 0.00 0.28
#> TCGA.DM.A28E.01 1 0.0000 0.937 1.00 0.00 0.00 0.00 0.00
#> TCGA.AU.3779.01 4 0.2077 0.924 0.04 0.00 0.00 0.92 0.04
#> TCGA.F4.6460.01 1 0.0000 0.937 1.00 0.00 0.00 0.00 0.00
#> TCGA.F5.6465.01 5 0.4262 1.000 0.00 0.44 0.00 0.00 0.56
#> TCGA.CM.5344.01 2 0.0000 0.962 0.00 1.00 0.00 0.00 0.00
#> TCGA.DM.A1D0.01 1 0.0000 0.937 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.D5.6929.01 5 0.0000 1.000 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.CM.6164.01 2 0.3647 0.747 0.00 0.64 0.00 0.00 0.36 0.00
#> TCGA.AG.3732.01 6 0.1480 0.823 0.00 0.04 0.00 0.02 0.00 0.94
#> TCGA.F5.6863.01 1 0.0000 0.878 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.G4.6309.01 6 0.3706 0.666 0.00 0.00 0.38 0.00 0.00 0.62
#> TCGA.CM.5868.01 2 0.3647 0.747 0.00 0.64 0.00 0.00 0.36 0.00
#> TCGA.AZ.4313.01 6 0.0000 0.823 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.CI.6624.01 2 0.5438 0.747 0.00 0.56 0.16 0.00 0.28 0.00
#> TCGA.DM.A0XF.01 4 0.2794 0.895 0.00 0.08 0.06 0.86 0.00 0.00
#> TCGA.DY.A0XA.01 1 0.4246 0.571 0.58 0.02 0.40 0.00 0.00 0.00
#> TCGA.DM.A28E.01 1 0.0000 0.878 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AU.3779.01 4 0.0547 0.895 0.02 0.00 0.00 0.98 0.00 0.00
#> TCGA.F4.6460.01 1 0.2260 0.823 0.86 0.14 0.00 0.00 0.00 0.00
#> TCGA.F5.6465.01 5 0.0000 1.000 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.CM.5344.01 2 0.5354 0.758 0.00 0.58 0.16 0.00 0.26 0.00
#> TCGA.DM.A1D0.01 1 0.0000 0.878 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.D5.6929.01 5 0.1886 0.969 0.00 0.12 0.00 0.00 0.88 0.00 0.00
#> TCGA.CM.6164.01 2 0.3745 0.783 0.26 0.70 0.00 0.00 0.04 0.00 0.00
#> TCGA.AG.3732.01 6 0.1363 0.774 0.00 0.00 0.00 0.00 0.02 0.94 0.04
#> TCGA.F5.6863.01 3 0.0000 0.836 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.G4.6309.01 6 0.4902 0.555 0.34 0.00 0.00 0.00 0.00 0.54 0.12
#> TCGA.CM.5868.01 2 0.3745 0.783 0.26 0.70 0.00 0.00 0.04 0.00 0.00
#> TCGA.AZ.4313.01 6 0.0000 0.774 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.CI.6624.01 2 0.0000 0.789 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DM.A0XF.01 4 0.4079 0.802 0.08 0.00 0.00 0.76 0.04 0.00 0.12
#> TCGA.DY.A0XA.01 7 0.3139 0.000 0.00 0.00 0.30 0.00 0.00 0.00 0.70
#> TCGA.DM.A28E.01 3 0.0504 0.829 0.00 0.00 0.98 0.00 0.02 0.00 0.00
#> TCGA.AU.3779.01 4 0.0000 0.802 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.F4.6460.01 3 0.3927 0.430 0.30 0.00 0.66 0.00 0.04 0.00 0.00
#> TCGA.F5.6465.01 5 0.2864 0.969 0.02 0.12 0.00 0.00 0.84 0.00 0.02
#> TCGA.CM.5344.01 2 0.0000 0.789 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DM.A1D0.01 3 0.0000 0.836 0.00 0.00 1.00 0.00 0.00 0.00 0.00
cbind(get_classes(res, k = 8), get_membership(res, k = 8))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7 p8
#> TCGA.D5.6929.01 5 0.366 0.866 0.06 0.06 0.00 0.00 0.78 0.0 0.10 0.00
#> TCGA.CM.6164.01 2 0.000 0.500 0.00 1.00 0.00 0.00 0.00 0.0 0.00 0.00
#> TCGA.AG.3732.01 6 0.202 0.733 0.00 0.00 0.00 0.00 0.02 0.9 0.02 0.06
#> TCGA.F5.6863.01 3 0.324 0.812 0.40 0.00 0.60 0.00 0.00 0.0 0.00 0.00
#> TCGA.G4.6309.01 6 0.476 0.499 0.36 0.00 0.00 0.00 0.00 0.5 0.00 0.14
#> TCGA.CM.5868.01 2 0.000 0.500 0.00 1.00 0.00 0.00 0.00 0.0 0.00 0.00
#> TCGA.AZ.4313.01 6 0.000 0.733 0.00 0.00 0.00 0.00 0.00 1.0 0.00 0.00
#> TCGA.CI.6624.01 2 0.495 -0.834 0.10 0.46 0.00 0.00 0.00 0.0 0.02 0.42
#> TCGA.DM.A0XF.01 4 0.000 0.719 0.00 0.00 0.00 1.00 0.00 0.0 0.00 0.00
#> TCGA.DY.A0XA.01 7 0.227 0.000 0.00 0.00 0.18 0.00 0.00 0.0 0.82 0.00
#> TCGA.DM.A28E.01 3 0.464 0.780 0.30 0.00 0.60 0.00 0.04 0.0 0.00 0.06
#> TCGA.AU.3779.01 4 0.440 0.719 0.08 0.00 0.00 0.68 0.00 0.0 0.04 0.20
#> TCGA.F4.6460.01 3 0.000 0.460 0.00 0.00 1.00 0.00 0.00 0.0 0.00 0.00
#> TCGA.F5.6465.01 5 0.109 0.866 0.00 0.06 0.00 0.00 0.94 0.0 0.00 0.00
#> TCGA.CM.5344.01 8 0.332 0.000 0.00 0.46 0.00 0.00 0.00 0.0 0.00 0.54
#> TCGA.DM.A1D0.01 3 0.324 0.812 0.40 0.00 0.60 0.00 0.00 0.0 0.00 0.00
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
consensus_heatmap(res, k = 7)
consensus_heatmap(res, k = 8)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
membership_heatmap(res, k = 7)
membership_heatmap(res, k = 8)
As soon as the classes for columns are determined, the signatures that are significantly different between subgroups can be looked for. Following are the heatmaps for signatures.
get_signatures(res, k = 2)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
get_signatures(res, k = 7)
get_signatures(res, k = 8)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. To get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows (which is done by automatically selecting number of clusters).If there are too many signatures, top_signatures = ... can be set to only show the
signatures with the highest FDRs:
# code only for demonstration
# e.g. to show the top 500 most significant rows
tb = get_signature(res, k = ..., top_signatures = 500)
If the signatures are defined as these which are uniquely high in current group, diff_method argument
can be set to "uniquely_high_in_one_group":
# code only for demonstration
tb = get_signature(res, k = ..., diff_method = "uniquely_high_in_one_group")
UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
dimension_reduction(res, k = 7, method = "UMAP")
dimension_reduction(res, k = 8, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
If matrix rows can be associated to genes, consider to use functional_enrichment(res,
...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.
Parent node: Node04. Child nodes: Node0111 , Node0112 , Node0121 , Node0122 , Node0211-leaf , Node0212 , Node0411-leaf , Node0412-leaf , Node0413-leaf , Node0414-leaf , Node0421-leaf , Node0422 , Node0423-leaf , Node0431-leaf , Node0432-leaf , Node0433-leaf .
The object with results only for a single top-value method and a single partitioning method can be extracted as:
res = res_rh["043"]
A summary of res and all the functions that can be applied to it:
res
#> A 'ConsensusPartition' object with k = 2, 3, 4, 5, 6, 7, 8.
#> On a matrix with 30000 rows and 17 columns.
#> Top rows (1000) are extracted by 'ATC' method.
#> Subgroups are detected by 'kmeans' method.
#> Performed in total 350 partitions by row resampling.
#> Best k for subgroups seems to be 3.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_partitions"
#> [7] "compare_signatures" "consensus_heatmap" "dimension_reduction"
#> [10] "functional_enrichment" "get_anno_col" "get_anno"
#> [13] "get_classes" "get_consensus" "get_matrix"
#> [16] "get_membership" "get_param" "get_signatures"
#> [19] "get_stats" "is_best_k" "is_stable_k"
#> [22] "membership_heatmap" "ncol" "nrow"
#> [25] "plot_ecdf" "predict_classes" "rownames"
#> [28] "select_partition_number" "show" "suggest_best_k"
#> [31] "test_to_known_factors" "top_rows_heatmap"
collect_plots() function collects all the plots made from res for all k (number of subgroups)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
The plots are:
k and the heatmap of
predicted classes for each k.k.k.k.All the plots in panels can be made by individual functions and they are plotted later in this section.
select_partition_number() produces several plots showing different
statistics for choosing “optimized” k. There are following statistics:
k;k, the area increased is defined as \(A_k - A_{k-1}\).The detailed explanations of these statistics can be found in the cola vignette.
Generally speaking, higher 1-PAC score, higher mean silhouette score or higher
concordance corresponds to better partition. Rand index and Jaccard index
measure how similar the current partition is compared to partition with k-1.
If they are too similar, we won't accept k is better than k-1.
select_partition_number(res)
The numeric values for all these statistics can be obtained by get_stats().
get_stats(res)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> 2 2 1.000 1.000 1.000 0.4858 0.515 0.515
#> 3 3 1.000 0.998 0.999 0.3940 0.765 0.562
#> 4 4 0.978 0.890 0.975 0.0402 0.978 0.932
#> 5 5 0.904 0.802 0.934 0.0406 0.985 0.951
#> 6 6 0.868 0.750 0.932 0.0521 0.949 0.821
#> 7 7 0.868 0.643 0.908 0.0472 0.956 0.812
#> 8 8 0.816 0.550 0.895 0.0404 0.971 0.846
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.DC.6157.01 2 0 1 0 1
#> TCGA.A6.A567.01 1 0 1 1 0
#> TCGA.EI.6885.01 2 0 1 0 1
#> TCGA.5M.AAT5.01 2 0 1 0 1
#> TCGA.G4.6317.02 2 0 1 0 1
#> TCGA.CK.4948.01 1 0 1 1 0
#> TCGA.AA.3494.01 2 0 1 0 1
#> TCGA.G4.6307.01 2 0 1 0 1
#> TCGA.F5.6810.01 1 0 1 1 0
#> TCGA.G4.6295.01 1 0 1 1 0
#> TCGA.AG.A01Y.01 2 0 1 0 1
#> TCGA.AZ.6603.01 2 0 1 0 1
#> TCGA.AF.6672.01 2 0 1 0 1
#> TCGA.NH.A8F7.01 2 0 1 0 1
#> TCGA.CA.5797.01 1 0 1 1 0
#> TCGA.EI.6513.01 1 0 1 1 0
#> TCGA.AZ.4681.01 2 0 1 0 1
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.DC.6157.01 2 0.0000 0.997 0 1.00 0.00
#> TCGA.A6.A567.01 3 0.0000 1.000 0 0.00 1.00
#> TCGA.EI.6885.01 3 0.0000 1.000 0 0.00 1.00
#> TCGA.5M.AAT5.01 2 0.0892 0.980 0 0.98 0.02
#> TCGA.G4.6317.02 2 0.0000 0.997 0 1.00 0.00
#> TCGA.CK.4948.01 1 0.0000 1.000 1 0.00 0.00
#> TCGA.AA.3494.01 2 0.0000 0.997 0 1.00 0.00
#> TCGA.G4.6307.01 2 0.0000 0.997 0 1.00 0.00
#> TCGA.F5.6810.01 1 0.0000 1.000 1 0.00 0.00
#> TCGA.G4.6295.01 1 0.0000 1.000 1 0.00 0.00
#> TCGA.AG.A01Y.01 3 0.0000 1.000 0 0.00 1.00
#> TCGA.AZ.6603.01 2 0.0000 0.997 0 1.00 0.00
#> TCGA.AF.6672.01 3 0.0000 1.000 0 0.00 1.00
#> TCGA.NH.A8F7.01 2 0.0000 0.997 0 1.00 0.00
#> TCGA.CA.5797.01 1 0.0000 1.000 1 0.00 0.00
#> TCGA.EI.6513.01 1 0.0000 1.000 1 0.00 0.00
#> TCGA.AZ.4681.01 2 0.0000 0.997 0 1.00 0.00
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> TCGA.DC.6157.01 2 0.0707 0.982 0 0.98 0.00 0.02
#> TCGA.A6.A567.01 4 0.0707 0.000 0 0.00 0.02 0.98
#> TCGA.EI.6885.01 3 0.0000 0.852 0 0.00 1.00 0.00
#> TCGA.5M.AAT5.01 2 0.1637 0.928 0 0.94 0.06 0.00
#> TCGA.G4.6317.02 2 0.0707 0.982 0 0.98 0.00 0.02
#> TCGA.CK.4948.01 1 0.0000 1.000 1 0.00 0.00 0.00
#> TCGA.AA.3494.01 2 0.0000 0.980 0 1.00 0.00 0.00
#> TCGA.G4.6307.01 2 0.0707 0.982 0 0.98 0.00 0.02
#> TCGA.F5.6810.01 1 0.0000 1.000 1 0.00 0.00 0.00
#> TCGA.G4.6295.01 1 0.0000 1.000 1 0.00 0.00 0.00
#> TCGA.AG.A01Y.01 3 0.0000 0.852 0 0.00 1.00 0.00
#> TCGA.AZ.6603.01 2 0.0000 0.980 0 1.00 0.00 0.00
#> TCGA.AF.6672.01 3 0.4134 0.639 0 0.00 0.74 0.26
#> TCGA.NH.A8F7.01 2 0.0707 0.982 0 0.98 0.00 0.02
#> TCGA.CA.5797.01 1 0.0000 1.000 1 0.00 0.00 0.00
#> TCGA.EI.6513.01 1 0.0000 1.000 1 0.00 0.00 0.00
#> TCGA.AZ.4681.01 2 0.0000 0.980 0 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.DC.6157.01 2 0.0000 0.938 0.00 1.00 0.00 0.00 0.00
#> TCGA.A6.A567.01 4 0.0000 0.000 0.00 0.00 0.00 1.00 0.00
#> TCGA.EI.6885.01 3 0.0000 1.000 0.00 0.00 1.00 0.00 0.00
#> TCGA.5M.AAT5.01 2 0.5351 0.391 0.00 0.56 0.06 0.00 0.38
#> TCGA.G4.6317.02 2 0.0000 0.938 0.00 1.00 0.00 0.00 0.00
#> TCGA.CK.4948.01 1 0.2732 0.848 0.84 0.00 0.00 0.00 0.16
#> TCGA.AA.3494.01 2 0.0000 0.938 0.00 1.00 0.00 0.00 0.00
#> TCGA.G4.6307.01 2 0.0000 0.938 0.00 1.00 0.00 0.00 0.00
#> TCGA.F5.6810.01 1 0.0000 0.959 1.00 0.00 0.00 0.00 0.00
#> TCGA.G4.6295.01 1 0.0000 0.959 1.00 0.00 0.00 0.00 0.00
#> TCGA.AG.A01Y.01 3 0.0000 1.000 0.00 0.00 1.00 0.00 0.00
#> TCGA.AZ.6603.01 2 0.0000 0.938 0.00 1.00 0.00 0.00 0.00
#> TCGA.AF.6672.01 5 0.5673 0.000 0.00 0.00 0.42 0.08 0.50
#> TCGA.NH.A8F7.01 2 0.0000 0.938 0.00 1.00 0.00 0.00 0.00
#> TCGA.CA.5797.01 1 0.0609 0.953 0.98 0.00 0.00 0.00 0.02
#> TCGA.EI.6513.01 1 0.0000 0.959 1.00 0.00 0.00 0.00 0.00
#> TCGA.AZ.4681.01 2 0.0000 0.938 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.DC.6157.01 2 0.0000 0.955 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.A6.A567.01 4 0.1267 0.000 0.00 0.00 0.00 0.94 0.06 0.00
#> TCGA.EI.6885.01 3 0.3198 1.000 0.00 0.00 0.74 0.00 0.26 0.00
#> TCGA.5M.AAT5.01 6 0.3678 0.000 0.00 0.18 0.02 0.00 0.02 0.78
#> TCGA.G4.6317.02 2 0.0000 0.955 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.CK.4948.01 1 0.4890 0.621 0.66 0.00 0.16 0.00 0.00 0.18
#> TCGA.AA.3494.01 2 0.1807 0.902 0.00 0.92 0.06 0.02 0.00 0.00
#> TCGA.G4.6307.01 2 0.0000 0.955 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.F5.6810.01 1 0.0000 0.911 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.G4.6295.01 1 0.0547 0.906 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.AG.A01Y.01 3 0.3198 1.000 0.00 0.00 0.74 0.00 0.26 0.00
#> TCGA.AZ.6603.01 2 0.0000 0.955 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.AF.6672.01 5 0.0000 0.000 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.NH.A8F7.01 2 0.0000 0.955 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.CA.5797.01 1 0.0547 0.906 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.EI.6513.01 1 0.0000 0.911 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AZ.4681.01 2 0.3045 0.821 0.00 0.84 0.10 0.06 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.DC.6157.01 2 0.0000 0.919 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.A6.A567.01 4 0.4866 0.000 0.00 0.00 0.00 0.48 0.10 0.42 0.00
#> TCGA.EI.6885.01 3 0.0863 0.964 0.00 0.00 0.96 0.00 0.00 0.00 0.04
#> TCGA.5M.AAT5.01 6 0.4778 0.000 0.00 0.06 0.00 0.00 0.02 0.58 0.34
#> TCGA.G4.6317.02 2 0.0504 0.907 0.00 0.98 0.00 0.02 0.00 0.00 0.00
#> TCGA.CK.4948.01 1 0.3562 0.421 0.50 0.00 0.00 0.50 0.00 0.00 0.00
#> TCGA.AA.3494.01 2 0.2081 0.682 0.00 0.86 0.00 0.00 0.00 0.00 0.14
#> TCGA.G4.6307.01 2 0.0000 0.919 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.F5.6810.01 1 0.0000 0.851 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.G4.6295.01 1 0.0504 0.847 0.98 0.00 0.00 0.00 0.02 0.00 0.00
#> TCGA.AG.A01Y.01 3 0.0000 0.964 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.AZ.6603.01 2 0.1363 0.876 0.00 0.94 0.00 0.02 0.00 0.00 0.04
#> TCGA.AF.6672.01 5 0.1433 0.000 0.00 0.00 0.08 0.00 0.92 0.00 0.00
#> TCGA.NH.A8F7.01 2 0.0000 0.919 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CA.5797.01 1 0.2278 0.807 0.88 0.00 0.00 0.04 0.00 0.00 0.08
#> TCGA.EI.6513.01 1 0.0000 0.851 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.AZ.4681.01 7 0.3546 0.000 0.00 0.46 0.00 0.00 0.00 0.00 0.54
cbind(get_classes(res, k = 8), get_membership(res, k = 8))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7 p8
#> TCGA.DC.6157.01 2 0.0000 0.861 0.00 1.00 0.00 0 0.00 0 0.00 0.00
#> TCGA.A6.A567.01 4 0.0000 0.000 0.00 0.00 0.00 1 0.00 0 0.00 0.00
#> TCGA.EI.6885.01 3 0.3757 0.684 0.00 0.00 0.68 0 0.00 0 0.06 0.26
#> TCGA.5M.AAT5.01 6 0.0000 0.000 0.00 0.00 0.00 0 0.00 1 0.00 0.00
#> TCGA.G4.6317.02 2 0.1563 0.819 0.00 0.90 0.00 0 0.00 0 0.00 0.10
#> TCGA.CK.4948.01 8 0.3272 0.000 0.42 0.00 0.00 0 0.00 0 0.00 0.58
#> TCGA.AA.3494.01 2 0.3991 0.492 0.00 0.70 0.00 0 0.02 0 0.22 0.06
#> TCGA.G4.6307.01 2 0.0000 0.861 0.00 1.00 0.00 0 0.00 0 0.00 0.00
#> TCGA.F5.6810.01 1 0.0000 0.890 1.00 0.00 0.00 0 0.00 0 0.00 0.00
#> TCGA.G4.6295.01 1 0.0471 0.877 0.98 0.00 0.00 0 0.00 0 0.02 0.00
#> TCGA.AG.A01Y.01 3 0.0000 0.684 0.00 0.00 1.00 0 0.00 0 0.00 0.00
#> TCGA.AZ.6603.01 2 0.3002 0.782 0.00 0.82 0.00 0 0.02 0 0.04 0.12
#> TCGA.AF.6672.01 5 0.1341 0.000 0.00 0.00 0.08 0 0.92 0 0.00 0.00
#> TCGA.NH.A8F7.01 2 0.0000 0.861 0.00 1.00 0.00 0 0.00 0 0.00 0.00
#> TCGA.CA.5797.01 1 0.3078 0.654 0.82 0.00 0.00 0 0.06 0 0.10 0.02
#> TCGA.EI.6513.01 1 0.0000 0.890 1.00 0.00 0.00 0 0.00 0 0.00 0.00
#> TCGA.AZ.4681.01 7 0.2267 0.000 0.00 0.18 0.00 0 0.00 0 0.82 0.00
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
consensus_heatmap(res, k = 7)
consensus_heatmap(res, k = 8)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
membership_heatmap(res, k = 7)
membership_heatmap(res, k = 8)
As soon as the classes for columns are determined, the signatures that are significantly different between subgroups can be looked for. Following are the heatmaps for signatures.
get_signatures(res, k = 2)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
get_signatures(res, k = 7)
get_signatures(res, k = 8)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. To get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows (which is done by automatically selecting number of clusters).If there are too many signatures, top_signatures = ... can be set to only show the
signatures with the highest FDRs:
# code only for demonstration
# e.g. to show the top 500 most significant rows
tb = get_signature(res, k = ..., top_signatures = 500)
If the signatures are defined as these which are uniquely high in current group, diff_method argument
can be set to "uniquely_high_in_one_group":
# code only for demonstration
tb = get_signature(res, k = ..., diff_method = "uniquely_high_in_one_group")
UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
dimension_reduction(res, k = 7, method = "UMAP")
dimension_reduction(res, k = 8, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
If matrix rows can be associated to genes, consider to use functional_enrichment(res,
...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.
sessionInfo()
#> R version 4.1.0 (2021-05-18)
#> Platform: x86_64-pc-linux-gnu (64-bit)
#> Running under: CentOS Linux 7 (Core)
#>
#> Matrix products: default
#> BLAS/LAPACK: /usr/lib64/libopenblas-r0.3.3.so
#>
#> locale:
#> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8
#> [4] LC_COLLATE=en_US.UTF-8 LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
#> [7] LC_PAPER=en_US.UTF-8 LC_NAME=C LC_ADDRESS=C
#> [10] LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
#>
#> attached base packages:
#> [1] grid stats graphics grDevices utils datasets methods base
#>
#> other attached packages:
#> [1] genefilter_1.74.0 ComplexHeatmap_2.8.0 markdown_1.1 knitr_1.33
#> [5] matrixStats_0.59.0 cola_1.9.4
#>
#> loaded via a namespace (and not attached):
#> [1] bitops_1.0-7 bit64_4.0.5 doParallel_1.0.16 RColorBrewer_1.1-2
#> [5] httr_1.4.2 GenomeInfoDb_1.28.1 data.tree_1.0.0 tools_4.1.0
#> [9] utf8_1.2.1 R6_2.5.0 irlba_2.3.3 DBI_1.1.1
#> [13] BiocGenerics_0.38.0 colorspace_2.0-2 GetoptLong_1.0.5 gridExtra_2.3
#> [17] tidyselect_1.1.1 bit_4.0.4 compiler_4.1.0 Biobase_2.52.0
#> [21] Cairo_1.5-12.2 xml2_1.3.2 microbenchmark_1.4-7 slam_0.1-48
#> [25] scales_1.1.1 askpass_1.1 stringr_1.4.0 digest_0.6.27
#> [29] XVector_0.32.0 pkgconfig_2.0.3 umap_0.2.7.0 fastmap_1.1.0
#> [33] highr_0.9 rlang_0.4.11 GlobalOptions_0.1.2 rstudioapi_0.13
#> [37] RSQLite_2.2.7 impute_1.66.0 generics_0.1.0 shape_1.4.6
#> [41] jsonlite_1.7.2 mclust_5.4.7 dplyr_1.0.7 dendextend_1.15.1
#> [45] RCurl_1.98-1.3 magrittr_2.0.1 GenomeInfoDbData_1.2.6 Matrix_1.3-4
#> [49] fansi_0.5.0 Rcpp_1.0.7 munsell_0.5.0 S4Vectors_0.30.0
#> [53] viridis_0.6.1 reticulate_1.20 lifecycle_1.0.0 scatterplot3d_0.3-41
#> [57] stringi_1.7.3 zlibbioc_1.38.0 blob_1.2.1 parallel_4.1.0
#> [61] crayon_1.4.1 lattice_0.20-44 Biostrings_2.60.1 splines_4.1.0
#> [65] annotate_1.70.0 circlize_0.4.13 KEGGREST_1.32.0 polylabelr_0.2.0
#> [69] pillar_1.6.1 rjson_0.2.20 codetools_0.2-18 stats4_4.1.0
#> [73] XML_3.99-0.6 glue_1.4.2 evaluate_0.14 png_0.1-7
#> [77] vctrs_0.3.8 foreach_1.5.1 polyclip_1.10-0 purrr_0.3.4
#> [81] gtable_0.3.0 openssl_1.4.4 assertthat_0.2.1 clue_0.3-59
#> [85] cachem_1.0.5 ggplot2_3.3.5 xfun_0.24 eulerr_6.1.0
#> [89] xtable_1.8-4 skmeans_0.2-13 RSpectra_0.16-0 viridisLite_0.4.0
#> [93] survival_3.2-11 tibble_3.1.2 Polychrome_1.3.1 iterators_1.0.13
#> [97] AnnotationDbi_1.54.1 memoise_2.0.0 IRanges_2.26.0 cluster_2.1.2
#> [101] ellipsis_0.3.2 brew_1.0-6