Date: 2021-07-22 19:16:08 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 375779 rows and 476 columns.
#> Performed in total 127400 partitions.
#> There are 61 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, 476 cols
#> |-- 01, 134 cols, 4105 signatures
#> | |-- 011, 44 cols, 2780 signatures
#> | | |-- 0111, 14 cols, 2616 signatures
#> | | | |-- 01111, 3 cols (b)
#> | | | |-- 01112, 8 cols (b)
#> | | | `-- 01113, 3 cols (b)
#> | | |-- 0112, 14 cols, 167 signatures (c)
#> | | `-- 0113, 16 cols, 2255 signatures
#> | | |-- 01131, 2 cols (b)
#> | | |-- 01132, 8 cols (b)
#> | | `-- 01133, 6 cols (b)
#> | |-- 012, 31 cols, 41067 signatures
#> | | |-- 0121, 7 cols (b)
#> | | |-- 0122, 9 cols (b)
#> | | |-- 0123, 5 cols (b)
#> | | |-- 0124, 7 cols (b)
#> | | `-- 0125, 3 cols (b)
#> | |-- 013, 31 cols, 29265 signatures
#> | | |-- 0131, 15 cols, 1969 signatures
#> | | | |-- 01311, 13 cols, 278 signatures (c)
#> | | | `-- 01312, 2 cols (b)
#> | | |-- 0132, 11 cols (b)
#> | | `-- 0133, 5 cols (b)
#> | `-- 014, 28 cols, 855 signatures (c)
#> |-- 02, 70 cols, 22901 signatures
#> | |-- 021, 28 cols, 4070 signatures
#> | | |-- 0211, 6 cols (b)
#> | | `-- 0212, 22 cols, 1564 signatures
#> | | |-- 02121, 6 cols (b)
#> | | |-- 02122, 11 cols (b)
#> | | `-- 02123, 5 cols (b)
#> | |-- 022, 23 cols, 2142 signatures
#> | | |-- 0221, 10 cols (b)
#> | | `-- 0222, 13 cols, 648 signatures (c)
#> | `-- 023, 19 cols, 244 signatures (c)
#> |-- 03, 73 cols, 1034 signatures
#> | |-- 031, 26 cols, 2328 signatures
#> | | |-- 0311, 17 cols, 2454 signatures
#> | | | |-- 03111, 6 cols (b)
#> | | | |-- 03112, 9 cols (b)
#> | | | `-- 03113, 2 cols (b)
#> | | `-- 0312, 9 cols (b)
#> | `-- 032, 47 cols, 23773 signatures
#> | |-- 0321, 13 cols, 662 signatures (c)
#> | |-- 0322, 20 cols, 1119 signatures
#> | | |-- 03221, 14 cols, 193 signatures (c)
#> | | `-- 03222, 6 cols (b)
#> | `-- 0323, 14 cols, 2164 signatures
#> | |-- 03231, 2 cols (b)
#> | |-- 03232, 8 cols (b)
#> | |-- 03233, 2 cols (b)
#> | `-- 03234, 2 cols (b)
#> |-- 04, 131 cols, 52804 signatures
#> | |-- 041, 42 cols, 3485 signatures
#> | | |-- 0411, 12 cols, 1144 signatures
#> | | | |-- 04111, 10 cols (b)
#> | | | `-- 04112, 2 cols (b)
#> | | |-- 0412, 22 cols, 2117 signatures
#> | | | |-- 04121, 5 cols (b)
#> | | | `-- 04122, 17 cols, 233 signatures (c)
#> | | `-- 0413, 8 cols (b)
#> | |-- 042, 30 cols, 11354 signatures
#> | | |-- 0421, 12 cols, 685 signatures (c)
#> | | |-- 0422, 7 cols (b)
#> | | `-- 0423, 11 cols (b)
#> | |-- 043, 17 cols, 2664 signatures
#> | | |-- 0431, 4 cols (b)
#> | | |-- 0432, 9 cols (b)
#> | | `-- 0433, 4 cols (b)
#> | `-- 044, 42 cols, 8228 signatures
#> | |-- 0441, 14 cols, 864 signatures (c)
#> | |-- 0442, 20 cols, 6230 signatures
#> | | |-- 04421, 12 cols, 318 signatures (c)
#> | | |-- 04422, 3 cols (b)
#> | | |-- 04423, 3 cols (b)
#> | | `-- 04424, 2 cols (b)
#> | `-- 0443, 8 cols (b)
#> `-- 05, 68 cols, 10240 signatures
#> |-- 051, 31 cols, 17313 signatures
#> | |-- 0511, 17 cols, 1831 signatures
#> | | |-- 05111, 4 cols (b)
#> | | |-- 05112, 7 cols (b)
#> | | `-- 05113, 6 cols (b)
#> | |-- 0512, 9 cols (b)
#> | `-- 0513, 5 cols (b)
#> `-- 052, 37 cols, 12706 signatures
#> |-- 0521, 12 cols, 403 signatures (c)
#> |-- 0522, 13 cols, 138 signatures (c)
#> |-- 0523, 8 cols (b)
#> `-- 0524, 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] 375779 476
All the methods that were tried:
res_rh@param$combination_method
#> [[1]]
#> [1] "SD" "kmeans"
#>
#> [[2]]
#> [1] "ATC" "kmeans"
#>
#> [[3]]
#> [1] "SD" "skmeans"
#>
#> [[4]]
#> [1] "ATC" "skmeans"
The density distribution for each sample is visualized as one column in the following heatmap. The clustering is based on the distance which is the Kolmogorov-Smirnov statistic between two distributions.
library(ComplexHeatmap)
densityHeatmap(mat, ylab = "value", cluster_columns = TRUE, show_column_names = FALSE,
mc.cores = 1)
Some values about the hierarchy:
all_nodes(res_rh)
#> [1] "0" "01" "011" "0111" "01111" "01112" "01113" "0112" "0113" "01131" "01132" "01133"
#> [13] "012" "0121" "0122" "0123" "0124" "0125" "013" "0131" "01311" "01312" "0132" "0133"
#> [25] "014" "02" "021" "0211" "0212" "02121" "02122" "02123" "022" "0221" "0222" "023"
#> [37] "03" "031" "0311" "03111" "03112" "03113" "0312" "032" "0321" "0322" "03221" "03222"
#> [49] "0323" "03231" "03232" "03233" "03234" "04" "041" "0411" "04111" "04112" "0412" "04121"
#> [61] "04122" "0413" "042" "0421" "0422" "0423" "043" "0431" "0432" "0433" "044" "0441"
#> [73] "0442" "04421" "04422" "04423" "04424" "0443" "05" "051" "0511" "05111" "05112" "05113"
#> [85] "0512" "0513" "052" "0521" "0522" "0523" "0524"
all_leaves(res_rh)
#> [1] "01111" "01112" "01113" "0112" "01131" "01132" "01133" "0121" "0122" "0123" "0124" "0125"
#> [13] "01311" "01312" "0132" "0133" "014" "0211" "02121" "02122" "02123" "0221" "0222" "023"
#> [25] "03111" "03112" "03113" "0312" "0321" "03221" "03222" "03231" "03232" "03233" "03234" "04111"
#> [37] "04112" "04121" "04122" "0413" "0421" "0422" "0423" "0431" "0432" "0433" "0441" "04421"
#> [49] "04422" "04423" "04424" "0443" "05111" "05112" "05113" "0512" "0513" "0521" "0522" "0523"
#> [61] "0524"
node_info(res_rh)
#> id best_method depth best_k n_columns n_signatures p_signatures is_leaf
#> 1 0 ATC:skmeans 1 5 476 57862 0.153979 FALSE
#> 2 01 SD:skmeans 2 4 134 4105 0.010924 FALSE
#> 3 011 ATC:kmeans 3 3 44 2780 0.007398 FALSE
#> 4 0111 ATC:skmeans 4 3 14 2616 0.006962 FALSE
#> 5 01111 not applied 5 NA 3 NA NA TRUE
#> 6 01112 not applied 5 NA 8 NA NA TRUE
#> 7 01113 not applied 5 NA 3 NA NA TRUE
#> 8 0112 ATC:skmeans 4 2 14 167 0.000444 TRUE
#> 9 0113 ATC:skmeans 4 3 16 2255 0.006001 FALSE
#> 10 01131 not applied 5 NA 2 NA NA TRUE
#> 11 01132 not applied 5 NA 8 NA NA TRUE
#> 12 01133 not applied 5 NA 6 NA NA TRUE
#> 13 012 ATC:skmeans 3 5 31 41067 0.109285 FALSE
#> 14 0121 not applied 4 NA 7 NA NA TRUE
#> 15 0122 not applied 4 NA 9 NA NA TRUE
#> 16 0123 not applied 4 NA 5 NA NA TRUE
#> 17 0124 not applied 4 NA 7 NA NA TRUE
#> 18 0125 not applied 4 NA 3 NA NA TRUE
#> 19 013 ATC:skmeans 3 3 31 29265 0.077878 FALSE
#> 20 0131 ATC:kmeans 4 2 15 1969 0.005240 FALSE
#> 21 01311 SD:kmeans 5 3 13 278 0.000740 TRUE
#> 22 01312 not applied 5 NA 2 NA NA TRUE
#> 23 0132 not applied 4 NA 11 NA NA TRUE
#> 24 0133 not applied 4 NA 5 NA NA TRUE
#> 25 014 ATC:skmeans 3 2 28 855 0.002275 TRUE
#> 26 02 ATC:kmeans 2 3 70 22901 0.060943 FALSE
#> 27 021 ATC:kmeans 3 2 28 4070 0.010831 FALSE
#> 28 0211 not applied 4 NA 6 NA NA TRUE
#> 29 0212 ATC:skmeans 4 3 22 1564 0.004162 FALSE
#> 30 02121 not applied 5 NA 6 NA NA TRUE
#> 31 02122 not applied 5 NA 11 NA NA TRUE
#> 32 02123 not applied 5 NA 5 NA NA TRUE
#> 33 022 SD:kmeans 3 2 23 2142 0.005700 FALSE
#> 34 0221 not applied 4 NA 10 NA NA TRUE
#> 35 0222 ATC:kmeans 4 3 13 648 0.001724 TRUE
#> 36 023 ATC:kmeans 3 3 19 244 0.000649 TRUE
#> 37 03 ATC:skmeans 2 2 73 1034 0.002752 FALSE
#> 38 031 ATC:kmeans 3 2 26 2328 0.006195 FALSE
#> 39 0311 ATC:skmeans 4 3 17 2454 0.006530 FALSE
#> 40 03111 not applied 5 NA 6 NA NA TRUE
#> 41 03112 not applied 5 NA 9 NA NA TRUE
#> 42 03113 not applied 5 NA 2 NA NA TRUE
#> 43 0312 not applied 4 NA 9 NA NA TRUE
#> 44 032 ATC:kmeans 3 3 47 23773 0.063263 FALSE
#> 45 0321 ATC:kmeans 4 4 13 662 0.001762 TRUE
#> 46 0322 ATC:kmeans 4 2 20 1119 0.002978 FALSE
#> 47 03221 ATC:kmeans 5 2 14 193 0.000514 TRUE
#> 48 03222 not applied 5 NA 6 NA NA TRUE
#> 49 0323 ATC:kmeans 4 4 14 2164 0.005759 FALSE
#> 50 03231 not applied 5 NA 2 NA NA TRUE
#> 51 03232 not applied 5 NA 8 NA NA TRUE
#> 52 03233 not applied 5 NA 2 NA NA TRUE
#> 53 03234 not applied 5 NA 2 NA NA TRUE
#> 54 04 ATC:kmeans 2 4 131 52804 0.140519 FALSE
#> 55 041 ATC:skmeans 3 3 42 3485 0.009274 FALSE
#> 56 0411 ATC:kmeans 4 2 12 1144 0.003044 FALSE
#> 57 04111 not applied 5 NA 10 NA NA TRUE
#> 58 04112 not applied 5 NA 2 NA NA TRUE
#> 59 0412 ATC:kmeans 4 2 22 2117 0.005634 FALSE
#> 60 04121 not applied 5 NA 5 NA NA TRUE
#> 61 04122 ATC:skmeans 5 2 17 233 0.000620 TRUE
#> 62 0413 not applied 4 NA 8 NA NA TRUE
#> 63 042 ATC:kmeans 3 3 30 11354 0.030215 FALSE
#> 64 0421 ATC:skmeans 4 3 12 685 0.001823 TRUE
#> 65 0422 not applied 4 NA 7 NA NA TRUE
#> 66 0423 not applied 4 NA 11 NA NA TRUE
#> 67 043 SD:kmeans 3 3 17 2664 0.007089 FALSE
#> 68 0431 not applied 4 NA 4 NA NA TRUE
#> 69 0432 not applied 4 NA 9 NA NA TRUE
#> 70 0433 not applied 4 NA 4 NA NA TRUE
#> 71 044 ATC:skmeans 3 3 42 8228 0.021896 FALSE
#> 72 0441 ATC:skmeans 4 3 14 864 0.002299 TRUE
#> 73 0442 ATC:skmeans 4 4 20 6230 0.016579 FALSE
#> 74 04421 ATC:skmeans 5 3 12 318 0.000846 TRUE
#> 75 04422 not applied 5 NA 3 NA NA TRUE
#> 76 04423 not applied 5 NA 3 NA NA TRUE
#> 77 04424 not applied 5 NA 2 NA NA TRUE
#> 78 0443 not applied 4 NA 8 NA NA TRUE
#> 79 05 SD:kmeans 2 2 68 10240 0.027250 FALSE
#> 80 051 ATC:kmeans 3 3 31 17313 0.046072 FALSE
#> 81 0511 ATC:skmeans 4 3 17 1831 0.004873 FALSE
#> 82 05111 not applied 5 NA 4 NA NA TRUE
#> 83 05112 not applied 5 NA 7 NA NA TRUE
#> 84 05113 not applied 5 NA 6 NA NA TRUE
#> 85 0512 not applied 4 NA 9 NA NA TRUE
#> 86 0513 not applied 4 NA 5 NA NA TRUE
#> 87 052 ATC:kmeans 3 4 37 12706 0.033812 FALSE
#> 88 0521 ATC:skmeans 4 3 12 403 0.001072 TRUE
#> 89 0522 ATC:skmeans 4 2 13 138 0.000367 TRUE
#> 90 0523 not applied 4 NA 8 NA NA TRUE
#> 91 0524 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:skmeans | 7 | 0.92 | 0.85 | 0.93 | 476 | * | |
| Node01 | SD:skmeans | 4 | 1.00 | 0.98 | 0.98 | 134 | ** | |
| Node011 | ATC:kmeans | 3 | 1.00 | 0.95 | 0.98 | 44 | ** | |
| Node0111 | ATC:skmeans | 3 | 1.00 | 0.99 | 0.99 | 14 | ** | |
| Node01111-leaf | not applied | ✓ (b) | 3 | |||||
| Node01112-leaf | not applied | ✓ (b) | 8 | |||||
| Node01113-leaf | not applied | ✓ (b) | 3 | |||||
| Node0112-leaf | ATC:skmeans | ✓ (c) | 8 | 0.95 | 0.57 | 0.93 | 14 | * |
| Node0113 | ATC:skmeans | 3 | 1.00 | 1.00 | 1.00 | 16 | ** | |
| Node01131-leaf | not applied | ✓ (b) | 2 | |||||
| Node01132-leaf | not applied | ✓ (b) | 8 | |||||
| Node01133-leaf | not applied | ✓ (b) | 6 | |||||
| Node012 | ATC:skmeans | 5 | 0.95 | 0.95 | 0.96 | 31 | * | |
| Node0121-leaf | not applied | ✓ (b) | 7 | |||||
| Node0122-leaf | not applied | ✓ (b) | 9 | |||||
| Node0123-leaf | not applied | ✓ (b) | 5 | |||||
| Node0124-leaf | not applied | ✓ (b) | 7 | |||||
| Node0125-leaf | not applied | ✓ (b) | 3 | |||||
| Node013 | ATC:skmeans | 4 | 0.96 | 0.94 | 0.96 | 31 | ** | |
| Node0131 | ATC:kmeans | 8 | 0.94 | 0.67 | 0.97 | 15 | * | |
| Node01311-leaf | SD:kmeans | ✓ (c) | 3 | 1.00 | 0.99 | 0.99 | 13 | ** |
| Node01312-leaf | not applied | ✓ (b) | 2 | |||||
| Node0132-leaf | not applied | ✓ (b) | 11 | |||||
| Node0133-leaf | not applied | ✓ (b) | 5 | |||||
| Node014-leaf | ATC:skmeans | ✓ (c) | 2 | 1.00 | 1.00 | 1.00 | 28 | ** |
| Node02 | ATC:kmeans | 2 | 1.00 | 1.00 | 1.00 | 70 | ** | |
| Node021 | ATC:kmeans | 6 | 0.94 | 0.92 | 0.95 | 28 | * | |
| Node0211-leaf | not applied | ✓ (b) | 6 | |||||
| Node0212 | ATC:skmeans | 3 | 1.00 | 0.98 | 0.99 | 22 | ** | |
| Node02121-leaf | not applied | ✓ (b) | 6 | |||||
| Node02122-leaf | not applied | ✓ (b) | 11 | |||||
| Node02123-leaf | not applied | ✓ (b) | 5 | |||||
| Node022 | SD:kmeans | 2 | 1.00 | 0.97 | 0.99 | 23 | ** | |
| Node0221-leaf | not applied | ✓ (b) | 10 | |||||
| Node0222-leaf | ATC:kmeans | ✓ (c) | 7 | 0.92 | 0.68 | 0.91 | 13 | * |
| Node023-leaf | ATC:kmeans | ✓ (c) | 3 | 0.92 | 0.98 | 0.99 | 19 | * |
| Node03 | ATC:skmeans | 2 | 1.00 | 0.99 | 1.00 | 73 | ** | |
| Node031 | ATC:kmeans | 2 | 1.00 | 1.00 | 1.00 | 26 | ** | |
| Node0311 | ATC:skmeans | 3 | 1.00 | 1.00 | 1.00 | 17 | ** | |
| Node03111-leaf | not applied | ✓ (b) | 6 | |||||
| Node03112-leaf | not applied | ✓ (b) | 9 | |||||
| Node03113-leaf | not applied | ✓ (b) | 2 | |||||
| Node0312-leaf | not applied | ✓ (b) | 9 | |||||
| Node032 | ATC:kmeans | 3 | 1.00 | 0.99 | 1.00 | 47 | ** | |
| Node0321-leaf | ATC:kmeans | ✓ (c) | 2 | 1.00 | 1.00 | 1.00 | 13 | ** |
| Node0322 | ATC:kmeans | 2 | 1.00 | 1.00 | 1.00 | 20 | ** | |
| Node03221-leaf | ATC:kmeans | ✓ (c) | 2 | 1.00 | 1.00 | 1.00 | 14 | ** |
| Node03222-leaf | not applied | ✓ (b) | 6 | |||||
| Node0323 | ATC:kmeans | 3 | 1.00 | 1.00 | 0.99 | 14 | ** | |
| Node03231-leaf | not applied | ✓ (b) | 2 | |||||
| Node03232-leaf | not applied | ✓ (b) | 8 | |||||
| Node03233-leaf | not applied | ✓ (b) | 2 | |||||
| Node03234-leaf | not applied | ✓ (b) | 2 | |||||
| Node04 | ATC:kmeans | 4 | 1.00 | 0.98 | 0.99 | 131 | ** | |
| Node041 | ATC:skmeans | 3 | 1.00 | 0.95 | 0.98 | 42 | ** | |
| Node0411 | ATC:kmeans | 4 | 1.00 | 0.91 | 1.00 | 12 | ** | |
| Node04111-leaf | not applied | ✓ (b) | 10 | |||||
| Node04112-leaf | not applied | ✓ (b) | 2 | |||||
| Node0412 | ATC:kmeans | 2 | 1.00 | 1.00 | 1.00 | 22 | ** | |
| Node04121-leaf | not applied | ✓ (b) | 5 | |||||
| Node04122-leaf | ATC:skmeans | ✓ (c) | 3 | 1.00 | 1.00 | 1.00 | 17 | ** |
| Node0413-leaf | not applied | ✓ (b) | 8 | |||||
| Node042 | ATC:kmeans | 3 | 1.00 | 0.97 | 0.99 | 30 | ** | |
| Node0421-leaf | ATC:skmeans | ✓ (c) | 8 | 0.92 | 0.47 | 0.97 | 12 | * |
| Node0422-leaf | not applied | ✓ (b) | 7 | |||||
| Node0423-leaf | not applied | ✓ (b) | 11 | |||||
| Node043 | SD:kmeans | 3 | 1.00 | 0.98 | 0.98 | 17 | ** | |
| Node0431-leaf | not applied | ✓ (b) | 4 | |||||
| Node0432-leaf | not applied | ✓ (b) | 9 | |||||
| Node0433-leaf | not applied | ✓ (b) | 4 | |||||
| Node044 | ATC:skmeans | 3 | 0.96 | 0.96 | 0.98 | 42 | ** | |
| Node0441-leaf | ATC:skmeans | ✓ (c) | 3 | 1.00 | 1.00 | 1.00 | 14 | ** |
| Node0442 | ATC:skmeans | 3 | 1.00 | 1.00 | 1.00 | 20 | ** | |
| Node04421-leaf | ATC:skmeans | ✓ (c) | 7 | 0.94 | 0.58 | 0.95 | 12 | * |
| Node04422-leaf | not applied | ✓ (b) | 3 | |||||
| Node04423-leaf | not applied | ✓ (b) | 3 | |||||
| Node04424-leaf | not applied | ✓ (b) | 2 | |||||
| Node0443-leaf | not applied | ✓ (b) | 8 | |||||
| Node05 | SD:kmeans | 2 | 1.00 | 0.98 | 0.99 | 68 | ** | |
| Node051 | ATC:kmeans | 3 | 1.00 | 1.00 | 1.00 | 31 | ** | |
| Node0511 | ATC:skmeans | 2 | 1.00 | 1.00 | 1.00 | 17 | ** | |
| Node05111-leaf | not applied | ✓ (b) | 4 | |||||
| Node05112-leaf | not applied | ✓ (b) | 7 | |||||
| Node05113-leaf | not applied | ✓ (b) | 6 | |||||
| Node0512-leaf | not applied | ✓ (b) | 9 | |||||
| Node0513-leaf | not applied | ✓ (b) | 5 | |||||
| Node052 | ATC:kmeans | 4 | 1.00 | 0.99 | 0.99 | 37 | ** | |
| Node0521-leaf | ATC:skmeans | ✓ (c) | 8 | 0.94 | 0.51 | 0.97 | 12 | * |
| Node0522-leaf | ATC:skmeans | ✓ (c) | 2 | 1.00 | 1.00 | 1.00 | 13 | ** |
| Node0523-leaf | not applied | ✓ (b) | 8 | |||||
| Node0524-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 = 1034))
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 1119))
#> Error in lt[[hierarchy[i, 1]]]$AddChildNode({: attempt to apply non-function
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 1144))
#> Error in lt[[hierarchy[i, 1]]]$AddChildNode({: attempt to apply non-function
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 1564))
#> Error in lt[[hierarchy[i, 1]]]$AddChildNode({: attempt to apply non-function
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 1831))
#> Error in lt[[hierarchy[i, 1]]]$AddChildNode({: attempt to apply non-function
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 1969))
#> Error in lt[[hierarchy[i, 1]]]$AddChildNode({: attempt to apply non-function
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 2117))
#> Error in lt[[hierarchy[i, 1]]]$AddChildNode({: attempt to apply non-function
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 2142))
#> Error in lt[[hierarchy[i, 1]]]$AddChildNode({: attempt to apply non-function
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 2164))
#> Error in lt[[hierarchy[i, 1]]]$AddChildNode({: attempt to apply non-function
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 2255))
#> Error in lt[[hierarchy[i, 1]]]$AddChildNode({: attempt to apply non-function
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 2328))
#> Error in lt[[hierarchy[i, 1]]]$AddChildNode({: attempt to apply non-function
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 2454))
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 2616))
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 2664))
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 2780))
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 3485))
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 4070))
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 4105))
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 6230))
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 8228))
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 10240))
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 11354))
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 12706))
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 17313))
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 22901))
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 23773))
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 29265))
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 41067))
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 52804))
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 57862))
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 = 1034))
#> TCGA.FR.A728.01 TCGA.GN.A4U8.11 TCGA.GN.A8LL.06 TCGA.FR.A8YC.06 TCGA.DA.A95X.06 TCGA.ER.A42K.06
#> "014" "01132" "03113" "0221" "0211" "0321"
#> TCGA.D3.A8GO.06 TCGA.D3.A8GK.06 TCGA.WE.A8JZ.06 TCGA.WE.A8ZO.06 TCGA.D3.A8GI.06 TCGA.FS.A4FC.06
#> "0124" "0524" "02121" "05113" "0512" "0421"
#> TCGA.FS.A4F2.06 TCGA.WE.A8ZM.06 TCGA.WE.A8ZT.06 TCGA.D3.A8GQ.06 TCGA.D3.A8GB.06 TCGA.DA.A95Y.06
#> "03221" "0522" "03112" "04112" "01311" "03111"
#> TCGA.EE.A3JI.06 TCGA.OD.A75X.06 TCGA.DA.A960.01 TCGA.D3.A8GV.06 TCGA.WE.A8ZN.06 TCGA.D3.A8GN.06
#> "0221" "023" "0211" "02121" "0112" "014"
#> TCGA.EB.A550.01 TCGA.BF.A5EQ.01 TCGA.EB.A3HV.01 TCGA.HR.A5NC.01 TCGA.DA.A95Z.06 TCGA.EB.A6QZ.01
#> "0122" "0421" "0521" "0523" "0221" "02122"
#> TCGA.FW.A3I3.06 TCGA.WE.A8K6.06 TCGA.D3.A8GP.06 TCGA.EB.A42Z.01 TCGA.GN.A4U4.06 TCGA.GF.A4EO.06
#> "023" "0321" "0222" "023" "02123" "014"
#> TCGA.GN.A8LK.06 TCGA.WE.A8K4.01 TCGA.DA.A95W.06 TCGA.FW.A5DX.01 TCGA.GN.A4U3.06 TCGA.EB.A6QY.01
#> "0521" "0112" "0221" "02121" "03111" "0133"
#> TCGA.EB.A5VU.01 TCGA.Z2.A8RT.06 TCGA.WE.A8K1.06 TCGA.EB.A41B.01 TCGA.WE.A8ZY.06 TCGA.D9.A6EG.06
#> "0443" "0321" "0112" "0321" "02122" "0222"
#> TCGA.BF.A5ER.01 TCGA.FR.A8YD.06 TCGA.FS.A4F9.06 TCGA.EB.A6R0.01 TCGA.ER.A42L.06 TCGA.D3.A8GJ.06
#> "0512" "05113" "05112" "03221" "01133" "04423"
#> TCGA.FR.A8YE.06 TCGA.WE.A8ZR.06 TCGA.BF.A9VF.01 TCGA.EE.A3JH.06 TCGA.DA.A95V.06 TCGA.GF.A769.01
#> "01132" "0432" "0521" "0112" "04122" "02123"
#> TCGA.D9.A4Z2.01 TCGA.FR.A44A.06 TCGA.EB.A5VV.06 TCGA.EE.A180.06 TCGA.D3.A8GC.06 TCGA.WE.A8K5.06
#> "03221" "014" "0123" "0222" "0513" "023"
#> TCGA.GN.A8LN.01 TCGA.EE.A3JB.06 TCGA.D3.A3MO.06 TCGA.ER.A42H.01 TCGA.WE.A8ZX.06 TCGA.GN.A4U5.01
#> "02122" "04111" "0522" "05112" "04122" "014"
#> TCGA.D3.A8GS.06 TCGA.WE.A8ZQ.06 TCGA.EE.A2MF.06 TCGA.D3.A5GU.06 TCGA.GN.A4U8.06 TCGA.EB.A42Y.01
#> "0441" "0523" "0222" "05113" "0413" "02122"
#> TCGA.D3.A3ML.06 TCGA.EB.A551.01 TCGA.D3.A8GM.06 TCGA.D3.A8GL.06 TCGA.D3.A3MU.06 TCGA.FS.A4F0.06
#> "05113" "04422" "04122" "0221" "0221" "0221"
#> TCGA.D3.A3MV.06 TCGA.GN.A4U7.06 TCGA.FR.A2OS.01 TCGA.D3.A2JE.06 TCGA.YD.A89C.06 TCGA.FR.A726.01
#> "03221" "03113" "0523" "0522" "04111" "04111"
#> TCGA.BF.A5EP.01 TCGA.D3.A3MR.06 TCGA.D3.A8GR.06 TCGA.GN.A4U9.06 TCGA.EB.A6L9.06 TCGA.D3.A5GL.06
#> "0312" "0112" "05111" "0522" "01311" "0312"
#> TCGA.EB.A430.01 TCGA.D3.A8GE.06 TCGA.D3.A8GD.06 TCGA.EB.A41A.01 TCGA.W3.A825.06 TCGA.EE.A183.06
#> "0133" "0132" "014" "0222" "0443" "01112"
#> TCGA.ER.A2NH.06 TCGA.D3.A5GR.06 TCGA.FR.A729.06 TCGA.D3.A1QA.06 TCGA.FS.A1YY.06 TCGA.EE.A2MK.06
#> "0112" "0441" "0441" "0211" "0312" "03112"
#> TCGA.EE.A2M8.06 TCGA.EB.A5KH.06 TCGA.FS.A1ZR.06 TCGA.EE.A3AE.06 TCGA.EE.A29P.06 TCGA.EB.A553.01
#> "0123" "02122" "0521" "03112" "04424" "0513"
#> TCGA.EE.A2MR.06 TCGA.GN.A26A.06 TCGA.FS.A1ZY.06 TCGA.EE.A20I.06 TCGA.DA.A1I5.06 TCGA.EE.A184.06
#> "01112" "04111" "02123" "04121" "0125" "023"
#> TCGA.EB.A85J.01 TCGA.RP.A6K9.06 TCGA.EE.A17Y.06 TCGA.D9.A149.06 TCGA.ER.A19D.06 TCGA.FS.A1ZZ.06
#> "0433" "0423" "04111" "0421" "0122" "023"
#> TCGA.EE.A2GP.06 TCGA.EE.A3AD.06 TCGA.D3.A1Q9.06 TCGA.GF.A2C7.01 TCGA.BF.A5ES.01 TCGA.ER.A199.06
#> "0524" "02122" "04121" "05112" "05111" "014"
#> TCGA.EE.A3AH.06 TCGA.W3.A828.06 TCGA.EE.A2A5.06 TCGA.ER.A19L.06 TCGA.BF.A1PX.01 TCGA.ER.A19T.06
#> "02121" "0133" "0522" "0432" "01112" "0431"
#> TCGA.EB.A51B.01 TCGA.FS.A1ZQ.06 TCGA.D3.A2JG.06 TCGA.EE.A2GH.06 TCGA.ER.A19F.06 TCGA.ER.A196.01
#> "0312" "03233" "0312" "0112" "03221" "0124"
#> TCGA.D3.A2JC.06 TCGA.EE.A3AG.06 TCGA.ER.A19S.06 TCGA.EE.A2GC.06 TCGA.EE.A29N.06 TCGA.FR.A7U8.06
#> "0441" "03221" "014" "0524" "01133" "023"
#> TCGA.BF.A5EO.01 TCGA.ER.A19B.06 TCGA.D3.A5GN.06 TCGA.D3.A2JB.06 TCGA.ER.A19J.06 TCGA.D3.A2JD.06
#> "04122" "03232" "03232" "0123" "023" "0112"
#> TCGA.FS.A1Z4.06 TCGA.FR.A7UA.06 TCGA.EE.A2M7.06 TCGA.D3.A1Q3.06 TCGA.EB.A85I.01 TCGA.EB.A82C.01
#> "01311" "014" "0441" "0431" "0421" "023"
#> TCGA.ER.A19E.06 TCGA.FS.A1ZK.06 TCGA.FS.A1ZU.06 TCGA.EB.A5FP.01 TCGA.EB.A4XL.01 TCGA.DA.A1I2.06
#> "0522" "0524" "0522" "02122" "03112" "0441"
#> TCGA.EE.A29L.06 TCGA.FS.A1ZN.01 TCGA.EB.A24D.01 TCGA.EE.A2GB.06 TCGA.DA.A1I7.06 TCGA.ER.A2NF.01
#> "0211" "02122" "05113" "03221" "0441" "0132"
#> TCGA.GN.A263.01 TCGA.EE.A20C.06 TCGA.EE.A2MQ.06 TCGA.ER.A19N.06 TCGA.FS.A1Z3.06 TCGA.DA.A1I8.06
#> "0132" "023" "0512" "0112" "0321" "03221"
#> TCGA.D3.A5GS.06 TCGA.EE.A181.06 TCGA.GN.A268.06 TCGA.W3.A824.06 TCGA.EE.A2GS.06 TCGA.FR.A7U9.06
#> "03232" "04121" "0221" "05112" "0321" "0121"
#> TCGA.ER.A19Q.06 TCGA.FS.A1ZM.06 TCGA.EE.A2MG.06 TCGA.EE.A2MC.06 TCGA.EE.A17Z.06 TCGA.D3.A2JP.06
#> "0125" "0441" "01311" "01312" "0522" "04122"
#> TCGA.ER.A19C.06 TCGA.EB.A82B.01 TCGA.EE.A2A0.06 TCGA.EE.A29G.06 TCGA.D3.A5GO.06 TCGA.GN.A269.01
#> "0443" "0423" "014" "01131" "03221" "01113"
#> TCGA.EE.A2A1.06 TCGA.ER.A1A1.06 TCGA.FS.A1ZG.06 TCGA.FS.A1ZE.06 TCGA.FS.A1ZH.06 TCGA.EE.A2MH.06
#> "01311" "01311" "0222" "0222" "04111" "01112"
#> TCGA.D3.A2J6.06 TCGA.EE.A29Q.06 TCGA.BF.A1PZ.01 TCGA.D3.A3BZ.06 TCGA.D3.A2JO.06 TCGA.GN.A267.06
#> "0423" "03232" "0321" "01311" "04422" "0432"
#> TCGA.EE.A2MN.06 TCGA.GN.A264.06 TCGA.ER.A197.06 TCGA.DA.A1IB.06 TCGA.D3.A3CC.06 TCGA.ER.A19T.01
#> "0513" "023" "014" "014" "0423" "0523"
#> TCGA.GN.A261.06 TCGA.FS.A1YW.06 TCGA.BF.A1PU.01 TCGA.D3.A1QB.06 TCGA.D3.A1Q6.06 TCGA.D3.A3C8.06
#> "0122" "023" "0443" "0124" "0441" "014"
#> TCGA.ER.A19A.06 TCGA.EE.A2GN.06 TCGA.EE.A29M.06 TCGA.D3.A2J7.06 TCGA.EB.A24C.01 TCGA.GN.A262.06
#> "01311" "0522" "0121" "01133" "0432" "02123"
#> TCGA.EE.A2GD.06 TCGA.D3.A2J9.06 TCGA.EE.A29B.06 TCGA.D9.A1JX.06 TCGA.EE.A29A.06 TCGA.D3.A2JL.06
#> "014" "01132" "05112" "03222" "0221" "04122"
#> TCGA.D3.A1Q4.06 TCGA.FS.A1ZS.06 TCGA.D3.A3C3.06 TCGA.D3.A2J8.06 TCGA.FS.A1ZF.06 TCGA.FS.A1ZC.06
#> "0122" "0423" "0413" "01311" "03232" "02121"
#> TCGA.EE.A20H.06 TCGA.EE.A29W.06 TCGA.D3.A1QA.07 TCGA.BF.A1PV.01 TCGA.EE.A29S.06 TCGA.DA.A1HV.06
#> "0522" "0321" "0413" "0512" "04424" "03222"
#> TCGA.FS.A1Z0.06 TCGA.EE.A2GO.06 TCGA.EB.A1NK.01 TCGA.GN.A26D.06 TCGA.EE.A2MJ.06 TCGA.ER.A198.06
#> "0122" "023" "0133" "0422" "01132" "0512"
#> TCGA.EE.A17X.06 TCGA.EE.A2M5.06 TCGA.GN.A266.06 TCGA.D3.A3C1.06 TCGA.D3.A2JH.06 TCGA.EE.A20F.06
#> "03111" "04122" "0443" "04421" "0112" "04111"
#> TCGA.EE.A29E.06 TCGA.ER.A2NG.06 TCGA.ER.A193.06 TCGA.FS.A1ZW.06 TCGA.ER.A19O.06 TCGA.EE.A2ME.06
#> "0133" "014" "0421" "0413" "04421" "01112"
#> TCGA.EE.A20B.06 TCGA.EE.A3AF.06 TCGA.GN.A265.06 TCGA.FS.A1YX.06 TCGA.FS.A1ZJ.06 TCGA.ER.A19H.06
#> "04111" "0312" "01132" "0441" "0523" "03221"
#> TCGA.EE.A3AC.06 TCGA.EE.A2MU.06 TCGA.ER.A194.01 TCGA.EE.A2MS.06 TCGA.EE.A29R.06 TCGA.D9.A1X3.06
#> "0521" "01133" "04423" "0433" "023" "0221"
#> TCGA.EE.A29X.06 TCGA.EE.A2GK.06 TCGA.EE.A3AA.06 TCGA.ER.A2NE.06 TCGA.EE.A2GR.06 TCGA.FS.A1ZD.06
#> "04421" "0123" "01112" "02122" "0521" "0523"
#> TCGA.ER.A19P.06 TCGA.D3.A1Q8.06 TCGA.ER.A2NC.06 TCGA.BF.A1Q0.01 TCGA.FS.A1ZP.06 TCGA.EE.A182.06
#> "014" "0112" "0443" "0421" "0522" "0432"
#> TCGA.D9.A1JW.06 TCGA.D3.A1Q7.06 TCGA.EE.A185.06 TCGA.EE.A2GJ.06 TCGA.D3.A3CB.06 TCGA.EE.A2GU.06
#> "0421" "014" "02122" "0431" "01111" "0421"
#> TCGA.ER.A195.06 TCGA.FS.A1Z7.06 TCGA.EE.A2M6.06 TCGA.ER.A19K.01 TCGA.DA.A1HY.06 TCGA.D3.A3C7.06
#> "0132" "0423" "02121" "04421" "03221" "0321"
#> TCGA.EE.A2MP.06 TCGA.EE.A29H.06 TCGA.FR.A3YO.06 TCGA.XV.AB01.01 TCGA.RP.A694.06 TCGA.EB.A5SF.01
#> "03232" "0312" "04421" "0312" "04423" "0122"
#> TCGA.ER.A19G.06 TCGA.EE.A2GE.06 TCGA.GF.A3OT.06 TCGA.ER.A2NF.06 TCGA.RP.A695.06 TCGA.BF.AAP7.01
#> "03222" "0112" "014" "0132" "0512" "0121"
#> TCGA.EB.A3Y7.01 TCGA.EB.A3XC.01 TCGA.ER.A19W.06 TCGA.FR.A69P.06 TCGA.RP.A693.06 TCGA.FW.A3TV.06
#> "0423" "03111" "014" "0321" "01111" "0124"
#> TCGA.FW.A3R5.11 TCGA.FW.A3TU.06 TCGA.BF.AAP8.01 TCGA.EE.A2MM.06 TCGA.DA.A1HW.06 TCGA.DA.A1IC.06
#> "0132" "05111" "0422" "0513" "0441" "0521"
#> TCGA.XV.AAZV.01 TCGA.D3.A3C6.06 TCGA.EE.A29C.06 TCGA.BF.AAP2.01 TCGA.EE.A2A2.06 TCGA.GF.A6C8.06
#> "0121" "03232" "0132" "02122" "03222" "0443"
#> TCGA.RP.A690.06 TCGA.FW.A5DY.06 TCGA.DA.A1I4.06 TCGA.EE.A29V.06 TCGA.GF.A6C9.06 TCGA.EE.A2GT.06
#> "0122" "014" "0132" "04122" "01132" "01312"
#> TCGA.GN.A9SD.06 TCGA.EE.A3AB.06 TCGA.BF.AAP6.01 TCGA.EB.A5SH.06 TCGA.D9.A6E9.06 TCGA.BF.AAP4.01
#> "014" "0413" "03221" "0431" "04421" "04421"
#> TCGA.EE.A2GM.06 TCGA.D3.A3CF.06 TCGA.D9.A6EC.06 TCGA.DA.A1I1.06 TCGA.HR.A2OH.06 TCGA.EE.A2MT.06
#> "02123" "0121" "023" "0413" "014" "0422"
#> TCGA.ER.A19M.06 TCGA.GN.A26C.01 TCGA.FS.A1ZA.06 TCGA.EB.A5SE.01 TCGA.ER.A3PL.06 TCGA.FR.A3R1.01
#> "04111" "01112" "04422" "0222" "0521" "0312"
#> TCGA.EE.A2MI.06 TCGA.D3.A3CE.06 TCGA.D3.A5GT.01 TCGA.ER.A2NB.01 TCGA.D3.A1Q5.06 TCGA.EB.A5UN.06
#> "0443" "0441" "05112" "0421" "0422" "01113"
#> TCGA.EB.A299.01 TCGA.DA.A1IA.06 TCGA.EB.A5SG.06 TCGA.D9.A6EA.06 TCGA.XV.AAZY.01 TCGA.EB.A57M.01
#> "03232" "05111" "014" "0222" "014" "04122"
#> TCGA.EE.A2A6.06 TCGA.D3.A2JA.06 TCGA.D3.A1Q1.06 TCGA.EB.A3XF.01 TCGA.D3.A2JF.06 TCGA.XV.AAZW.01
#> "0421" "0132" "0422" "03112" "03234" "03112"
#> TCGA.EB.A3Y6.01 TCGA.EB.A3XE.01 TCGA.D9.A3Z4.01 TCGA.FW.A3R5.06 TCGA.EE.A2GI.06 TCGA.EE.A2GL.06
#> "0441" "0432" "0523" "0432" "04111" "014"
#> TCGA.EB.A3XB.01 TCGA.BF.AAOU.01 TCGA.EB.A3XD.01 TCGA.EE.A2MD.06 TCGA.YD.A9TB.06 TCGA.W3.AA1V.06
#> "04421" "014" "0124" "04421" "0521" "0441"
#> TCGA.ER.A2ND.06 TCGA.D3.A2JK.06 TCGA.FS.A1ZB.06 TCGA.EE.A29D.06 TCGA.EB.A5UM.01 TCGA.QB.A6FS.06
#> "0521" "04122" "0112" "0222" "0432" "0132"
#> TCGA.D9.A3Z1.06 TCGA.D3.A2JN.06 TCGA.FR.A3YN.06 TCGA.FS.A1ZT.06 TCGA.D9.A148.06 TCGA.HR.A2OG.06
#> "01133" "014" "03233" "0132" "04121" "0125"
#> TCGA.EE.A2ML.06 TCGA.EB.A5UL.06 TCGA.EE.A29T.06 TCGA.D9.A3Z3.06 TCGA.D9.A4Z3.01 TCGA.ER.A3ES.06
#> "0413" "04122" "0432" "0124" "0522" "0422"
#> TCGA.XV.A9VZ.01 TCGA.QB.AA9O.06 TCGA.EB.A44Q.06 TCGA.EB.A44R.06 TCGA.BF.A3DJ.01 TCGA.EE.A3JD.06
#> "0122" "03111" "04421" "0433" "03112" "01311"
#> TCGA.D3.A51N.06 TCGA.EB.A44N.01 TCGA.EE.A3J3.06 TCGA.XV.A9W5.01 TCGA.D3.A51G.06 TCGA.EB.A4P0.01
#> "0413" "01133" "0321" "04122" "03234" "03112"
#> TCGA.BF.AAP1.01 TCGA.EE.A3J4.06 TCGA.Z2.AA3V.06 TCGA.LH.A9QB.06 TCGA.D3.A51J.06 TCGA.3N.A9WC.06
#> "023" "05112" "0121" "023" "04421" "0421"
#> TCGA.DA.A3F8.06 TCGA.D9.A4Z6.06 TCGA.D3.A51R.06 TCGA.EB.A4OZ.01 TCGA.FS.A4FB.06 TCGA.EE.A3JE.06
#> "01132" "04122" "03221" "0121" "03112" "01132"
#> TCGA.W3.AA1W.06 TCGA.DA.A1I0.06 TCGA.D3.A51F.06 TCGA.IH.A3EA.01 TCGA.EB.A431.01 TCGA.EB.A97M.01
#> "01111" "04122" "01311" "0512" "04122" "0222"
#> TCGA.BF.AAOX.01 TCGA.DA.A3F5.06 TCGA.YD.A9TA.06 TCGA.DA.A3F2.06 TCGA.EB.A44O.01 TCGA.EB.A4IQ.01
#> "04121" "0423" "04112" "01311" "0521" "0421"
#> TCGA.EB.A4IS.01 TCGA.YG.AA3O.06 TCGA.ER.A3EV.06 TCGA.3N.A9WD.06 TCGA.BF.A3DM.01 TCGA.XV.A9W2.01
#> "0112" "0512" "0433" "01131" "0321" "0423"
#> TCGA.W3.AA1Q.06 TCGA.WE.AAA0.06 TCGA.W3.AA1R.06 TCGA.EE.A3J5.06 TCGA.EB.A4OY.01 TCGA.FS.A4FD.06
#> "0512" "04122" "03222" "04122" "0122" "0422"
#> TCGA.BF.AAP0.06 TCGA.YG.AA3P.06 TCGA.EE.A3JA.06 TCGA.W3.AA21.06 TCGA.WE.AAA3.06 TCGA.FS.A4F4.06
#> "0123" "0523" "03231" "0211" "0423" "03111"
#> TCGA.BF.A3DN.01 TCGA.ER.A3ET.06 TCGA.W3.AA1O.06 TCGA.D3.A51E.06 TCGA.Z2.AA3S.06 TCGA.YG.AA3N.01
#> "0321" "0423" "0513" "03221" "0222" "04421"
#> TCGA.WE.AA9Y.06 TCGA.FS.A4F5.06 TCGA.EE.A3J7.06 TCGA.FS.A4F8.06 TCGA.DA.A3F3.06 TCGA.D3.A51H.06
#> "01113" "023" "05113" "01112" "03231" "01311"
#> TCGA.BF.A3DL.01 TCGA.D3.A51T.06 TCGA.D3.A51K.06 TCGA.EB.A44P.01 TCGA.D9.A4Z5.01 TCGA.WE.AAA4.06
#> "0124" "03222" "0522" "0521" "023" "014"
#> TCGA.3N.A9WB.06 TCGA.EE.A3J8.06
#> "0222" "0211"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 1119))
#> TCGA.FR.A728.01 TCGA.GN.A4U8.11 TCGA.GN.A8LL.06 TCGA.FR.A8YC.06 TCGA.DA.A95X.06 TCGA.ER.A42K.06
#> "014" "01132" "03113" "0221" "0211" "03"
#> TCGA.D3.A8GO.06 TCGA.D3.A8GK.06 TCGA.WE.A8JZ.06 TCGA.WE.A8ZO.06 TCGA.D3.A8GI.06 TCGA.FS.A4FC.06
#> "0124" "0524" "02121" "05113" "0512" "0421"
#> TCGA.FS.A4F2.06 TCGA.WE.A8ZM.06 TCGA.WE.A8ZT.06 TCGA.D3.A8GQ.06 TCGA.D3.A8GB.06 TCGA.DA.A95Y.06
#> "03221" "0522" "03112" "04112" "01311" "03111"
#> TCGA.EE.A3JI.06 TCGA.OD.A75X.06 TCGA.DA.A960.01 TCGA.D3.A8GV.06 TCGA.WE.A8ZN.06 TCGA.D3.A8GN.06
#> "0221" "023" "0211" "02121" "0112" "014"
#> TCGA.EB.A550.01 TCGA.BF.A5EQ.01 TCGA.EB.A3HV.01 TCGA.HR.A5NC.01 TCGA.DA.A95Z.06 TCGA.EB.A6QZ.01
#> "0122" "0421" "0521" "0523" "0221" "02122"
#> TCGA.FW.A3I3.06 TCGA.WE.A8K6.06 TCGA.D3.A8GP.06 TCGA.EB.A42Z.01 TCGA.GN.A4U4.06 TCGA.GF.A4EO.06
#> "023" "03" "0222" "023" "02123" "014"
#> TCGA.GN.A8LK.06 TCGA.WE.A8K4.01 TCGA.DA.A95W.06 TCGA.FW.A5DX.01 TCGA.GN.A4U3.06 TCGA.EB.A6QY.01
#> "0521" "0112" "0221" "02121" "03111" "0133"
#> TCGA.EB.A5VU.01 TCGA.Z2.A8RT.06 TCGA.WE.A8K1.06 TCGA.EB.A41B.01 TCGA.WE.A8ZY.06 TCGA.D9.A6EG.06
#> "0443" "03" "0112" "03" "02122" "0222"
#> TCGA.BF.A5ER.01 TCGA.FR.A8YD.06 TCGA.FS.A4F9.06 TCGA.EB.A6R0.01 TCGA.ER.A42L.06 TCGA.D3.A8GJ.06
#> "0512" "05113" "05112" "03221" "01133" "04423"
#> TCGA.FR.A8YE.06 TCGA.WE.A8ZR.06 TCGA.BF.A9VF.01 TCGA.EE.A3JH.06 TCGA.DA.A95V.06 TCGA.GF.A769.01
#> "01132" "0432" "0521" "0112" "04122" "02123"
#> TCGA.D9.A4Z2.01 TCGA.FR.A44A.06 TCGA.EB.A5VV.06 TCGA.EE.A180.06 TCGA.D3.A8GC.06 TCGA.WE.A8K5.06
#> "03221" "014" "0123" "0222" "0513" "023"
#> TCGA.GN.A8LN.01 TCGA.EE.A3JB.06 TCGA.D3.A3MO.06 TCGA.ER.A42H.01 TCGA.WE.A8ZX.06 TCGA.GN.A4U5.01
#> "02122" "04111" "0522" "05112" "04122" "014"
#> TCGA.D3.A8GS.06 TCGA.WE.A8ZQ.06 TCGA.EE.A2MF.06 TCGA.D3.A5GU.06 TCGA.GN.A4U8.06 TCGA.EB.A42Y.01
#> "0441" "0523" "0222" "05113" "0413" "02122"
#> TCGA.D3.A3ML.06 TCGA.EB.A551.01 TCGA.D3.A8GM.06 TCGA.D3.A8GL.06 TCGA.D3.A3MU.06 TCGA.FS.A4F0.06
#> "05113" "04422" "04122" "0221" "0221" "0221"
#> TCGA.D3.A3MV.06 TCGA.GN.A4U7.06 TCGA.FR.A2OS.01 TCGA.D3.A2JE.06 TCGA.YD.A89C.06 TCGA.FR.A726.01
#> "03221" "03113" "0523" "0522" "04111" "04111"
#> TCGA.BF.A5EP.01 TCGA.D3.A3MR.06 TCGA.D3.A8GR.06 TCGA.GN.A4U9.06 TCGA.EB.A6L9.06 TCGA.D3.A5GL.06
#> "03" "0112" "05111" "0522" "01311" "03"
#> TCGA.EB.A430.01 TCGA.D3.A8GE.06 TCGA.D3.A8GD.06 TCGA.EB.A41A.01 TCGA.W3.A825.06 TCGA.EE.A183.06
#> "0133" "0132" "014" "0222" "0443" "01112"
#> TCGA.ER.A2NH.06 TCGA.D3.A5GR.06 TCGA.FR.A729.06 TCGA.D3.A1QA.06 TCGA.FS.A1YY.06 TCGA.EE.A2MK.06
#> "0112" "0441" "0441" "0211" "03" "03112"
#> TCGA.EE.A2M8.06 TCGA.EB.A5KH.06 TCGA.FS.A1ZR.06 TCGA.EE.A3AE.06 TCGA.EE.A29P.06 TCGA.EB.A553.01
#> "0123" "02122" "0521" "03112" "04424" "0513"
#> TCGA.EE.A2MR.06 TCGA.GN.A26A.06 TCGA.FS.A1ZY.06 TCGA.EE.A20I.06 TCGA.DA.A1I5.06 TCGA.EE.A184.06
#> "01112" "04111" "02123" "04121" "0125" "023"
#> TCGA.EB.A85J.01 TCGA.RP.A6K9.06 TCGA.EE.A17Y.06 TCGA.D9.A149.06 TCGA.ER.A19D.06 TCGA.FS.A1ZZ.06
#> "0433" "0423" "04111" "0421" "0122" "023"
#> TCGA.EE.A2GP.06 TCGA.EE.A3AD.06 TCGA.D3.A1Q9.06 TCGA.GF.A2C7.01 TCGA.BF.A5ES.01 TCGA.ER.A199.06
#> "0524" "02122" "04121" "05112" "05111" "014"
#> TCGA.EE.A3AH.06 TCGA.W3.A828.06 TCGA.EE.A2A5.06 TCGA.ER.A19L.06 TCGA.BF.A1PX.01 TCGA.ER.A19T.06
#> "02121" "0133" "0522" "0432" "01112" "0431"
#> TCGA.EB.A51B.01 TCGA.FS.A1ZQ.06 TCGA.D3.A2JG.06 TCGA.EE.A2GH.06 TCGA.ER.A19F.06 TCGA.ER.A196.01
#> "03" "03233" "03" "0112" "03221" "0124"
#> TCGA.D3.A2JC.06 TCGA.EE.A3AG.06 TCGA.ER.A19S.06 TCGA.EE.A2GC.06 TCGA.EE.A29N.06 TCGA.FR.A7U8.06
#> "0441" "03221" "014" "0524" "01133" "023"
#> TCGA.BF.A5EO.01 TCGA.ER.A19B.06 TCGA.D3.A5GN.06 TCGA.D3.A2JB.06 TCGA.ER.A19J.06 TCGA.D3.A2JD.06
#> "04122" "03232" "03232" "0123" "023" "0112"
#> TCGA.FS.A1Z4.06 TCGA.FR.A7UA.06 TCGA.EE.A2M7.06 TCGA.D3.A1Q3.06 TCGA.EB.A85I.01 TCGA.EB.A82C.01
#> "01311" "014" "0441" "0431" "0421" "023"
#> TCGA.ER.A19E.06 TCGA.FS.A1ZK.06 TCGA.FS.A1ZU.06 TCGA.EB.A5FP.01 TCGA.EB.A4XL.01 TCGA.DA.A1I2.06
#> "0522" "0524" "0522" "02122" "03112" "0441"
#> TCGA.EE.A29L.06 TCGA.FS.A1ZN.01 TCGA.EB.A24D.01 TCGA.EE.A2GB.06 TCGA.DA.A1I7.06 TCGA.ER.A2NF.01
#> "0211" "02122" "05113" "03221" "0441" "0132"
#> TCGA.GN.A263.01 TCGA.EE.A20C.06 TCGA.EE.A2MQ.06 TCGA.ER.A19N.06 TCGA.FS.A1Z3.06 TCGA.DA.A1I8.06
#> "0132" "023" "0512" "0112" "03" "03221"
#> TCGA.D3.A5GS.06 TCGA.EE.A181.06 TCGA.GN.A268.06 TCGA.W3.A824.06 TCGA.EE.A2GS.06 TCGA.FR.A7U9.06
#> "03232" "04121" "0221" "05112" "03" "0121"
#> TCGA.ER.A19Q.06 TCGA.FS.A1ZM.06 TCGA.EE.A2MG.06 TCGA.EE.A2MC.06 TCGA.EE.A17Z.06 TCGA.D3.A2JP.06
#> "0125" "0441" "01311" "01312" "0522" "04122"
#> TCGA.ER.A19C.06 TCGA.EB.A82B.01 TCGA.EE.A2A0.06 TCGA.EE.A29G.06 TCGA.D3.A5GO.06 TCGA.GN.A269.01
#> "0443" "0423" "014" "01131" "03221" "01113"
#> TCGA.EE.A2A1.06 TCGA.ER.A1A1.06 TCGA.FS.A1ZG.06 TCGA.FS.A1ZE.06 TCGA.FS.A1ZH.06 TCGA.EE.A2MH.06
#> "01311" "01311" "0222" "0222" "04111" "01112"
#> TCGA.D3.A2J6.06 TCGA.EE.A29Q.06 TCGA.BF.A1PZ.01 TCGA.D3.A3BZ.06 TCGA.D3.A2JO.06 TCGA.GN.A267.06
#> "0423" "03232" "03" "01311" "04422" "0432"
#> TCGA.EE.A2MN.06 TCGA.GN.A264.06 TCGA.ER.A197.06 TCGA.DA.A1IB.06 TCGA.D3.A3CC.06 TCGA.ER.A19T.01
#> "0513" "023" "014" "014" "0423" "0523"
#> TCGA.GN.A261.06 TCGA.FS.A1YW.06 TCGA.BF.A1PU.01 TCGA.D3.A1QB.06 TCGA.D3.A1Q6.06 TCGA.D3.A3C8.06
#> "0122" "023" "0443" "0124" "0441" "014"
#> TCGA.ER.A19A.06 TCGA.EE.A2GN.06 TCGA.EE.A29M.06 TCGA.D3.A2J7.06 TCGA.EB.A24C.01 TCGA.GN.A262.06
#> "01311" "0522" "0121" "01133" "0432" "02123"
#> TCGA.EE.A2GD.06 TCGA.D3.A2J9.06 TCGA.EE.A29B.06 TCGA.D9.A1JX.06 TCGA.EE.A29A.06 TCGA.D3.A2JL.06
#> "014" "01132" "05112" "03222" "0221" "04122"
#> TCGA.D3.A1Q4.06 TCGA.FS.A1ZS.06 TCGA.D3.A3C3.06 TCGA.D3.A2J8.06 TCGA.FS.A1ZF.06 TCGA.FS.A1ZC.06
#> "0122" "0423" "0413" "01311" "03232" "02121"
#> TCGA.EE.A20H.06 TCGA.EE.A29W.06 TCGA.D3.A1QA.07 TCGA.BF.A1PV.01 TCGA.EE.A29S.06 TCGA.DA.A1HV.06
#> "0522" "03" "0413" "0512" "04424" "03222"
#> TCGA.FS.A1Z0.06 TCGA.EE.A2GO.06 TCGA.EB.A1NK.01 TCGA.GN.A26D.06 TCGA.EE.A2MJ.06 TCGA.ER.A198.06
#> "0122" "023" "0133" "0422" "01132" "0512"
#> TCGA.EE.A17X.06 TCGA.EE.A2M5.06 TCGA.GN.A266.06 TCGA.D3.A3C1.06 TCGA.D3.A2JH.06 TCGA.EE.A20F.06
#> "03111" "04122" "0443" "04421" "0112" "04111"
#> TCGA.EE.A29E.06 TCGA.ER.A2NG.06 TCGA.ER.A193.06 TCGA.FS.A1ZW.06 TCGA.ER.A19O.06 TCGA.EE.A2ME.06
#> "0133" "014" "0421" "0413" "04421" "01112"
#> TCGA.EE.A20B.06 TCGA.EE.A3AF.06 TCGA.GN.A265.06 TCGA.FS.A1YX.06 TCGA.FS.A1ZJ.06 TCGA.ER.A19H.06
#> "04111" "03" "01132" "0441" "0523" "03221"
#> TCGA.EE.A3AC.06 TCGA.EE.A2MU.06 TCGA.ER.A194.01 TCGA.EE.A2MS.06 TCGA.EE.A29R.06 TCGA.D9.A1X3.06
#> "0521" "01133" "04423" "0433" "023" "0221"
#> TCGA.EE.A29X.06 TCGA.EE.A2GK.06 TCGA.EE.A3AA.06 TCGA.ER.A2NE.06 TCGA.EE.A2GR.06 TCGA.FS.A1ZD.06
#> "04421" "0123" "01112" "02122" "0521" "0523"
#> TCGA.ER.A19P.06 TCGA.D3.A1Q8.06 TCGA.ER.A2NC.06 TCGA.BF.A1Q0.01 TCGA.FS.A1ZP.06 TCGA.EE.A182.06
#> "014" "0112" "0443" "0421" "0522" "0432"
#> TCGA.D9.A1JW.06 TCGA.D3.A1Q7.06 TCGA.EE.A185.06 TCGA.EE.A2GJ.06 TCGA.D3.A3CB.06 TCGA.EE.A2GU.06
#> "0421" "014" "02122" "0431" "01111" "0421"
#> TCGA.ER.A195.06 TCGA.FS.A1Z7.06 TCGA.EE.A2M6.06 TCGA.ER.A19K.01 TCGA.DA.A1HY.06 TCGA.D3.A3C7.06
#> "0132" "0423" "02121" "04421" "03221" "03"
#> TCGA.EE.A2MP.06 TCGA.EE.A29H.06 TCGA.FR.A3YO.06 TCGA.XV.AB01.01 TCGA.RP.A694.06 TCGA.EB.A5SF.01
#> "03232" "03" "04421" "03" "04423" "0122"
#> TCGA.ER.A19G.06 TCGA.EE.A2GE.06 TCGA.GF.A3OT.06 TCGA.ER.A2NF.06 TCGA.RP.A695.06 TCGA.BF.AAP7.01
#> "03222" "0112" "014" "0132" "0512" "0121"
#> TCGA.EB.A3Y7.01 TCGA.EB.A3XC.01 TCGA.ER.A19W.06 TCGA.FR.A69P.06 TCGA.RP.A693.06 TCGA.FW.A3TV.06
#> "0423" "03111" "014" "03" "01111" "0124"
#> TCGA.FW.A3R5.11 TCGA.FW.A3TU.06 TCGA.BF.AAP8.01 TCGA.EE.A2MM.06 TCGA.DA.A1HW.06 TCGA.DA.A1IC.06
#> "0132" "05111" "0422" "0513" "0441" "0521"
#> TCGA.XV.AAZV.01 TCGA.D3.A3C6.06 TCGA.EE.A29C.06 TCGA.BF.AAP2.01 TCGA.EE.A2A2.06 TCGA.GF.A6C8.06
#> "0121" "03232" "0132" "02122" "03222" "0443"
#> TCGA.RP.A690.06 TCGA.FW.A5DY.06 TCGA.DA.A1I4.06 TCGA.EE.A29V.06 TCGA.GF.A6C9.06 TCGA.EE.A2GT.06
#> "0122" "014" "0132" "04122" "01132" "01312"
#> TCGA.GN.A9SD.06 TCGA.EE.A3AB.06 TCGA.BF.AAP6.01 TCGA.EB.A5SH.06 TCGA.D9.A6E9.06 TCGA.BF.AAP4.01
#> "014" "0413" "03221" "0431" "04421" "04421"
#> TCGA.EE.A2GM.06 TCGA.D3.A3CF.06 TCGA.D9.A6EC.06 TCGA.DA.A1I1.06 TCGA.HR.A2OH.06 TCGA.EE.A2MT.06
#> "02123" "0121" "023" "0413" "014" "0422"
#> TCGA.ER.A19M.06 TCGA.GN.A26C.01 TCGA.FS.A1ZA.06 TCGA.EB.A5SE.01 TCGA.ER.A3PL.06 TCGA.FR.A3R1.01
#> "04111" "01112" "04422" "0222" "0521" "03"
#> TCGA.EE.A2MI.06 TCGA.D3.A3CE.06 TCGA.D3.A5GT.01 TCGA.ER.A2NB.01 TCGA.D3.A1Q5.06 TCGA.EB.A5UN.06
#> "0443" "0441" "05112" "0421" "0422" "01113"
#> TCGA.EB.A299.01 TCGA.DA.A1IA.06 TCGA.EB.A5SG.06 TCGA.D9.A6EA.06 TCGA.XV.AAZY.01 TCGA.EB.A57M.01
#> "03232" "05111" "014" "0222" "014" "04122"
#> TCGA.EE.A2A6.06 TCGA.D3.A2JA.06 TCGA.D3.A1Q1.06 TCGA.EB.A3XF.01 TCGA.D3.A2JF.06 TCGA.XV.AAZW.01
#> "0421" "0132" "0422" "03112" "03234" "03112"
#> TCGA.EB.A3Y6.01 TCGA.EB.A3XE.01 TCGA.D9.A3Z4.01 TCGA.FW.A3R5.06 TCGA.EE.A2GI.06 TCGA.EE.A2GL.06
#> "0441" "0432" "0523" "0432" "04111" "014"
#> TCGA.EB.A3XB.01 TCGA.BF.AAOU.01 TCGA.EB.A3XD.01 TCGA.EE.A2MD.06 TCGA.YD.A9TB.06 TCGA.W3.AA1V.06
#> "04421" "014" "0124" "04421" "0521" "0441"
#> TCGA.ER.A2ND.06 TCGA.D3.A2JK.06 TCGA.FS.A1ZB.06 TCGA.EE.A29D.06 TCGA.EB.A5UM.01 TCGA.QB.A6FS.06
#> "0521" "04122" "0112" "0222" "0432" "0132"
#> TCGA.D9.A3Z1.06 TCGA.D3.A2JN.06 TCGA.FR.A3YN.06 TCGA.FS.A1ZT.06 TCGA.D9.A148.06 TCGA.HR.A2OG.06
#> "01133" "014" "03233" "0132" "04121" "0125"
#> TCGA.EE.A2ML.06 TCGA.EB.A5UL.06 TCGA.EE.A29T.06 TCGA.D9.A3Z3.06 TCGA.D9.A4Z3.01 TCGA.ER.A3ES.06
#> "0413" "04122" "0432" "0124" "0522" "0422"
#> TCGA.XV.A9VZ.01 TCGA.QB.AA9O.06 TCGA.EB.A44Q.06 TCGA.EB.A44R.06 TCGA.BF.A3DJ.01 TCGA.EE.A3JD.06
#> "0122" "03111" "04421" "0433" "03112" "01311"
#> TCGA.D3.A51N.06 TCGA.EB.A44N.01 TCGA.EE.A3J3.06 TCGA.XV.A9W5.01 TCGA.D3.A51G.06 TCGA.EB.A4P0.01
#> "0413" "01133" "03" "04122" "03234" "03112"
#> TCGA.BF.AAP1.01 TCGA.EE.A3J4.06 TCGA.Z2.AA3V.06 TCGA.LH.A9QB.06 TCGA.D3.A51J.06 TCGA.3N.A9WC.06
#> "023" "05112" "0121" "023" "04421" "0421"
#> TCGA.DA.A3F8.06 TCGA.D9.A4Z6.06 TCGA.D3.A51R.06 TCGA.EB.A4OZ.01 TCGA.FS.A4FB.06 TCGA.EE.A3JE.06
#> "01132" "04122" "03221" "0121" "03112" "01132"
#> TCGA.W3.AA1W.06 TCGA.DA.A1I0.06 TCGA.D3.A51F.06 TCGA.IH.A3EA.01 TCGA.EB.A431.01 TCGA.EB.A97M.01
#> "01111" "04122" "01311" "0512" "04122" "0222"
#> TCGA.BF.AAOX.01 TCGA.DA.A3F5.06 TCGA.YD.A9TA.06 TCGA.DA.A3F2.06 TCGA.EB.A44O.01 TCGA.EB.A4IQ.01
#> "04121" "0423" "04112" "01311" "0521" "0421"
#> TCGA.EB.A4IS.01 TCGA.YG.AA3O.06 TCGA.ER.A3EV.06 TCGA.3N.A9WD.06 TCGA.BF.A3DM.01 TCGA.XV.A9W2.01
#> "0112" "0512" "0433" "01131" "03" "0423"
#> TCGA.W3.AA1Q.06 TCGA.WE.AAA0.06 TCGA.W3.AA1R.06 TCGA.EE.A3J5.06 TCGA.EB.A4OY.01 TCGA.FS.A4FD.06
#> "0512" "04122" "03222" "04122" "0122" "0422"
#> TCGA.BF.AAP0.06 TCGA.YG.AA3P.06 TCGA.EE.A3JA.06 TCGA.W3.AA21.06 TCGA.WE.AAA3.06 TCGA.FS.A4F4.06
#> "0123" "0523" "03231" "0211" "0423" "03111"
#> TCGA.BF.A3DN.01 TCGA.ER.A3ET.06 TCGA.W3.AA1O.06 TCGA.D3.A51E.06 TCGA.Z2.AA3S.06 TCGA.YG.AA3N.01
#> "03" "0423" "0513" "03221" "0222" "04421"
#> TCGA.WE.AA9Y.06 TCGA.FS.A4F5.06 TCGA.EE.A3J7.06 TCGA.FS.A4F8.06 TCGA.DA.A3F3.06 TCGA.D3.A51H.06
#> "01113" "023" "05113" "01112" "03231" "01311"
#> TCGA.BF.A3DL.01 TCGA.D3.A51T.06 TCGA.D3.A51K.06 TCGA.EB.A44P.01 TCGA.D9.A4Z5.01 TCGA.WE.AAA4.06
#> "0124" "03222" "0522" "0521" "023" "014"
#> TCGA.3N.A9WB.06 TCGA.EE.A3J8.06
#> "0222" "0211"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 1144))
#> TCGA.FR.A728.01 TCGA.GN.A4U8.11 TCGA.GN.A8LL.06 TCGA.FR.A8YC.06 TCGA.DA.A95X.06 TCGA.ER.A42K.06
#> "014" "01132" "03113" "0221" "0211" "03"
#> TCGA.D3.A8GO.06 TCGA.D3.A8GK.06 TCGA.WE.A8JZ.06 TCGA.WE.A8ZO.06 TCGA.D3.A8GI.06 TCGA.FS.A4FC.06
#> "0124" "0524" "02121" "05113" "0512" "0421"
#> TCGA.FS.A4F2.06 TCGA.WE.A8ZM.06 TCGA.WE.A8ZT.06 TCGA.D3.A8GQ.06 TCGA.D3.A8GB.06 TCGA.DA.A95Y.06
#> "03" "0522" "03112" "04112" "01311" "03111"
#> TCGA.EE.A3JI.06 TCGA.OD.A75X.06 TCGA.DA.A960.01 TCGA.D3.A8GV.06 TCGA.WE.A8ZN.06 TCGA.D3.A8GN.06
#> "0221" "023" "0211" "02121" "0112" "014"
#> TCGA.EB.A550.01 TCGA.BF.A5EQ.01 TCGA.EB.A3HV.01 TCGA.HR.A5NC.01 TCGA.DA.A95Z.06 TCGA.EB.A6QZ.01
#> "0122" "0421" "0521" "0523" "0221" "02122"
#> TCGA.FW.A3I3.06 TCGA.WE.A8K6.06 TCGA.D3.A8GP.06 TCGA.EB.A42Z.01 TCGA.GN.A4U4.06 TCGA.GF.A4EO.06
#> "023" "03" "0222" "023" "02123" "014"
#> TCGA.GN.A8LK.06 TCGA.WE.A8K4.01 TCGA.DA.A95W.06 TCGA.FW.A5DX.01 TCGA.GN.A4U3.06 TCGA.EB.A6QY.01
#> "0521" "0112" "0221" "02121" "03111" "0133"
#> TCGA.EB.A5VU.01 TCGA.Z2.A8RT.06 TCGA.WE.A8K1.06 TCGA.EB.A41B.01 TCGA.WE.A8ZY.06 TCGA.D9.A6EG.06
#> "0443" "03" "0112" "03" "02122" "0222"
#> TCGA.BF.A5ER.01 TCGA.FR.A8YD.06 TCGA.FS.A4F9.06 TCGA.EB.A6R0.01 TCGA.ER.A42L.06 TCGA.D3.A8GJ.06
#> "0512" "05113" "05112" "03" "01133" "04423"
#> TCGA.FR.A8YE.06 TCGA.WE.A8ZR.06 TCGA.BF.A9VF.01 TCGA.EE.A3JH.06 TCGA.DA.A95V.06 TCGA.GF.A769.01
#> "01132" "0432" "0521" "0112" "04122" "02123"
#> TCGA.D9.A4Z2.01 TCGA.FR.A44A.06 TCGA.EB.A5VV.06 TCGA.EE.A180.06 TCGA.D3.A8GC.06 TCGA.WE.A8K5.06
#> "03" "014" "0123" "0222" "0513" "023"
#> TCGA.GN.A8LN.01 TCGA.EE.A3JB.06 TCGA.D3.A3MO.06 TCGA.ER.A42H.01 TCGA.WE.A8ZX.06 TCGA.GN.A4U5.01
#> "02122" "04111" "0522" "05112" "04122" "014"
#> TCGA.D3.A8GS.06 TCGA.WE.A8ZQ.06 TCGA.EE.A2MF.06 TCGA.D3.A5GU.06 TCGA.GN.A4U8.06 TCGA.EB.A42Y.01
#> "0441" "0523" "0222" "05113" "0413" "02122"
#> TCGA.D3.A3ML.06 TCGA.EB.A551.01 TCGA.D3.A8GM.06 TCGA.D3.A8GL.06 TCGA.D3.A3MU.06 TCGA.FS.A4F0.06
#> "05113" "04422" "04122" "0221" "0221" "0221"
#> TCGA.D3.A3MV.06 TCGA.GN.A4U7.06 TCGA.FR.A2OS.01 TCGA.D3.A2JE.06 TCGA.YD.A89C.06 TCGA.FR.A726.01
#> "03" "03113" "0523" "0522" "04111" "04111"
#> TCGA.BF.A5EP.01 TCGA.D3.A3MR.06 TCGA.D3.A8GR.06 TCGA.GN.A4U9.06 TCGA.EB.A6L9.06 TCGA.D3.A5GL.06
#> "03" "0112" "05111" "0522" "01311" "03"
#> TCGA.EB.A430.01 TCGA.D3.A8GE.06 TCGA.D3.A8GD.06 TCGA.EB.A41A.01 TCGA.W3.A825.06 TCGA.EE.A183.06
#> "0133" "0132" "014" "0222" "0443" "01112"
#> TCGA.ER.A2NH.06 TCGA.D3.A5GR.06 TCGA.FR.A729.06 TCGA.D3.A1QA.06 TCGA.FS.A1YY.06 TCGA.EE.A2MK.06
#> "0112" "0441" "0441" "0211" "03" "03112"
#> TCGA.EE.A2M8.06 TCGA.EB.A5KH.06 TCGA.FS.A1ZR.06 TCGA.EE.A3AE.06 TCGA.EE.A29P.06 TCGA.EB.A553.01
#> "0123" "02122" "0521" "03112" "04424" "0513"
#> TCGA.EE.A2MR.06 TCGA.GN.A26A.06 TCGA.FS.A1ZY.06 TCGA.EE.A20I.06 TCGA.DA.A1I5.06 TCGA.EE.A184.06
#> "01112" "04111" "02123" "04121" "0125" "023"
#> TCGA.EB.A85J.01 TCGA.RP.A6K9.06 TCGA.EE.A17Y.06 TCGA.D9.A149.06 TCGA.ER.A19D.06 TCGA.FS.A1ZZ.06
#> "0433" "0423" "04111" "0421" "0122" "023"
#> TCGA.EE.A2GP.06 TCGA.EE.A3AD.06 TCGA.D3.A1Q9.06 TCGA.GF.A2C7.01 TCGA.BF.A5ES.01 TCGA.ER.A199.06
#> "0524" "02122" "04121" "05112" "05111" "014"
#> TCGA.EE.A3AH.06 TCGA.W3.A828.06 TCGA.EE.A2A5.06 TCGA.ER.A19L.06 TCGA.BF.A1PX.01 TCGA.ER.A19T.06
#> "02121" "0133" "0522" "0432" "01112" "0431"
#> TCGA.EB.A51B.01 TCGA.FS.A1ZQ.06 TCGA.D3.A2JG.06 TCGA.EE.A2GH.06 TCGA.ER.A19F.06 TCGA.ER.A196.01
#> "03" "03233" "03" "0112" "03" "0124"
#> TCGA.D3.A2JC.06 TCGA.EE.A3AG.06 TCGA.ER.A19S.06 TCGA.EE.A2GC.06 TCGA.EE.A29N.06 TCGA.FR.A7U8.06
#> "0441" "03" "014" "0524" "01133" "023"
#> TCGA.BF.A5EO.01 TCGA.ER.A19B.06 TCGA.D3.A5GN.06 TCGA.D3.A2JB.06 TCGA.ER.A19J.06 TCGA.D3.A2JD.06
#> "04122" "03232" "03232" "0123" "023" "0112"
#> TCGA.FS.A1Z4.06 TCGA.FR.A7UA.06 TCGA.EE.A2M7.06 TCGA.D3.A1Q3.06 TCGA.EB.A85I.01 TCGA.EB.A82C.01
#> "01311" "014" "0441" "0431" "0421" "023"
#> TCGA.ER.A19E.06 TCGA.FS.A1ZK.06 TCGA.FS.A1ZU.06 TCGA.EB.A5FP.01 TCGA.EB.A4XL.01 TCGA.DA.A1I2.06
#> "0522" "0524" "0522" "02122" "03112" "0441"
#> TCGA.EE.A29L.06 TCGA.FS.A1ZN.01 TCGA.EB.A24D.01 TCGA.EE.A2GB.06 TCGA.DA.A1I7.06 TCGA.ER.A2NF.01
#> "0211" "02122" "05113" "03" "0441" "0132"
#> TCGA.GN.A263.01 TCGA.EE.A20C.06 TCGA.EE.A2MQ.06 TCGA.ER.A19N.06 TCGA.FS.A1Z3.06 TCGA.DA.A1I8.06
#> "0132" "023" "0512" "0112" "03" "03"
#> TCGA.D3.A5GS.06 TCGA.EE.A181.06 TCGA.GN.A268.06 TCGA.W3.A824.06 TCGA.EE.A2GS.06 TCGA.FR.A7U9.06
#> "03232" "04121" "0221" "05112" "03" "0121"
#> TCGA.ER.A19Q.06 TCGA.FS.A1ZM.06 TCGA.EE.A2MG.06 TCGA.EE.A2MC.06 TCGA.EE.A17Z.06 TCGA.D3.A2JP.06
#> "0125" "0441" "01311" "01312" "0522" "04122"
#> TCGA.ER.A19C.06 TCGA.EB.A82B.01 TCGA.EE.A2A0.06 TCGA.EE.A29G.06 TCGA.D3.A5GO.06 TCGA.GN.A269.01
#> "0443" "0423" "014" "01131" "03" "01113"
#> TCGA.EE.A2A1.06 TCGA.ER.A1A1.06 TCGA.FS.A1ZG.06 TCGA.FS.A1ZE.06 TCGA.FS.A1ZH.06 TCGA.EE.A2MH.06
#> "01311" "01311" "0222" "0222" "04111" "01112"
#> TCGA.D3.A2J6.06 TCGA.EE.A29Q.06 TCGA.BF.A1PZ.01 TCGA.D3.A3BZ.06 TCGA.D3.A2JO.06 TCGA.GN.A267.06
#> "0423" "03232" "03" "01311" "04422" "0432"
#> TCGA.EE.A2MN.06 TCGA.GN.A264.06 TCGA.ER.A197.06 TCGA.DA.A1IB.06 TCGA.D3.A3CC.06 TCGA.ER.A19T.01
#> "0513" "023" "014" "014" "0423" "0523"
#> TCGA.GN.A261.06 TCGA.FS.A1YW.06 TCGA.BF.A1PU.01 TCGA.D3.A1QB.06 TCGA.D3.A1Q6.06 TCGA.D3.A3C8.06
#> "0122" "023" "0443" "0124" "0441" "014"
#> TCGA.ER.A19A.06 TCGA.EE.A2GN.06 TCGA.EE.A29M.06 TCGA.D3.A2J7.06 TCGA.EB.A24C.01 TCGA.GN.A262.06
#> "01311" "0522" "0121" "01133" "0432" "02123"
#> TCGA.EE.A2GD.06 TCGA.D3.A2J9.06 TCGA.EE.A29B.06 TCGA.D9.A1JX.06 TCGA.EE.A29A.06 TCGA.D3.A2JL.06
#> "014" "01132" "05112" "03" "0221" "04122"
#> TCGA.D3.A1Q4.06 TCGA.FS.A1ZS.06 TCGA.D3.A3C3.06 TCGA.D3.A2J8.06 TCGA.FS.A1ZF.06 TCGA.FS.A1ZC.06
#> "0122" "0423" "0413" "01311" "03232" "02121"
#> TCGA.EE.A20H.06 TCGA.EE.A29W.06 TCGA.D3.A1QA.07 TCGA.BF.A1PV.01 TCGA.EE.A29S.06 TCGA.DA.A1HV.06
#> "0522" "03" "0413" "0512" "04424" "03"
#> TCGA.FS.A1Z0.06 TCGA.EE.A2GO.06 TCGA.EB.A1NK.01 TCGA.GN.A26D.06 TCGA.EE.A2MJ.06 TCGA.ER.A198.06
#> "0122" "023" "0133" "0422" "01132" "0512"
#> TCGA.EE.A17X.06 TCGA.EE.A2M5.06 TCGA.GN.A266.06 TCGA.D3.A3C1.06 TCGA.D3.A2JH.06 TCGA.EE.A20F.06
#> "03111" "04122" "0443" "04421" "0112" "04111"
#> TCGA.EE.A29E.06 TCGA.ER.A2NG.06 TCGA.ER.A193.06 TCGA.FS.A1ZW.06 TCGA.ER.A19O.06 TCGA.EE.A2ME.06
#> "0133" "014" "0421" "0413" "04421" "01112"
#> TCGA.EE.A20B.06 TCGA.EE.A3AF.06 TCGA.GN.A265.06 TCGA.FS.A1YX.06 TCGA.FS.A1ZJ.06 TCGA.ER.A19H.06
#> "04111" "03" "01132" "0441" "0523" "03"
#> TCGA.EE.A3AC.06 TCGA.EE.A2MU.06 TCGA.ER.A194.01 TCGA.EE.A2MS.06 TCGA.EE.A29R.06 TCGA.D9.A1X3.06
#> "0521" "01133" "04423" "0433" "023" "0221"
#> TCGA.EE.A29X.06 TCGA.EE.A2GK.06 TCGA.EE.A3AA.06 TCGA.ER.A2NE.06 TCGA.EE.A2GR.06 TCGA.FS.A1ZD.06
#> "04421" "0123" "01112" "02122" "0521" "0523"
#> TCGA.ER.A19P.06 TCGA.D3.A1Q8.06 TCGA.ER.A2NC.06 TCGA.BF.A1Q0.01 TCGA.FS.A1ZP.06 TCGA.EE.A182.06
#> "014" "0112" "0443" "0421" "0522" "0432"
#> TCGA.D9.A1JW.06 TCGA.D3.A1Q7.06 TCGA.EE.A185.06 TCGA.EE.A2GJ.06 TCGA.D3.A3CB.06 TCGA.EE.A2GU.06
#> "0421" "014" "02122" "0431" "01111" "0421"
#> TCGA.ER.A195.06 TCGA.FS.A1Z7.06 TCGA.EE.A2M6.06 TCGA.ER.A19K.01 TCGA.DA.A1HY.06 TCGA.D3.A3C7.06
#> "0132" "0423" "02121" "04421" "03" "03"
#> TCGA.EE.A2MP.06 TCGA.EE.A29H.06 TCGA.FR.A3YO.06 TCGA.XV.AB01.01 TCGA.RP.A694.06 TCGA.EB.A5SF.01
#> "03232" "03" "04421" "03" "04423" "0122"
#> TCGA.ER.A19G.06 TCGA.EE.A2GE.06 TCGA.GF.A3OT.06 TCGA.ER.A2NF.06 TCGA.RP.A695.06 TCGA.BF.AAP7.01
#> "03" "0112" "014" "0132" "0512" "0121"
#> TCGA.EB.A3Y7.01 TCGA.EB.A3XC.01 TCGA.ER.A19W.06 TCGA.FR.A69P.06 TCGA.RP.A693.06 TCGA.FW.A3TV.06
#> "0423" "03111" "014" "03" "01111" "0124"
#> TCGA.FW.A3R5.11 TCGA.FW.A3TU.06 TCGA.BF.AAP8.01 TCGA.EE.A2MM.06 TCGA.DA.A1HW.06 TCGA.DA.A1IC.06
#> "0132" "05111" "0422" "0513" "0441" "0521"
#> TCGA.XV.AAZV.01 TCGA.D3.A3C6.06 TCGA.EE.A29C.06 TCGA.BF.AAP2.01 TCGA.EE.A2A2.06 TCGA.GF.A6C8.06
#> "0121" "03232" "0132" "02122" "03" "0443"
#> TCGA.RP.A690.06 TCGA.FW.A5DY.06 TCGA.DA.A1I4.06 TCGA.EE.A29V.06 TCGA.GF.A6C9.06 TCGA.EE.A2GT.06
#> "0122" "014" "0132" "04122" "01132" "01312"
#> TCGA.GN.A9SD.06 TCGA.EE.A3AB.06 TCGA.BF.AAP6.01 TCGA.EB.A5SH.06 TCGA.D9.A6E9.06 TCGA.BF.AAP4.01
#> "014" "0413" "03" "0431" "04421" "04421"
#> TCGA.EE.A2GM.06 TCGA.D3.A3CF.06 TCGA.D9.A6EC.06 TCGA.DA.A1I1.06 TCGA.HR.A2OH.06 TCGA.EE.A2MT.06
#> "02123" "0121" "023" "0413" "014" "0422"
#> TCGA.ER.A19M.06 TCGA.GN.A26C.01 TCGA.FS.A1ZA.06 TCGA.EB.A5SE.01 TCGA.ER.A3PL.06 TCGA.FR.A3R1.01
#> "04111" "01112" "04422" "0222" "0521" "03"
#> TCGA.EE.A2MI.06 TCGA.D3.A3CE.06 TCGA.D3.A5GT.01 TCGA.ER.A2NB.01 TCGA.D3.A1Q5.06 TCGA.EB.A5UN.06
#> "0443" "0441" "05112" "0421" "0422" "01113"
#> TCGA.EB.A299.01 TCGA.DA.A1IA.06 TCGA.EB.A5SG.06 TCGA.D9.A6EA.06 TCGA.XV.AAZY.01 TCGA.EB.A57M.01
#> "03232" "05111" "014" "0222" "014" "04122"
#> TCGA.EE.A2A6.06 TCGA.D3.A2JA.06 TCGA.D3.A1Q1.06 TCGA.EB.A3XF.01 TCGA.D3.A2JF.06 TCGA.XV.AAZW.01
#> "0421" "0132" "0422" "03112" "03234" "03112"
#> TCGA.EB.A3Y6.01 TCGA.EB.A3XE.01 TCGA.D9.A3Z4.01 TCGA.FW.A3R5.06 TCGA.EE.A2GI.06 TCGA.EE.A2GL.06
#> "0441" "0432" "0523" "0432" "04111" "014"
#> TCGA.EB.A3XB.01 TCGA.BF.AAOU.01 TCGA.EB.A3XD.01 TCGA.EE.A2MD.06 TCGA.YD.A9TB.06 TCGA.W3.AA1V.06
#> "04421" "014" "0124" "04421" "0521" "0441"
#> TCGA.ER.A2ND.06 TCGA.D3.A2JK.06 TCGA.FS.A1ZB.06 TCGA.EE.A29D.06 TCGA.EB.A5UM.01 TCGA.QB.A6FS.06
#> "0521" "04122" "0112" "0222" "0432" "0132"
#> TCGA.D9.A3Z1.06 TCGA.D3.A2JN.06 TCGA.FR.A3YN.06 TCGA.FS.A1ZT.06 TCGA.D9.A148.06 TCGA.HR.A2OG.06
#> "01133" "014" "03233" "0132" "04121" "0125"
#> TCGA.EE.A2ML.06 TCGA.EB.A5UL.06 TCGA.EE.A29T.06 TCGA.D9.A3Z3.06 TCGA.D9.A4Z3.01 TCGA.ER.A3ES.06
#> "0413" "04122" "0432" "0124" "0522" "0422"
#> TCGA.XV.A9VZ.01 TCGA.QB.AA9O.06 TCGA.EB.A44Q.06 TCGA.EB.A44R.06 TCGA.BF.A3DJ.01 TCGA.EE.A3JD.06
#> "0122" "03111" "04421" "0433" "03112" "01311"
#> TCGA.D3.A51N.06 TCGA.EB.A44N.01 TCGA.EE.A3J3.06 TCGA.XV.A9W5.01 TCGA.D3.A51G.06 TCGA.EB.A4P0.01
#> "0413" "01133" "03" "04122" "03234" "03112"
#> TCGA.BF.AAP1.01 TCGA.EE.A3J4.06 TCGA.Z2.AA3V.06 TCGA.LH.A9QB.06 TCGA.D3.A51J.06 TCGA.3N.A9WC.06
#> "023" "05112" "0121" "023" "04421" "0421"
#> TCGA.DA.A3F8.06 TCGA.D9.A4Z6.06 TCGA.D3.A51R.06 TCGA.EB.A4OZ.01 TCGA.FS.A4FB.06 TCGA.EE.A3JE.06
#> "01132" "04122" "03" "0121" "03112" "01132"
#> TCGA.W3.AA1W.06 TCGA.DA.A1I0.06 TCGA.D3.A51F.06 TCGA.IH.A3EA.01 TCGA.EB.A431.01 TCGA.EB.A97M.01
#> "01111" "04122" "01311" "0512" "04122" "0222"
#> TCGA.BF.AAOX.01 TCGA.DA.A3F5.06 TCGA.YD.A9TA.06 TCGA.DA.A3F2.06 TCGA.EB.A44O.01 TCGA.EB.A4IQ.01
#> "04121" "0423" "04112" "01311" "0521" "0421"
#> TCGA.EB.A4IS.01 TCGA.YG.AA3O.06 TCGA.ER.A3EV.06 TCGA.3N.A9WD.06 TCGA.BF.A3DM.01 TCGA.XV.A9W2.01
#> "0112" "0512" "0433" "01131" "03" "0423"
#> TCGA.W3.AA1Q.06 TCGA.WE.AAA0.06 TCGA.W3.AA1R.06 TCGA.EE.A3J5.06 TCGA.EB.A4OY.01 TCGA.FS.A4FD.06
#> "0512" "04122" "03" "04122" "0122" "0422"
#> TCGA.BF.AAP0.06 TCGA.YG.AA3P.06 TCGA.EE.A3JA.06 TCGA.W3.AA21.06 TCGA.WE.AAA3.06 TCGA.FS.A4F4.06
#> "0123" "0523" "03231" "0211" "0423" "03111"
#> TCGA.BF.A3DN.01 TCGA.ER.A3ET.06 TCGA.W3.AA1O.06 TCGA.D3.A51E.06 TCGA.Z2.AA3S.06 TCGA.YG.AA3N.01
#> "03" "0423" "0513" "03" "0222" "04421"
#> TCGA.WE.AA9Y.06 TCGA.FS.A4F5.06 TCGA.EE.A3J7.06 TCGA.FS.A4F8.06 TCGA.DA.A3F3.06 TCGA.D3.A51H.06
#> "01113" "023" "05113" "01112" "03231" "01311"
#> TCGA.BF.A3DL.01 TCGA.D3.A51T.06 TCGA.D3.A51K.06 TCGA.EB.A44P.01 TCGA.D9.A4Z5.01 TCGA.WE.AAA4.06
#> "0124" "03" "0522" "0521" "023" "014"
#> TCGA.3N.A9WB.06 TCGA.EE.A3J8.06
#> "0222" "0211"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 1564))
#> TCGA.FR.A728.01 TCGA.GN.A4U8.11 TCGA.GN.A8LL.06 TCGA.FR.A8YC.06 TCGA.DA.A95X.06 TCGA.ER.A42K.06
#> "014" "01132" "03113" "0221" "0211" "03"
#> TCGA.D3.A8GO.06 TCGA.D3.A8GK.06 TCGA.WE.A8JZ.06 TCGA.WE.A8ZO.06 TCGA.D3.A8GI.06 TCGA.FS.A4FC.06
#> "0124" "0524" "02121" "05113" "0512" "0421"
#> TCGA.FS.A4F2.06 TCGA.WE.A8ZM.06 TCGA.WE.A8ZT.06 TCGA.D3.A8GQ.06 TCGA.D3.A8GB.06 TCGA.DA.A95Y.06
#> "03" "0522" "03112" "0411" "01311" "03111"
#> TCGA.EE.A3JI.06 TCGA.OD.A75X.06 TCGA.DA.A960.01 TCGA.D3.A8GV.06 TCGA.WE.A8ZN.06 TCGA.D3.A8GN.06
#> "0221" "023" "0211" "02121" "0112" "014"
#> TCGA.EB.A550.01 TCGA.BF.A5EQ.01 TCGA.EB.A3HV.01 TCGA.HR.A5NC.01 TCGA.DA.A95Z.06 TCGA.EB.A6QZ.01
#> "0122" "0421" "0521" "0523" "0221" "02122"
#> TCGA.FW.A3I3.06 TCGA.WE.A8K6.06 TCGA.D3.A8GP.06 TCGA.EB.A42Z.01 TCGA.GN.A4U4.06 TCGA.GF.A4EO.06
#> "023" "03" "0222" "023" "02123" "014"
#> TCGA.GN.A8LK.06 TCGA.WE.A8K4.01 TCGA.DA.A95W.06 TCGA.FW.A5DX.01 TCGA.GN.A4U3.06 TCGA.EB.A6QY.01
#> "0521" "0112" "0221" "02121" "03111" "0133"
#> TCGA.EB.A5VU.01 TCGA.Z2.A8RT.06 TCGA.WE.A8K1.06 TCGA.EB.A41B.01 TCGA.WE.A8ZY.06 TCGA.D9.A6EG.06
#> "0443" "03" "0112" "03" "02122" "0222"
#> TCGA.BF.A5ER.01 TCGA.FR.A8YD.06 TCGA.FS.A4F9.06 TCGA.EB.A6R0.01 TCGA.ER.A42L.06 TCGA.D3.A8GJ.06
#> "0512" "05113" "05112" "03" "01133" "04423"
#> TCGA.FR.A8YE.06 TCGA.WE.A8ZR.06 TCGA.BF.A9VF.01 TCGA.EE.A3JH.06 TCGA.DA.A95V.06 TCGA.GF.A769.01
#> "01132" "0432" "0521" "0112" "04122" "02123"
#> TCGA.D9.A4Z2.01 TCGA.FR.A44A.06 TCGA.EB.A5VV.06 TCGA.EE.A180.06 TCGA.D3.A8GC.06 TCGA.WE.A8K5.06
#> "03" "014" "0123" "0222" "0513" "023"
#> TCGA.GN.A8LN.01 TCGA.EE.A3JB.06 TCGA.D3.A3MO.06 TCGA.ER.A42H.01 TCGA.WE.A8ZX.06 TCGA.GN.A4U5.01
#> "02122" "0411" "0522" "05112" "04122" "014"
#> TCGA.D3.A8GS.06 TCGA.WE.A8ZQ.06 TCGA.EE.A2MF.06 TCGA.D3.A5GU.06 TCGA.GN.A4U8.06 TCGA.EB.A42Y.01
#> "0441" "0523" "0222" "05113" "0413" "02122"
#> TCGA.D3.A3ML.06 TCGA.EB.A551.01 TCGA.D3.A8GM.06 TCGA.D3.A8GL.06 TCGA.D3.A3MU.06 TCGA.FS.A4F0.06
#> "05113" "04422" "04122" "0221" "0221" "0221"
#> TCGA.D3.A3MV.06 TCGA.GN.A4U7.06 TCGA.FR.A2OS.01 TCGA.D3.A2JE.06 TCGA.YD.A89C.06 TCGA.FR.A726.01
#> "03" "03113" "0523" "0522" "0411" "0411"
#> TCGA.BF.A5EP.01 TCGA.D3.A3MR.06 TCGA.D3.A8GR.06 TCGA.GN.A4U9.06 TCGA.EB.A6L9.06 TCGA.D3.A5GL.06
#> "03" "0112" "05111" "0522" "01311" "03"
#> TCGA.EB.A430.01 TCGA.D3.A8GE.06 TCGA.D3.A8GD.06 TCGA.EB.A41A.01 TCGA.W3.A825.06 TCGA.EE.A183.06
#> "0133" "0132" "014" "0222" "0443" "01112"
#> TCGA.ER.A2NH.06 TCGA.D3.A5GR.06 TCGA.FR.A729.06 TCGA.D3.A1QA.06 TCGA.FS.A1YY.06 TCGA.EE.A2MK.06
#> "0112" "0441" "0441" "0211" "03" "03112"
#> TCGA.EE.A2M8.06 TCGA.EB.A5KH.06 TCGA.FS.A1ZR.06 TCGA.EE.A3AE.06 TCGA.EE.A29P.06 TCGA.EB.A553.01
#> "0123" "02122" "0521" "03112" "04424" "0513"
#> TCGA.EE.A2MR.06 TCGA.GN.A26A.06 TCGA.FS.A1ZY.06 TCGA.EE.A20I.06 TCGA.DA.A1I5.06 TCGA.EE.A184.06
#> "01112" "0411" "02123" "04121" "0125" "023"
#> TCGA.EB.A85J.01 TCGA.RP.A6K9.06 TCGA.EE.A17Y.06 TCGA.D9.A149.06 TCGA.ER.A19D.06 TCGA.FS.A1ZZ.06
#> "0433" "0423" "0411" "0421" "0122" "023"
#> TCGA.EE.A2GP.06 TCGA.EE.A3AD.06 TCGA.D3.A1Q9.06 TCGA.GF.A2C7.01 TCGA.BF.A5ES.01 TCGA.ER.A199.06
#> "0524" "02122" "04121" "05112" "05111" "014"
#> TCGA.EE.A3AH.06 TCGA.W3.A828.06 TCGA.EE.A2A5.06 TCGA.ER.A19L.06 TCGA.BF.A1PX.01 TCGA.ER.A19T.06
#> "02121" "0133" "0522" "0432" "01112" "0431"
#> TCGA.EB.A51B.01 TCGA.FS.A1ZQ.06 TCGA.D3.A2JG.06 TCGA.EE.A2GH.06 TCGA.ER.A19F.06 TCGA.ER.A196.01
#> "03" "03233" "03" "0112" "03" "0124"
#> TCGA.D3.A2JC.06 TCGA.EE.A3AG.06 TCGA.ER.A19S.06 TCGA.EE.A2GC.06 TCGA.EE.A29N.06 TCGA.FR.A7U8.06
#> "0441" "03" "014" "0524" "01133" "023"
#> TCGA.BF.A5EO.01 TCGA.ER.A19B.06 TCGA.D3.A5GN.06 TCGA.D3.A2JB.06 TCGA.ER.A19J.06 TCGA.D3.A2JD.06
#> "04122" "03232" "03232" "0123" "023" "0112"
#> TCGA.FS.A1Z4.06 TCGA.FR.A7UA.06 TCGA.EE.A2M7.06 TCGA.D3.A1Q3.06 TCGA.EB.A85I.01 TCGA.EB.A82C.01
#> "01311" "014" "0441" "0431" "0421" "023"
#> TCGA.ER.A19E.06 TCGA.FS.A1ZK.06 TCGA.FS.A1ZU.06 TCGA.EB.A5FP.01 TCGA.EB.A4XL.01 TCGA.DA.A1I2.06
#> "0522" "0524" "0522" "02122" "03112" "0441"
#> TCGA.EE.A29L.06 TCGA.FS.A1ZN.01 TCGA.EB.A24D.01 TCGA.EE.A2GB.06 TCGA.DA.A1I7.06 TCGA.ER.A2NF.01
#> "0211" "02122" "05113" "03" "0441" "0132"
#> TCGA.GN.A263.01 TCGA.EE.A20C.06 TCGA.EE.A2MQ.06 TCGA.ER.A19N.06 TCGA.FS.A1Z3.06 TCGA.DA.A1I8.06
#> "0132" "023" "0512" "0112" "03" "03"
#> TCGA.D3.A5GS.06 TCGA.EE.A181.06 TCGA.GN.A268.06 TCGA.W3.A824.06 TCGA.EE.A2GS.06 TCGA.FR.A7U9.06
#> "03232" "04121" "0221" "05112" "03" "0121"
#> TCGA.ER.A19Q.06 TCGA.FS.A1ZM.06 TCGA.EE.A2MG.06 TCGA.EE.A2MC.06 TCGA.EE.A17Z.06 TCGA.D3.A2JP.06
#> "0125" "0441" "01311" "01312" "0522" "04122"
#> TCGA.ER.A19C.06 TCGA.EB.A82B.01 TCGA.EE.A2A0.06 TCGA.EE.A29G.06 TCGA.D3.A5GO.06 TCGA.GN.A269.01
#> "0443" "0423" "014" "01131" "03" "01113"
#> TCGA.EE.A2A1.06 TCGA.ER.A1A1.06 TCGA.FS.A1ZG.06 TCGA.FS.A1ZE.06 TCGA.FS.A1ZH.06 TCGA.EE.A2MH.06
#> "01311" "01311" "0222" "0222" "0411" "01112"
#> TCGA.D3.A2J6.06 TCGA.EE.A29Q.06 TCGA.BF.A1PZ.01 TCGA.D3.A3BZ.06 TCGA.D3.A2JO.06 TCGA.GN.A267.06
#> "0423" "03232" "03" "01311" "04422" "0432"
#> TCGA.EE.A2MN.06 TCGA.GN.A264.06 TCGA.ER.A197.06 TCGA.DA.A1IB.06 TCGA.D3.A3CC.06 TCGA.ER.A19T.01
#> "0513" "023" "014" "014" "0423" "0523"
#> TCGA.GN.A261.06 TCGA.FS.A1YW.06 TCGA.BF.A1PU.01 TCGA.D3.A1QB.06 TCGA.D3.A1Q6.06 TCGA.D3.A3C8.06
#> "0122" "023" "0443" "0124" "0441" "014"
#> TCGA.ER.A19A.06 TCGA.EE.A2GN.06 TCGA.EE.A29M.06 TCGA.D3.A2J7.06 TCGA.EB.A24C.01 TCGA.GN.A262.06
#> "01311" "0522" "0121" "01133" "0432" "02123"
#> TCGA.EE.A2GD.06 TCGA.D3.A2J9.06 TCGA.EE.A29B.06 TCGA.D9.A1JX.06 TCGA.EE.A29A.06 TCGA.D3.A2JL.06
#> "014" "01132" "05112" "03" "0221" "04122"
#> TCGA.D3.A1Q4.06 TCGA.FS.A1ZS.06 TCGA.D3.A3C3.06 TCGA.D3.A2J8.06 TCGA.FS.A1ZF.06 TCGA.FS.A1ZC.06
#> "0122" "0423" "0413" "01311" "03232" "02121"
#> TCGA.EE.A20H.06 TCGA.EE.A29W.06 TCGA.D3.A1QA.07 TCGA.BF.A1PV.01 TCGA.EE.A29S.06 TCGA.DA.A1HV.06
#> "0522" "03" "0413" "0512" "04424" "03"
#> TCGA.FS.A1Z0.06 TCGA.EE.A2GO.06 TCGA.EB.A1NK.01 TCGA.GN.A26D.06 TCGA.EE.A2MJ.06 TCGA.ER.A198.06
#> "0122" "023" "0133" "0422" "01132" "0512"
#> TCGA.EE.A17X.06 TCGA.EE.A2M5.06 TCGA.GN.A266.06 TCGA.D3.A3C1.06 TCGA.D3.A2JH.06 TCGA.EE.A20F.06
#> "03111" "04122" "0443" "04421" "0112" "0411"
#> TCGA.EE.A29E.06 TCGA.ER.A2NG.06 TCGA.ER.A193.06 TCGA.FS.A1ZW.06 TCGA.ER.A19O.06 TCGA.EE.A2ME.06
#> "0133" "014" "0421" "0413" "04421" "01112"
#> TCGA.EE.A20B.06 TCGA.EE.A3AF.06 TCGA.GN.A265.06 TCGA.FS.A1YX.06 TCGA.FS.A1ZJ.06 TCGA.ER.A19H.06
#> "0411" "03" "01132" "0441" "0523" "03"
#> TCGA.EE.A3AC.06 TCGA.EE.A2MU.06 TCGA.ER.A194.01 TCGA.EE.A2MS.06 TCGA.EE.A29R.06 TCGA.D9.A1X3.06
#> "0521" "01133" "04423" "0433" "023" "0221"
#> TCGA.EE.A29X.06 TCGA.EE.A2GK.06 TCGA.EE.A3AA.06 TCGA.ER.A2NE.06 TCGA.EE.A2GR.06 TCGA.FS.A1ZD.06
#> "04421" "0123" "01112" "02122" "0521" "0523"
#> TCGA.ER.A19P.06 TCGA.D3.A1Q8.06 TCGA.ER.A2NC.06 TCGA.BF.A1Q0.01 TCGA.FS.A1ZP.06 TCGA.EE.A182.06
#> "014" "0112" "0443" "0421" "0522" "0432"
#> TCGA.D9.A1JW.06 TCGA.D3.A1Q7.06 TCGA.EE.A185.06 TCGA.EE.A2GJ.06 TCGA.D3.A3CB.06 TCGA.EE.A2GU.06
#> "0421" "014" "02122" "0431" "01111" "0421"
#> TCGA.ER.A195.06 TCGA.FS.A1Z7.06 TCGA.EE.A2M6.06 TCGA.ER.A19K.01 TCGA.DA.A1HY.06 TCGA.D3.A3C7.06
#> "0132" "0423" "02121" "04421" "03" "03"
#> TCGA.EE.A2MP.06 TCGA.EE.A29H.06 TCGA.FR.A3YO.06 TCGA.XV.AB01.01 TCGA.RP.A694.06 TCGA.EB.A5SF.01
#> "03232" "03" "04421" "03" "04423" "0122"
#> TCGA.ER.A19G.06 TCGA.EE.A2GE.06 TCGA.GF.A3OT.06 TCGA.ER.A2NF.06 TCGA.RP.A695.06 TCGA.BF.AAP7.01
#> "03" "0112" "014" "0132" "0512" "0121"
#> TCGA.EB.A3Y7.01 TCGA.EB.A3XC.01 TCGA.ER.A19W.06 TCGA.FR.A69P.06 TCGA.RP.A693.06 TCGA.FW.A3TV.06
#> "0423" "03111" "014" "03" "01111" "0124"
#> TCGA.FW.A3R5.11 TCGA.FW.A3TU.06 TCGA.BF.AAP8.01 TCGA.EE.A2MM.06 TCGA.DA.A1HW.06 TCGA.DA.A1IC.06
#> "0132" "05111" "0422" "0513" "0441" "0521"
#> TCGA.XV.AAZV.01 TCGA.D3.A3C6.06 TCGA.EE.A29C.06 TCGA.BF.AAP2.01 TCGA.EE.A2A2.06 TCGA.GF.A6C8.06
#> "0121" "03232" "0132" "02122" "03" "0443"
#> TCGA.RP.A690.06 TCGA.FW.A5DY.06 TCGA.DA.A1I4.06 TCGA.EE.A29V.06 TCGA.GF.A6C9.06 TCGA.EE.A2GT.06
#> "0122" "014" "0132" "04122" "01132" "01312"
#> TCGA.GN.A9SD.06 TCGA.EE.A3AB.06 TCGA.BF.AAP6.01 TCGA.EB.A5SH.06 TCGA.D9.A6E9.06 TCGA.BF.AAP4.01
#> "014" "0413" "03" "0431" "04421" "04421"
#> TCGA.EE.A2GM.06 TCGA.D3.A3CF.06 TCGA.D9.A6EC.06 TCGA.DA.A1I1.06 TCGA.HR.A2OH.06 TCGA.EE.A2MT.06
#> "02123" "0121" "023" "0413" "014" "0422"
#> TCGA.ER.A19M.06 TCGA.GN.A26C.01 TCGA.FS.A1ZA.06 TCGA.EB.A5SE.01 TCGA.ER.A3PL.06 TCGA.FR.A3R1.01
#> "0411" "01112" "04422" "0222" "0521" "03"
#> TCGA.EE.A2MI.06 TCGA.D3.A3CE.06 TCGA.D3.A5GT.01 TCGA.ER.A2NB.01 TCGA.D3.A1Q5.06 TCGA.EB.A5UN.06
#> "0443" "0441" "05112" "0421" "0422" "01113"
#> TCGA.EB.A299.01 TCGA.DA.A1IA.06 TCGA.EB.A5SG.06 TCGA.D9.A6EA.06 TCGA.XV.AAZY.01 TCGA.EB.A57M.01
#> "03232" "05111" "014" "0222" "014" "04122"
#> TCGA.EE.A2A6.06 TCGA.D3.A2JA.06 TCGA.D3.A1Q1.06 TCGA.EB.A3XF.01 TCGA.D3.A2JF.06 TCGA.XV.AAZW.01
#> "0421" "0132" "0422" "03112" "03234" "03112"
#> TCGA.EB.A3Y6.01 TCGA.EB.A3XE.01 TCGA.D9.A3Z4.01 TCGA.FW.A3R5.06 TCGA.EE.A2GI.06 TCGA.EE.A2GL.06
#> "0441" "0432" "0523" "0432" "0411" "014"
#> TCGA.EB.A3XB.01 TCGA.BF.AAOU.01 TCGA.EB.A3XD.01 TCGA.EE.A2MD.06 TCGA.YD.A9TB.06 TCGA.W3.AA1V.06
#> "04421" "014" "0124" "04421" "0521" "0441"
#> TCGA.ER.A2ND.06 TCGA.D3.A2JK.06 TCGA.FS.A1ZB.06 TCGA.EE.A29D.06 TCGA.EB.A5UM.01 TCGA.QB.A6FS.06
#> "0521" "04122" "0112" "0222" "0432" "0132"
#> TCGA.D9.A3Z1.06 TCGA.D3.A2JN.06 TCGA.FR.A3YN.06 TCGA.FS.A1ZT.06 TCGA.D9.A148.06 TCGA.HR.A2OG.06
#> "01133" "014" "03233" "0132" "04121" "0125"
#> TCGA.EE.A2ML.06 TCGA.EB.A5UL.06 TCGA.EE.A29T.06 TCGA.D9.A3Z3.06 TCGA.D9.A4Z3.01 TCGA.ER.A3ES.06
#> "0413" "04122" "0432" "0124" "0522" "0422"
#> TCGA.XV.A9VZ.01 TCGA.QB.AA9O.06 TCGA.EB.A44Q.06 TCGA.EB.A44R.06 TCGA.BF.A3DJ.01 TCGA.EE.A3JD.06
#> "0122" "03111" "04421" "0433" "03112" "01311"
#> TCGA.D3.A51N.06 TCGA.EB.A44N.01 TCGA.EE.A3J3.06 TCGA.XV.A9W5.01 TCGA.D3.A51G.06 TCGA.EB.A4P0.01
#> "0413" "01133" "03" "04122" "03234" "03112"
#> TCGA.BF.AAP1.01 TCGA.EE.A3J4.06 TCGA.Z2.AA3V.06 TCGA.LH.A9QB.06 TCGA.D3.A51J.06 TCGA.3N.A9WC.06
#> "023" "05112" "0121" "023" "04421" "0421"
#> TCGA.DA.A3F8.06 TCGA.D9.A4Z6.06 TCGA.D3.A51R.06 TCGA.EB.A4OZ.01 TCGA.FS.A4FB.06 TCGA.EE.A3JE.06
#> "01132" "04122" "03" "0121" "03112" "01132"
#> TCGA.W3.AA1W.06 TCGA.DA.A1I0.06 TCGA.D3.A51F.06 TCGA.IH.A3EA.01 TCGA.EB.A431.01 TCGA.EB.A97M.01
#> "01111" "04122" "01311" "0512" "04122" "0222"
#> TCGA.BF.AAOX.01 TCGA.DA.A3F5.06 TCGA.YD.A9TA.06 TCGA.DA.A3F2.06 TCGA.EB.A44O.01 TCGA.EB.A4IQ.01
#> "04121" "0423" "0411" "01311" "0521" "0421"
#> TCGA.EB.A4IS.01 TCGA.YG.AA3O.06 TCGA.ER.A3EV.06 TCGA.3N.A9WD.06 TCGA.BF.A3DM.01 TCGA.XV.A9W2.01
#> "0112" "0512" "0433" "01131" "03" "0423"
#> TCGA.W3.AA1Q.06 TCGA.WE.AAA0.06 TCGA.W3.AA1R.06 TCGA.EE.A3J5.06 TCGA.EB.A4OY.01 TCGA.FS.A4FD.06
#> "0512" "04122" "03" "04122" "0122" "0422"
#> TCGA.BF.AAP0.06 TCGA.YG.AA3P.06 TCGA.EE.A3JA.06 TCGA.W3.AA21.06 TCGA.WE.AAA3.06 TCGA.FS.A4F4.06
#> "0123" "0523" "03231" "0211" "0423" "03111"
#> TCGA.BF.A3DN.01 TCGA.ER.A3ET.06 TCGA.W3.AA1O.06 TCGA.D3.A51E.06 TCGA.Z2.AA3S.06 TCGA.YG.AA3N.01
#> "03" "0423" "0513" "03" "0222" "04421"
#> TCGA.WE.AA9Y.06 TCGA.FS.A4F5.06 TCGA.EE.A3J7.06 TCGA.FS.A4F8.06 TCGA.DA.A3F3.06 TCGA.D3.A51H.06
#> "01113" "023" "05113" "01112" "03231" "01311"
#> TCGA.BF.A3DL.01 TCGA.D3.A51T.06 TCGA.D3.A51K.06 TCGA.EB.A44P.01 TCGA.D9.A4Z5.01 TCGA.WE.AAA4.06
#> "0124" "03" "0522" "0521" "023" "014"
#> TCGA.3N.A9WB.06 TCGA.EE.A3J8.06
#> "0222" "0211"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 1831))
#> TCGA.FR.A728.01 TCGA.GN.A4U8.11 TCGA.GN.A8LL.06 TCGA.FR.A8YC.06 TCGA.DA.A95X.06 TCGA.ER.A42K.06
#> "014" "01132" "03113" "0221" "0211" "03"
#> TCGA.D3.A8GO.06 TCGA.D3.A8GK.06 TCGA.WE.A8JZ.06 TCGA.WE.A8ZO.06 TCGA.D3.A8GI.06 TCGA.FS.A4FC.06
#> "0124" "0524" "0212" "05113" "0512" "0421"
#> TCGA.FS.A4F2.06 TCGA.WE.A8ZM.06 TCGA.WE.A8ZT.06 TCGA.D3.A8GQ.06 TCGA.D3.A8GB.06 TCGA.DA.A95Y.06
#> "03" "0522" "03112" "0411" "01311" "03111"
#> TCGA.EE.A3JI.06 TCGA.OD.A75X.06 TCGA.DA.A960.01 TCGA.D3.A8GV.06 TCGA.WE.A8ZN.06 TCGA.D3.A8GN.06
#> "0221" "023" "0211" "0212" "0112" "014"
#> TCGA.EB.A550.01 TCGA.BF.A5EQ.01 TCGA.EB.A3HV.01 TCGA.HR.A5NC.01 TCGA.DA.A95Z.06 TCGA.EB.A6QZ.01
#> "0122" "0421" "0521" "0523" "0221" "0212"
#> TCGA.FW.A3I3.06 TCGA.WE.A8K6.06 TCGA.D3.A8GP.06 TCGA.EB.A42Z.01 TCGA.GN.A4U4.06 TCGA.GF.A4EO.06
#> "023" "03" "0222" "023" "0212" "014"
#> TCGA.GN.A8LK.06 TCGA.WE.A8K4.01 TCGA.DA.A95W.06 TCGA.FW.A5DX.01 TCGA.GN.A4U3.06 TCGA.EB.A6QY.01
#> "0521" "0112" "0221" "0212" "03111" "0133"
#> TCGA.EB.A5VU.01 TCGA.Z2.A8RT.06 TCGA.WE.A8K1.06 TCGA.EB.A41B.01 TCGA.WE.A8ZY.06 TCGA.D9.A6EG.06
#> "0443" "03" "0112" "03" "0212" "0222"
#> TCGA.BF.A5ER.01 TCGA.FR.A8YD.06 TCGA.FS.A4F9.06 TCGA.EB.A6R0.01 TCGA.ER.A42L.06 TCGA.D3.A8GJ.06
#> "0512" "05113" "05112" "03" "01133" "04423"
#> TCGA.FR.A8YE.06 TCGA.WE.A8ZR.06 TCGA.BF.A9VF.01 TCGA.EE.A3JH.06 TCGA.DA.A95V.06 TCGA.GF.A769.01
#> "01132" "0432" "0521" "0112" "04122" "0212"
#> TCGA.D9.A4Z2.01 TCGA.FR.A44A.06 TCGA.EB.A5VV.06 TCGA.EE.A180.06 TCGA.D3.A8GC.06 TCGA.WE.A8K5.06
#> "03" "014" "0123" "0222" "0513" "023"
#> TCGA.GN.A8LN.01 TCGA.EE.A3JB.06 TCGA.D3.A3MO.06 TCGA.ER.A42H.01 TCGA.WE.A8ZX.06 TCGA.GN.A4U5.01
#> "0212" "0411" "0522" "05112" "04122" "014"
#> TCGA.D3.A8GS.06 TCGA.WE.A8ZQ.06 TCGA.EE.A2MF.06 TCGA.D3.A5GU.06 TCGA.GN.A4U8.06 TCGA.EB.A42Y.01
#> "0441" "0523" "0222" "05113" "0413" "0212"
#> TCGA.D3.A3ML.06 TCGA.EB.A551.01 TCGA.D3.A8GM.06 TCGA.D3.A8GL.06 TCGA.D3.A3MU.06 TCGA.FS.A4F0.06
#> "05113" "04422" "04122" "0221" "0221" "0221"
#> TCGA.D3.A3MV.06 TCGA.GN.A4U7.06 TCGA.FR.A2OS.01 TCGA.D3.A2JE.06 TCGA.YD.A89C.06 TCGA.FR.A726.01
#> "03" "03113" "0523" "0522" "0411" "0411"
#> TCGA.BF.A5EP.01 TCGA.D3.A3MR.06 TCGA.D3.A8GR.06 TCGA.GN.A4U9.06 TCGA.EB.A6L9.06 TCGA.D3.A5GL.06
#> "03" "0112" "05111" "0522" "01311" "03"
#> TCGA.EB.A430.01 TCGA.D3.A8GE.06 TCGA.D3.A8GD.06 TCGA.EB.A41A.01 TCGA.W3.A825.06 TCGA.EE.A183.06
#> "0133" "0132" "014" "0222" "0443" "01112"
#> TCGA.ER.A2NH.06 TCGA.D3.A5GR.06 TCGA.FR.A729.06 TCGA.D3.A1QA.06 TCGA.FS.A1YY.06 TCGA.EE.A2MK.06
#> "0112" "0441" "0441" "0211" "03" "03112"
#> TCGA.EE.A2M8.06 TCGA.EB.A5KH.06 TCGA.FS.A1ZR.06 TCGA.EE.A3AE.06 TCGA.EE.A29P.06 TCGA.EB.A553.01
#> "0123" "0212" "0521" "03112" "04424" "0513"
#> TCGA.EE.A2MR.06 TCGA.GN.A26A.06 TCGA.FS.A1ZY.06 TCGA.EE.A20I.06 TCGA.DA.A1I5.06 TCGA.EE.A184.06
#> "01112" "0411" "0212" "04121" "0125" "023"
#> TCGA.EB.A85J.01 TCGA.RP.A6K9.06 TCGA.EE.A17Y.06 TCGA.D9.A149.06 TCGA.ER.A19D.06 TCGA.FS.A1ZZ.06
#> "0433" "0423" "0411" "0421" "0122" "023"
#> TCGA.EE.A2GP.06 TCGA.EE.A3AD.06 TCGA.D3.A1Q9.06 TCGA.GF.A2C7.01 TCGA.BF.A5ES.01 TCGA.ER.A199.06
#> "0524" "0212" "04121" "05112" "05111" "014"
#> TCGA.EE.A3AH.06 TCGA.W3.A828.06 TCGA.EE.A2A5.06 TCGA.ER.A19L.06 TCGA.BF.A1PX.01 TCGA.ER.A19T.06
#> "0212" "0133" "0522" "0432" "01112" "0431"
#> TCGA.EB.A51B.01 TCGA.FS.A1ZQ.06 TCGA.D3.A2JG.06 TCGA.EE.A2GH.06 TCGA.ER.A19F.06 TCGA.ER.A196.01
#> "03" "03233" "03" "0112" "03" "0124"
#> TCGA.D3.A2JC.06 TCGA.EE.A3AG.06 TCGA.ER.A19S.06 TCGA.EE.A2GC.06 TCGA.EE.A29N.06 TCGA.FR.A7U8.06
#> "0441" "03" "014" "0524" "01133" "023"
#> TCGA.BF.A5EO.01 TCGA.ER.A19B.06 TCGA.D3.A5GN.06 TCGA.D3.A2JB.06 TCGA.ER.A19J.06 TCGA.D3.A2JD.06
#> "04122" "03232" "03232" "0123" "023" "0112"
#> TCGA.FS.A1Z4.06 TCGA.FR.A7UA.06 TCGA.EE.A2M7.06 TCGA.D3.A1Q3.06 TCGA.EB.A85I.01 TCGA.EB.A82C.01
#> "01311" "014" "0441" "0431" "0421" "023"
#> TCGA.ER.A19E.06 TCGA.FS.A1ZK.06 TCGA.FS.A1ZU.06 TCGA.EB.A5FP.01 TCGA.EB.A4XL.01 TCGA.DA.A1I2.06
#> "0522" "0524" "0522" "0212" "03112" "0441"
#> TCGA.EE.A29L.06 TCGA.FS.A1ZN.01 TCGA.EB.A24D.01 TCGA.EE.A2GB.06 TCGA.DA.A1I7.06 TCGA.ER.A2NF.01
#> "0211" "0212" "05113" "03" "0441" "0132"
#> TCGA.GN.A263.01 TCGA.EE.A20C.06 TCGA.EE.A2MQ.06 TCGA.ER.A19N.06 TCGA.FS.A1Z3.06 TCGA.DA.A1I8.06
#> "0132" "023" "0512" "0112" "03" "03"
#> TCGA.D3.A5GS.06 TCGA.EE.A181.06 TCGA.GN.A268.06 TCGA.W3.A824.06 TCGA.EE.A2GS.06 TCGA.FR.A7U9.06
#> "03232" "04121" "0221" "05112" "03" "0121"
#> TCGA.ER.A19Q.06 TCGA.FS.A1ZM.06 TCGA.EE.A2MG.06 TCGA.EE.A2MC.06 TCGA.EE.A17Z.06 TCGA.D3.A2JP.06
#> "0125" "0441" "01311" "01312" "0522" "04122"
#> TCGA.ER.A19C.06 TCGA.EB.A82B.01 TCGA.EE.A2A0.06 TCGA.EE.A29G.06 TCGA.D3.A5GO.06 TCGA.GN.A269.01
#> "0443" "0423" "014" "01131" "03" "01113"
#> TCGA.EE.A2A1.06 TCGA.ER.A1A1.06 TCGA.FS.A1ZG.06 TCGA.FS.A1ZE.06 TCGA.FS.A1ZH.06 TCGA.EE.A2MH.06
#> "01311" "01311" "0222" "0222" "0411" "01112"
#> TCGA.D3.A2J6.06 TCGA.EE.A29Q.06 TCGA.BF.A1PZ.01 TCGA.D3.A3BZ.06 TCGA.D3.A2JO.06 TCGA.GN.A267.06
#> "0423" "03232" "03" "01311" "04422" "0432"
#> TCGA.EE.A2MN.06 TCGA.GN.A264.06 TCGA.ER.A197.06 TCGA.DA.A1IB.06 TCGA.D3.A3CC.06 TCGA.ER.A19T.01
#> "0513" "023" "014" "014" "0423" "0523"
#> TCGA.GN.A261.06 TCGA.FS.A1YW.06 TCGA.BF.A1PU.01 TCGA.D3.A1QB.06 TCGA.D3.A1Q6.06 TCGA.D3.A3C8.06
#> "0122" "023" "0443" "0124" "0441" "014"
#> TCGA.ER.A19A.06 TCGA.EE.A2GN.06 TCGA.EE.A29M.06 TCGA.D3.A2J7.06 TCGA.EB.A24C.01 TCGA.GN.A262.06
#> "01311" "0522" "0121" "01133" "0432" "0212"
#> TCGA.EE.A2GD.06 TCGA.D3.A2J9.06 TCGA.EE.A29B.06 TCGA.D9.A1JX.06 TCGA.EE.A29A.06 TCGA.D3.A2JL.06
#> "014" "01132" "05112" "03" "0221" "04122"
#> TCGA.D3.A1Q4.06 TCGA.FS.A1ZS.06 TCGA.D3.A3C3.06 TCGA.D3.A2J8.06 TCGA.FS.A1ZF.06 TCGA.FS.A1ZC.06
#> "0122" "0423" "0413" "01311" "03232" "0212"
#> TCGA.EE.A20H.06 TCGA.EE.A29W.06 TCGA.D3.A1QA.07 TCGA.BF.A1PV.01 TCGA.EE.A29S.06 TCGA.DA.A1HV.06
#> "0522" "03" "0413" "0512" "04424" "03"
#> TCGA.FS.A1Z0.06 TCGA.EE.A2GO.06 TCGA.EB.A1NK.01 TCGA.GN.A26D.06 TCGA.EE.A2MJ.06 TCGA.ER.A198.06
#> "0122" "023" "0133" "0422" "01132" "0512"
#> TCGA.EE.A17X.06 TCGA.EE.A2M5.06 TCGA.GN.A266.06 TCGA.D3.A3C1.06 TCGA.D3.A2JH.06 TCGA.EE.A20F.06
#> "03111" "04122" "0443" "04421" "0112" "0411"
#> TCGA.EE.A29E.06 TCGA.ER.A2NG.06 TCGA.ER.A193.06 TCGA.FS.A1ZW.06 TCGA.ER.A19O.06 TCGA.EE.A2ME.06
#> "0133" "014" "0421" "0413" "04421" "01112"
#> TCGA.EE.A20B.06 TCGA.EE.A3AF.06 TCGA.GN.A265.06 TCGA.FS.A1YX.06 TCGA.FS.A1ZJ.06 TCGA.ER.A19H.06
#> "0411" "03" "01132" "0441" "0523" "03"
#> TCGA.EE.A3AC.06 TCGA.EE.A2MU.06 TCGA.ER.A194.01 TCGA.EE.A2MS.06 TCGA.EE.A29R.06 TCGA.D9.A1X3.06
#> "0521" "01133" "04423" "0433" "023" "0221"
#> TCGA.EE.A29X.06 TCGA.EE.A2GK.06 TCGA.EE.A3AA.06 TCGA.ER.A2NE.06 TCGA.EE.A2GR.06 TCGA.FS.A1ZD.06
#> "04421" "0123" "01112" "0212" "0521" "0523"
#> TCGA.ER.A19P.06 TCGA.D3.A1Q8.06 TCGA.ER.A2NC.06 TCGA.BF.A1Q0.01 TCGA.FS.A1ZP.06 TCGA.EE.A182.06
#> "014" "0112" "0443" "0421" "0522" "0432"
#> TCGA.D9.A1JW.06 TCGA.D3.A1Q7.06 TCGA.EE.A185.06 TCGA.EE.A2GJ.06 TCGA.D3.A3CB.06 TCGA.EE.A2GU.06
#> "0421" "014" "0212" "0431" "01111" "0421"
#> TCGA.ER.A195.06 TCGA.FS.A1Z7.06 TCGA.EE.A2M6.06 TCGA.ER.A19K.01 TCGA.DA.A1HY.06 TCGA.D3.A3C7.06
#> "0132" "0423" "0212" "04421" "03" "03"
#> TCGA.EE.A2MP.06 TCGA.EE.A29H.06 TCGA.FR.A3YO.06 TCGA.XV.AB01.01 TCGA.RP.A694.06 TCGA.EB.A5SF.01
#> "03232" "03" "04421" "03" "04423" "0122"
#> TCGA.ER.A19G.06 TCGA.EE.A2GE.06 TCGA.GF.A3OT.06 TCGA.ER.A2NF.06 TCGA.RP.A695.06 TCGA.BF.AAP7.01
#> "03" "0112" "014" "0132" "0512" "0121"
#> TCGA.EB.A3Y7.01 TCGA.EB.A3XC.01 TCGA.ER.A19W.06 TCGA.FR.A69P.06 TCGA.RP.A693.06 TCGA.FW.A3TV.06
#> "0423" "03111" "014" "03" "01111" "0124"
#> TCGA.FW.A3R5.11 TCGA.FW.A3TU.06 TCGA.BF.AAP8.01 TCGA.EE.A2MM.06 TCGA.DA.A1HW.06 TCGA.DA.A1IC.06
#> "0132" "05111" "0422" "0513" "0441" "0521"
#> TCGA.XV.AAZV.01 TCGA.D3.A3C6.06 TCGA.EE.A29C.06 TCGA.BF.AAP2.01 TCGA.EE.A2A2.06 TCGA.GF.A6C8.06
#> "0121" "03232" "0132" "0212" "03" "0443"
#> TCGA.RP.A690.06 TCGA.FW.A5DY.06 TCGA.DA.A1I4.06 TCGA.EE.A29V.06 TCGA.GF.A6C9.06 TCGA.EE.A2GT.06
#> "0122" "014" "0132" "04122" "01132" "01312"
#> TCGA.GN.A9SD.06 TCGA.EE.A3AB.06 TCGA.BF.AAP6.01 TCGA.EB.A5SH.06 TCGA.D9.A6E9.06 TCGA.BF.AAP4.01
#> "014" "0413" "03" "0431" "04421" "04421"
#> TCGA.EE.A2GM.06 TCGA.D3.A3CF.06 TCGA.D9.A6EC.06 TCGA.DA.A1I1.06 TCGA.HR.A2OH.06 TCGA.EE.A2MT.06
#> "0212" "0121" "023" "0413" "014" "0422"
#> TCGA.ER.A19M.06 TCGA.GN.A26C.01 TCGA.FS.A1ZA.06 TCGA.EB.A5SE.01 TCGA.ER.A3PL.06 TCGA.FR.A3R1.01
#> "0411" "01112" "04422" "0222" "0521" "03"
#> TCGA.EE.A2MI.06 TCGA.D3.A3CE.06 TCGA.D3.A5GT.01 TCGA.ER.A2NB.01 TCGA.D3.A1Q5.06 TCGA.EB.A5UN.06
#> "0443" "0441" "05112" "0421" "0422" "01113"
#> TCGA.EB.A299.01 TCGA.DA.A1IA.06 TCGA.EB.A5SG.06 TCGA.D9.A6EA.06 TCGA.XV.AAZY.01 TCGA.EB.A57M.01
#> "03232" "05111" "014" "0222" "014" "04122"
#> TCGA.EE.A2A6.06 TCGA.D3.A2JA.06 TCGA.D3.A1Q1.06 TCGA.EB.A3XF.01 TCGA.D3.A2JF.06 TCGA.XV.AAZW.01
#> "0421" "0132" "0422" "03112" "03234" "03112"
#> TCGA.EB.A3Y6.01 TCGA.EB.A3XE.01 TCGA.D9.A3Z4.01 TCGA.FW.A3R5.06 TCGA.EE.A2GI.06 TCGA.EE.A2GL.06
#> "0441" "0432" "0523" "0432" "0411" "014"
#> TCGA.EB.A3XB.01 TCGA.BF.AAOU.01 TCGA.EB.A3XD.01 TCGA.EE.A2MD.06 TCGA.YD.A9TB.06 TCGA.W3.AA1V.06
#> "04421" "014" "0124" "04421" "0521" "0441"
#> TCGA.ER.A2ND.06 TCGA.D3.A2JK.06 TCGA.FS.A1ZB.06 TCGA.EE.A29D.06 TCGA.EB.A5UM.01 TCGA.QB.A6FS.06
#> "0521" "04122" "0112" "0222" "0432" "0132"
#> TCGA.D9.A3Z1.06 TCGA.D3.A2JN.06 TCGA.FR.A3YN.06 TCGA.FS.A1ZT.06 TCGA.D9.A148.06 TCGA.HR.A2OG.06
#> "01133" "014" "03233" "0132" "04121" "0125"
#> TCGA.EE.A2ML.06 TCGA.EB.A5UL.06 TCGA.EE.A29T.06 TCGA.D9.A3Z3.06 TCGA.D9.A4Z3.01 TCGA.ER.A3ES.06
#> "0413" "04122" "0432" "0124" "0522" "0422"
#> TCGA.XV.A9VZ.01 TCGA.QB.AA9O.06 TCGA.EB.A44Q.06 TCGA.EB.A44R.06 TCGA.BF.A3DJ.01 TCGA.EE.A3JD.06
#> "0122" "03111" "04421" "0433" "03112" "01311"
#> TCGA.D3.A51N.06 TCGA.EB.A44N.01 TCGA.EE.A3J3.06 TCGA.XV.A9W5.01 TCGA.D3.A51G.06 TCGA.EB.A4P0.01
#> "0413" "01133" "03" "04122" "03234" "03112"
#> TCGA.BF.AAP1.01 TCGA.EE.A3J4.06 TCGA.Z2.AA3V.06 TCGA.LH.A9QB.06 TCGA.D3.A51J.06 TCGA.3N.A9WC.06
#> "023" "05112" "0121" "023" "04421" "0421"
#> TCGA.DA.A3F8.06 TCGA.D9.A4Z6.06 TCGA.D3.A51R.06 TCGA.EB.A4OZ.01 TCGA.FS.A4FB.06 TCGA.EE.A3JE.06
#> "01132" "04122" "03" "0121" "03112" "01132"
#> TCGA.W3.AA1W.06 TCGA.DA.A1I0.06 TCGA.D3.A51F.06 TCGA.IH.A3EA.01 TCGA.EB.A431.01 TCGA.EB.A97M.01
#> "01111" "04122" "01311" "0512" "04122" "0222"
#> TCGA.BF.AAOX.01 TCGA.DA.A3F5.06 TCGA.YD.A9TA.06 TCGA.DA.A3F2.06 TCGA.EB.A44O.01 TCGA.EB.A4IQ.01
#> "04121" "0423" "0411" "01311" "0521" "0421"
#> TCGA.EB.A4IS.01 TCGA.YG.AA3O.06 TCGA.ER.A3EV.06 TCGA.3N.A9WD.06 TCGA.BF.A3DM.01 TCGA.XV.A9W2.01
#> "0112" "0512" "0433" "01131" "03" "0423"
#> TCGA.W3.AA1Q.06 TCGA.WE.AAA0.06 TCGA.W3.AA1R.06 TCGA.EE.A3J5.06 TCGA.EB.A4OY.01 TCGA.FS.A4FD.06
#> "0512" "04122" "03" "04122" "0122" "0422"
#> TCGA.BF.AAP0.06 TCGA.YG.AA3P.06 TCGA.EE.A3JA.06 TCGA.W3.AA21.06 TCGA.WE.AAA3.06 TCGA.FS.A4F4.06
#> "0123" "0523" "03231" "0211" "0423" "03111"
#> TCGA.BF.A3DN.01 TCGA.ER.A3ET.06 TCGA.W3.AA1O.06 TCGA.D3.A51E.06 TCGA.Z2.AA3S.06 TCGA.YG.AA3N.01
#> "03" "0423" "0513" "03" "0222" "04421"
#> TCGA.WE.AA9Y.06 TCGA.FS.A4F5.06 TCGA.EE.A3J7.06 TCGA.FS.A4F8.06 TCGA.DA.A3F3.06 TCGA.D3.A51H.06
#> "01113" "023" "05113" "01112" "03231" "01311"
#> TCGA.BF.A3DL.01 TCGA.D3.A51T.06 TCGA.D3.A51K.06 TCGA.EB.A44P.01 TCGA.D9.A4Z5.01 TCGA.WE.AAA4.06
#> "0124" "03" "0522" "0521" "023" "014"
#> TCGA.3N.A9WB.06 TCGA.EE.A3J8.06
#> "0222" "0211"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 1969))
#> TCGA.FR.A728.01 TCGA.GN.A4U8.11 TCGA.GN.A8LL.06 TCGA.FR.A8YC.06 TCGA.DA.A95X.06 TCGA.ER.A42K.06
#> "014" "01132" "03113" "0221" "0211" "03"
#> TCGA.D3.A8GO.06 TCGA.D3.A8GK.06 TCGA.WE.A8JZ.06 TCGA.WE.A8ZO.06 TCGA.D3.A8GI.06 TCGA.FS.A4FC.06
#> "0124" "0524" "0212" "0511" "0512" "0421"
#> TCGA.FS.A4F2.06 TCGA.WE.A8ZM.06 TCGA.WE.A8ZT.06 TCGA.D3.A8GQ.06 TCGA.D3.A8GB.06 TCGA.DA.A95Y.06
#> "03" "0522" "03112" "0411" "01311" "03111"
#> TCGA.EE.A3JI.06 TCGA.OD.A75X.06 TCGA.DA.A960.01 TCGA.D3.A8GV.06 TCGA.WE.A8ZN.06 TCGA.D3.A8GN.06
#> "0221" "023" "0211" "0212" "0112" "014"
#> TCGA.EB.A550.01 TCGA.BF.A5EQ.01 TCGA.EB.A3HV.01 TCGA.HR.A5NC.01 TCGA.DA.A95Z.06 TCGA.EB.A6QZ.01
#> "0122" "0421" "0521" "0523" "0221" "0212"
#> TCGA.FW.A3I3.06 TCGA.WE.A8K6.06 TCGA.D3.A8GP.06 TCGA.EB.A42Z.01 TCGA.GN.A4U4.06 TCGA.GF.A4EO.06
#> "023" "03" "0222" "023" "0212" "014"
#> TCGA.GN.A8LK.06 TCGA.WE.A8K4.01 TCGA.DA.A95W.06 TCGA.FW.A5DX.01 TCGA.GN.A4U3.06 TCGA.EB.A6QY.01
#> "0521" "0112" "0221" "0212" "03111" "0133"
#> TCGA.EB.A5VU.01 TCGA.Z2.A8RT.06 TCGA.WE.A8K1.06 TCGA.EB.A41B.01 TCGA.WE.A8ZY.06 TCGA.D9.A6EG.06
#> "0443" "03" "0112" "03" "0212" "0222"
#> TCGA.BF.A5ER.01 TCGA.FR.A8YD.06 TCGA.FS.A4F9.06 TCGA.EB.A6R0.01 TCGA.ER.A42L.06 TCGA.D3.A8GJ.06
#> "0512" "0511" "0511" "03" "01133" "04423"
#> TCGA.FR.A8YE.06 TCGA.WE.A8ZR.06 TCGA.BF.A9VF.01 TCGA.EE.A3JH.06 TCGA.DA.A95V.06 TCGA.GF.A769.01
#> "01132" "0432" "0521" "0112" "04122" "0212"
#> TCGA.D9.A4Z2.01 TCGA.FR.A44A.06 TCGA.EB.A5VV.06 TCGA.EE.A180.06 TCGA.D3.A8GC.06 TCGA.WE.A8K5.06
#> "03" "014" "0123" "0222" "0513" "023"
#> TCGA.GN.A8LN.01 TCGA.EE.A3JB.06 TCGA.D3.A3MO.06 TCGA.ER.A42H.01 TCGA.WE.A8ZX.06 TCGA.GN.A4U5.01
#> "0212" "0411" "0522" "0511" "04122" "014"
#> TCGA.D3.A8GS.06 TCGA.WE.A8ZQ.06 TCGA.EE.A2MF.06 TCGA.D3.A5GU.06 TCGA.GN.A4U8.06 TCGA.EB.A42Y.01
#> "0441" "0523" "0222" "0511" "0413" "0212"
#> TCGA.D3.A3ML.06 TCGA.EB.A551.01 TCGA.D3.A8GM.06 TCGA.D3.A8GL.06 TCGA.D3.A3MU.06 TCGA.FS.A4F0.06
#> "0511" "04422" "04122" "0221" "0221" "0221"
#> TCGA.D3.A3MV.06 TCGA.GN.A4U7.06 TCGA.FR.A2OS.01 TCGA.D3.A2JE.06 TCGA.YD.A89C.06 TCGA.FR.A726.01
#> "03" "03113" "0523" "0522" "0411" "0411"
#> TCGA.BF.A5EP.01 TCGA.D3.A3MR.06 TCGA.D3.A8GR.06 TCGA.GN.A4U9.06 TCGA.EB.A6L9.06 TCGA.D3.A5GL.06
#> "03" "0112" "0511" "0522" "01311" "03"
#> TCGA.EB.A430.01 TCGA.D3.A8GE.06 TCGA.D3.A8GD.06 TCGA.EB.A41A.01 TCGA.W3.A825.06 TCGA.EE.A183.06
#> "0133" "0132" "014" "0222" "0443" "01112"
#> TCGA.ER.A2NH.06 TCGA.D3.A5GR.06 TCGA.FR.A729.06 TCGA.D3.A1QA.06 TCGA.FS.A1YY.06 TCGA.EE.A2MK.06
#> "0112" "0441" "0441" "0211" "03" "03112"
#> TCGA.EE.A2M8.06 TCGA.EB.A5KH.06 TCGA.FS.A1ZR.06 TCGA.EE.A3AE.06 TCGA.EE.A29P.06 TCGA.EB.A553.01
#> "0123" "0212" "0521" "03112" "04424" "0513"
#> TCGA.EE.A2MR.06 TCGA.GN.A26A.06 TCGA.FS.A1ZY.06 TCGA.EE.A20I.06 TCGA.DA.A1I5.06 TCGA.EE.A184.06
#> "01112" "0411" "0212" "04121" "0125" "023"
#> TCGA.EB.A85J.01 TCGA.RP.A6K9.06 TCGA.EE.A17Y.06 TCGA.D9.A149.06 TCGA.ER.A19D.06 TCGA.FS.A1ZZ.06
#> "0433" "0423" "0411" "0421" "0122" "023"
#> TCGA.EE.A2GP.06 TCGA.EE.A3AD.06 TCGA.D3.A1Q9.06 TCGA.GF.A2C7.01 TCGA.BF.A5ES.01 TCGA.ER.A199.06
#> "0524" "0212" "04121" "0511" "0511" "014"
#> TCGA.EE.A3AH.06 TCGA.W3.A828.06 TCGA.EE.A2A5.06 TCGA.ER.A19L.06 TCGA.BF.A1PX.01 TCGA.ER.A19T.06
#> "0212" "0133" "0522" "0432" "01112" "0431"
#> TCGA.EB.A51B.01 TCGA.FS.A1ZQ.06 TCGA.D3.A2JG.06 TCGA.EE.A2GH.06 TCGA.ER.A19F.06 TCGA.ER.A196.01
#> "03" "03233" "03" "0112" "03" "0124"
#> TCGA.D3.A2JC.06 TCGA.EE.A3AG.06 TCGA.ER.A19S.06 TCGA.EE.A2GC.06 TCGA.EE.A29N.06 TCGA.FR.A7U8.06
#> "0441" "03" "014" "0524" "01133" "023"
#> TCGA.BF.A5EO.01 TCGA.ER.A19B.06 TCGA.D3.A5GN.06 TCGA.D3.A2JB.06 TCGA.ER.A19J.06 TCGA.D3.A2JD.06
#> "04122" "03232" "03232" "0123" "023" "0112"
#> TCGA.FS.A1Z4.06 TCGA.FR.A7UA.06 TCGA.EE.A2M7.06 TCGA.D3.A1Q3.06 TCGA.EB.A85I.01 TCGA.EB.A82C.01
#> "01311" "014" "0441" "0431" "0421" "023"
#> TCGA.ER.A19E.06 TCGA.FS.A1ZK.06 TCGA.FS.A1ZU.06 TCGA.EB.A5FP.01 TCGA.EB.A4XL.01 TCGA.DA.A1I2.06
#> "0522" "0524" "0522" "0212" "03112" "0441"
#> TCGA.EE.A29L.06 TCGA.FS.A1ZN.01 TCGA.EB.A24D.01 TCGA.EE.A2GB.06 TCGA.DA.A1I7.06 TCGA.ER.A2NF.01
#> "0211" "0212" "0511" "03" "0441" "0132"
#> TCGA.GN.A263.01 TCGA.EE.A20C.06 TCGA.EE.A2MQ.06 TCGA.ER.A19N.06 TCGA.FS.A1Z3.06 TCGA.DA.A1I8.06
#> "0132" "023" "0512" "0112" "03" "03"
#> TCGA.D3.A5GS.06 TCGA.EE.A181.06 TCGA.GN.A268.06 TCGA.W3.A824.06 TCGA.EE.A2GS.06 TCGA.FR.A7U9.06
#> "03232" "04121" "0221" "0511" "03" "0121"
#> TCGA.ER.A19Q.06 TCGA.FS.A1ZM.06 TCGA.EE.A2MG.06 TCGA.EE.A2MC.06 TCGA.EE.A17Z.06 TCGA.D3.A2JP.06
#> "0125" "0441" "01311" "01312" "0522" "04122"
#> TCGA.ER.A19C.06 TCGA.EB.A82B.01 TCGA.EE.A2A0.06 TCGA.EE.A29G.06 TCGA.D3.A5GO.06 TCGA.GN.A269.01
#> "0443" "0423" "014" "01131" "03" "01113"
#> TCGA.EE.A2A1.06 TCGA.ER.A1A1.06 TCGA.FS.A1ZG.06 TCGA.FS.A1ZE.06 TCGA.FS.A1ZH.06 TCGA.EE.A2MH.06
#> "01311" "01311" "0222" "0222" "0411" "01112"
#> TCGA.D3.A2J6.06 TCGA.EE.A29Q.06 TCGA.BF.A1PZ.01 TCGA.D3.A3BZ.06 TCGA.D3.A2JO.06 TCGA.GN.A267.06
#> "0423" "03232" "03" "01311" "04422" "0432"
#> TCGA.EE.A2MN.06 TCGA.GN.A264.06 TCGA.ER.A197.06 TCGA.DA.A1IB.06 TCGA.D3.A3CC.06 TCGA.ER.A19T.01
#> "0513" "023" "014" "014" "0423" "0523"
#> TCGA.GN.A261.06 TCGA.FS.A1YW.06 TCGA.BF.A1PU.01 TCGA.D3.A1QB.06 TCGA.D3.A1Q6.06 TCGA.D3.A3C8.06
#> "0122" "023" "0443" "0124" "0441" "014"
#> TCGA.ER.A19A.06 TCGA.EE.A2GN.06 TCGA.EE.A29M.06 TCGA.D3.A2J7.06 TCGA.EB.A24C.01 TCGA.GN.A262.06
#> "01311" "0522" "0121" "01133" "0432" "0212"
#> TCGA.EE.A2GD.06 TCGA.D3.A2J9.06 TCGA.EE.A29B.06 TCGA.D9.A1JX.06 TCGA.EE.A29A.06 TCGA.D3.A2JL.06
#> "014" "01132" "0511" "03" "0221" "04122"
#> TCGA.D3.A1Q4.06 TCGA.FS.A1ZS.06 TCGA.D3.A3C3.06 TCGA.D3.A2J8.06 TCGA.FS.A1ZF.06 TCGA.FS.A1ZC.06
#> "0122" "0423" "0413" "01311" "03232" "0212"
#> TCGA.EE.A20H.06 TCGA.EE.A29W.06 TCGA.D3.A1QA.07 TCGA.BF.A1PV.01 TCGA.EE.A29S.06 TCGA.DA.A1HV.06
#> "0522" "03" "0413" "0512" "04424" "03"
#> TCGA.FS.A1Z0.06 TCGA.EE.A2GO.06 TCGA.EB.A1NK.01 TCGA.GN.A26D.06 TCGA.EE.A2MJ.06 TCGA.ER.A198.06
#> "0122" "023" "0133" "0422" "01132" "0512"
#> TCGA.EE.A17X.06 TCGA.EE.A2M5.06 TCGA.GN.A266.06 TCGA.D3.A3C1.06 TCGA.D3.A2JH.06 TCGA.EE.A20F.06
#> "03111" "04122" "0443" "04421" "0112" "0411"
#> TCGA.EE.A29E.06 TCGA.ER.A2NG.06 TCGA.ER.A193.06 TCGA.FS.A1ZW.06 TCGA.ER.A19O.06 TCGA.EE.A2ME.06
#> "0133" "014" "0421" "0413" "04421" "01112"
#> TCGA.EE.A20B.06 TCGA.EE.A3AF.06 TCGA.GN.A265.06 TCGA.FS.A1YX.06 TCGA.FS.A1ZJ.06 TCGA.ER.A19H.06
#> "0411" "03" "01132" "0441" "0523" "03"
#> TCGA.EE.A3AC.06 TCGA.EE.A2MU.06 TCGA.ER.A194.01 TCGA.EE.A2MS.06 TCGA.EE.A29R.06 TCGA.D9.A1X3.06
#> "0521" "01133" "04423" "0433" "023" "0221"
#> TCGA.EE.A29X.06 TCGA.EE.A2GK.06 TCGA.EE.A3AA.06 TCGA.ER.A2NE.06 TCGA.EE.A2GR.06 TCGA.FS.A1ZD.06
#> "04421" "0123" "01112" "0212" "0521" "0523"
#> TCGA.ER.A19P.06 TCGA.D3.A1Q8.06 TCGA.ER.A2NC.06 TCGA.BF.A1Q0.01 TCGA.FS.A1ZP.06 TCGA.EE.A182.06
#> "014" "0112" "0443" "0421" "0522" "0432"
#> TCGA.D9.A1JW.06 TCGA.D3.A1Q7.06 TCGA.EE.A185.06 TCGA.EE.A2GJ.06 TCGA.D3.A3CB.06 TCGA.EE.A2GU.06
#> "0421" "014" "0212" "0431" "01111" "0421"
#> TCGA.ER.A195.06 TCGA.FS.A1Z7.06 TCGA.EE.A2M6.06 TCGA.ER.A19K.01 TCGA.DA.A1HY.06 TCGA.D3.A3C7.06
#> "0132" "0423" "0212" "04421" "03" "03"
#> TCGA.EE.A2MP.06 TCGA.EE.A29H.06 TCGA.FR.A3YO.06 TCGA.XV.AB01.01 TCGA.RP.A694.06 TCGA.EB.A5SF.01
#> "03232" "03" "04421" "03" "04423" "0122"
#> TCGA.ER.A19G.06 TCGA.EE.A2GE.06 TCGA.GF.A3OT.06 TCGA.ER.A2NF.06 TCGA.RP.A695.06 TCGA.BF.AAP7.01
#> "03" "0112" "014" "0132" "0512" "0121"
#> TCGA.EB.A3Y7.01 TCGA.EB.A3XC.01 TCGA.ER.A19W.06 TCGA.FR.A69P.06 TCGA.RP.A693.06 TCGA.FW.A3TV.06
#> "0423" "03111" "014" "03" "01111" "0124"
#> TCGA.FW.A3R5.11 TCGA.FW.A3TU.06 TCGA.BF.AAP8.01 TCGA.EE.A2MM.06 TCGA.DA.A1HW.06 TCGA.DA.A1IC.06
#> "0132" "0511" "0422" "0513" "0441" "0521"
#> TCGA.XV.AAZV.01 TCGA.D3.A3C6.06 TCGA.EE.A29C.06 TCGA.BF.AAP2.01 TCGA.EE.A2A2.06 TCGA.GF.A6C8.06
#> "0121" "03232" "0132" "0212" "03" "0443"
#> TCGA.RP.A690.06 TCGA.FW.A5DY.06 TCGA.DA.A1I4.06 TCGA.EE.A29V.06 TCGA.GF.A6C9.06 TCGA.EE.A2GT.06
#> "0122" "014" "0132" "04122" "01132" "01312"
#> TCGA.GN.A9SD.06 TCGA.EE.A3AB.06 TCGA.BF.AAP6.01 TCGA.EB.A5SH.06 TCGA.D9.A6E9.06 TCGA.BF.AAP4.01
#> "014" "0413" "03" "0431" "04421" "04421"
#> TCGA.EE.A2GM.06 TCGA.D3.A3CF.06 TCGA.D9.A6EC.06 TCGA.DA.A1I1.06 TCGA.HR.A2OH.06 TCGA.EE.A2MT.06
#> "0212" "0121" "023" "0413" "014" "0422"
#> TCGA.ER.A19M.06 TCGA.GN.A26C.01 TCGA.FS.A1ZA.06 TCGA.EB.A5SE.01 TCGA.ER.A3PL.06 TCGA.FR.A3R1.01
#> "0411" "01112" "04422" "0222" "0521" "03"
#> TCGA.EE.A2MI.06 TCGA.D3.A3CE.06 TCGA.D3.A5GT.01 TCGA.ER.A2NB.01 TCGA.D3.A1Q5.06 TCGA.EB.A5UN.06
#> "0443" "0441" "0511" "0421" "0422" "01113"
#> TCGA.EB.A299.01 TCGA.DA.A1IA.06 TCGA.EB.A5SG.06 TCGA.D9.A6EA.06 TCGA.XV.AAZY.01 TCGA.EB.A57M.01
#> "03232" "0511" "014" "0222" "014" "04122"
#> TCGA.EE.A2A6.06 TCGA.D3.A2JA.06 TCGA.D3.A1Q1.06 TCGA.EB.A3XF.01 TCGA.D3.A2JF.06 TCGA.XV.AAZW.01
#> "0421" "0132" "0422" "03112" "03234" "03112"
#> TCGA.EB.A3Y6.01 TCGA.EB.A3XE.01 TCGA.D9.A3Z4.01 TCGA.FW.A3R5.06 TCGA.EE.A2GI.06 TCGA.EE.A2GL.06
#> "0441" "0432" "0523" "0432" "0411" "014"
#> TCGA.EB.A3XB.01 TCGA.BF.AAOU.01 TCGA.EB.A3XD.01 TCGA.EE.A2MD.06 TCGA.YD.A9TB.06 TCGA.W3.AA1V.06
#> "04421" "014" "0124" "04421" "0521" "0441"
#> TCGA.ER.A2ND.06 TCGA.D3.A2JK.06 TCGA.FS.A1ZB.06 TCGA.EE.A29D.06 TCGA.EB.A5UM.01 TCGA.QB.A6FS.06
#> "0521" "04122" "0112" "0222" "0432" "0132"
#> TCGA.D9.A3Z1.06 TCGA.D3.A2JN.06 TCGA.FR.A3YN.06 TCGA.FS.A1ZT.06 TCGA.D9.A148.06 TCGA.HR.A2OG.06
#> "01133" "014" "03233" "0132" "04121" "0125"
#> TCGA.EE.A2ML.06 TCGA.EB.A5UL.06 TCGA.EE.A29T.06 TCGA.D9.A3Z3.06 TCGA.D9.A4Z3.01 TCGA.ER.A3ES.06
#> "0413" "04122" "0432" "0124" "0522" "0422"
#> TCGA.XV.A9VZ.01 TCGA.QB.AA9O.06 TCGA.EB.A44Q.06 TCGA.EB.A44R.06 TCGA.BF.A3DJ.01 TCGA.EE.A3JD.06
#> "0122" "03111" "04421" "0433" "03112" "01311"
#> TCGA.D3.A51N.06 TCGA.EB.A44N.01 TCGA.EE.A3J3.06 TCGA.XV.A9W5.01 TCGA.D3.A51G.06 TCGA.EB.A4P0.01
#> "0413" "01133" "03" "04122" "03234" "03112"
#> TCGA.BF.AAP1.01 TCGA.EE.A3J4.06 TCGA.Z2.AA3V.06 TCGA.LH.A9QB.06 TCGA.D3.A51J.06 TCGA.3N.A9WC.06
#> "023" "0511" "0121" "023" "04421" "0421"
#> TCGA.DA.A3F8.06 TCGA.D9.A4Z6.06 TCGA.D3.A51R.06 TCGA.EB.A4OZ.01 TCGA.FS.A4FB.06 TCGA.EE.A3JE.06
#> "01132" "04122" "03" "0121" "03112" "01132"
#> TCGA.W3.AA1W.06 TCGA.DA.A1I0.06 TCGA.D3.A51F.06 TCGA.IH.A3EA.01 TCGA.EB.A431.01 TCGA.EB.A97M.01
#> "01111" "04122" "01311" "0512" "04122" "0222"
#> TCGA.BF.AAOX.01 TCGA.DA.A3F5.06 TCGA.YD.A9TA.06 TCGA.DA.A3F2.06 TCGA.EB.A44O.01 TCGA.EB.A4IQ.01
#> "04121" "0423" "0411" "01311" "0521" "0421"
#> TCGA.EB.A4IS.01 TCGA.YG.AA3O.06 TCGA.ER.A3EV.06 TCGA.3N.A9WD.06 TCGA.BF.A3DM.01 TCGA.XV.A9W2.01
#> "0112" "0512" "0433" "01131" "03" "0423"
#> TCGA.W3.AA1Q.06 TCGA.WE.AAA0.06 TCGA.W3.AA1R.06 TCGA.EE.A3J5.06 TCGA.EB.A4OY.01 TCGA.FS.A4FD.06
#> "0512" "04122" "03" "04122" "0122" "0422"
#> TCGA.BF.AAP0.06 TCGA.YG.AA3P.06 TCGA.EE.A3JA.06 TCGA.W3.AA21.06 TCGA.WE.AAA3.06 TCGA.FS.A4F4.06
#> "0123" "0523" "03231" "0211" "0423" "03111"
#> TCGA.BF.A3DN.01 TCGA.ER.A3ET.06 TCGA.W3.AA1O.06 TCGA.D3.A51E.06 TCGA.Z2.AA3S.06 TCGA.YG.AA3N.01
#> "03" "0423" "0513" "03" "0222" "04421"
#> TCGA.WE.AA9Y.06 TCGA.FS.A4F5.06 TCGA.EE.A3J7.06 TCGA.FS.A4F8.06 TCGA.DA.A3F3.06 TCGA.D3.A51H.06
#> "01113" "023" "0511" "01112" "03231" "01311"
#> TCGA.BF.A3DL.01 TCGA.D3.A51T.06 TCGA.D3.A51K.06 TCGA.EB.A44P.01 TCGA.D9.A4Z5.01 TCGA.WE.AAA4.06
#> "0124" "03" "0522" "0521" "023" "014"
#> TCGA.3N.A9WB.06 TCGA.EE.A3J8.06
#> "0222" "0211"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 2117))
#> TCGA.FR.A728.01 TCGA.GN.A4U8.11 TCGA.GN.A8LL.06 TCGA.FR.A8YC.06 TCGA.DA.A95X.06 TCGA.ER.A42K.06
#> "014" "01132" "03113" "0221" "0211" "03"
#> TCGA.D3.A8GO.06 TCGA.D3.A8GK.06 TCGA.WE.A8JZ.06 TCGA.WE.A8ZO.06 TCGA.D3.A8GI.06 TCGA.FS.A4FC.06
#> "0124" "0524" "0212" "0511" "0512" "0421"
#> TCGA.FS.A4F2.06 TCGA.WE.A8ZM.06 TCGA.WE.A8ZT.06 TCGA.D3.A8GQ.06 TCGA.D3.A8GB.06 TCGA.DA.A95Y.06
#> "03" "0522" "03112" "0411" "0131" "03111"
#> TCGA.EE.A3JI.06 TCGA.OD.A75X.06 TCGA.DA.A960.01 TCGA.D3.A8GV.06 TCGA.WE.A8ZN.06 TCGA.D3.A8GN.06
#> "0221" "023" "0211" "0212" "0112" "014"
#> TCGA.EB.A550.01 TCGA.BF.A5EQ.01 TCGA.EB.A3HV.01 TCGA.HR.A5NC.01 TCGA.DA.A95Z.06 TCGA.EB.A6QZ.01
#> "0122" "0421" "0521" "0523" "0221" "0212"
#> TCGA.FW.A3I3.06 TCGA.WE.A8K6.06 TCGA.D3.A8GP.06 TCGA.EB.A42Z.01 TCGA.GN.A4U4.06 TCGA.GF.A4EO.06
#> "023" "03" "0222" "023" "0212" "014"
#> TCGA.GN.A8LK.06 TCGA.WE.A8K4.01 TCGA.DA.A95W.06 TCGA.FW.A5DX.01 TCGA.GN.A4U3.06 TCGA.EB.A6QY.01
#> "0521" "0112" "0221" "0212" "03111" "0133"
#> TCGA.EB.A5VU.01 TCGA.Z2.A8RT.06 TCGA.WE.A8K1.06 TCGA.EB.A41B.01 TCGA.WE.A8ZY.06 TCGA.D9.A6EG.06
#> "0443" "03" "0112" "03" "0212" "0222"
#> TCGA.BF.A5ER.01 TCGA.FR.A8YD.06 TCGA.FS.A4F9.06 TCGA.EB.A6R0.01 TCGA.ER.A42L.06 TCGA.D3.A8GJ.06
#> "0512" "0511" "0511" "03" "01133" "04423"
#> TCGA.FR.A8YE.06 TCGA.WE.A8ZR.06 TCGA.BF.A9VF.01 TCGA.EE.A3JH.06 TCGA.DA.A95V.06 TCGA.GF.A769.01
#> "01132" "0432" "0521" "0112" "04122" "0212"
#> TCGA.D9.A4Z2.01 TCGA.FR.A44A.06 TCGA.EB.A5VV.06 TCGA.EE.A180.06 TCGA.D3.A8GC.06 TCGA.WE.A8K5.06
#> "03" "014" "0123" "0222" "0513" "023"
#> TCGA.GN.A8LN.01 TCGA.EE.A3JB.06 TCGA.D3.A3MO.06 TCGA.ER.A42H.01 TCGA.WE.A8ZX.06 TCGA.GN.A4U5.01
#> "0212" "0411" "0522" "0511" "04122" "014"
#> TCGA.D3.A8GS.06 TCGA.WE.A8ZQ.06 TCGA.EE.A2MF.06 TCGA.D3.A5GU.06 TCGA.GN.A4U8.06 TCGA.EB.A42Y.01
#> "0441" "0523" "0222" "0511" "0413" "0212"
#> TCGA.D3.A3ML.06 TCGA.EB.A551.01 TCGA.D3.A8GM.06 TCGA.D3.A8GL.06 TCGA.D3.A3MU.06 TCGA.FS.A4F0.06
#> "0511" "04422" "04122" "0221" "0221" "0221"
#> TCGA.D3.A3MV.06 TCGA.GN.A4U7.06 TCGA.FR.A2OS.01 TCGA.D3.A2JE.06 TCGA.YD.A89C.06 TCGA.FR.A726.01
#> "03" "03113" "0523" "0522" "0411" "0411"
#> TCGA.BF.A5EP.01 TCGA.D3.A3MR.06 TCGA.D3.A8GR.06 TCGA.GN.A4U9.06 TCGA.EB.A6L9.06 TCGA.D3.A5GL.06
#> "03" "0112" "0511" "0522" "0131" "03"
#> TCGA.EB.A430.01 TCGA.D3.A8GE.06 TCGA.D3.A8GD.06 TCGA.EB.A41A.01 TCGA.W3.A825.06 TCGA.EE.A183.06
#> "0133" "0132" "014" "0222" "0443" "01112"
#> TCGA.ER.A2NH.06 TCGA.D3.A5GR.06 TCGA.FR.A729.06 TCGA.D3.A1QA.06 TCGA.FS.A1YY.06 TCGA.EE.A2MK.06
#> "0112" "0441" "0441" "0211" "03" "03112"
#> TCGA.EE.A2M8.06 TCGA.EB.A5KH.06 TCGA.FS.A1ZR.06 TCGA.EE.A3AE.06 TCGA.EE.A29P.06 TCGA.EB.A553.01
#> "0123" "0212" "0521" "03112" "04424" "0513"
#> TCGA.EE.A2MR.06 TCGA.GN.A26A.06 TCGA.FS.A1ZY.06 TCGA.EE.A20I.06 TCGA.DA.A1I5.06 TCGA.EE.A184.06
#> "01112" "0411" "0212" "04121" "0125" "023"
#> TCGA.EB.A85J.01 TCGA.RP.A6K9.06 TCGA.EE.A17Y.06 TCGA.D9.A149.06 TCGA.ER.A19D.06 TCGA.FS.A1ZZ.06
#> "0433" "0423" "0411" "0421" "0122" "023"
#> TCGA.EE.A2GP.06 TCGA.EE.A3AD.06 TCGA.D3.A1Q9.06 TCGA.GF.A2C7.01 TCGA.BF.A5ES.01 TCGA.ER.A199.06
#> "0524" "0212" "04121" "0511" "0511" "014"
#> TCGA.EE.A3AH.06 TCGA.W3.A828.06 TCGA.EE.A2A5.06 TCGA.ER.A19L.06 TCGA.BF.A1PX.01 TCGA.ER.A19T.06
#> "0212" "0133" "0522" "0432" "01112" "0431"
#> TCGA.EB.A51B.01 TCGA.FS.A1ZQ.06 TCGA.D3.A2JG.06 TCGA.EE.A2GH.06 TCGA.ER.A19F.06 TCGA.ER.A196.01
#> "03" "03233" "03" "0112" "03" "0124"
#> TCGA.D3.A2JC.06 TCGA.EE.A3AG.06 TCGA.ER.A19S.06 TCGA.EE.A2GC.06 TCGA.EE.A29N.06 TCGA.FR.A7U8.06
#> "0441" "03" "014" "0524" "01133" "023"
#> TCGA.BF.A5EO.01 TCGA.ER.A19B.06 TCGA.D3.A5GN.06 TCGA.D3.A2JB.06 TCGA.ER.A19J.06 TCGA.D3.A2JD.06
#> "04122" "03232" "03232" "0123" "023" "0112"
#> TCGA.FS.A1Z4.06 TCGA.FR.A7UA.06 TCGA.EE.A2M7.06 TCGA.D3.A1Q3.06 TCGA.EB.A85I.01 TCGA.EB.A82C.01
#> "0131" "014" "0441" "0431" "0421" "023"
#> TCGA.ER.A19E.06 TCGA.FS.A1ZK.06 TCGA.FS.A1ZU.06 TCGA.EB.A5FP.01 TCGA.EB.A4XL.01 TCGA.DA.A1I2.06
#> "0522" "0524" "0522" "0212" "03112" "0441"
#> TCGA.EE.A29L.06 TCGA.FS.A1ZN.01 TCGA.EB.A24D.01 TCGA.EE.A2GB.06 TCGA.DA.A1I7.06 TCGA.ER.A2NF.01
#> "0211" "0212" "0511" "03" "0441" "0132"
#> TCGA.GN.A263.01 TCGA.EE.A20C.06 TCGA.EE.A2MQ.06 TCGA.ER.A19N.06 TCGA.FS.A1Z3.06 TCGA.DA.A1I8.06
#> "0132" "023" "0512" "0112" "03" "03"
#> TCGA.D3.A5GS.06 TCGA.EE.A181.06 TCGA.GN.A268.06 TCGA.W3.A824.06 TCGA.EE.A2GS.06 TCGA.FR.A7U9.06
#> "03232" "04121" "0221" "0511" "03" "0121"
#> TCGA.ER.A19Q.06 TCGA.FS.A1ZM.06 TCGA.EE.A2MG.06 TCGA.EE.A2MC.06 TCGA.EE.A17Z.06 TCGA.D3.A2JP.06
#> "0125" "0441" "0131" "0131" "0522" "04122"
#> TCGA.ER.A19C.06 TCGA.EB.A82B.01 TCGA.EE.A2A0.06 TCGA.EE.A29G.06 TCGA.D3.A5GO.06 TCGA.GN.A269.01
#> "0443" "0423" "014" "01131" "03" "01113"
#> TCGA.EE.A2A1.06 TCGA.ER.A1A1.06 TCGA.FS.A1ZG.06 TCGA.FS.A1ZE.06 TCGA.FS.A1ZH.06 TCGA.EE.A2MH.06
#> "0131" "0131" "0222" "0222" "0411" "01112"
#> TCGA.D3.A2J6.06 TCGA.EE.A29Q.06 TCGA.BF.A1PZ.01 TCGA.D3.A3BZ.06 TCGA.D3.A2JO.06 TCGA.GN.A267.06
#> "0423" "03232" "03" "0131" "04422" "0432"
#> TCGA.EE.A2MN.06 TCGA.GN.A264.06 TCGA.ER.A197.06 TCGA.DA.A1IB.06 TCGA.D3.A3CC.06 TCGA.ER.A19T.01
#> "0513" "023" "014" "014" "0423" "0523"
#> TCGA.GN.A261.06 TCGA.FS.A1YW.06 TCGA.BF.A1PU.01 TCGA.D3.A1QB.06 TCGA.D3.A1Q6.06 TCGA.D3.A3C8.06
#> "0122" "023" "0443" "0124" "0441" "014"
#> TCGA.ER.A19A.06 TCGA.EE.A2GN.06 TCGA.EE.A29M.06 TCGA.D3.A2J7.06 TCGA.EB.A24C.01 TCGA.GN.A262.06
#> "0131" "0522" "0121" "01133" "0432" "0212"
#> TCGA.EE.A2GD.06 TCGA.D3.A2J9.06 TCGA.EE.A29B.06 TCGA.D9.A1JX.06 TCGA.EE.A29A.06 TCGA.D3.A2JL.06
#> "014" "01132" "0511" "03" "0221" "04122"
#> TCGA.D3.A1Q4.06 TCGA.FS.A1ZS.06 TCGA.D3.A3C3.06 TCGA.D3.A2J8.06 TCGA.FS.A1ZF.06 TCGA.FS.A1ZC.06
#> "0122" "0423" "0413" "0131" "03232" "0212"
#> TCGA.EE.A20H.06 TCGA.EE.A29W.06 TCGA.D3.A1QA.07 TCGA.BF.A1PV.01 TCGA.EE.A29S.06 TCGA.DA.A1HV.06
#> "0522" "03" "0413" "0512" "04424" "03"
#> TCGA.FS.A1Z0.06 TCGA.EE.A2GO.06 TCGA.EB.A1NK.01 TCGA.GN.A26D.06 TCGA.EE.A2MJ.06 TCGA.ER.A198.06
#> "0122" "023" "0133" "0422" "01132" "0512"
#> TCGA.EE.A17X.06 TCGA.EE.A2M5.06 TCGA.GN.A266.06 TCGA.D3.A3C1.06 TCGA.D3.A2JH.06 TCGA.EE.A20F.06
#> "03111" "04122" "0443" "04421" "0112" "0411"
#> TCGA.EE.A29E.06 TCGA.ER.A2NG.06 TCGA.ER.A193.06 TCGA.FS.A1ZW.06 TCGA.ER.A19O.06 TCGA.EE.A2ME.06
#> "0133" "014" "0421" "0413" "04421" "01112"
#> TCGA.EE.A20B.06 TCGA.EE.A3AF.06 TCGA.GN.A265.06 TCGA.FS.A1YX.06 TCGA.FS.A1ZJ.06 TCGA.ER.A19H.06
#> "0411" "03" "01132" "0441" "0523" "03"
#> TCGA.EE.A3AC.06 TCGA.EE.A2MU.06 TCGA.ER.A194.01 TCGA.EE.A2MS.06 TCGA.EE.A29R.06 TCGA.D9.A1X3.06
#> "0521" "01133" "04423" "0433" "023" "0221"
#> TCGA.EE.A29X.06 TCGA.EE.A2GK.06 TCGA.EE.A3AA.06 TCGA.ER.A2NE.06 TCGA.EE.A2GR.06 TCGA.FS.A1ZD.06
#> "04421" "0123" "01112" "0212" "0521" "0523"
#> TCGA.ER.A19P.06 TCGA.D3.A1Q8.06 TCGA.ER.A2NC.06 TCGA.BF.A1Q0.01 TCGA.FS.A1ZP.06 TCGA.EE.A182.06
#> "014" "0112" "0443" "0421" "0522" "0432"
#> TCGA.D9.A1JW.06 TCGA.D3.A1Q7.06 TCGA.EE.A185.06 TCGA.EE.A2GJ.06 TCGA.D3.A3CB.06 TCGA.EE.A2GU.06
#> "0421" "014" "0212" "0431" "01111" "0421"
#> TCGA.ER.A195.06 TCGA.FS.A1Z7.06 TCGA.EE.A2M6.06 TCGA.ER.A19K.01 TCGA.DA.A1HY.06 TCGA.D3.A3C7.06
#> "0132" "0423" "0212" "04421" "03" "03"
#> TCGA.EE.A2MP.06 TCGA.EE.A29H.06 TCGA.FR.A3YO.06 TCGA.XV.AB01.01 TCGA.RP.A694.06 TCGA.EB.A5SF.01
#> "03232" "03" "04421" "03" "04423" "0122"
#> TCGA.ER.A19G.06 TCGA.EE.A2GE.06 TCGA.GF.A3OT.06 TCGA.ER.A2NF.06 TCGA.RP.A695.06 TCGA.BF.AAP7.01
#> "03" "0112" "014" "0132" "0512" "0121"
#> TCGA.EB.A3Y7.01 TCGA.EB.A3XC.01 TCGA.ER.A19W.06 TCGA.FR.A69P.06 TCGA.RP.A693.06 TCGA.FW.A3TV.06
#> "0423" "03111" "014" "03" "01111" "0124"
#> TCGA.FW.A3R5.11 TCGA.FW.A3TU.06 TCGA.BF.AAP8.01 TCGA.EE.A2MM.06 TCGA.DA.A1HW.06 TCGA.DA.A1IC.06
#> "0132" "0511" "0422" "0513" "0441" "0521"
#> TCGA.XV.AAZV.01 TCGA.D3.A3C6.06 TCGA.EE.A29C.06 TCGA.BF.AAP2.01 TCGA.EE.A2A2.06 TCGA.GF.A6C8.06
#> "0121" "03232" "0132" "0212" "03" "0443"
#> TCGA.RP.A690.06 TCGA.FW.A5DY.06 TCGA.DA.A1I4.06 TCGA.EE.A29V.06 TCGA.GF.A6C9.06 TCGA.EE.A2GT.06
#> "0122" "014" "0132" "04122" "01132" "0131"
#> TCGA.GN.A9SD.06 TCGA.EE.A3AB.06 TCGA.BF.AAP6.01 TCGA.EB.A5SH.06 TCGA.D9.A6E9.06 TCGA.BF.AAP4.01
#> "014" "0413" "03" "0431" "04421" "04421"
#> TCGA.EE.A2GM.06 TCGA.D3.A3CF.06 TCGA.D9.A6EC.06 TCGA.DA.A1I1.06 TCGA.HR.A2OH.06 TCGA.EE.A2MT.06
#> "0212" "0121" "023" "0413" "014" "0422"
#> TCGA.ER.A19M.06 TCGA.GN.A26C.01 TCGA.FS.A1ZA.06 TCGA.EB.A5SE.01 TCGA.ER.A3PL.06 TCGA.FR.A3R1.01
#> "0411" "01112" "04422" "0222" "0521" "03"
#> TCGA.EE.A2MI.06 TCGA.D3.A3CE.06 TCGA.D3.A5GT.01 TCGA.ER.A2NB.01 TCGA.D3.A1Q5.06 TCGA.EB.A5UN.06
#> "0443" "0441" "0511" "0421" "0422" "01113"
#> TCGA.EB.A299.01 TCGA.DA.A1IA.06 TCGA.EB.A5SG.06 TCGA.D9.A6EA.06 TCGA.XV.AAZY.01 TCGA.EB.A57M.01
#> "03232" "0511" "014" "0222" "014" "04122"
#> TCGA.EE.A2A6.06 TCGA.D3.A2JA.06 TCGA.D3.A1Q1.06 TCGA.EB.A3XF.01 TCGA.D3.A2JF.06 TCGA.XV.AAZW.01
#> "0421" "0132" "0422" "03112" "03234" "03112"
#> TCGA.EB.A3Y6.01 TCGA.EB.A3XE.01 TCGA.D9.A3Z4.01 TCGA.FW.A3R5.06 TCGA.EE.A2GI.06 TCGA.EE.A2GL.06
#> "0441" "0432" "0523" "0432" "0411" "014"
#> TCGA.EB.A3XB.01 TCGA.BF.AAOU.01 TCGA.EB.A3XD.01 TCGA.EE.A2MD.06 TCGA.YD.A9TB.06 TCGA.W3.AA1V.06
#> "04421" "014" "0124" "04421" "0521" "0441"
#> TCGA.ER.A2ND.06 TCGA.D3.A2JK.06 TCGA.FS.A1ZB.06 TCGA.EE.A29D.06 TCGA.EB.A5UM.01 TCGA.QB.A6FS.06
#> "0521" "04122" "0112" "0222" "0432" "0132"
#> TCGA.D9.A3Z1.06 TCGA.D3.A2JN.06 TCGA.FR.A3YN.06 TCGA.FS.A1ZT.06 TCGA.D9.A148.06 TCGA.HR.A2OG.06
#> "01133" "014" "03233" "0132" "04121" "0125"
#> TCGA.EE.A2ML.06 TCGA.EB.A5UL.06 TCGA.EE.A29T.06 TCGA.D9.A3Z3.06 TCGA.D9.A4Z3.01 TCGA.ER.A3ES.06
#> "0413" "04122" "0432" "0124" "0522" "0422"
#> TCGA.XV.A9VZ.01 TCGA.QB.AA9O.06 TCGA.EB.A44Q.06 TCGA.EB.A44R.06 TCGA.BF.A3DJ.01 TCGA.EE.A3JD.06
#> "0122" "03111" "04421" "0433" "03112" "0131"
#> TCGA.D3.A51N.06 TCGA.EB.A44N.01 TCGA.EE.A3J3.06 TCGA.XV.A9W5.01 TCGA.D3.A51G.06 TCGA.EB.A4P0.01
#> "0413" "01133" "03" "04122" "03234" "03112"
#> TCGA.BF.AAP1.01 TCGA.EE.A3J4.06 TCGA.Z2.AA3V.06 TCGA.LH.A9QB.06 TCGA.D3.A51J.06 TCGA.3N.A9WC.06
#> "023" "0511" "0121" "023" "04421" "0421"
#> TCGA.DA.A3F8.06 TCGA.D9.A4Z6.06 TCGA.D3.A51R.06 TCGA.EB.A4OZ.01 TCGA.FS.A4FB.06 TCGA.EE.A3JE.06
#> "01132" "04122" "03" "0121" "03112" "01132"
#> TCGA.W3.AA1W.06 TCGA.DA.A1I0.06 TCGA.D3.A51F.06 TCGA.IH.A3EA.01 TCGA.EB.A431.01 TCGA.EB.A97M.01
#> "01111" "04122" "0131" "0512" "04122" "0222"
#> TCGA.BF.AAOX.01 TCGA.DA.A3F5.06 TCGA.YD.A9TA.06 TCGA.DA.A3F2.06 TCGA.EB.A44O.01 TCGA.EB.A4IQ.01
#> "04121" "0423" "0411" "0131" "0521" "0421"
#> TCGA.EB.A4IS.01 TCGA.YG.AA3O.06 TCGA.ER.A3EV.06 TCGA.3N.A9WD.06 TCGA.BF.A3DM.01 TCGA.XV.A9W2.01
#> "0112" "0512" "0433" "01131" "03" "0423"
#> TCGA.W3.AA1Q.06 TCGA.WE.AAA0.06 TCGA.W3.AA1R.06 TCGA.EE.A3J5.06 TCGA.EB.A4OY.01 TCGA.FS.A4FD.06
#> "0512" "04122" "03" "04122" "0122" "0422"
#> TCGA.BF.AAP0.06 TCGA.YG.AA3P.06 TCGA.EE.A3JA.06 TCGA.W3.AA21.06 TCGA.WE.AAA3.06 TCGA.FS.A4F4.06
#> "0123" "0523" "03231" "0211" "0423" "03111"
#> TCGA.BF.A3DN.01 TCGA.ER.A3ET.06 TCGA.W3.AA1O.06 TCGA.D3.A51E.06 TCGA.Z2.AA3S.06 TCGA.YG.AA3N.01
#> "03" "0423" "0513" "03" "0222" "04421"
#> TCGA.WE.AA9Y.06 TCGA.FS.A4F5.06 TCGA.EE.A3J7.06 TCGA.FS.A4F8.06 TCGA.DA.A3F3.06 TCGA.D3.A51H.06
#> "01113" "023" "0511" "01112" "03231" "0131"
#> TCGA.BF.A3DL.01 TCGA.D3.A51T.06 TCGA.D3.A51K.06 TCGA.EB.A44P.01 TCGA.D9.A4Z5.01 TCGA.WE.AAA4.06
#> "0124" "03" "0522" "0521" "023" "014"
#> TCGA.3N.A9WB.06 TCGA.EE.A3J8.06
#> "0222" "0211"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 2142))
#> TCGA.FR.A728.01 TCGA.GN.A4U8.11 TCGA.GN.A8LL.06 TCGA.FR.A8YC.06 TCGA.DA.A95X.06 TCGA.ER.A42K.06
#> "014" "01132" "03113" "0221" "0211" "03"
#> TCGA.D3.A8GO.06 TCGA.D3.A8GK.06 TCGA.WE.A8JZ.06 TCGA.WE.A8ZO.06 TCGA.D3.A8GI.06 TCGA.FS.A4FC.06
#> "0124" "0524" "0212" "0511" "0512" "0421"
#> TCGA.FS.A4F2.06 TCGA.WE.A8ZM.06 TCGA.WE.A8ZT.06 TCGA.D3.A8GQ.06 TCGA.D3.A8GB.06 TCGA.DA.A95Y.06
#> "03" "0522" "03112" "0411" "0131" "03111"
#> TCGA.EE.A3JI.06 TCGA.OD.A75X.06 TCGA.DA.A960.01 TCGA.D3.A8GV.06 TCGA.WE.A8ZN.06 TCGA.D3.A8GN.06
#> "0221" "023" "0211" "0212" "0112" "014"
#> TCGA.EB.A550.01 TCGA.BF.A5EQ.01 TCGA.EB.A3HV.01 TCGA.HR.A5NC.01 TCGA.DA.A95Z.06 TCGA.EB.A6QZ.01
#> "0122" "0421" "0521" "0523" "0221" "0212"
#> TCGA.FW.A3I3.06 TCGA.WE.A8K6.06 TCGA.D3.A8GP.06 TCGA.EB.A42Z.01 TCGA.GN.A4U4.06 TCGA.GF.A4EO.06
#> "023" "03" "0222" "023" "0212" "014"
#> TCGA.GN.A8LK.06 TCGA.WE.A8K4.01 TCGA.DA.A95W.06 TCGA.FW.A5DX.01 TCGA.GN.A4U3.06 TCGA.EB.A6QY.01
#> "0521" "0112" "0221" "0212" "03111" "0133"
#> TCGA.EB.A5VU.01 TCGA.Z2.A8RT.06 TCGA.WE.A8K1.06 TCGA.EB.A41B.01 TCGA.WE.A8ZY.06 TCGA.D9.A6EG.06
#> "0443" "03" "0112" "03" "0212" "0222"
#> TCGA.BF.A5ER.01 TCGA.FR.A8YD.06 TCGA.FS.A4F9.06 TCGA.EB.A6R0.01 TCGA.ER.A42L.06 TCGA.D3.A8GJ.06
#> "0512" "0511" "0511" "03" "01133" "04423"
#> TCGA.FR.A8YE.06 TCGA.WE.A8ZR.06 TCGA.BF.A9VF.01 TCGA.EE.A3JH.06 TCGA.DA.A95V.06 TCGA.GF.A769.01
#> "01132" "0432" "0521" "0112" "0412" "0212"
#> TCGA.D9.A4Z2.01 TCGA.FR.A44A.06 TCGA.EB.A5VV.06 TCGA.EE.A180.06 TCGA.D3.A8GC.06 TCGA.WE.A8K5.06
#> "03" "014" "0123" "0222" "0513" "023"
#> TCGA.GN.A8LN.01 TCGA.EE.A3JB.06 TCGA.D3.A3MO.06 TCGA.ER.A42H.01 TCGA.WE.A8ZX.06 TCGA.GN.A4U5.01
#> "0212" "0411" "0522" "0511" "0412" "014"
#> TCGA.D3.A8GS.06 TCGA.WE.A8ZQ.06 TCGA.EE.A2MF.06 TCGA.D3.A5GU.06 TCGA.GN.A4U8.06 TCGA.EB.A42Y.01
#> "0441" "0523" "0222" "0511" "0413" "0212"
#> TCGA.D3.A3ML.06 TCGA.EB.A551.01 TCGA.D3.A8GM.06 TCGA.D3.A8GL.06 TCGA.D3.A3MU.06 TCGA.FS.A4F0.06
#> "0511" "04422" "0412" "0221" "0221" "0221"
#> TCGA.D3.A3MV.06 TCGA.GN.A4U7.06 TCGA.FR.A2OS.01 TCGA.D3.A2JE.06 TCGA.YD.A89C.06 TCGA.FR.A726.01
#> "03" "03113" "0523" "0522" "0411" "0411"
#> TCGA.BF.A5EP.01 TCGA.D3.A3MR.06 TCGA.D3.A8GR.06 TCGA.GN.A4U9.06 TCGA.EB.A6L9.06 TCGA.D3.A5GL.06
#> "03" "0112" "0511" "0522" "0131" "03"
#> TCGA.EB.A430.01 TCGA.D3.A8GE.06 TCGA.D3.A8GD.06 TCGA.EB.A41A.01 TCGA.W3.A825.06 TCGA.EE.A183.06
#> "0133" "0132" "014" "0222" "0443" "01112"
#> TCGA.ER.A2NH.06 TCGA.D3.A5GR.06 TCGA.FR.A729.06 TCGA.D3.A1QA.06 TCGA.FS.A1YY.06 TCGA.EE.A2MK.06
#> "0112" "0441" "0441" "0211" "03" "03112"
#> TCGA.EE.A2M8.06 TCGA.EB.A5KH.06 TCGA.FS.A1ZR.06 TCGA.EE.A3AE.06 TCGA.EE.A29P.06 TCGA.EB.A553.01
#> "0123" "0212" "0521" "03112" "04424" "0513"
#> TCGA.EE.A2MR.06 TCGA.GN.A26A.06 TCGA.FS.A1ZY.06 TCGA.EE.A20I.06 TCGA.DA.A1I5.06 TCGA.EE.A184.06
#> "01112" "0411" "0212" "0412" "0125" "023"
#> TCGA.EB.A85J.01 TCGA.RP.A6K9.06 TCGA.EE.A17Y.06 TCGA.D9.A149.06 TCGA.ER.A19D.06 TCGA.FS.A1ZZ.06
#> "0433" "0423" "0411" "0421" "0122" "023"
#> TCGA.EE.A2GP.06 TCGA.EE.A3AD.06 TCGA.D3.A1Q9.06 TCGA.GF.A2C7.01 TCGA.BF.A5ES.01 TCGA.ER.A199.06
#> "0524" "0212" "0412" "0511" "0511" "014"
#> TCGA.EE.A3AH.06 TCGA.W3.A828.06 TCGA.EE.A2A5.06 TCGA.ER.A19L.06 TCGA.BF.A1PX.01 TCGA.ER.A19T.06
#> "0212" "0133" "0522" "0432" "01112" "0431"
#> TCGA.EB.A51B.01 TCGA.FS.A1ZQ.06 TCGA.D3.A2JG.06 TCGA.EE.A2GH.06 TCGA.ER.A19F.06 TCGA.ER.A196.01
#> "03" "03233" "03" "0112" "03" "0124"
#> TCGA.D3.A2JC.06 TCGA.EE.A3AG.06 TCGA.ER.A19S.06 TCGA.EE.A2GC.06 TCGA.EE.A29N.06 TCGA.FR.A7U8.06
#> "0441" "03" "014" "0524" "01133" "023"
#> TCGA.BF.A5EO.01 TCGA.ER.A19B.06 TCGA.D3.A5GN.06 TCGA.D3.A2JB.06 TCGA.ER.A19J.06 TCGA.D3.A2JD.06
#> "0412" "03232" "03232" "0123" "023" "0112"
#> TCGA.FS.A1Z4.06 TCGA.FR.A7UA.06 TCGA.EE.A2M7.06 TCGA.D3.A1Q3.06 TCGA.EB.A85I.01 TCGA.EB.A82C.01
#> "0131" "014" "0441" "0431" "0421" "023"
#> TCGA.ER.A19E.06 TCGA.FS.A1ZK.06 TCGA.FS.A1ZU.06 TCGA.EB.A5FP.01 TCGA.EB.A4XL.01 TCGA.DA.A1I2.06
#> "0522" "0524" "0522" "0212" "03112" "0441"
#> TCGA.EE.A29L.06 TCGA.FS.A1ZN.01 TCGA.EB.A24D.01 TCGA.EE.A2GB.06 TCGA.DA.A1I7.06 TCGA.ER.A2NF.01
#> "0211" "0212" "0511" "03" "0441" "0132"
#> TCGA.GN.A263.01 TCGA.EE.A20C.06 TCGA.EE.A2MQ.06 TCGA.ER.A19N.06 TCGA.FS.A1Z3.06 TCGA.DA.A1I8.06
#> "0132" "023" "0512" "0112" "03" "03"
#> TCGA.D3.A5GS.06 TCGA.EE.A181.06 TCGA.GN.A268.06 TCGA.W3.A824.06 TCGA.EE.A2GS.06 TCGA.FR.A7U9.06
#> "03232" "0412" "0221" "0511" "03" "0121"
#> TCGA.ER.A19Q.06 TCGA.FS.A1ZM.06 TCGA.EE.A2MG.06 TCGA.EE.A2MC.06 TCGA.EE.A17Z.06 TCGA.D3.A2JP.06
#> "0125" "0441" "0131" "0131" "0522" "0412"
#> TCGA.ER.A19C.06 TCGA.EB.A82B.01 TCGA.EE.A2A0.06 TCGA.EE.A29G.06 TCGA.D3.A5GO.06 TCGA.GN.A269.01
#> "0443" "0423" "014" "01131" "03" "01113"
#> TCGA.EE.A2A1.06 TCGA.ER.A1A1.06 TCGA.FS.A1ZG.06 TCGA.FS.A1ZE.06 TCGA.FS.A1ZH.06 TCGA.EE.A2MH.06
#> "0131" "0131" "0222" "0222" "0411" "01112"
#> TCGA.D3.A2J6.06 TCGA.EE.A29Q.06 TCGA.BF.A1PZ.01 TCGA.D3.A3BZ.06 TCGA.D3.A2JO.06 TCGA.GN.A267.06
#> "0423" "03232" "03" "0131" "04422" "0432"
#> TCGA.EE.A2MN.06 TCGA.GN.A264.06 TCGA.ER.A197.06 TCGA.DA.A1IB.06 TCGA.D3.A3CC.06 TCGA.ER.A19T.01
#> "0513" "023" "014" "014" "0423" "0523"
#> TCGA.GN.A261.06 TCGA.FS.A1YW.06 TCGA.BF.A1PU.01 TCGA.D3.A1QB.06 TCGA.D3.A1Q6.06 TCGA.D3.A3C8.06
#> "0122" "023" "0443" "0124" "0441" "014"
#> TCGA.ER.A19A.06 TCGA.EE.A2GN.06 TCGA.EE.A29M.06 TCGA.D3.A2J7.06 TCGA.EB.A24C.01 TCGA.GN.A262.06
#> "0131" "0522" "0121" "01133" "0432" "0212"
#> TCGA.EE.A2GD.06 TCGA.D3.A2J9.06 TCGA.EE.A29B.06 TCGA.D9.A1JX.06 TCGA.EE.A29A.06 TCGA.D3.A2JL.06
#> "014" "01132" "0511" "03" "0221" "0412"
#> TCGA.D3.A1Q4.06 TCGA.FS.A1ZS.06 TCGA.D3.A3C3.06 TCGA.D3.A2J8.06 TCGA.FS.A1ZF.06 TCGA.FS.A1ZC.06
#> "0122" "0423" "0413" "0131" "03232" "0212"
#> TCGA.EE.A20H.06 TCGA.EE.A29W.06 TCGA.D3.A1QA.07 TCGA.BF.A1PV.01 TCGA.EE.A29S.06 TCGA.DA.A1HV.06
#> "0522" "03" "0413" "0512" "04424" "03"
#> TCGA.FS.A1Z0.06 TCGA.EE.A2GO.06 TCGA.EB.A1NK.01 TCGA.GN.A26D.06 TCGA.EE.A2MJ.06 TCGA.ER.A198.06
#> "0122" "023" "0133" "0422" "01132" "0512"
#> TCGA.EE.A17X.06 TCGA.EE.A2M5.06 TCGA.GN.A266.06 TCGA.D3.A3C1.06 TCGA.D3.A2JH.06 TCGA.EE.A20F.06
#> "03111" "0412" "0443" "04421" "0112" "0411"
#> TCGA.EE.A29E.06 TCGA.ER.A2NG.06 TCGA.ER.A193.06 TCGA.FS.A1ZW.06 TCGA.ER.A19O.06 TCGA.EE.A2ME.06
#> "0133" "014" "0421" "0413" "04421" "01112"
#> TCGA.EE.A20B.06 TCGA.EE.A3AF.06 TCGA.GN.A265.06 TCGA.FS.A1YX.06 TCGA.FS.A1ZJ.06 TCGA.ER.A19H.06
#> "0411" "03" "01132" "0441" "0523" "03"
#> TCGA.EE.A3AC.06 TCGA.EE.A2MU.06 TCGA.ER.A194.01 TCGA.EE.A2MS.06 TCGA.EE.A29R.06 TCGA.D9.A1X3.06
#> "0521" "01133" "04423" "0433" "023" "0221"
#> TCGA.EE.A29X.06 TCGA.EE.A2GK.06 TCGA.EE.A3AA.06 TCGA.ER.A2NE.06 TCGA.EE.A2GR.06 TCGA.FS.A1ZD.06
#> "04421" "0123" "01112" "0212" "0521" "0523"
#> TCGA.ER.A19P.06 TCGA.D3.A1Q8.06 TCGA.ER.A2NC.06 TCGA.BF.A1Q0.01 TCGA.FS.A1ZP.06 TCGA.EE.A182.06
#> "014" "0112" "0443" "0421" "0522" "0432"
#> TCGA.D9.A1JW.06 TCGA.D3.A1Q7.06 TCGA.EE.A185.06 TCGA.EE.A2GJ.06 TCGA.D3.A3CB.06 TCGA.EE.A2GU.06
#> "0421" "014" "0212" "0431" "01111" "0421"
#> TCGA.ER.A195.06 TCGA.FS.A1Z7.06 TCGA.EE.A2M6.06 TCGA.ER.A19K.01 TCGA.DA.A1HY.06 TCGA.D3.A3C7.06
#> "0132" "0423" "0212" "04421" "03" "03"
#> TCGA.EE.A2MP.06 TCGA.EE.A29H.06 TCGA.FR.A3YO.06 TCGA.XV.AB01.01 TCGA.RP.A694.06 TCGA.EB.A5SF.01
#> "03232" "03" "04421" "03" "04423" "0122"
#> TCGA.ER.A19G.06 TCGA.EE.A2GE.06 TCGA.GF.A3OT.06 TCGA.ER.A2NF.06 TCGA.RP.A695.06 TCGA.BF.AAP7.01
#> "03" "0112" "014" "0132" "0512" "0121"
#> TCGA.EB.A3Y7.01 TCGA.EB.A3XC.01 TCGA.ER.A19W.06 TCGA.FR.A69P.06 TCGA.RP.A693.06 TCGA.FW.A3TV.06
#> "0423" "03111" "014" "03" "01111" "0124"
#> TCGA.FW.A3R5.11 TCGA.FW.A3TU.06 TCGA.BF.AAP8.01 TCGA.EE.A2MM.06 TCGA.DA.A1HW.06 TCGA.DA.A1IC.06
#> "0132" "0511" "0422" "0513" "0441" "0521"
#> TCGA.XV.AAZV.01 TCGA.D3.A3C6.06 TCGA.EE.A29C.06 TCGA.BF.AAP2.01 TCGA.EE.A2A2.06 TCGA.GF.A6C8.06
#> "0121" "03232" "0132" "0212" "03" "0443"
#> TCGA.RP.A690.06 TCGA.FW.A5DY.06 TCGA.DA.A1I4.06 TCGA.EE.A29V.06 TCGA.GF.A6C9.06 TCGA.EE.A2GT.06
#> "0122" "014" "0132" "0412" "01132" "0131"
#> TCGA.GN.A9SD.06 TCGA.EE.A3AB.06 TCGA.BF.AAP6.01 TCGA.EB.A5SH.06 TCGA.D9.A6E9.06 TCGA.BF.AAP4.01
#> "014" "0413" "03" "0431" "04421" "04421"
#> TCGA.EE.A2GM.06 TCGA.D3.A3CF.06 TCGA.D9.A6EC.06 TCGA.DA.A1I1.06 TCGA.HR.A2OH.06 TCGA.EE.A2MT.06
#> "0212" "0121" "023" "0413" "014" "0422"
#> TCGA.ER.A19M.06 TCGA.GN.A26C.01 TCGA.FS.A1ZA.06 TCGA.EB.A5SE.01 TCGA.ER.A3PL.06 TCGA.FR.A3R1.01
#> "0411" "01112" "04422" "0222" "0521" "03"
#> TCGA.EE.A2MI.06 TCGA.D3.A3CE.06 TCGA.D3.A5GT.01 TCGA.ER.A2NB.01 TCGA.D3.A1Q5.06 TCGA.EB.A5UN.06
#> "0443" "0441" "0511" "0421" "0422" "01113"
#> TCGA.EB.A299.01 TCGA.DA.A1IA.06 TCGA.EB.A5SG.06 TCGA.D9.A6EA.06 TCGA.XV.AAZY.01 TCGA.EB.A57M.01
#> "03232" "0511" "014" "0222" "014" "0412"
#> TCGA.EE.A2A6.06 TCGA.D3.A2JA.06 TCGA.D3.A1Q1.06 TCGA.EB.A3XF.01 TCGA.D3.A2JF.06 TCGA.XV.AAZW.01
#> "0421" "0132" "0422" "03112" "03234" "03112"
#> TCGA.EB.A3Y6.01 TCGA.EB.A3XE.01 TCGA.D9.A3Z4.01 TCGA.FW.A3R5.06 TCGA.EE.A2GI.06 TCGA.EE.A2GL.06
#> "0441" "0432" "0523" "0432" "0411" "014"
#> TCGA.EB.A3XB.01 TCGA.BF.AAOU.01 TCGA.EB.A3XD.01 TCGA.EE.A2MD.06 TCGA.YD.A9TB.06 TCGA.W3.AA1V.06
#> "04421" "014" "0124" "04421" "0521" "0441"
#> TCGA.ER.A2ND.06 TCGA.D3.A2JK.06 TCGA.FS.A1ZB.06 TCGA.EE.A29D.06 TCGA.EB.A5UM.01 TCGA.QB.A6FS.06
#> "0521" "0412" "0112" "0222" "0432" "0132"
#> TCGA.D9.A3Z1.06 TCGA.D3.A2JN.06 TCGA.FR.A3YN.06 TCGA.FS.A1ZT.06 TCGA.D9.A148.06 TCGA.HR.A2OG.06
#> "01133" "014" "03233" "0132" "0412" "0125"
#> TCGA.EE.A2ML.06 TCGA.EB.A5UL.06 TCGA.EE.A29T.06 TCGA.D9.A3Z3.06 TCGA.D9.A4Z3.01 TCGA.ER.A3ES.06
#> "0413" "0412" "0432" "0124" "0522" "0422"
#> TCGA.XV.A9VZ.01 TCGA.QB.AA9O.06 TCGA.EB.A44Q.06 TCGA.EB.A44R.06 TCGA.BF.A3DJ.01 TCGA.EE.A3JD.06
#> "0122" "03111" "04421" "0433" "03112" "0131"
#> TCGA.D3.A51N.06 TCGA.EB.A44N.01 TCGA.EE.A3J3.06 TCGA.XV.A9W5.01 TCGA.D3.A51G.06 TCGA.EB.A4P0.01
#> "0413" "01133" "03" "0412" "03234" "03112"
#> TCGA.BF.AAP1.01 TCGA.EE.A3J4.06 TCGA.Z2.AA3V.06 TCGA.LH.A9QB.06 TCGA.D3.A51J.06 TCGA.3N.A9WC.06
#> "023" "0511" "0121" "023" "04421" "0421"
#> TCGA.DA.A3F8.06 TCGA.D9.A4Z6.06 TCGA.D3.A51R.06 TCGA.EB.A4OZ.01 TCGA.FS.A4FB.06 TCGA.EE.A3JE.06
#> "01132" "0412" "03" "0121" "03112" "01132"
#> TCGA.W3.AA1W.06 TCGA.DA.A1I0.06 TCGA.D3.A51F.06 TCGA.IH.A3EA.01 TCGA.EB.A431.01 TCGA.EB.A97M.01
#> "01111" "0412" "0131" "0512" "0412" "0222"
#> TCGA.BF.AAOX.01 TCGA.DA.A3F5.06 TCGA.YD.A9TA.06 TCGA.DA.A3F2.06 TCGA.EB.A44O.01 TCGA.EB.A4IQ.01
#> "0412" "0423" "0411" "0131" "0521" "0421"
#> TCGA.EB.A4IS.01 TCGA.YG.AA3O.06 TCGA.ER.A3EV.06 TCGA.3N.A9WD.06 TCGA.BF.A3DM.01 TCGA.XV.A9W2.01
#> "0112" "0512" "0433" "01131" "03" "0423"
#> TCGA.W3.AA1Q.06 TCGA.WE.AAA0.06 TCGA.W3.AA1R.06 TCGA.EE.A3J5.06 TCGA.EB.A4OY.01 TCGA.FS.A4FD.06
#> "0512" "0412" "03" "0412" "0122" "0422"
#> TCGA.BF.AAP0.06 TCGA.YG.AA3P.06 TCGA.EE.A3JA.06 TCGA.W3.AA21.06 TCGA.WE.AAA3.06 TCGA.FS.A4F4.06
#> "0123" "0523" "03231" "0211" "0423" "03111"
#> TCGA.BF.A3DN.01 TCGA.ER.A3ET.06 TCGA.W3.AA1O.06 TCGA.D3.A51E.06 TCGA.Z2.AA3S.06 TCGA.YG.AA3N.01
#> "03" "0423" "0513" "03" "0222" "04421"
#> TCGA.WE.AA9Y.06 TCGA.FS.A4F5.06 TCGA.EE.A3J7.06 TCGA.FS.A4F8.06 TCGA.DA.A3F3.06 TCGA.D3.A51H.06
#> "01113" "023" "0511" "01112" "03231" "0131"
#> TCGA.BF.A3DL.01 TCGA.D3.A51T.06 TCGA.D3.A51K.06 TCGA.EB.A44P.01 TCGA.D9.A4Z5.01 TCGA.WE.AAA4.06
#> "0124" "03" "0522" "0521" "023" "014"
#> TCGA.3N.A9WB.06 TCGA.EE.A3J8.06
#> "0222" "0211"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 2164))
#> TCGA.FR.A728.01 TCGA.GN.A4U8.11 TCGA.GN.A8LL.06 TCGA.FR.A8YC.06 TCGA.DA.A95X.06 TCGA.ER.A42K.06
#> "014" "01132" "03113" "022" "0211" "03"
#> TCGA.D3.A8GO.06 TCGA.D3.A8GK.06 TCGA.WE.A8JZ.06 TCGA.WE.A8ZO.06 TCGA.D3.A8GI.06 TCGA.FS.A4FC.06
#> "0124" "0524" "0212" "0511" "0512" "0421"
#> TCGA.FS.A4F2.06 TCGA.WE.A8ZM.06 TCGA.WE.A8ZT.06 TCGA.D3.A8GQ.06 TCGA.D3.A8GB.06 TCGA.DA.A95Y.06
#> "03" "0522" "03112" "0411" "0131" "03111"
#> TCGA.EE.A3JI.06 TCGA.OD.A75X.06 TCGA.DA.A960.01 TCGA.D3.A8GV.06 TCGA.WE.A8ZN.06 TCGA.D3.A8GN.06
#> "022" "023" "0211" "0212" "0112" "014"
#> TCGA.EB.A550.01 TCGA.BF.A5EQ.01 TCGA.EB.A3HV.01 TCGA.HR.A5NC.01 TCGA.DA.A95Z.06 TCGA.EB.A6QZ.01
#> "0122" "0421" "0521" "0523" "022" "0212"
#> TCGA.FW.A3I3.06 TCGA.WE.A8K6.06 TCGA.D3.A8GP.06 TCGA.EB.A42Z.01 TCGA.GN.A4U4.06 TCGA.GF.A4EO.06
#> "023" "03" "022" "023" "0212" "014"
#> TCGA.GN.A8LK.06 TCGA.WE.A8K4.01 TCGA.DA.A95W.06 TCGA.FW.A5DX.01 TCGA.GN.A4U3.06 TCGA.EB.A6QY.01
#> "0521" "0112" "022" "0212" "03111" "0133"
#> TCGA.EB.A5VU.01 TCGA.Z2.A8RT.06 TCGA.WE.A8K1.06 TCGA.EB.A41B.01 TCGA.WE.A8ZY.06 TCGA.D9.A6EG.06
#> "0443" "03" "0112" "03" "0212" "022"
#> TCGA.BF.A5ER.01 TCGA.FR.A8YD.06 TCGA.FS.A4F9.06 TCGA.EB.A6R0.01 TCGA.ER.A42L.06 TCGA.D3.A8GJ.06
#> "0512" "0511" "0511" "03" "01133" "04423"
#> TCGA.FR.A8YE.06 TCGA.WE.A8ZR.06 TCGA.BF.A9VF.01 TCGA.EE.A3JH.06 TCGA.DA.A95V.06 TCGA.GF.A769.01
#> "01132" "0432" "0521" "0112" "0412" "0212"
#> TCGA.D9.A4Z2.01 TCGA.FR.A44A.06 TCGA.EB.A5VV.06 TCGA.EE.A180.06 TCGA.D3.A8GC.06 TCGA.WE.A8K5.06
#> "03" "014" "0123" "022" "0513" "023"
#> TCGA.GN.A8LN.01 TCGA.EE.A3JB.06 TCGA.D3.A3MO.06 TCGA.ER.A42H.01 TCGA.WE.A8ZX.06 TCGA.GN.A4U5.01
#> "0212" "0411" "0522" "0511" "0412" "014"
#> TCGA.D3.A8GS.06 TCGA.WE.A8ZQ.06 TCGA.EE.A2MF.06 TCGA.D3.A5GU.06 TCGA.GN.A4U8.06 TCGA.EB.A42Y.01
#> "0441" "0523" "022" "0511" "0413" "0212"
#> TCGA.D3.A3ML.06 TCGA.EB.A551.01 TCGA.D3.A8GM.06 TCGA.D3.A8GL.06 TCGA.D3.A3MU.06 TCGA.FS.A4F0.06
#> "0511" "04422" "0412" "022" "022" "022"
#> TCGA.D3.A3MV.06 TCGA.GN.A4U7.06 TCGA.FR.A2OS.01 TCGA.D3.A2JE.06 TCGA.YD.A89C.06 TCGA.FR.A726.01
#> "03" "03113" "0523" "0522" "0411" "0411"
#> TCGA.BF.A5EP.01 TCGA.D3.A3MR.06 TCGA.D3.A8GR.06 TCGA.GN.A4U9.06 TCGA.EB.A6L9.06 TCGA.D3.A5GL.06
#> "03" "0112" "0511" "0522" "0131" "03"
#> TCGA.EB.A430.01 TCGA.D3.A8GE.06 TCGA.D3.A8GD.06 TCGA.EB.A41A.01 TCGA.W3.A825.06 TCGA.EE.A183.06
#> "0133" "0132" "014" "022" "0443" "01112"
#> TCGA.ER.A2NH.06 TCGA.D3.A5GR.06 TCGA.FR.A729.06 TCGA.D3.A1QA.06 TCGA.FS.A1YY.06 TCGA.EE.A2MK.06
#> "0112" "0441" "0441" "0211" "03" "03112"
#> TCGA.EE.A2M8.06 TCGA.EB.A5KH.06 TCGA.FS.A1ZR.06 TCGA.EE.A3AE.06 TCGA.EE.A29P.06 TCGA.EB.A553.01
#> "0123" "0212" "0521" "03112" "04424" "0513"
#> TCGA.EE.A2MR.06 TCGA.GN.A26A.06 TCGA.FS.A1ZY.06 TCGA.EE.A20I.06 TCGA.DA.A1I5.06 TCGA.EE.A184.06
#> "01112" "0411" "0212" "0412" "0125" "023"
#> TCGA.EB.A85J.01 TCGA.RP.A6K9.06 TCGA.EE.A17Y.06 TCGA.D9.A149.06 TCGA.ER.A19D.06 TCGA.FS.A1ZZ.06
#> "0433" "0423" "0411" "0421" "0122" "023"
#> TCGA.EE.A2GP.06 TCGA.EE.A3AD.06 TCGA.D3.A1Q9.06 TCGA.GF.A2C7.01 TCGA.BF.A5ES.01 TCGA.ER.A199.06
#> "0524" "0212" "0412" "0511" "0511" "014"
#> TCGA.EE.A3AH.06 TCGA.W3.A828.06 TCGA.EE.A2A5.06 TCGA.ER.A19L.06 TCGA.BF.A1PX.01 TCGA.ER.A19T.06
#> "0212" "0133" "0522" "0432" "01112" "0431"
#> TCGA.EB.A51B.01 TCGA.FS.A1ZQ.06 TCGA.D3.A2JG.06 TCGA.EE.A2GH.06 TCGA.ER.A19F.06 TCGA.ER.A196.01
#> "03" "03233" "03" "0112" "03" "0124"
#> TCGA.D3.A2JC.06 TCGA.EE.A3AG.06 TCGA.ER.A19S.06 TCGA.EE.A2GC.06 TCGA.EE.A29N.06 TCGA.FR.A7U8.06
#> "0441" "03" "014" "0524" "01133" "023"
#> TCGA.BF.A5EO.01 TCGA.ER.A19B.06 TCGA.D3.A5GN.06 TCGA.D3.A2JB.06 TCGA.ER.A19J.06 TCGA.D3.A2JD.06
#> "0412" "03232" "03232" "0123" "023" "0112"
#> TCGA.FS.A1Z4.06 TCGA.FR.A7UA.06 TCGA.EE.A2M7.06 TCGA.D3.A1Q3.06 TCGA.EB.A85I.01 TCGA.EB.A82C.01
#> "0131" "014" "0441" "0431" "0421" "023"
#> TCGA.ER.A19E.06 TCGA.FS.A1ZK.06 TCGA.FS.A1ZU.06 TCGA.EB.A5FP.01 TCGA.EB.A4XL.01 TCGA.DA.A1I2.06
#> "0522" "0524" "0522" "0212" "03112" "0441"
#> TCGA.EE.A29L.06 TCGA.FS.A1ZN.01 TCGA.EB.A24D.01 TCGA.EE.A2GB.06 TCGA.DA.A1I7.06 TCGA.ER.A2NF.01
#> "0211" "0212" "0511" "03" "0441" "0132"
#> TCGA.GN.A263.01 TCGA.EE.A20C.06 TCGA.EE.A2MQ.06 TCGA.ER.A19N.06 TCGA.FS.A1Z3.06 TCGA.DA.A1I8.06
#> "0132" "023" "0512" "0112" "03" "03"
#> TCGA.D3.A5GS.06 TCGA.EE.A181.06 TCGA.GN.A268.06 TCGA.W3.A824.06 TCGA.EE.A2GS.06 TCGA.FR.A7U9.06
#> "03232" "0412" "022" "0511" "03" "0121"
#> TCGA.ER.A19Q.06 TCGA.FS.A1ZM.06 TCGA.EE.A2MG.06 TCGA.EE.A2MC.06 TCGA.EE.A17Z.06 TCGA.D3.A2JP.06
#> "0125" "0441" "0131" "0131" "0522" "0412"
#> TCGA.ER.A19C.06 TCGA.EB.A82B.01 TCGA.EE.A2A0.06 TCGA.EE.A29G.06 TCGA.D3.A5GO.06 TCGA.GN.A269.01
#> "0443" "0423" "014" "01131" "03" "01113"
#> TCGA.EE.A2A1.06 TCGA.ER.A1A1.06 TCGA.FS.A1ZG.06 TCGA.FS.A1ZE.06 TCGA.FS.A1ZH.06 TCGA.EE.A2MH.06
#> "0131" "0131" "022" "022" "0411" "01112"
#> TCGA.D3.A2J6.06 TCGA.EE.A29Q.06 TCGA.BF.A1PZ.01 TCGA.D3.A3BZ.06 TCGA.D3.A2JO.06 TCGA.GN.A267.06
#> "0423" "03232" "03" "0131" "04422" "0432"
#> TCGA.EE.A2MN.06 TCGA.GN.A264.06 TCGA.ER.A197.06 TCGA.DA.A1IB.06 TCGA.D3.A3CC.06 TCGA.ER.A19T.01
#> "0513" "023" "014" "014" "0423" "0523"
#> TCGA.GN.A261.06 TCGA.FS.A1YW.06 TCGA.BF.A1PU.01 TCGA.D3.A1QB.06 TCGA.D3.A1Q6.06 TCGA.D3.A3C8.06
#> "0122" "023" "0443" "0124" "0441" "014"
#> TCGA.ER.A19A.06 TCGA.EE.A2GN.06 TCGA.EE.A29M.06 TCGA.D3.A2J7.06 TCGA.EB.A24C.01 TCGA.GN.A262.06
#> "0131" "0522" "0121" "01133" "0432" "0212"
#> TCGA.EE.A2GD.06 TCGA.D3.A2J9.06 TCGA.EE.A29B.06 TCGA.D9.A1JX.06 TCGA.EE.A29A.06 TCGA.D3.A2JL.06
#> "014" "01132" "0511" "03" "022" "0412"
#> TCGA.D3.A1Q4.06 TCGA.FS.A1ZS.06 TCGA.D3.A3C3.06 TCGA.D3.A2J8.06 TCGA.FS.A1ZF.06 TCGA.FS.A1ZC.06
#> "0122" "0423" "0413" "0131" "03232" "0212"
#> TCGA.EE.A20H.06 TCGA.EE.A29W.06 TCGA.D3.A1QA.07 TCGA.BF.A1PV.01 TCGA.EE.A29S.06 TCGA.DA.A1HV.06
#> "0522" "03" "0413" "0512" "04424" "03"
#> TCGA.FS.A1Z0.06 TCGA.EE.A2GO.06 TCGA.EB.A1NK.01 TCGA.GN.A26D.06 TCGA.EE.A2MJ.06 TCGA.ER.A198.06
#> "0122" "023" "0133" "0422" "01132" "0512"
#> TCGA.EE.A17X.06 TCGA.EE.A2M5.06 TCGA.GN.A266.06 TCGA.D3.A3C1.06 TCGA.D3.A2JH.06 TCGA.EE.A20F.06
#> "03111" "0412" "0443" "04421" "0112" "0411"
#> TCGA.EE.A29E.06 TCGA.ER.A2NG.06 TCGA.ER.A193.06 TCGA.FS.A1ZW.06 TCGA.ER.A19O.06 TCGA.EE.A2ME.06
#> "0133" "014" "0421" "0413" "04421" "01112"
#> TCGA.EE.A20B.06 TCGA.EE.A3AF.06 TCGA.GN.A265.06 TCGA.FS.A1YX.06 TCGA.FS.A1ZJ.06 TCGA.ER.A19H.06
#> "0411" "03" "01132" "0441" "0523" "03"
#> TCGA.EE.A3AC.06 TCGA.EE.A2MU.06 TCGA.ER.A194.01 TCGA.EE.A2MS.06 TCGA.EE.A29R.06 TCGA.D9.A1X3.06
#> "0521" "01133" "04423" "0433" "023" "022"
#> TCGA.EE.A29X.06 TCGA.EE.A2GK.06 TCGA.EE.A3AA.06 TCGA.ER.A2NE.06 TCGA.EE.A2GR.06 TCGA.FS.A1ZD.06
#> "04421" "0123" "01112" "0212" "0521" "0523"
#> TCGA.ER.A19P.06 TCGA.D3.A1Q8.06 TCGA.ER.A2NC.06 TCGA.BF.A1Q0.01 TCGA.FS.A1ZP.06 TCGA.EE.A182.06
#> "014" "0112" "0443" "0421" "0522" "0432"
#> TCGA.D9.A1JW.06 TCGA.D3.A1Q7.06 TCGA.EE.A185.06 TCGA.EE.A2GJ.06 TCGA.D3.A3CB.06 TCGA.EE.A2GU.06
#> "0421" "014" "0212" "0431" "01111" "0421"
#> TCGA.ER.A195.06 TCGA.FS.A1Z7.06 TCGA.EE.A2M6.06 TCGA.ER.A19K.01 TCGA.DA.A1HY.06 TCGA.D3.A3C7.06
#> "0132" "0423" "0212" "04421" "03" "03"
#> TCGA.EE.A2MP.06 TCGA.EE.A29H.06 TCGA.FR.A3YO.06 TCGA.XV.AB01.01 TCGA.RP.A694.06 TCGA.EB.A5SF.01
#> "03232" "03" "04421" "03" "04423" "0122"
#> TCGA.ER.A19G.06 TCGA.EE.A2GE.06 TCGA.GF.A3OT.06 TCGA.ER.A2NF.06 TCGA.RP.A695.06 TCGA.BF.AAP7.01
#> "03" "0112" "014" "0132" "0512" "0121"
#> TCGA.EB.A3Y7.01 TCGA.EB.A3XC.01 TCGA.ER.A19W.06 TCGA.FR.A69P.06 TCGA.RP.A693.06 TCGA.FW.A3TV.06
#> "0423" "03111" "014" "03" "01111" "0124"
#> TCGA.FW.A3R5.11 TCGA.FW.A3TU.06 TCGA.BF.AAP8.01 TCGA.EE.A2MM.06 TCGA.DA.A1HW.06 TCGA.DA.A1IC.06
#> "0132" "0511" "0422" "0513" "0441" "0521"
#> TCGA.XV.AAZV.01 TCGA.D3.A3C6.06 TCGA.EE.A29C.06 TCGA.BF.AAP2.01 TCGA.EE.A2A2.06 TCGA.GF.A6C8.06
#> "0121" "03232" "0132" "0212" "03" "0443"
#> TCGA.RP.A690.06 TCGA.FW.A5DY.06 TCGA.DA.A1I4.06 TCGA.EE.A29V.06 TCGA.GF.A6C9.06 TCGA.EE.A2GT.06
#> "0122" "014" "0132" "0412" "01132" "0131"
#> TCGA.GN.A9SD.06 TCGA.EE.A3AB.06 TCGA.BF.AAP6.01 TCGA.EB.A5SH.06 TCGA.D9.A6E9.06 TCGA.BF.AAP4.01
#> "014" "0413" "03" "0431" "04421" "04421"
#> TCGA.EE.A2GM.06 TCGA.D3.A3CF.06 TCGA.D9.A6EC.06 TCGA.DA.A1I1.06 TCGA.HR.A2OH.06 TCGA.EE.A2MT.06
#> "0212" "0121" "023" "0413" "014" "0422"
#> TCGA.ER.A19M.06 TCGA.GN.A26C.01 TCGA.FS.A1ZA.06 TCGA.EB.A5SE.01 TCGA.ER.A3PL.06 TCGA.FR.A3R1.01
#> "0411" "01112" "04422" "022" "0521" "03"
#> TCGA.EE.A2MI.06 TCGA.D3.A3CE.06 TCGA.D3.A5GT.01 TCGA.ER.A2NB.01 TCGA.D3.A1Q5.06 TCGA.EB.A5UN.06
#> "0443" "0441" "0511" "0421" "0422" "01113"
#> TCGA.EB.A299.01 TCGA.DA.A1IA.06 TCGA.EB.A5SG.06 TCGA.D9.A6EA.06 TCGA.XV.AAZY.01 TCGA.EB.A57M.01
#> "03232" "0511" "014" "022" "014" "0412"
#> TCGA.EE.A2A6.06 TCGA.D3.A2JA.06 TCGA.D3.A1Q1.06 TCGA.EB.A3XF.01 TCGA.D3.A2JF.06 TCGA.XV.AAZW.01
#> "0421" "0132" "0422" "03112" "03234" "03112"
#> TCGA.EB.A3Y6.01 TCGA.EB.A3XE.01 TCGA.D9.A3Z4.01 TCGA.FW.A3R5.06 TCGA.EE.A2GI.06 TCGA.EE.A2GL.06
#> "0441" "0432" "0523" "0432" "0411" "014"
#> TCGA.EB.A3XB.01 TCGA.BF.AAOU.01 TCGA.EB.A3XD.01 TCGA.EE.A2MD.06 TCGA.YD.A9TB.06 TCGA.W3.AA1V.06
#> "04421" "014" "0124" "04421" "0521" "0441"
#> TCGA.ER.A2ND.06 TCGA.D3.A2JK.06 TCGA.FS.A1ZB.06 TCGA.EE.A29D.06 TCGA.EB.A5UM.01 TCGA.QB.A6FS.06
#> "0521" "0412" "0112" "022" "0432" "0132"
#> TCGA.D9.A3Z1.06 TCGA.D3.A2JN.06 TCGA.FR.A3YN.06 TCGA.FS.A1ZT.06 TCGA.D9.A148.06 TCGA.HR.A2OG.06
#> "01133" "014" "03233" "0132" "0412" "0125"
#> TCGA.EE.A2ML.06 TCGA.EB.A5UL.06 TCGA.EE.A29T.06 TCGA.D9.A3Z3.06 TCGA.D9.A4Z3.01 TCGA.ER.A3ES.06
#> "0413" "0412" "0432" "0124" "0522" "0422"
#> TCGA.XV.A9VZ.01 TCGA.QB.AA9O.06 TCGA.EB.A44Q.06 TCGA.EB.A44R.06 TCGA.BF.A3DJ.01 TCGA.EE.A3JD.06
#> "0122" "03111" "04421" "0433" "03112" "0131"
#> TCGA.D3.A51N.06 TCGA.EB.A44N.01 TCGA.EE.A3J3.06 TCGA.XV.A9W5.01 TCGA.D3.A51G.06 TCGA.EB.A4P0.01
#> "0413" "01133" "03" "0412" "03234" "03112"
#> TCGA.BF.AAP1.01 TCGA.EE.A3J4.06 TCGA.Z2.AA3V.06 TCGA.LH.A9QB.06 TCGA.D3.A51J.06 TCGA.3N.A9WC.06
#> "023" "0511" "0121" "023" "04421" "0421"
#> TCGA.DA.A3F8.06 TCGA.D9.A4Z6.06 TCGA.D3.A51R.06 TCGA.EB.A4OZ.01 TCGA.FS.A4FB.06 TCGA.EE.A3JE.06
#> "01132" "0412" "03" "0121" "03112" "01132"
#> TCGA.W3.AA1W.06 TCGA.DA.A1I0.06 TCGA.D3.A51F.06 TCGA.IH.A3EA.01 TCGA.EB.A431.01 TCGA.EB.A97M.01
#> "01111" "0412" "0131" "0512" "0412" "022"
#> TCGA.BF.AAOX.01 TCGA.DA.A3F5.06 TCGA.YD.A9TA.06 TCGA.DA.A3F2.06 TCGA.EB.A44O.01 TCGA.EB.A4IQ.01
#> "0412" "0423" "0411" "0131" "0521" "0421"
#> TCGA.EB.A4IS.01 TCGA.YG.AA3O.06 TCGA.ER.A3EV.06 TCGA.3N.A9WD.06 TCGA.BF.A3DM.01 TCGA.XV.A9W2.01
#> "0112" "0512" "0433" "01131" "03" "0423"
#> TCGA.W3.AA1Q.06 TCGA.WE.AAA0.06 TCGA.W3.AA1R.06 TCGA.EE.A3J5.06 TCGA.EB.A4OY.01 TCGA.FS.A4FD.06
#> "0512" "0412" "03" "0412" "0122" "0422"
#> TCGA.BF.AAP0.06 TCGA.YG.AA3P.06 TCGA.EE.A3JA.06 TCGA.W3.AA21.06 TCGA.WE.AAA3.06 TCGA.FS.A4F4.06
#> "0123" "0523" "03231" "0211" "0423" "03111"
#> TCGA.BF.A3DN.01 TCGA.ER.A3ET.06 TCGA.W3.AA1O.06 TCGA.D3.A51E.06 TCGA.Z2.AA3S.06 TCGA.YG.AA3N.01
#> "03" "0423" "0513" "03" "022" "04421"
#> TCGA.WE.AA9Y.06 TCGA.FS.A4F5.06 TCGA.EE.A3J7.06 TCGA.FS.A4F8.06 TCGA.DA.A3F3.06 TCGA.D3.A51H.06
#> "01113" "023" "0511" "01112" "03231" "0131"
#> TCGA.BF.A3DL.01 TCGA.D3.A51T.06 TCGA.D3.A51K.06 TCGA.EB.A44P.01 TCGA.D9.A4Z5.01 TCGA.WE.AAA4.06
#> "0124" "03" "0522" "0521" "023" "014"
#> TCGA.3N.A9WB.06 TCGA.EE.A3J8.06
#> "022" "0211"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 2255))
#> TCGA.FR.A728.01 TCGA.GN.A4U8.11 TCGA.GN.A8LL.06 TCGA.FR.A8YC.06 TCGA.DA.A95X.06 TCGA.ER.A42K.06
#> "014" "01132" "03113" "022" "0211" "03"
#> TCGA.D3.A8GO.06 TCGA.D3.A8GK.06 TCGA.WE.A8JZ.06 TCGA.WE.A8ZO.06 TCGA.D3.A8GI.06 TCGA.FS.A4FC.06
#> "0124" "0524" "0212" "0511" "0512" "0421"
#> TCGA.FS.A4F2.06 TCGA.WE.A8ZM.06 TCGA.WE.A8ZT.06 TCGA.D3.A8GQ.06 TCGA.D3.A8GB.06 TCGA.DA.A95Y.06
#> "03" "0522" "03112" "0411" "0131" "03111"
#> TCGA.EE.A3JI.06 TCGA.OD.A75X.06 TCGA.DA.A960.01 TCGA.D3.A8GV.06 TCGA.WE.A8ZN.06 TCGA.D3.A8GN.06
#> "022" "023" "0211" "0212" "0112" "014"
#> TCGA.EB.A550.01 TCGA.BF.A5EQ.01 TCGA.EB.A3HV.01 TCGA.HR.A5NC.01 TCGA.DA.A95Z.06 TCGA.EB.A6QZ.01
#> "0122" "0421" "0521" "0523" "022" "0212"
#> TCGA.FW.A3I3.06 TCGA.WE.A8K6.06 TCGA.D3.A8GP.06 TCGA.EB.A42Z.01 TCGA.GN.A4U4.06 TCGA.GF.A4EO.06
#> "023" "03" "022" "023" "0212" "014"
#> TCGA.GN.A8LK.06 TCGA.WE.A8K4.01 TCGA.DA.A95W.06 TCGA.FW.A5DX.01 TCGA.GN.A4U3.06 TCGA.EB.A6QY.01
#> "0521" "0112" "022" "0212" "03111" "0133"
#> TCGA.EB.A5VU.01 TCGA.Z2.A8RT.06 TCGA.WE.A8K1.06 TCGA.EB.A41B.01 TCGA.WE.A8ZY.06 TCGA.D9.A6EG.06
#> "0443" "03" "0112" "03" "0212" "022"
#> TCGA.BF.A5ER.01 TCGA.FR.A8YD.06 TCGA.FS.A4F9.06 TCGA.EB.A6R0.01 TCGA.ER.A42L.06 TCGA.D3.A8GJ.06
#> "0512" "0511" "0511" "03" "01133" "04423"
#> TCGA.FR.A8YE.06 TCGA.WE.A8ZR.06 TCGA.BF.A9VF.01 TCGA.EE.A3JH.06 TCGA.DA.A95V.06 TCGA.GF.A769.01
#> "01132" "0432" "0521" "0112" "0412" "0212"
#> TCGA.D9.A4Z2.01 TCGA.FR.A44A.06 TCGA.EB.A5VV.06 TCGA.EE.A180.06 TCGA.D3.A8GC.06 TCGA.WE.A8K5.06
#> "03" "014" "0123" "022" "0513" "023"
#> TCGA.GN.A8LN.01 TCGA.EE.A3JB.06 TCGA.D3.A3MO.06 TCGA.ER.A42H.01 TCGA.WE.A8ZX.06 TCGA.GN.A4U5.01
#> "0212" "0411" "0522" "0511" "0412" "014"
#> TCGA.D3.A8GS.06 TCGA.WE.A8ZQ.06 TCGA.EE.A2MF.06 TCGA.D3.A5GU.06 TCGA.GN.A4U8.06 TCGA.EB.A42Y.01
#> "0441" "0523" "022" "0511" "0413" "0212"
#> TCGA.D3.A3ML.06 TCGA.EB.A551.01 TCGA.D3.A8GM.06 TCGA.D3.A8GL.06 TCGA.D3.A3MU.06 TCGA.FS.A4F0.06
#> "0511" "04422" "0412" "022" "022" "022"
#> TCGA.D3.A3MV.06 TCGA.GN.A4U7.06 TCGA.FR.A2OS.01 TCGA.D3.A2JE.06 TCGA.YD.A89C.06 TCGA.FR.A726.01
#> "03" "03113" "0523" "0522" "0411" "0411"
#> TCGA.BF.A5EP.01 TCGA.D3.A3MR.06 TCGA.D3.A8GR.06 TCGA.GN.A4U9.06 TCGA.EB.A6L9.06 TCGA.D3.A5GL.06
#> "03" "0112" "0511" "0522" "0131" "03"
#> TCGA.EB.A430.01 TCGA.D3.A8GE.06 TCGA.D3.A8GD.06 TCGA.EB.A41A.01 TCGA.W3.A825.06 TCGA.EE.A183.06
#> "0133" "0132" "014" "022" "0443" "01112"
#> TCGA.ER.A2NH.06 TCGA.D3.A5GR.06 TCGA.FR.A729.06 TCGA.D3.A1QA.06 TCGA.FS.A1YY.06 TCGA.EE.A2MK.06
#> "0112" "0441" "0441" "0211" "03" "03112"
#> TCGA.EE.A2M8.06 TCGA.EB.A5KH.06 TCGA.FS.A1ZR.06 TCGA.EE.A3AE.06 TCGA.EE.A29P.06 TCGA.EB.A553.01
#> "0123" "0212" "0521" "03112" "04424" "0513"
#> TCGA.EE.A2MR.06 TCGA.GN.A26A.06 TCGA.FS.A1ZY.06 TCGA.EE.A20I.06 TCGA.DA.A1I5.06 TCGA.EE.A184.06
#> "01112" "0411" "0212" "0412" "0125" "023"
#> TCGA.EB.A85J.01 TCGA.RP.A6K9.06 TCGA.EE.A17Y.06 TCGA.D9.A149.06 TCGA.ER.A19D.06 TCGA.FS.A1ZZ.06
#> "0433" "0423" "0411" "0421" "0122" "023"
#> TCGA.EE.A2GP.06 TCGA.EE.A3AD.06 TCGA.D3.A1Q9.06 TCGA.GF.A2C7.01 TCGA.BF.A5ES.01 TCGA.ER.A199.06
#> "0524" "0212" "0412" "0511" "0511" "014"
#> TCGA.EE.A3AH.06 TCGA.W3.A828.06 TCGA.EE.A2A5.06 TCGA.ER.A19L.06 TCGA.BF.A1PX.01 TCGA.ER.A19T.06
#> "0212" "0133" "0522" "0432" "01112" "0431"
#> TCGA.EB.A51B.01 TCGA.FS.A1ZQ.06 TCGA.D3.A2JG.06 TCGA.EE.A2GH.06 TCGA.ER.A19F.06 TCGA.ER.A196.01
#> "03" "03" "03" "0112" "03" "0124"
#> TCGA.D3.A2JC.06 TCGA.EE.A3AG.06 TCGA.ER.A19S.06 TCGA.EE.A2GC.06 TCGA.EE.A29N.06 TCGA.FR.A7U8.06
#> "0441" "03" "014" "0524" "01133" "023"
#> TCGA.BF.A5EO.01 TCGA.ER.A19B.06 TCGA.D3.A5GN.06 TCGA.D3.A2JB.06 TCGA.ER.A19J.06 TCGA.D3.A2JD.06
#> "0412" "03" "03" "0123" "023" "0112"
#> TCGA.FS.A1Z4.06 TCGA.FR.A7UA.06 TCGA.EE.A2M7.06 TCGA.D3.A1Q3.06 TCGA.EB.A85I.01 TCGA.EB.A82C.01
#> "0131" "014" "0441" "0431" "0421" "023"
#> TCGA.ER.A19E.06 TCGA.FS.A1ZK.06 TCGA.FS.A1ZU.06 TCGA.EB.A5FP.01 TCGA.EB.A4XL.01 TCGA.DA.A1I2.06
#> "0522" "0524" "0522" "0212" "03112" "0441"
#> TCGA.EE.A29L.06 TCGA.FS.A1ZN.01 TCGA.EB.A24D.01 TCGA.EE.A2GB.06 TCGA.DA.A1I7.06 TCGA.ER.A2NF.01
#> "0211" "0212" "0511" "03" "0441" "0132"
#> TCGA.GN.A263.01 TCGA.EE.A20C.06 TCGA.EE.A2MQ.06 TCGA.ER.A19N.06 TCGA.FS.A1Z3.06 TCGA.DA.A1I8.06
#> "0132" "023" "0512" "0112" "03" "03"
#> TCGA.D3.A5GS.06 TCGA.EE.A181.06 TCGA.GN.A268.06 TCGA.W3.A824.06 TCGA.EE.A2GS.06 TCGA.FR.A7U9.06
#> "03" "0412" "022" "0511" "03" "0121"
#> TCGA.ER.A19Q.06 TCGA.FS.A1ZM.06 TCGA.EE.A2MG.06 TCGA.EE.A2MC.06 TCGA.EE.A17Z.06 TCGA.D3.A2JP.06
#> "0125" "0441" "0131" "0131" "0522" "0412"
#> TCGA.ER.A19C.06 TCGA.EB.A82B.01 TCGA.EE.A2A0.06 TCGA.EE.A29G.06 TCGA.D3.A5GO.06 TCGA.GN.A269.01
#> "0443" "0423" "014" "01131" "03" "01113"
#> TCGA.EE.A2A1.06 TCGA.ER.A1A1.06 TCGA.FS.A1ZG.06 TCGA.FS.A1ZE.06 TCGA.FS.A1ZH.06 TCGA.EE.A2MH.06
#> "0131" "0131" "022" "022" "0411" "01112"
#> TCGA.D3.A2J6.06 TCGA.EE.A29Q.06 TCGA.BF.A1PZ.01 TCGA.D3.A3BZ.06 TCGA.D3.A2JO.06 TCGA.GN.A267.06
#> "0423" "03" "03" "0131" "04422" "0432"
#> TCGA.EE.A2MN.06 TCGA.GN.A264.06 TCGA.ER.A197.06 TCGA.DA.A1IB.06 TCGA.D3.A3CC.06 TCGA.ER.A19T.01
#> "0513" "023" "014" "014" "0423" "0523"
#> TCGA.GN.A261.06 TCGA.FS.A1YW.06 TCGA.BF.A1PU.01 TCGA.D3.A1QB.06 TCGA.D3.A1Q6.06 TCGA.D3.A3C8.06
#> "0122" "023" "0443" "0124" "0441" "014"
#> TCGA.ER.A19A.06 TCGA.EE.A2GN.06 TCGA.EE.A29M.06 TCGA.D3.A2J7.06 TCGA.EB.A24C.01 TCGA.GN.A262.06
#> "0131" "0522" "0121" "01133" "0432" "0212"
#> TCGA.EE.A2GD.06 TCGA.D3.A2J9.06 TCGA.EE.A29B.06 TCGA.D9.A1JX.06 TCGA.EE.A29A.06 TCGA.D3.A2JL.06
#> "014" "01132" "0511" "03" "022" "0412"
#> TCGA.D3.A1Q4.06 TCGA.FS.A1ZS.06 TCGA.D3.A3C3.06 TCGA.D3.A2J8.06 TCGA.FS.A1ZF.06 TCGA.FS.A1ZC.06
#> "0122" "0423" "0413" "0131" "03" "0212"
#> TCGA.EE.A20H.06 TCGA.EE.A29W.06 TCGA.D3.A1QA.07 TCGA.BF.A1PV.01 TCGA.EE.A29S.06 TCGA.DA.A1HV.06
#> "0522" "03" "0413" "0512" "04424" "03"
#> TCGA.FS.A1Z0.06 TCGA.EE.A2GO.06 TCGA.EB.A1NK.01 TCGA.GN.A26D.06 TCGA.EE.A2MJ.06 TCGA.ER.A198.06
#> "0122" "023" "0133" "0422" "01132" "0512"
#> TCGA.EE.A17X.06 TCGA.EE.A2M5.06 TCGA.GN.A266.06 TCGA.D3.A3C1.06 TCGA.D3.A2JH.06 TCGA.EE.A20F.06
#> "03111" "0412" "0443" "04421" "0112" "0411"
#> TCGA.EE.A29E.06 TCGA.ER.A2NG.06 TCGA.ER.A193.06 TCGA.FS.A1ZW.06 TCGA.ER.A19O.06 TCGA.EE.A2ME.06
#> "0133" "014" "0421" "0413" "04421" "01112"
#> TCGA.EE.A20B.06 TCGA.EE.A3AF.06 TCGA.GN.A265.06 TCGA.FS.A1YX.06 TCGA.FS.A1ZJ.06 TCGA.ER.A19H.06
#> "0411" "03" "01132" "0441" "0523" "03"
#> TCGA.EE.A3AC.06 TCGA.EE.A2MU.06 TCGA.ER.A194.01 TCGA.EE.A2MS.06 TCGA.EE.A29R.06 TCGA.D9.A1X3.06
#> "0521" "01133" "04423" "0433" "023" "022"
#> TCGA.EE.A29X.06 TCGA.EE.A2GK.06 TCGA.EE.A3AA.06 TCGA.ER.A2NE.06 TCGA.EE.A2GR.06 TCGA.FS.A1ZD.06
#> "04421" "0123" "01112" "0212" "0521" "0523"
#> TCGA.ER.A19P.06 TCGA.D3.A1Q8.06 TCGA.ER.A2NC.06 TCGA.BF.A1Q0.01 TCGA.FS.A1ZP.06 TCGA.EE.A182.06
#> "014" "0112" "0443" "0421" "0522" "0432"
#> TCGA.D9.A1JW.06 TCGA.D3.A1Q7.06 TCGA.EE.A185.06 TCGA.EE.A2GJ.06 TCGA.D3.A3CB.06 TCGA.EE.A2GU.06
#> "0421" "014" "0212" "0431" "01111" "0421"
#> TCGA.ER.A195.06 TCGA.FS.A1Z7.06 TCGA.EE.A2M6.06 TCGA.ER.A19K.01 TCGA.DA.A1HY.06 TCGA.D3.A3C7.06
#> "0132" "0423" "0212" "04421" "03" "03"
#> TCGA.EE.A2MP.06 TCGA.EE.A29H.06 TCGA.FR.A3YO.06 TCGA.XV.AB01.01 TCGA.RP.A694.06 TCGA.EB.A5SF.01
#> "03" "03" "04421" "03" "04423" "0122"
#> TCGA.ER.A19G.06 TCGA.EE.A2GE.06 TCGA.GF.A3OT.06 TCGA.ER.A2NF.06 TCGA.RP.A695.06 TCGA.BF.AAP7.01
#> "03" "0112" "014" "0132" "0512" "0121"
#> TCGA.EB.A3Y7.01 TCGA.EB.A3XC.01 TCGA.ER.A19W.06 TCGA.FR.A69P.06 TCGA.RP.A693.06 TCGA.FW.A3TV.06
#> "0423" "03111" "014" "03" "01111" "0124"
#> TCGA.FW.A3R5.11 TCGA.FW.A3TU.06 TCGA.BF.AAP8.01 TCGA.EE.A2MM.06 TCGA.DA.A1HW.06 TCGA.DA.A1IC.06
#> "0132" "0511" "0422" "0513" "0441" "0521"
#> TCGA.XV.AAZV.01 TCGA.D3.A3C6.06 TCGA.EE.A29C.06 TCGA.BF.AAP2.01 TCGA.EE.A2A2.06 TCGA.GF.A6C8.06
#> "0121" "03" "0132" "0212" "03" "0443"
#> TCGA.RP.A690.06 TCGA.FW.A5DY.06 TCGA.DA.A1I4.06 TCGA.EE.A29V.06 TCGA.GF.A6C9.06 TCGA.EE.A2GT.06
#> "0122" "014" "0132" "0412" "01132" "0131"
#> TCGA.GN.A9SD.06 TCGA.EE.A3AB.06 TCGA.BF.AAP6.01 TCGA.EB.A5SH.06 TCGA.D9.A6E9.06 TCGA.BF.AAP4.01
#> "014" "0413" "03" "0431" "04421" "04421"
#> TCGA.EE.A2GM.06 TCGA.D3.A3CF.06 TCGA.D9.A6EC.06 TCGA.DA.A1I1.06 TCGA.HR.A2OH.06 TCGA.EE.A2MT.06
#> "0212" "0121" "023" "0413" "014" "0422"
#> TCGA.ER.A19M.06 TCGA.GN.A26C.01 TCGA.FS.A1ZA.06 TCGA.EB.A5SE.01 TCGA.ER.A3PL.06 TCGA.FR.A3R1.01
#> "0411" "01112" "04422" "022" "0521" "03"
#> TCGA.EE.A2MI.06 TCGA.D3.A3CE.06 TCGA.D3.A5GT.01 TCGA.ER.A2NB.01 TCGA.D3.A1Q5.06 TCGA.EB.A5UN.06
#> "0443" "0441" "0511" "0421" "0422" "01113"
#> TCGA.EB.A299.01 TCGA.DA.A1IA.06 TCGA.EB.A5SG.06 TCGA.D9.A6EA.06 TCGA.XV.AAZY.01 TCGA.EB.A57M.01
#> "03" "0511" "014" "022" "014" "0412"
#> TCGA.EE.A2A6.06 TCGA.D3.A2JA.06 TCGA.D3.A1Q1.06 TCGA.EB.A3XF.01 TCGA.D3.A2JF.06 TCGA.XV.AAZW.01
#> "0421" "0132" "0422" "03112" "03" "03112"
#> TCGA.EB.A3Y6.01 TCGA.EB.A3XE.01 TCGA.D9.A3Z4.01 TCGA.FW.A3R5.06 TCGA.EE.A2GI.06 TCGA.EE.A2GL.06
#> "0441" "0432" "0523" "0432" "0411" "014"
#> TCGA.EB.A3XB.01 TCGA.BF.AAOU.01 TCGA.EB.A3XD.01 TCGA.EE.A2MD.06 TCGA.YD.A9TB.06 TCGA.W3.AA1V.06
#> "04421" "014" "0124" "04421" "0521" "0441"
#> TCGA.ER.A2ND.06 TCGA.D3.A2JK.06 TCGA.FS.A1ZB.06 TCGA.EE.A29D.06 TCGA.EB.A5UM.01 TCGA.QB.A6FS.06
#> "0521" "0412" "0112" "022" "0432" "0132"
#> TCGA.D9.A3Z1.06 TCGA.D3.A2JN.06 TCGA.FR.A3YN.06 TCGA.FS.A1ZT.06 TCGA.D9.A148.06 TCGA.HR.A2OG.06
#> "01133" "014" "03" "0132" "0412" "0125"
#> TCGA.EE.A2ML.06 TCGA.EB.A5UL.06 TCGA.EE.A29T.06 TCGA.D9.A3Z3.06 TCGA.D9.A4Z3.01 TCGA.ER.A3ES.06
#> "0413" "0412" "0432" "0124" "0522" "0422"
#> TCGA.XV.A9VZ.01 TCGA.QB.AA9O.06 TCGA.EB.A44Q.06 TCGA.EB.A44R.06 TCGA.BF.A3DJ.01 TCGA.EE.A3JD.06
#> "0122" "03111" "04421" "0433" "03112" "0131"
#> TCGA.D3.A51N.06 TCGA.EB.A44N.01 TCGA.EE.A3J3.06 TCGA.XV.A9W5.01 TCGA.D3.A51G.06 TCGA.EB.A4P0.01
#> "0413" "01133" "03" "0412" "03" "03112"
#> TCGA.BF.AAP1.01 TCGA.EE.A3J4.06 TCGA.Z2.AA3V.06 TCGA.LH.A9QB.06 TCGA.D3.A51J.06 TCGA.3N.A9WC.06
#> "023" "0511" "0121" "023" "04421" "0421"
#> TCGA.DA.A3F8.06 TCGA.D9.A4Z6.06 TCGA.D3.A51R.06 TCGA.EB.A4OZ.01 TCGA.FS.A4FB.06 TCGA.EE.A3JE.06
#> "01132" "0412" "03" "0121" "03112" "01132"
#> TCGA.W3.AA1W.06 TCGA.DA.A1I0.06 TCGA.D3.A51F.06 TCGA.IH.A3EA.01 TCGA.EB.A431.01 TCGA.EB.A97M.01
#> "01111" "0412" "0131" "0512" "0412" "022"
#> TCGA.BF.AAOX.01 TCGA.DA.A3F5.06 TCGA.YD.A9TA.06 TCGA.DA.A3F2.06 TCGA.EB.A44O.01 TCGA.EB.A4IQ.01
#> "0412" "0423" "0411" "0131" "0521" "0421"
#> TCGA.EB.A4IS.01 TCGA.YG.AA3O.06 TCGA.ER.A3EV.06 TCGA.3N.A9WD.06 TCGA.BF.A3DM.01 TCGA.XV.A9W2.01
#> "0112" "0512" "0433" "01131" "03" "0423"
#> TCGA.W3.AA1Q.06 TCGA.WE.AAA0.06 TCGA.W3.AA1R.06 TCGA.EE.A3J5.06 TCGA.EB.A4OY.01 TCGA.FS.A4FD.06
#> "0512" "0412" "03" "0412" "0122" "0422"
#> TCGA.BF.AAP0.06 TCGA.YG.AA3P.06 TCGA.EE.A3JA.06 TCGA.W3.AA21.06 TCGA.WE.AAA3.06 TCGA.FS.A4F4.06
#> "0123" "0523" "03" "0211" "0423" "03111"
#> TCGA.BF.A3DN.01 TCGA.ER.A3ET.06 TCGA.W3.AA1O.06 TCGA.D3.A51E.06 TCGA.Z2.AA3S.06 TCGA.YG.AA3N.01
#> "03" "0423" "0513" "03" "022" "04421"
#> TCGA.WE.AA9Y.06 TCGA.FS.A4F5.06 TCGA.EE.A3J7.06 TCGA.FS.A4F8.06 TCGA.DA.A3F3.06 TCGA.D3.A51H.06
#> "01113" "023" "0511" "01112" "03" "0131"
#> TCGA.BF.A3DL.01 TCGA.D3.A51T.06 TCGA.D3.A51K.06 TCGA.EB.A44P.01 TCGA.D9.A4Z5.01 TCGA.WE.AAA4.06
#> "0124" "03" "0522" "0521" "023" "014"
#> TCGA.3N.A9WB.06 TCGA.EE.A3J8.06
#> "022" "0211"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 2328))
#> TCGA.FR.A728.01 TCGA.GN.A4U8.11 TCGA.GN.A8LL.06 TCGA.FR.A8YC.06 TCGA.DA.A95X.06 TCGA.ER.A42K.06
#> "014" "0113" "03113" "022" "0211" "03"
#> TCGA.D3.A8GO.06 TCGA.D3.A8GK.06 TCGA.WE.A8JZ.06 TCGA.WE.A8ZO.06 TCGA.D3.A8GI.06 TCGA.FS.A4FC.06
#> "0124" "0524" "0212" "0511" "0512" "0421"
#> TCGA.FS.A4F2.06 TCGA.WE.A8ZM.06 TCGA.WE.A8ZT.06 TCGA.D3.A8GQ.06 TCGA.D3.A8GB.06 TCGA.DA.A95Y.06
#> "03" "0522" "03112" "0411" "0131" "03111"
#> TCGA.EE.A3JI.06 TCGA.OD.A75X.06 TCGA.DA.A960.01 TCGA.D3.A8GV.06 TCGA.WE.A8ZN.06 TCGA.D3.A8GN.06
#> "022" "023" "0211" "0212" "0112" "014"
#> TCGA.EB.A550.01 TCGA.BF.A5EQ.01 TCGA.EB.A3HV.01 TCGA.HR.A5NC.01 TCGA.DA.A95Z.06 TCGA.EB.A6QZ.01
#> "0122" "0421" "0521" "0523" "022" "0212"
#> TCGA.FW.A3I3.06 TCGA.WE.A8K6.06 TCGA.D3.A8GP.06 TCGA.EB.A42Z.01 TCGA.GN.A4U4.06 TCGA.GF.A4EO.06
#> "023" "03" "022" "023" "0212" "014"
#> TCGA.GN.A8LK.06 TCGA.WE.A8K4.01 TCGA.DA.A95W.06 TCGA.FW.A5DX.01 TCGA.GN.A4U3.06 TCGA.EB.A6QY.01
#> "0521" "0112" "022" "0212" "03111" "0133"
#> TCGA.EB.A5VU.01 TCGA.Z2.A8RT.06 TCGA.WE.A8K1.06 TCGA.EB.A41B.01 TCGA.WE.A8ZY.06 TCGA.D9.A6EG.06
#> "0443" "03" "0112" "03" "0212" "022"
#> TCGA.BF.A5ER.01 TCGA.FR.A8YD.06 TCGA.FS.A4F9.06 TCGA.EB.A6R0.01 TCGA.ER.A42L.06 TCGA.D3.A8GJ.06
#> "0512" "0511" "0511" "03" "0113" "04423"
#> TCGA.FR.A8YE.06 TCGA.WE.A8ZR.06 TCGA.BF.A9VF.01 TCGA.EE.A3JH.06 TCGA.DA.A95V.06 TCGA.GF.A769.01
#> "0113" "0432" "0521" "0112" "0412" "0212"
#> TCGA.D9.A4Z2.01 TCGA.FR.A44A.06 TCGA.EB.A5VV.06 TCGA.EE.A180.06 TCGA.D3.A8GC.06 TCGA.WE.A8K5.06
#> "03" "014" "0123" "022" "0513" "023"
#> TCGA.GN.A8LN.01 TCGA.EE.A3JB.06 TCGA.D3.A3MO.06 TCGA.ER.A42H.01 TCGA.WE.A8ZX.06 TCGA.GN.A4U5.01
#> "0212" "0411" "0522" "0511" "0412" "014"
#> TCGA.D3.A8GS.06 TCGA.WE.A8ZQ.06 TCGA.EE.A2MF.06 TCGA.D3.A5GU.06 TCGA.GN.A4U8.06 TCGA.EB.A42Y.01
#> "0441" "0523" "022" "0511" "0413" "0212"
#> TCGA.D3.A3ML.06 TCGA.EB.A551.01 TCGA.D3.A8GM.06 TCGA.D3.A8GL.06 TCGA.D3.A3MU.06 TCGA.FS.A4F0.06
#> "0511" "04422" "0412" "022" "022" "022"
#> TCGA.D3.A3MV.06 TCGA.GN.A4U7.06 TCGA.FR.A2OS.01 TCGA.D3.A2JE.06 TCGA.YD.A89C.06 TCGA.FR.A726.01
#> "03" "03113" "0523" "0522" "0411" "0411"
#> TCGA.BF.A5EP.01 TCGA.D3.A3MR.06 TCGA.D3.A8GR.06 TCGA.GN.A4U9.06 TCGA.EB.A6L9.06 TCGA.D3.A5GL.06
#> "03" "0112" "0511" "0522" "0131" "03"
#> TCGA.EB.A430.01 TCGA.D3.A8GE.06 TCGA.D3.A8GD.06 TCGA.EB.A41A.01 TCGA.W3.A825.06 TCGA.EE.A183.06
#> "0133" "0132" "014" "022" "0443" "01112"
#> TCGA.ER.A2NH.06 TCGA.D3.A5GR.06 TCGA.FR.A729.06 TCGA.D3.A1QA.06 TCGA.FS.A1YY.06 TCGA.EE.A2MK.06
#> "0112" "0441" "0441" "0211" "03" "03112"
#> TCGA.EE.A2M8.06 TCGA.EB.A5KH.06 TCGA.FS.A1ZR.06 TCGA.EE.A3AE.06 TCGA.EE.A29P.06 TCGA.EB.A553.01
#> "0123" "0212" "0521" "03112" "04424" "0513"
#> TCGA.EE.A2MR.06 TCGA.GN.A26A.06 TCGA.FS.A1ZY.06 TCGA.EE.A20I.06 TCGA.DA.A1I5.06 TCGA.EE.A184.06
#> "01112" "0411" "0212" "0412" "0125" "023"
#> TCGA.EB.A85J.01 TCGA.RP.A6K9.06 TCGA.EE.A17Y.06 TCGA.D9.A149.06 TCGA.ER.A19D.06 TCGA.FS.A1ZZ.06
#> "0433" "0423" "0411" "0421" "0122" "023"
#> TCGA.EE.A2GP.06 TCGA.EE.A3AD.06 TCGA.D3.A1Q9.06 TCGA.GF.A2C7.01 TCGA.BF.A5ES.01 TCGA.ER.A199.06
#> "0524" "0212" "0412" "0511" "0511" "014"
#> TCGA.EE.A3AH.06 TCGA.W3.A828.06 TCGA.EE.A2A5.06 TCGA.ER.A19L.06 TCGA.BF.A1PX.01 TCGA.ER.A19T.06
#> "0212" "0133" "0522" "0432" "01112" "0431"
#> TCGA.EB.A51B.01 TCGA.FS.A1ZQ.06 TCGA.D3.A2JG.06 TCGA.EE.A2GH.06 TCGA.ER.A19F.06 TCGA.ER.A196.01
#> "03" "03" "03" "0112" "03" "0124"
#> TCGA.D3.A2JC.06 TCGA.EE.A3AG.06 TCGA.ER.A19S.06 TCGA.EE.A2GC.06 TCGA.EE.A29N.06 TCGA.FR.A7U8.06
#> "0441" "03" "014" "0524" "0113" "023"
#> TCGA.BF.A5EO.01 TCGA.ER.A19B.06 TCGA.D3.A5GN.06 TCGA.D3.A2JB.06 TCGA.ER.A19J.06 TCGA.D3.A2JD.06
#> "0412" "03" "03" "0123" "023" "0112"
#> TCGA.FS.A1Z4.06 TCGA.FR.A7UA.06 TCGA.EE.A2M7.06 TCGA.D3.A1Q3.06 TCGA.EB.A85I.01 TCGA.EB.A82C.01
#> "0131" "014" "0441" "0431" "0421" "023"
#> TCGA.ER.A19E.06 TCGA.FS.A1ZK.06 TCGA.FS.A1ZU.06 TCGA.EB.A5FP.01 TCGA.EB.A4XL.01 TCGA.DA.A1I2.06
#> "0522" "0524" "0522" "0212" "03112" "0441"
#> TCGA.EE.A29L.06 TCGA.FS.A1ZN.01 TCGA.EB.A24D.01 TCGA.EE.A2GB.06 TCGA.DA.A1I7.06 TCGA.ER.A2NF.01
#> "0211" "0212" "0511" "03" "0441" "0132"
#> TCGA.GN.A263.01 TCGA.EE.A20C.06 TCGA.EE.A2MQ.06 TCGA.ER.A19N.06 TCGA.FS.A1Z3.06 TCGA.DA.A1I8.06
#> "0132" "023" "0512" "0112" "03" "03"
#> TCGA.D3.A5GS.06 TCGA.EE.A181.06 TCGA.GN.A268.06 TCGA.W3.A824.06 TCGA.EE.A2GS.06 TCGA.FR.A7U9.06
#> "03" "0412" "022" "0511" "03" "0121"
#> TCGA.ER.A19Q.06 TCGA.FS.A1ZM.06 TCGA.EE.A2MG.06 TCGA.EE.A2MC.06 TCGA.EE.A17Z.06 TCGA.D3.A2JP.06
#> "0125" "0441" "0131" "0131" "0522" "0412"
#> TCGA.ER.A19C.06 TCGA.EB.A82B.01 TCGA.EE.A2A0.06 TCGA.EE.A29G.06 TCGA.D3.A5GO.06 TCGA.GN.A269.01
#> "0443" "0423" "014" "0113" "03" "01113"
#> TCGA.EE.A2A1.06 TCGA.ER.A1A1.06 TCGA.FS.A1ZG.06 TCGA.FS.A1ZE.06 TCGA.FS.A1ZH.06 TCGA.EE.A2MH.06
#> "0131" "0131" "022" "022" "0411" "01112"
#> TCGA.D3.A2J6.06 TCGA.EE.A29Q.06 TCGA.BF.A1PZ.01 TCGA.D3.A3BZ.06 TCGA.D3.A2JO.06 TCGA.GN.A267.06
#> "0423" "03" "03" "0131" "04422" "0432"
#> TCGA.EE.A2MN.06 TCGA.GN.A264.06 TCGA.ER.A197.06 TCGA.DA.A1IB.06 TCGA.D3.A3CC.06 TCGA.ER.A19T.01
#> "0513" "023" "014" "014" "0423" "0523"
#> TCGA.GN.A261.06 TCGA.FS.A1YW.06 TCGA.BF.A1PU.01 TCGA.D3.A1QB.06 TCGA.D3.A1Q6.06 TCGA.D3.A3C8.06
#> "0122" "023" "0443" "0124" "0441" "014"
#> TCGA.ER.A19A.06 TCGA.EE.A2GN.06 TCGA.EE.A29M.06 TCGA.D3.A2J7.06 TCGA.EB.A24C.01 TCGA.GN.A262.06
#> "0131" "0522" "0121" "0113" "0432" "0212"
#> TCGA.EE.A2GD.06 TCGA.D3.A2J9.06 TCGA.EE.A29B.06 TCGA.D9.A1JX.06 TCGA.EE.A29A.06 TCGA.D3.A2JL.06
#> "014" "0113" "0511" "03" "022" "0412"
#> TCGA.D3.A1Q4.06 TCGA.FS.A1ZS.06 TCGA.D3.A3C3.06 TCGA.D3.A2J8.06 TCGA.FS.A1ZF.06 TCGA.FS.A1ZC.06
#> "0122" "0423" "0413" "0131" "03" "0212"
#> TCGA.EE.A20H.06 TCGA.EE.A29W.06 TCGA.D3.A1QA.07 TCGA.BF.A1PV.01 TCGA.EE.A29S.06 TCGA.DA.A1HV.06
#> "0522" "03" "0413" "0512" "04424" "03"
#> TCGA.FS.A1Z0.06 TCGA.EE.A2GO.06 TCGA.EB.A1NK.01 TCGA.GN.A26D.06 TCGA.EE.A2MJ.06 TCGA.ER.A198.06
#> "0122" "023" "0133" "0422" "0113" "0512"
#> TCGA.EE.A17X.06 TCGA.EE.A2M5.06 TCGA.GN.A266.06 TCGA.D3.A3C1.06 TCGA.D3.A2JH.06 TCGA.EE.A20F.06
#> "03111" "0412" "0443" "04421" "0112" "0411"
#> TCGA.EE.A29E.06 TCGA.ER.A2NG.06 TCGA.ER.A193.06 TCGA.FS.A1ZW.06 TCGA.ER.A19O.06 TCGA.EE.A2ME.06
#> "0133" "014" "0421" "0413" "04421" "01112"
#> TCGA.EE.A20B.06 TCGA.EE.A3AF.06 TCGA.GN.A265.06 TCGA.FS.A1YX.06 TCGA.FS.A1ZJ.06 TCGA.ER.A19H.06
#> "0411" "03" "0113" "0441" "0523" "03"
#> TCGA.EE.A3AC.06 TCGA.EE.A2MU.06 TCGA.ER.A194.01 TCGA.EE.A2MS.06 TCGA.EE.A29R.06 TCGA.D9.A1X3.06
#> "0521" "0113" "04423" "0433" "023" "022"
#> TCGA.EE.A29X.06 TCGA.EE.A2GK.06 TCGA.EE.A3AA.06 TCGA.ER.A2NE.06 TCGA.EE.A2GR.06 TCGA.FS.A1ZD.06
#> "04421" "0123" "01112" "0212" "0521" "0523"
#> TCGA.ER.A19P.06 TCGA.D3.A1Q8.06 TCGA.ER.A2NC.06 TCGA.BF.A1Q0.01 TCGA.FS.A1ZP.06 TCGA.EE.A182.06
#> "014" "0112" "0443" "0421" "0522" "0432"
#> TCGA.D9.A1JW.06 TCGA.D3.A1Q7.06 TCGA.EE.A185.06 TCGA.EE.A2GJ.06 TCGA.D3.A3CB.06 TCGA.EE.A2GU.06
#> "0421" "014" "0212" "0431" "01111" "0421"
#> TCGA.ER.A195.06 TCGA.FS.A1Z7.06 TCGA.EE.A2M6.06 TCGA.ER.A19K.01 TCGA.DA.A1HY.06 TCGA.D3.A3C7.06
#> "0132" "0423" "0212" "04421" "03" "03"
#> TCGA.EE.A2MP.06 TCGA.EE.A29H.06 TCGA.FR.A3YO.06 TCGA.XV.AB01.01 TCGA.RP.A694.06 TCGA.EB.A5SF.01
#> "03" "03" "04421" "03" "04423" "0122"
#> TCGA.ER.A19G.06 TCGA.EE.A2GE.06 TCGA.GF.A3OT.06 TCGA.ER.A2NF.06 TCGA.RP.A695.06 TCGA.BF.AAP7.01
#> "03" "0112" "014" "0132" "0512" "0121"
#> TCGA.EB.A3Y7.01 TCGA.EB.A3XC.01 TCGA.ER.A19W.06 TCGA.FR.A69P.06 TCGA.RP.A693.06 TCGA.FW.A3TV.06
#> "0423" "03111" "014" "03" "01111" "0124"
#> TCGA.FW.A3R5.11 TCGA.FW.A3TU.06 TCGA.BF.AAP8.01 TCGA.EE.A2MM.06 TCGA.DA.A1HW.06 TCGA.DA.A1IC.06
#> "0132" "0511" "0422" "0513" "0441" "0521"
#> TCGA.XV.AAZV.01 TCGA.D3.A3C6.06 TCGA.EE.A29C.06 TCGA.BF.AAP2.01 TCGA.EE.A2A2.06 TCGA.GF.A6C8.06
#> "0121" "03" "0132" "0212" "03" "0443"
#> TCGA.RP.A690.06 TCGA.FW.A5DY.06 TCGA.DA.A1I4.06 TCGA.EE.A29V.06 TCGA.GF.A6C9.06 TCGA.EE.A2GT.06
#> "0122" "014" "0132" "0412" "0113" "0131"
#> TCGA.GN.A9SD.06 TCGA.EE.A3AB.06 TCGA.BF.AAP6.01 TCGA.EB.A5SH.06 TCGA.D9.A6E9.06 TCGA.BF.AAP4.01
#> "014" "0413" "03" "0431" "04421" "04421"
#> TCGA.EE.A2GM.06 TCGA.D3.A3CF.06 TCGA.D9.A6EC.06 TCGA.DA.A1I1.06 TCGA.HR.A2OH.06 TCGA.EE.A2MT.06
#> "0212" "0121" "023" "0413" "014" "0422"
#> TCGA.ER.A19M.06 TCGA.GN.A26C.01 TCGA.FS.A1ZA.06 TCGA.EB.A5SE.01 TCGA.ER.A3PL.06 TCGA.FR.A3R1.01
#> "0411" "01112" "04422" "022" "0521" "03"
#> TCGA.EE.A2MI.06 TCGA.D3.A3CE.06 TCGA.D3.A5GT.01 TCGA.ER.A2NB.01 TCGA.D3.A1Q5.06 TCGA.EB.A5UN.06
#> "0443" "0441" "0511" "0421" "0422" "01113"
#> TCGA.EB.A299.01 TCGA.DA.A1IA.06 TCGA.EB.A5SG.06 TCGA.D9.A6EA.06 TCGA.XV.AAZY.01 TCGA.EB.A57M.01
#> "03" "0511" "014" "022" "014" "0412"
#> TCGA.EE.A2A6.06 TCGA.D3.A2JA.06 TCGA.D3.A1Q1.06 TCGA.EB.A3XF.01 TCGA.D3.A2JF.06 TCGA.XV.AAZW.01
#> "0421" "0132" "0422" "03112" "03" "03112"
#> TCGA.EB.A3Y6.01 TCGA.EB.A3XE.01 TCGA.D9.A3Z4.01 TCGA.FW.A3R5.06 TCGA.EE.A2GI.06 TCGA.EE.A2GL.06
#> "0441" "0432" "0523" "0432" "0411" "014"
#> TCGA.EB.A3XB.01 TCGA.BF.AAOU.01 TCGA.EB.A3XD.01 TCGA.EE.A2MD.06 TCGA.YD.A9TB.06 TCGA.W3.AA1V.06
#> "04421" "014" "0124" "04421" "0521" "0441"
#> TCGA.ER.A2ND.06 TCGA.D3.A2JK.06 TCGA.FS.A1ZB.06 TCGA.EE.A29D.06 TCGA.EB.A5UM.01 TCGA.QB.A6FS.06
#> "0521" "0412" "0112" "022" "0432" "0132"
#> TCGA.D9.A3Z1.06 TCGA.D3.A2JN.06 TCGA.FR.A3YN.06 TCGA.FS.A1ZT.06 TCGA.D9.A148.06 TCGA.HR.A2OG.06
#> "0113" "014" "03" "0132" "0412" "0125"
#> TCGA.EE.A2ML.06 TCGA.EB.A5UL.06 TCGA.EE.A29T.06 TCGA.D9.A3Z3.06 TCGA.D9.A4Z3.01 TCGA.ER.A3ES.06
#> "0413" "0412" "0432" "0124" "0522" "0422"
#> TCGA.XV.A9VZ.01 TCGA.QB.AA9O.06 TCGA.EB.A44Q.06 TCGA.EB.A44R.06 TCGA.BF.A3DJ.01 TCGA.EE.A3JD.06
#> "0122" "03111" "04421" "0433" "03112" "0131"
#> TCGA.D3.A51N.06 TCGA.EB.A44N.01 TCGA.EE.A3J3.06 TCGA.XV.A9W5.01 TCGA.D3.A51G.06 TCGA.EB.A4P0.01
#> "0413" "0113" "03" "0412" "03" "03112"
#> TCGA.BF.AAP1.01 TCGA.EE.A3J4.06 TCGA.Z2.AA3V.06 TCGA.LH.A9QB.06 TCGA.D3.A51J.06 TCGA.3N.A9WC.06
#> "023" "0511" "0121" "023" "04421" "0421"
#> TCGA.DA.A3F8.06 TCGA.D9.A4Z6.06 TCGA.D3.A51R.06 TCGA.EB.A4OZ.01 TCGA.FS.A4FB.06 TCGA.EE.A3JE.06
#> "0113" "0412" "03" "0121" "03112" "0113"
#> TCGA.W3.AA1W.06 TCGA.DA.A1I0.06 TCGA.D3.A51F.06 TCGA.IH.A3EA.01 TCGA.EB.A431.01 TCGA.EB.A97M.01
#> "01111" "0412" "0131" "0512" "0412" "022"
#> TCGA.BF.AAOX.01 TCGA.DA.A3F5.06 TCGA.YD.A9TA.06 TCGA.DA.A3F2.06 TCGA.EB.A44O.01 TCGA.EB.A4IQ.01
#> "0412" "0423" "0411" "0131" "0521" "0421"
#> TCGA.EB.A4IS.01 TCGA.YG.AA3O.06 TCGA.ER.A3EV.06 TCGA.3N.A9WD.06 TCGA.BF.A3DM.01 TCGA.XV.A9W2.01
#> "0112" "0512" "0433" "0113" "03" "0423"
#> TCGA.W3.AA1Q.06 TCGA.WE.AAA0.06 TCGA.W3.AA1R.06 TCGA.EE.A3J5.06 TCGA.EB.A4OY.01 TCGA.FS.A4FD.06
#> "0512" "0412" "03" "0412" "0122" "0422"
#> TCGA.BF.AAP0.06 TCGA.YG.AA3P.06 TCGA.EE.A3JA.06 TCGA.W3.AA21.06 TCGA.WE.AAA3.06 TCGA.FS.A4F4.06
#> "0123" "0523" "03" "0211" "0423" "03111"
#> TCGA.BF.A3DN.01 TCGA.ER.A3ET.06 TCGA.W3.AA1O.06 TCGA.D3.A51E.06 TCGA.Z2.AA3S.06 TCGA.YG.AA3N.01
#> "03" "0423" "0513" "03" "022" "04421"
#> TCGA.WE.AA9Y.06 TCGA.FS.A4F5.06 TCGA.EE.A3J7.06 TCGA.FS.A4F8.06 TCGA.DA.A3F3.06 TCGA.D3.A51H.06
#> "01113" "023" "0511" "01112" "03" "0131"
#> TCGA.BF.A3DL.01 TCGA.D3.A51T.06 TCGA.D3.A51K.06 TCGA.EB.A44P.01 TCGA.D9.A4Z5.01 TCGA.WE.AAA4.06
#> "0124" "03" "0522" "0521" "023" "014"
#> TCGA.3N.A9WB.06 TCGA.EE.A3J8.06
#> "022" "0211"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 2454))
#> TCGA.FR.A728.01 TCGA.GN.A4U8.11 TCGA.GN.A8LL.06 TCGA.FR.A8YC.06 TCGA.DA.A95X.06 TCGA.ER.A42K.06
#> "014" "0113" "03" "022" "0211" "03"
#> TCGA.D3.A8GO.06 TCGA.D3.A8GK.06 TCGA.WE.A8JZ.06 TCGA.WE.A8ZO.06 TCGA.D3.A8GI.06 TCGA.FS.A4FC.06
#> "0124" "0524" "0212" "0511" "0512" "0421"
#> TCGA.FS.A4F2.06 TCGA.WE.A8ZM.06 TCGA.WE.A8ZT.06 TCGA.D3.A8GQ.06 TCGA.D3.A8GB.06 TCGA.DA.A95Y.06
#> "03" "0522" "03" "0411" "0131" "03"
#> TCGA.EE.A3JI.06 TCGA.OD.A75X.06 TCGA.DA.A960.01 TCGA.D3.A8GV.06 TCGA.WE.A8ZN.06 TCGA.D3.A8GN.06
#> "022" "023" "0211" "0212" "0112" "014"
#> TCGA.EB.A550.01 TCGA.BF.A5EQ.01 TCGA.EB.A3HV.01 TCGA.HR.A5NC.01 TCGA.DA.A95Z.06 TCGA.EB.A6QZ.01
#> "0122" "0421" "0521" "0523" "022" "0212"
#> TCGA.FW.A3I3.06 TCGA.WE.A8K6.06 TCGA.D3.A8GP.06 TCGA.EB.A42Z.01 TCGA.GN.A4U4.06 TCGA.GF.A4EO.06
#> "023" "03" "022" "023" "0212" "014"
#> TCGA.GN.A8LK.06 TCGA.WE.A8K4.01 TCGA.DA.A95W.06 TCGA.FW.A5DX.01 TCGA.GN.A4U3.06 TCGA.EB.A6QY.01
#> "0521" "0112" "022" "0212" "03" "0133"
#> TCGA.EB.A5VU.01 TCGA.Z2.A8RT.06 TCGA.WE.A8K1.06 TCGA.EB.A41B.01 TCGA.WE.A8ZY.06 TCGA.D9.A6EG.06
#> "0443" "03" "0112" "03" "0212" "022"
#> TCGA.BF.A5ER.01 TCGA.FR.A8YD.06 TCGA.FS.A4F9.06 TCGA.EB.A6R0.01 TCGA.ER.A42L.06 TCGA.D3.A8GJ.06
#> "0512" "0511" "0511" "03" "0113" "04423"
#> TCGA.FR.A8YE.06 TCGA.WE.A8ZR.06 TCGA.BF.A9VF.01 TCGA.EE.A3JH.06 TCGA.DA.A95V.06 TCGA.GF.A769.01
#> "0113" "0432" "0521" "0112" "0412" "0212"
#> TCGA.D9.A4Z2.01 TCGA.FR.A44A.06 TCGA.EB.A5VV.06 TCGA.EE.A180.06 TCGA.D3.A8GC.06 TCGA.WE.A8K5.06
#> "03" "014" "0123" "022" "0513" "023"
#> TCGA.GN.A8LN.01 TCGA.EE.A3JB.06 TCGA.D3.A3MO.06 TCGA.ER.A42H.01 TCGA.WE.A8ZX.06 TCGA.GN.A4U5.01
#> "0212" "0411" "0522" "0511" "0412" "014"
#> TCGA.D3.A8GS.06 TCGA.WE.A8ZQ.06 TCGA.EE.A2MF.06 TCGA.D3.A5GU.06 TCGA.GN.A4U8.06 TCGA.EB.A42Y.01
#> "0441" "0523" "022" "0511" "0413" "0212"
#> TCGA.D3.A3ML.06 TCGA.EB.A551.01 TCGA.D3.A8GM.06 TCGA.D3.A8GL.06 TCGA.D3.A3MU.06 TCGA.FS.A4F0.06
#> "0511" "04422" "0412" "022" "022" "022"
#> TCGA.D3.A3MV.06 TCGA.GN.A4U7.06 TCGA.FR.A2OS.01 TCGA.D3.A2JE.06 TCGA.YD.A89C.06 TCGA.FR.A726.01
#> "03" "03" "0523" "0522" "0411" "0411"
#> TCGA.BF.A5EP.01 TCGA.D3.A3MR.06 TCGA.D3.A8GR.06 TCGA.GN.A4U9.06 TCGA.EB.A6L9.06 TCGA.D3.A5GL.06
#> "03" "0112" "0511" "0522" "0131" "03"
#> TCGA.EB.A430.01 TCGA.D3.A8GE.06 TCGA.D3.A8GD.06 TCGA.EB.A41A.01 TCGA.W3.A825.06 TCGA.EE.A183.06
#> "0133" "0132" "014" "022" "0443" "01112"
#> TCGA.ER.A2NH.06 TCGA.D3.A5GR.06 TCGA.FR.A729.06 TCGA.D3.A1QA.06 TCGA.FS.A1YY.06 TCGA.EE.A2MK.06
#> "0112" "0441" "0441" "0211" "03" "03"
#> TCGA.EE.A2M8.06 TCGA.EB.A5KH.06 TCGA.FS.A1ZR.06 TCGA.EE.A3AE.06 TCGA.EE.A29P.06 TCGA.EB.A553.01
#> "0123" "0212" "0521" "03" "04424" "0513"
#> TCGA.EE.A2MR.06 TCGA.GN.A26A.06 TCGA.FS.A1ZY.06 TCGA.EE.A20I.06 TCGA.DA.A1I5.06 TCGA.EE.A184.06
#> "01112" "0411" "0212" "0412" "0125" "023"
#> TCGA.EB.A85J.01 TCGA.RP.A6K9.06 TCGA.EE.A17Y.06 TCGA.D9.A149.06 TCGA.ER.A19D.06 TCGA.FS.A1ZZ.06
#> "0433" "0423" "0411" "0421" "0122" "023"
#> TCGA.EE.A2GP.06 TCGA.EE.A3AD.06 TCGA.D3.A1Q9.06 TCGA.GF.A2C7.01 TCGA.BF.A5ES.01 TCGA.ER.A199.06
#> "0524" "0212" "0412" "0511" "0511" "014"
#> TCGA.EE.A3AH.06 TCGA.W3.A828.06 TCGA.EE.A2A5.06 TCGA.ER.A19L.06 TCGA.BF.A1PX.01 TCGA.ER.A19T.06
#> "0212" "0133" "0522" "0432" "01112" "0431"
#> TCGA.EB.A51B.01 TCGA.FS.A1ZQ.06 TCGA.D3.A2JG.06 TCGA.EE.A2GH.06 TCGA.ER.A19F.06 TCGA.ER.A196.01
#> "03" "03" "03" "0112" "03" "0124"
#> TCGA.D3.A2JC.06 TCGA.EE.A3AG.06 TCGA.ER.A19S.06 TCGA.EE.A2GC.06 TCGA.EE.A29N.06 TCGA.FR.A7U8.06
#> "0441" "03" "014" "0524" "0113" "023"
#> TCGA.BF.A5EO.01 TCGA.ER.A19B.06 TCGA.D3.A5GN.06 TCGA.D3.A2JB.06 TCGA.ER.A19J.06 TCGA.D3.A2JD.06
#> "0412" "03" "03" "0123" "023" "0112"
#> TCGA.FS.A1Z4.06 TCGA.FR.A7UA.06 TCGA.EE.A2M7.06 TCGA.D3.A1Q3.06 TCGA.EB.A85I.01 TCGA.EB.A82C.01
#> "0131" "014" "0441" "0431" "0421" "023"
#> TCGA.ER.A19E.06 TCGA.FS.A1ZK.06 TCGA.FS.A1ZU.06 TCGA.EB.A5FP.01 TCGA.EB.A4XL.01 TCGA.DA.A1I2.06
#> "0522" "0524" "0522" "0212" "03" "0441"
#> TCGA.EE.A29L.06 TCGA.FS.A1ZN.01 TCGA.EB.A24D.01 TCGA.EE.A2GB.06 TCGA.DA.A1I7.06 TCGA.ER.A2NF.01
#> "0211" "0212" "0511" "03" "0441" "0132"
#> TCGA.GN.A263.01 TCGA.EE.A20C.06 TCGA.EE.A2MQ.06 TCGA.ER.A19N.06 TCGA.FS.A1Z3.06 TCGA.DA.A1I8.06
#> "0132" "023" "0512" "0112" "03" "03"
#> TCGA.D3.A5GS.06 TCGA.EE.A181.06 TCGA.GN.A268.06 TCGA.W3.A824.06 TCGA.EE.A2GS.06 TCGA.FR.A7U9.06
#> "03" "0412" "022" "0511" "03" "0121"
#> TCGA.ER.A19Q.06 TCGA.FS.A1ZM.06 TCGA.EE.A2MG.06 TCGA.EE.A2MC.06 TCGA.EE.A17Z.06 TCGA.D3.A2JP.06
#> "0125" "0441" "0131" "0131" "0522" "0412"
#> TCGA.ER.A19C.06 TCGA.EB.A82B.01 TCGA.EE.A2A0.06 TCGA.EE.A29G.06 TCGA.D3.A5GO.06 TCGA.GN.A269.01
#> "0443" "0423" "014" "0113" "03" "01113"
#> TCGA.EE.A2A1.06 TCGA.ER.A1A1.06 TCGA.FS.A1ZG.06 TCGA.FS.A1ZE.06 TCGA.FS.A1ZH.06 TCGA.EE.A2MH.06
#> "0131" "0131" "022" "022" "0411" "01112"
#> TCGA.D3.A2J6.06 TCGA.EE.A29Q.06 TCGA.BF.A1PZ.01 TCGA.D3.A3BZ.06 TCGA.D3.A2JO.06 TCGA.GN.A267.06
#> "0423" "03" "03" "0131" "04422" "0432"
#> TCGA.EE.A2MN.06 TCGA.GN.A264.06 TCGA.ER.A197.06 TCGA.DA.A1IB.06 TCGA.D3.A3CC.06 TCGA.ER.A19T.01
#> "0513" "023" "014" "014" "0423" "0523"
#> TCGA.GN.A261.06 TCGA.FS.A1YW.06 TCGA.BF.A1PU.01 TCGA.D3.A1QB.06 TCGA.D3.A1Q6.06 TCGA.D3.A3C8.06
#> "0122" "023" "0443" "0124" "0441" "014"
#> TCGA.ER.A19A.06 TCGA.EE.A2GN.06 TCGA.EE.A29M.06 TCGA.D3.A2J7.06 TCGA.EB.A24C.01 TCGA.GN.A262.06
#> "0131" "0522" "0121" "0113" "0432" "0212"
#> TCGA.EE.A2GD.06 TCGA.D3.A2J9.06 TCGA.EE.A29B.06 TCGA.D9.A1JX.06 TCGA.EE.A29A.06 TCGA.D3.A2JL.06
#> "014" "0113" "0511" "03" "022" "0412"
#> TCGA.D3.A1Q4.06 TCGA.FS.A1ZS.06 TCGA.D3.A3C3.06 TCGA.D3.A2J8.06 TCGA.FS.A1ZF.06 TCGA.FS.A1ZC.06
#> "0122" "0423" "0413" "0131" "03" "0212"
#> TCGA.EE.A20H.06 TCGA.EE.A29W.06 TCGA.D3.A1QA.07 TCGA.BF.A1PV.01 TCGA.EE.A29S.06 TCGA.DA.A1HV.06
#> "0522" "03" "0413" "0512" "04424" "03"
#> TCGA.FS.A1Z0.06 TCGA.EE.A2GO.06 TCGA.EB.A1NK.01 TCGA.GN.A26D.06 TCGA.EE.A2MJ.06 TCGA.ER.A198.06
#> "0122" "023" "0133" "0422" "0113" "0512"
#> TCGA.EE.A17X.06 TCGA.EE.A2M5.06 TCGA.GN.A266.06 TCGA.D3.A3C1.06 TCGA.D3.A2JH.06 TCGA.EE.A20F.06
#> "03" "0412" "0443" "04421" "0112" "0411"
#> TCGA.EE.A29E.06 TCGA.ER.A2NG.06 TCGA.ER.A193.06 TCGA.FS.A1ZW.06 TCGA.ER.A19O.06 TCGA.EE.A2ME.06
#> "0133" "014" "0421" "0413" "04421" "01112"
#> TCGA.EE.A20B.06 TCGA.EE.A3AF.06 TCGA.GN.A265.06 TCGA.FS.A1YX.06 TCGA.FS.A1ZJ.06 TCGA.ER.A19H.06
#> "0411" "03" "0113" "0441" "0523" "03"
#> TCGA.EE.A3AC.06 TCGA.EE.A2MU.06 TCGA.ER.A194.01 TCGA.EE.A2MS.06 TCGA.EE.A29R.06 TCGA.D9.A1X3.06
#> "0521" "0113" "04423" "0433" "023" "022"
#> TCGA.EE.A29X.06 TCGA.EE.A2GK.06 TCGA.EE.A3AA.06 TCGA.ER.A2NE.06 TCGA.EE.A2GR.06 TCGA.FS.A1ZD.06
#> "04421" "0123" "01112" "0212" "0521" "0523"
#> TCGA.ER.A19P.06 TCGA.D3.A1Q8.06 TCGA.ER.A2NC.06 TCGA.BF.A1Q0.01 TCGA.FS.A1ZP.06 TCGA.EE.A182.06
#> "014" "0112" "0443" "0421" "0522" "0432"
#> TCGA.D9.A1JW.06 TCGA.D3.A1Q7.06 TCGA.EE.A185.06 TCGA.EE.A2GJ.06 TCGA.D3.A3CB.06 TCGA.EE.A2GU.06
#> "0421" "014" "0212" "0431" "01111" "0421"
#> TCGA.ER.A195.06 TCGA.FS.A1Z7.06 TCGA.EE.A2M6.06 TCGA.ER.A19K.01 TCGA.DA.A1HY.06 TCGA.D3.A3C7.06
#> "0132" "0423" "0212" "04421" "03" "03"
#> TCGA.EE.A2MP.06 TCGA.EE.A29H.06 TCGA.FR.A3YO.06 TCGA.XV.AB01.01 TCGA.RP.A694.06 TCGA.EB.A5SF.01
#> "03" "03" "04421" "03" "04423" "0122"
#> TCGA.ER.A19G.06 TCGA.EE.A2GE.06 TCGA.GF.A3OT.06 TCGA.ER.A2NF.06 TCGA.RP.A695.06 TCGA.BF.AAP7.01
#> "03" "0112" "014" "0132" "0512" "0121"
#> TCGA.EB.A3Y7.01 TCGA.EB.A3XC.01 TCGA.ER.A19W.06 TCGA.FR.A69P.06 TCGA.RP.A693.06 TCGA.FW.A3TV.06
#> "0423" "03" "014" "03" "01111" "0124"
#> TCGA.FW.A3R5.11 TCGA.FW.A3TU.06 TCGA.BF.AAP8.01 TCGA.EE.A2MM.06 TCGA.DA.A1HW.06 TCGA.DA.A1IC.06
#> "0132" "0511" "0422" "0513" "0441" "0521"
#> TCGA.XV.AAZV.01 TCGA.D3.A3C6.06 TCGA.EE.A29C.06 TCGA.BF.AAP2.01 TCGA.EE.A2A2.06 TCGA.GF.A6C8.06
#> "0121" "03" "0132" "0212" "03" "0443"
#> TCGA.RP.A690.06 TCGA.FW.A5DY.06 TCGA.DA.A1I4.06 TCGA.EE.A29V.06 TCGA.GF.A6C9.06 TCGA.EE.A2GT.06
#> "0122" "014" "0132" "0412" "0113" "0131"
#> TCGA.GN.A9SD.06 TCGA.EE.A3AB.06 TCGA.BF.AAP6.01 TCGA.EB.A5SH.06 TCGA.D9.A6E9.06 TCGA.BF.AAP4.01
#> "014" "0413" "03" "0431" "04421" "04421"
#> TCGA.EE.A2GM.06 TCGA.D3.A3CF.06 TCGA.D9.A6EC.06 TCGA.DA.A1I1.06 TCGA.HR.A2OH.06 TCGA.EE.A2MT.06
#> "0212" "0121" "023" "0413" "014" "0422"
#> TCGA.ER.A19M.06 TCGA.GN.A26C.01 TCGA.FS.A1ZA.06 TCGA.EB.A5SE.01 TCGA.ER.A3PL.06 TCGA.FR.A3R1.01
#> "0411" "01112" "04422" "022" "0521" "03"
#> TCGA.EE.A2MI.06 TCGA.D3.A3CE.06 TCGA.D3.A5GT.01 TCGA.ER.A2NB.01 TCGA.D3.A1Q5.06 TCGA.EB.A5UN.06
#> "0443" "0441" "0511" "0421" "0422" "01113"
#> TCGA.EB.A299.01 TCGA.DA.A1IA.06 TCGA.EB.A5SG.06 TCGA.D9.A6EA.06 TCGA.XV.AAZY.01 TCGA.EB.A57M.01
#> "03" "0511" "014" "022" "014" "0412"
#> TCGA.EE.A2A6.06 TCGA.D3.A2JA.06 TCGA.D3.A1Q1.06 TCGA.EB.A3XF.01 TCGA.D3.A2JF.06 TCGA.XV.AAZW.01
#> "0421" "0132" "0422" "03" "03" "03"
#> TCGA.EB.A3Y6.01 TCGA.EB.A3XE.01 TCGA.D9.A3Z4.01 TCGA.FW.A3R5.06 TCGA.EE.A2GI.06 TCGA.EE.A2GL.06
#> "0441" "0432" "0523" "0432" "0411" "014"
#> TCGA.EB.A3XB.01 TCGA.BF.AAOU.01 TCGA.EB.A3XD.01 TCGA.EE.A2MD.06 TCGA.YD.A9TB.06 TCGA.W3.AA1V.06
#> "04421" "014" "0124" "04421" "0521" "0441"
#> TCGA.ER.A2ND.06 TCGA.D3.A2JK.06 TCGA.FS.A1ZB.06 TCGA.EE.A29D.06 TCGA.EB.A5UM.01 TCGA.QB.A6FS.06
#> "0521" "0412" "0112" "022" "0432" "0132"
#> TCGA.D9.A3Z1.06 TCGA.D3.A2JN.06 TCGA.FR.A3YN.06 TCGA.FS.A1ZT.06 TCGA.D9.A148.06 TCGA.HR.A2OG.06
#> "0113" "014" "03" "0132" "0412" "0125"
#> TCGA.EE.A2ML.06 TCGA.EB.A5UL.06 TCGA.EE.A29T.06 TCGA.D9.A3Z3.06 TCGA.D9.A4Z3.01 TCGA.ER.A3ES.06
#> "0413" "0412" "0432" "0124" "0522" "0422"
#> TCGA.XV.A9VZ.01 TCGA.QB.AA9O.06 TCGA.EB.A44Q.06 TCGA.EB.A44R.06 TCGA.BF.A3DJ.01 TCGA.EE.A3JD.06
#> "0122" "03" "04421" "0433" "03" "0131"
#> TCGA.D3.A51N.06 TCGA.EB.A44N.01 TCGA.EE.A3J3.06 TCGA.XV.A9W5.01 TCGA.D3.A51G.06 TCGA.EB.A4P0.01
#> "0413" "0113" "03" "0412" "03" "03"
#> TCGA.BF.AAP1.01 TCGA.EE.A3J4.06 TCGA.Z2.AA3V.06 TCGA.LH.A9QB.06 TCGA.D3.A51J.06 TCGA.3N.A9WC.06
#> "023" "0511" "0121" "023" "04421" "0421"
#> TCGA.DA.A3F8.06 TCGA.D9.A4Z6.06 TCGA.D3.A51R.06 TCGA.EB.A4OZ.01 TCGA.FS.A4FB.06 TCGA.EE.A3JE.06
#> "0113" "0412" "03" "0121" "03" "0113"
#> TCGA.W3.AA1W.06 TCGA.DA.A1I0.06 TCGA.D3.A51F.06 TCGA.IH.A3EA.01 TCGA.EB.A431.01 TCGA.EB.A97M.01
#> "01111" "0412" "0131" "0512" "0412" "022"
#> TCGA.BF.AAOX.01 TCGA.DA.A3F5.06 TCGA.YD.A9TA.06 TCGA.DA.A3F2.06 TCGA.EB.A44O.01 TCGA.EB.A4IQ.01
#> "0412" "0423" "0411" "0131" "0521" "0421"
#> TCGA.EB.A4IS.01 TCGA.YG.AA3O.06 TCGA.ER.A3EV.06 TCGA.3N.A9WD.06 TCGA.BF.A3DM.01 TCGA.XV.A9W2.01
#> "0112" "0512" "0433" "0113" "03" "0423"
#> TCGA.W3.AA1Q.06 TCGA.WE.AAA0.06 TCGA.W3.AA1R.06 TCGA.EE.A3J5.06 TCGA.EB.A4OY.01 TCGA.FS.A4FD.06
#> "0512" "0412" "03" "0412" "0122" "0422"
#> TCGA.BF.AAP0.06 TCGA.YG.AA3P.06 TCGA.EE.A3JA.06 TCGA.W3.AA21.06 TCGA.WE.AAA3.06 TCGA.FS.A4F4.06
#> "0123" "0523" "03" "0211" "0423" "03"
#> TCGA.BF.A3DN.01 TCGA.ER.A3ET.06 TCGA.W3.AA1O.06 TCGA.D3.A51E.06 TCGA.Z2.AA3S.06 TCGA.YG.AA3N.01
#> "03" "0423" "0513" "03" "022" "04421"
#> TCGA.WE.AA9Y.06 TCGA.FS.A4F5.06 TCGA.EE.A3J7.06 TCGA.FS.A4F8.06 TCGA.DA.A3F3.06 TCGA.D3.A51H.06
#> "01113" "023" "0511" "01112" "03" "0131"
#> TCGA.BF.A3DL.01 TCGA.D3.A51T.06 TCGA.D3.A51K.06 TCGA.EB.A44P.01 TCGA.D9.A4Z5.01 TCGA.WE.AAA4.06
#> "0124" "03" "0522" "0521" "023" "014"
#> TCGA.3N.A9WB.06 TCGA.EE.A3J8.06
#> "022" "0211"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 2616))
#> TCGA.FR.A728.01 TCGA.GN.A4U8.11 TCGA.GN.A8LL.06 TCGA.FR.A8YC.06 TCGA.DA.A95X.06 TCGA.ER.A42K.06
#> "014" "0113" "03" "022" "0211" "03"
#> TCGA.D3.A8GO.06 TCGA.D3.A8GK.06 TCGA.WE.A8JZ.06 TCGA.WE.A8ZO.06 TCGA.D3.A8GI.06 TCGA.FS.A4FC.06
#> "0124" "0524" "0212" "0511" "0512" "0421"
#> TCGA.FS.A4F2.06 TCGA.WE.A8ZM.06 TCGA.WE.A8ZT.06 TCGA.D3.A8GQ.06 TCGA.D3.A8GB.06 TCGA.DA.A95Y.06
#> "03" "0522" "03" "0411" "0131" "03"
#> TCGA.EE.A3JI.06 TCGA.OD.A75X.06 TCGA.DA.A960.01 TCGA.D3.A8GV.06 TCGA.WE.A8ZN.06 TCGA.D3.A8GN.06
#> "022" "023" "0211" "0212" "0112" "014"
#> TCGA.EB.A550.01 TCGA.BF.A5EQ.01 TCGA.EB.A3HV.01 TCGA.HR.A5NC.01 TCGA.DA.A95Z.06 TCGA.EB.A6QZ.01
#> "0122" "0421" "0521" "0523" "022" "0212"
#> TCGA.FW.A3I3.06 TCGA.WE.A8K6.06 TCGA.D3.A8GP.06 TCGA.EB.A42Z.01 TCGA.GN.A4U4.06 TCGA.GF.A4EO.06
#> "023" "03" "022" "023" "0212" "014"
#> TCGA.GN.A8LK.06 TCGA.WE.A8K4.01 TCGA.DA.A95W.06 TCGA.FW.A5DX.01 TCGA.GN.A4U3.06 TCGA.EB.A6QY.01
#> "0521" "0112" "022" "0212" "03" "0133"
#> TCGA.EB.A5VU.01 TCGA.Z2.A8RT.06 TCGA.WE.A8K1.06 TCGA.EB.A41B.01 TCGA.WE.A8ZY.06 TCGA.D9.A6EG.06
#> "0443" "03" "0112" "03" "0212" "022"
#> TCGA.BF.A5ER.01 TCGA.FR.A8YD.06 TCGA.FS.A4F9.06 TCGA.EB.A6R0.01 TCGA.ER.A42L.06 TCGA.D3.A8GJ.06
#> "0512" "0511" "0511" "03" "0113" "04423"
#> TCGA.FR.A8YE.06 TCGA.WE.A8ZR.06 TCGA.BF.A9VF.01 TCGA.EE.A3JH.06 TCGA.DA.A95V.06 TCGA.GF.A769.01
#> "0113" "0432" "0521" "0112" "0412" "0212"
#> TCGA.D9.A4Z2.01 TCGA.FR.A44A.06 TCGA.EB.A5VV.06 TCGA.EE.A180.06 TCGA.D3.A8GC.06 TCGA.WE.A8K5.06
#> "03" "014" "0123" "022" "0513" "023"
#> TCGA.GN.A8LN.01 TCGA.EE.A3JB.06 TCGA.D3.A3MO.06 TCGA.ER.A42H.01 TCGA.WE.A8ZX.06 TCGA.GN.A4U5.01
#> "0212" "0411" "0522" "0511" "0412" "014"
#> TCGA.D3.A8GS.06 TCGA.WE.A8ZQ.06 TCGA.EE.A2MF.06 TCGA.D3.A5GU.06 TCGA.GN.A4U8.06 TCGA.EB.A42Y.01
#> "0441" "0523" "022" "0511" "0413" "0212"
#> TCGA.D3.A3ML.06 TCGA.EB.A551.01 TCGA.D3.A8GM.06 TCGA.D3.A8GL.06 TCGA.D3.A3MU.06 TCGA.FS.A4F0.06
#> "0511" "04422" "0412" "022" "022" "022"
#> TCGA.D3.A3MV.06 TCGA.GN.A4U7.06 TCGA.FR.A2OS.01 TCGA.D3.A2JE.06 TCGA.YD.A89C.06 TCGA.FR.A726.01
#> "03" "03" "0523" "0522" "0411" "0411"
#> TCGA.BF.A5EP.01 TCGA.D3.A3MR.06 TCGA.D3.A8GR.06 TCGA.GN.A4U9.06 TCGA.EB.A6L9.06 TCGA.D3.A5GL.06
#> "03" "0112" "0511" "0522" "0131" "03"
#> TCGA.EB.A430.01 TCGA.D3.A8GE.06 TCGA.D3.A8GD.06 TCGA.EB.A41A.01 TCGA.W3.A825.06 TCGA.EE.A183.06
#> "0133" "0132" "014" "022" "0443" "01112"
#> TCGA.ER.A2NH.06 TCGA.D3.A5GR.06 TCGA.FR.A729.06 TCGA.D3.A1QA.06 TCGA.FS.A1YY.06 TCGA.EE.A2MK.06
#> "0112" "0441" "0441" "0211" "03" "03"
#> TCGA.EE.A2M8.06 TCGA.EB.A5KH.06 TCGA.FS.A1ZR.06 TCGA.EE.A3AE.06 TCGA.EE.A29P.06 TCGA.EB.A553.01
#> "0123" "0212" "0521" "03" "04424" "0513"
#> TCGA.EE.A2MR.06 TCGA.GN.A26A.06 TCGA.FS.A1ZY.06 TCGA.EE.A20I.06 TCGA.DA.A1I5.06 TCGA.EE.A184.06
#> "01112" "0411" "0212" "0412" "0125" "023"
#> TCGA.EB.A85J.01 TCGA.RP.A6K9.06 TCGA.EE.A17Y.06 TCGA.D9.A149.06 TCGA.ER.A19D.06 TCGA.FS.A1ZZ.06
#> "0433" "0423" "0411" "0421" "0122" "023"
#> TCGA.EE.A2GP.06 TCGA.EE.A3AD.06 TCGA.D3.A1Q9.06 TCGA.GF.A2C7.01 TCGA.BF.A5ES.01 TCGA.ER.A199.06
#> "0524" "0212" "0412" "0511" "0511" "014"
#> TCGA.EE.A3AH.06 TCGA.W3.A828.06 TCGA.EE.A2A5.06 TCGA.ER.A19L.06 TCGA.BF.A1PX.01 TCGA.ER.A19T.06
#> "0212" "0133" "0522" "0432" "01112" "0431"
#> TCGA.EB.A51B.01 TCGA.FS.A1ZQ.06 TCGA.D3.A2JG.06 TCGA.EE.A2GH.06 TCGA.ER.A19F.06 TCGA.ER.A196.01
#> "03" "03" "03" "0112" "03" "0124"
#> TCGA.D3.A2JC.06 TCGA.EE.A3AG.06 TCGA.ER.A19S.06 TCGA.EE.A2GC.06 TCGA.EE.A29N.06 TCGA.FR.A7U8.06
#> "0441" "03" "014" "0524" "0113" "023"
#> TCGA.BF.A5EO.01 TCGA.ER.A19B.06 TCGA.D3.A5GN.06 TCGA.D3.A2JB.06 TCGA.ER.A19J.06 TCGA.D3.A2JD.06
#> "0412" "03" "03" "0123" "023" "0112"
#> TCGA.FS.A1Z4.06 TCGA.FR.A7UA.06 TCGA.EE.A2M7.06 TCGA.D3.A1Q3.06 TCGA.EB.A85I.01 TCGA.EB.A82C.01
#> "0131" "014" "0441" "0431" "0421" "023"
#> TCGA.ER.A19E.06 TCGA.FS.A1ZK.06 TCGA.FS.A1ZU.06 TCGA.EB.A5FP.01 TCGA.EB.A4XL.01 TCGA.DA.A1I2.06
#> "0522" "0524" "0522" "0212" "03" "0441"
#> TCGA.EE.A29L.06 TCGA.FS.A1ZN.01 TCGA.EB.A24D.01 TCGA.EE.A2GB.06 TCGA.DA.A1I7.06 TCGA.ER.A2NF.01
#> "0211" "0212" "0511" "03" "0441" "0132"
#> TCGA.GN.A263.01 TCGA.EE.A20C.06 TCGA.EE.A2MQ.06 TCGA.ER.A19N.06 TCGA.FS.A1Z3.06 TCGA.DA.A1I8.06
#> "0132" "023" "0512" "0112" "03" "03"
#> TCGA.D3.A5GS.06 TCGA.EE.A181.06 TCGA.GN.A268.06 TCGA.W3.A824.06 TCGA.EE.A2GS.06 TCGA.FR.A7U9.06
#> "03" "0412" "022" "0511" "03" "0121"
#> TCGA.ER.A19Q.06 TCGA.FS.A1ZM.06 TCGA.EE.A2MG.06 TCGA.EE.A2MC.06 TCGA.EE.A17Z.06 TCGA.D3.A2JP.06
#> "0125" "0441" "0131" "0131" "0522" "0412"
#> TCGA.ER.A19C.06 TCGA.EB.A82B.01 TCGA.EE.A2A0.06 TCGA.EE.A29G.06 TCGA.D3.A5GO.06 TCGA.GN.A269.01
#> "0443" "0423" "014" "0113" "03" "01113"
#> TCGA.EE.A2A1.06 TCGA.ER.A1A1.06 TCGA.FS.A1ZG.06 TCGA.FS.A1ZE.06 TCGA.FS.A1ZH.06 TCGA.EE.A2MH.06
#> "0131" "0131" "022" "022" "0411" "01112"
#> TCGA.D3.A2J6.06 TCGA.EE.A29Q.06 TCGA.BF.A1PZ.01 TCGA.D3.A3BZ.06 TCGA.D3.A2JO.06 TCGA.GN.A267.06
#> "0423" "03" "03" "0131" "04422" "0432"
#> TCGA.EE.A2MN.06 TCGA.GN.A264.06 TCGA.ER.A197.06 TCGA.DA.A1IB.06 TCGA.D3.A3CC.06 TCGA.ER.A19T.01
#> "0513" "023" "014" "014" "0423" "0523"
#> TCGA.GN.A261.06 TCGA.FS.A1YW.06 TCGA.BF.A1PU.01 TCGA.D3.A1QB.06 TCGA.D3.A1Q6.06 TCGA.D3.A3C8.06
#> "0122" "023" "0443" "0124" "0441" "014"
#> TCGA.ER.A19A.06 TCGA.EE.A2GN.06 TCGA.EE.A29M.06 TCGA.D3.A2J7.06 TCGA.EB.A24C.01 TCGA.GN.A262.06
#> "0131" "0522" "0121" "0113" "0432" "0212"
#> TCGA.EE.A2GD.06 TCGA.D3.A2J9.06 TCGA.EE.A29B.06 TCGA.D9.A1JX.06 TCGA.EE.A29A.06 TCGA.D3.A2JL.06
#> "014" "0113" "0511" "03" "022" "0412"
#> TCGA.D3.A1Q4.06 TCGA.FS.A1ZS.06 TCGA.D3.A3C3.06 TCGA.D3.A2J8.06 TCGA.FS.A1ZF.06 TCGA.FS.A1ZC.06
#> "0122" "0423" "0413" "0131" "03" "0212"
#> TCGA.EE.A20H.06 TCGA.EE.A29W.06 TCGA.D3.A1QA.07 TCGA.BF.A1PV.01 TCGA.EE.A29S.06 TCGA.DA.A1HV.06
#> "0522" "03" "0413" "0512" "04424" "03"
#> TCGA.FS.A1Z0.06 TCGA.EE.A2GO.06 TCGA.EB.A1NK.01 TCGA.GN.A26D.06 TCGA.EE.A2MJ.06 TCGA.ER.A198.06
#> "0122" "023" "0133" "0422" "0113" "0512"
#> TCGA.EE.A17X.06 TCGA.EE.A2M5.06 TCGA.GN.A266.06 TCGA.D3.A3C1.06 TCGA.D3.A2JH.06 TCGA.EE.A20F.06
#> "03" "0412" "0443" "04421" "0112" "0411"
#> TCGA.EE.A29E.06 TCGA.ER.A2NG.06 TCGA.ER.A193.06 TCGA.FS.A1ZW.06 TCGA.ER.A19O.06 TCGA.EE.A2ME.06
#> "0133" "014" "0421" "0413" "04421" "01112"
#> TCGA.EE.A20B.06 TCGA.EE.A3AF.06 TCGA.GN.A265.06 TCGA.FS.A1YX.06 TCGA.FS.A1ZJ.06 TCGA.ER.A19H.06
#> "0411" "03" "0113" "0441" "0523" "03"
#> TCGA.EE.A3AC.06 TCGA.EE.A2MU.06 TCGA.ER.A194.01 TCGA.EE.A2MS.06 TCGA.EE.A29R.06 TCGA.D9.A1X3.06
#> "0521" "0113" "04423" "0433" "023" "022"
#> TCGA.EE.A29X.06 TCGA.EE.A2GK.06 TCGA.EE.A3AA.06 TCGA.ER.A2NE.06 TCGA.EE.A2GR.06 TCGA.FS.A1ZD.06
#> "04421" "0123" "01112" "0212" "0521" "0523"
#> TCGA.ER.A19P.06 TCGA.D3.A1Q8.06 TCGA.ER.A2NC.06 TCGA.BF.A1Q0.01 TCGA.FS.A1ZP.06 TCGA.EE.A182.06
#> "014" "0112" "0443" "0421" "0522" "0432"
#> TCGA.D9.A1JW.06 TCGA.D3.A1Q7.06 TCGA.EE.A185.06 TCGA.EE.A2GJ.06 TCGA.D3.A3CB.06 TCGA.EE.A2GU.06
#> "0421" "014" "0212" "0431" "01111" "0421"
#> TCGA.ER.A195.06 TCGA.FS.A1Z7.06 TCGA.EE.A2M6.06 TCGA.ER.A19K.01 TCGA.DA.A1HY.06 TCGA.D3.A3C7.06
#> "0132" "0423" "0212" "04421" "03" "03"
#> TCGA.EE.A2MP.06 TCGA.EE.A29H.06 TCGA.FR.A3YO.06 TCGA.XV.AB01.01 TCGA.RP.A694.06 TCGA.EB.A5SF.01
#> "03" "03" "04421" "03" "04423" "0122"
#> TCGA.ER.A19G.06 TCGA.EE.A2GE.06 TCGA.GF.A3OT.06 TCGA.ER.A2NF.06 TCGA.RP.A695.06 TCGA.BF.AAP7.01
#> "03" "0112" "014" "0132" "0512" "0121"
#> TCGA.EB.A3Y7.01 TCGA.EB.A3XC.01 TCGA.ER.A19W.06 TCGA.FR.A69P.06 TCGA.RP.A693.06 TCGA.FW.A3TV.06
#> "0423" "03" "014" "03" "01111" "0124"
#> TCGA.FW.A3R5.11 TCGA.FW.A3TU.06 TCGA.BF.AAP8.01 TCGA.EE.A2MM.06 TCGA.DA.A1HW.06 TCGA.DA.A1IC.06
#> "0132" "0511" "0422" "0513" "0441" "0521"
#> TCGA.XV.AAZV.01 TCGA.D3.A3C6.06 TCGA.EE.A29C.06 TCGA.BF.AAP2.01 TCGA.EE.A2A2.06 TCGA.GF.A6C8.06
#> "0121" "03" "0132" "0212" "03" "0443"
#> TCGA.RP.A690.06 TCGA.FW.A5DY.06 TCGA.DA.A1I4.06 TCGA.EE.A29V.06 TCGA.GF.A6C9.06 TCGA.EE.A2GT.06
#> "0122" "014" "0132" "0412" "0113" "0131"
#> TCGA.GN.A9SD.06 TCGA.EE.A3AB.06 TCGA.BF.AAP6.01 TCGA.EB.A5SH.06 TCGA.D9.A6E9.06 TCGA.BF.AAP4.01
#> "014" "0413" "03" "0431" "04421" "04421"
#> TCGA.EE.A2GM.06 TCGA.D3.A3CF.06 TCGA.D9.A6EC.06 TCGA.DA.A1I1.06 TCGA.HR.A2OH.06 TCGA.EE.A2MT.06
#> "0212" "0121" "023" "0413" "014" "0422"
#> TCGA.ER.A19M.06 TCGA.GN.A26C.01 TCGA.FS.A1ZA.06 TCGA.EB.A5SE.01 TCGA.ER.A3PL.06 TCGA.FR.A3R1.01
#> "0411" "01112" "04422" "022" "0521" "03"
#> TCGA.EE.A2MI.06 TCGA.D3.A3CE.06 TCGA.D3.A5GT.01 TCGA.ER.A2NB.01 TCGA.D3.A1Q5.06 TCGA.EB.A5UN.06
#> "0443" "0441" "0511" "0421" "0422" "01113"
#> TCGA.EB.A299.01 TCGA.DA.A1IA.06 TCGA.EB.A5SG.06 TCGA.D9.A6EA.06 TCGA.XV.AAZY.01 TCGA.EB.A57M.01
#> "03" "0511" "014" "022" "014" "0412"
#> TCGA.EE.A2A6.06 TCGA.D3.A2JA.06 TCGA.D3.A1Q1.06 TCGA.EB.A3XF.01 TCGA.D3.A2JF.06 TCGA.XV.AAZW.01
#> "0421" "0132" "0422" "03" "03" "03"
#> TCGA.EB.A3Y6.01 TCGA.EB.A3XE.01 TCGA.D9.A3Z4.01 TCGA.FW.A3R5.06 TCGA.EE.A2GI.06 TCGA.EE.A2GL.06
#> "0441" "0432" "0523" "0432" "0411" "014"
#> TCGA.EB.A3XB.01 TCGA.BF.AAOU.01 TCGA.EB.A3XD.01 TCGA.EE.A2MD.06 TCGA.YD.A9TB.06 TCGA.W3.AA1V.06
#> "04421" "014" "0124" "04421" "0521" "0441"
#> TCGA.ER.A2ND.06 TCGA.D3.A2JK.06 TCGA.FS.A1ZB.06 TCGA.EE.A29D.06 TCGA.EB.A5UM.01 TCGA.QB.A6FS.06
#> "0521" "0412" "0112" "022" "0432" "0132"
#> TCGA.D9.A3Z1.06 TCGA.D3.A2JN.06 TCGA.FR.A3YN.06 TCGA.FS.A1ZT.06 TCGA.D9.A148.06 TCGA.HR.A2OG.06
#> "0113" "014" "03" "0132" "0412" "0125"
#> TCGA.EE.A2ML.06 TCGA.EB.A5UL.06 TCGA.EE.A29T.06 TCGA.D9.A3Z3.06 TCGA.D9.A4Z3.01 TCGA.ER.A3ES.06
#> "0413" "0412" "0432" "0124" "0522" "0422"
#> TCGA.XV.A9VZ.01 TCGA.QB.AA9O.06 TCGA.EB.A44Q.06 TCGA.EB.A44R.06 TCGA.BF.A3DJ.01 TCGA.EE.A3JD.06
#> "0122" "03" "04421" "0433" "03" "0131"
#> TCGA.D3.A51N.06 TCGA.EB.A44N.01 TCGA.EE.A3J3.06 TCGA.XV.A9W5.01 TCGA.D3.A51G.06 TCGA.EB.A4P0.01
#> "0413" "0113" "03" "0412" "03" "03"
#> TCGA.BF.AAP1.01 TCGA.EE.A3J4.06 TCGA.Z2.AA3V.06 TCGA.LH.A9QB.06 TCGA.D3.A51J.06 TCGA.3N.A9WC.06
#> "023" "0511" "0121" "023" "04421" "0421"
#> TCGA.DA.A3F8.06 TCGA.D9.A4Z6.06 TCGA.D3.A51R.06 TCGA.EB.A4OZ.01 TCGA.FS.A4FB.06 TCGA.EE.A3JE.06
#> "0113" "0412" "03" "0121" "03" "0113"
#> TCGA.W3.AA1W.06 TCGA.DA.A1I0.06 TCGA.D3.A51F.06 TCGA.IH.A3EA.01 TCGA.EB.A431.01 TCGA.EB.A97M.01
#> "01111" "0412" "0131" "0512" "0412" "022"
#> TCGA.BF.AAOX.01 TCGA.DA.A3F5.06 TCGA.YD.A9TA.06 TCGA.DA.A3F2.06 TCGA.EB.A44O.01 TCGA.EB.A4IQ.01
#> "0412" "0423" "0411" "0131" "0521" "0421"
#> TCGA.EB.A4IS.01 TCGA.YG.AA3O.06 TCGA.ER.A3EV.06 TCGA.3N.A9WD.06 TCGA.BF.A3DM.01 TCGA.XV.A9W2.01
#> "0112" "0512" "0433" "0113" "03" "0423"
#> TCGA.W3.AA1Q.06 TCGA.WE.AAA0.06 TCGA.W3.AA1R.06 TCGA.EE.A3J5.06 TCGA.EB.A4OY.01 TCGA.FS.A4FD.06
#> "0512" "0412" "03" "0412" "0122" "0422"
#> TCGA.BF.AAP0.06 TCGA.YG.AA3P.06 TCGA.EE.A3JA.06 TCGA.W3.AA21.06 TCGA.WE.AAA3.06 TCGA.FS.A4F4.06
#> "0123" "0523" "03" "0211" "0423" "03"
#> TCGA.BF.A3DN.01 TCGA.ER.A3ET.06 TCGA.W3.AA1O.06 TCGA.D3.A51E.06 TCGA.Z2.AA3S.06 TCGA.YG.AA3N.01
#> "03" "0423" "0513" "03" "022" "04421"
#> TCGA.WE.AA9Y.06 TCGA.FS.A4F5.06 TCGA.EE.A3J7.06 TCGA.FS.A4F8.06 TCGA.DA.A3F3.06 TCGA.D3.A51H.06
#> "01113" "023" "0511" "01112" "03" "0131"
#> TCGA.BF.A3DL.01 TCGA.D3.A51T.06 TCGA.D3.A51K.06 TCGA.EB.A44P.01 TCGA.D9.A4Z5.01 TCGA.WE.AAA4.06
#> "0124" "03" "0522" "0521" "023" "014"
#> TCGA.3N.A9WB.06 TCGA.EE.A3J8.06
#> "022" "0211"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 2664))
#> TCGA.FR.A728.01 TCGA.GN.A4U8.11 TCGA.GN.A8LL.06 TCGA.FR.A8YC.06 TCGA.DA.A95X.06 TCGA.ER.A42K.06
#> "014" "0113" "03" "022" "0211" "03"
#> TCGA.D3.A8GO.06 TCGA.D3.A8GK.06 TCGA.WE.A8JZ.06 TCGA.WE.A8ZO.06 TCGA.D3.A8GI.06 TCGA.FS.A4FC.06
#> "0124" "0524" "0212" "0511" "0512" "0421"
#> TCGA.FS.A4F2.06 TCGA.WE.A8ZM.06 TCGA.WE.A8ZT.06 TCGA.D3.A8GQ.06 TCGA.D3.A8GB.06 TCGA.DA.A95Y.06
#> "03" "0522" "03" "0411" "0131" "03"
#> TCGA.EE.A3JI.06 TCGA.OD.A75X.06 TCGA.DA.A960.01 TCGA.D3.A8GV.06 TCGA.WE.A8ZN.06 TCGA.D3.A8GN.06
#> "022" "023" "0211" "0212" "0112" "014"
#> TCGA.EB.A550.01 TCGA.BF.A5EQ.01 TCGA.EB.A3HV.01 TCGA.HR.A5NC.01 TCGA.DA.A95Z.06 TCGA.EB.A6QZ.01
#> "0122" "0421" "0521" "0523" "022" "0212"
#> TCGA.FW.A3I3.06 TCGA.WE.A8K6.06 TCGA.D3.A8GP.06 TCGA.EB.A42Z.01 TCGA.GN.A4U4.06 TCGA.GF.A4EO.06
#> "023" "03" "022" "023" "0212" "014"
#> TCGA.GN.A8LK.06 TCGA.WE.A8K4.01 TCGA.DA.A95W.06 TCGA.FW.A5DX.01 TCGA.GN.A4U3.06 TCGA.EB.A6QY.01
#> "0521" "0112" "022" "0212" "03" "0133"
#> TCGA.EB.A5VU.01 TCGA.Z2.A8RT.06 TCGA.WE.A8K1.06 TCGA.EB.A41B.01 TCGA.WE.A8ZY.06 TCGA.D9.A6EG.06
#> "0443" "03" "0112" "03" "0212" "022"
#> TCGA.BF.A5ER.01 TCGA.FR.A8YD.06 TCGA.FS.A4F9.06 TCGA.EB.A6R0.01 TCGA.ER.A42L.06 TCGA.D3.A8GJ.06
#> "0512" "0511" "0511" "03" "0113" "04423"
#> TCGA.FR.A8YE.06 TCGA.WE.A8ZR.06 TCGA.BF.A9VF.01 TCGA.EE.A3JH.06 TCGA.DA.A95V.06 TCGA.GF.A769.01
#> "0113" "0432" "0521" "0112" "0412" "0212"
#> TCGA.D9.A4Z2.01 TCGA.FR.A44A.06 TCGA.EB.A5VV.06 TCGA.EE.A180.06 TCGA.D3.A8GC.06 TCGA.WE.A8K5.06
#> "03" "014" "0123" "022" "0513" "023"
#> TCGA.GN.A8LN.01 TCGA.EE.A3JB.06 TCGA.D3.A3MO.06 TCGA.ER.A42H.01 TCGA.WE.A8ZX.06 TCGA.GN.A4U5.01
#> "0212" "0411" "0522" "0511" "0412" "014"
#> TCGA.D3.A8GS.06 TCGA.WE.A8ZQ.06 TCGA.EE.A2MF.06 TCGA.D3.A5GU.06 TCGA.GN.A4U8.06 TCGA.EB.A42Y.01
#> "0441" "0523" "022" "0511" "0413" "0212"
#> TCGA.D3.A3ML.06 TCGA.EB.A551.01 TCGA.D3.A8GM.06 TCGA.D3.A8GL.06 TCGA.D3.A3MU.06 TCGA.FS.A4F0.06
#> "0511" "04422" "0412" "022" "022" "022"
#> TCGA.D3.A3MV.06 TCGA.GN.A4U7.06 TCGA.FR.A2OS.01 TCGA.D3.A2JE.06 TCGA.YD.A89C.06 TCGA.FR.A726.01
#> "03" "03" "0523" "0522" "0411" "0411"
#> TCGA.BF.A5EP.01 TCGA.D3.A3MR.06 TCGA.D3.A8GR.06 TCGA.GN.A4U9.06 TCGA.EB.A6L9.06 TCGA.D3.A5GL.06
#> "03" "0112" "0511" "0522" "0131" "03"
#> TCGA.EB.A430.01 TCGA.D3.A8GE.06 TCGA.D3.A8GD.06 TCGA.EB.A41A.01 TCGA.W3.A825.06 TCGA.EE.A183.06
#> "0133" "0132" "014" "022" "0443" "0111"
#> TCGA.ER.A2NH.06 TCGA.D3.A5GR.06 TCGA.FR.A729.06 TCGA.D3.A1QA.06 TCGA.FS.A1YY.06 TCGA.EE.A2MK.06
#> "0112" "0441" "0441" "0211" "03" "03"
#> TCGA.EE.A2M8.06 TCGA.EB.A5KH.06 TCGA.FS.A1ZR.06 TCGA.EE.A3AE.06 TCGA.EE.A29P.06 TCGA.EB.A553.01
#> "0123" "0212" "0521" "03" "04424" "0513"
#> TCGA.EE.A2MR.06 TCGA.GN.A26A.06 TCGA.FS.A1ZY.06 TCGA.EE.A20I.06 TCGA.DA.A1I5.06 TCGA.EE.A184.06
#> "0111" "0411" "0212" "0412" "0125" "023"
#> TCGA.EB.A85J.01 TCGA.RP.A6K9.06 TCGA.EE.A17Y.06 TCGA.D9.A149.06 TCGA.ER.A19D.06 TCGA.FS.A1ZZ.06
#> "0433" "0423" "0411" "0421" "0122" "023"
#> TCGA.EE.A2GP.06 TCGA.EE.A3AD.06 TCGA.D3.A1Q9.06 TCGA.GF.A2C7.01 TCGA.BF.A5ES.01 TCGA.ER.A199.06
#> "0524" "0212" "0412" "0511" "0511" "014"
#> TCGA.EE.A3AH.06 TCGA.W3.A828.06 TCGA.EE.A2A5.06 TCGA.ER.A19L.06 TCGA.BF.A1PX.01 TCGA.ER.A19T.06
#> "0212" "0133" "0522" "0432" "0111" "0431"
#> TCGA.EB.A51B.01 TCGA.FS.A1ZQ.06 TCGA.D3.A2JG.06 TCGA.EE.A2GH.06 TCGA.ER.A19F.06 TCGA.ER.A196.01
#> "03" "03" "03" "0112" "03" "0124"
#> TCGA.D3.A2JC.06 TCGA.EE.A3AG.06 TCGA.ER.A19S.06 TCGA.EE.A2GC.06 TCGA.EE.A29N.06 TCGA.FR.A7U8.06
#> "0441" "03" "014" "0524" "0113" "023"
#> TCGA.BF.A5EO.01 TCGA.ER.A19B.06 TCGA.D3.A5GN.06 TCGA.D3.A2JB.06 TCGA.ER.A19J.06 TCGA.D3.A2JD.06
#> "0412" "03" "03" "0123" "023" "0112"
#> TCGA.FS.A1Z4.06 TCGA.FR.A7UA.06 TCGA.EE.A2M7.06 TCGA.D3.A1Q3.06 TCGA.EB.A85I.01 TCGA.EB.A82C.01
#> "0131" "014" "0441" "0431" "0421" "023"
#> TCGA.ER.A19E.06 TCGA.FS.A1ZK.06 TCGA.FS.A1ZU.06 TCGA.EB.A5FP.01 TCGA.EB.A4XL.01 TCGA.DA.A1I2.06
#> "0522" "0524" "0522" "0212" "03" "0441"
#> TCGA.EE.A29L.06 TCGA.FS.A1ZN.01 TCGA.EB.A24D.01 TCGA.EE.A2GB.06 TCGA.DA.A1I7.06 TCGA.ER.A2NF.01
#> "0211" "0212" "0511" "03" "0441" "0132"
#> TCGA.GN.A263.01 TCGA.EE.A20C.06 TCGA.EE.A2MQ.06 TCGA.ER.A19N.06 TCGA.FS.A1Z3.06 TCGA.DA.A1I8.06
#> "0132" "023" "0512" "0112" "03" "03"
#> TCGA.D3.A5GS.06 TCGA.EE.A181.06 TCGA.GN.A268.06 TCGA.W3.A824.06 TCGA.EE.A2GS.06 TCGA.FR.A7U9.06
#> "03" "0412" "022" "0511" "03" "0121"
#> TCGA.ER.A19Q.06 TCGA.FS.A1ZM.06 TCGA.EE.A2MG.06 TCGA.EE.A2MC.06 TCGA.EE.A17Z.06 TCGA.D3.A2JP.06
#> "0125" "0441" "0131" "0131" "0522" "0412"
#> TCGA.ER.A19C.06 TCGA.EB.A82B.01 TCGA.EE.A2A0.06 TCGA.EE.A29G.06 TCGA.D3.A5GO.06 TCGA.GN.A269.01
#> "0443" "0423" "014" "0113" "03" "0111"
#> TCGA.EE.A2A1.06 TCGA.ER.A1A1.06 TCGA.FS.A1ZG.06 TCGA.FS.A1ZE.06 TCGA.FS.A1ZH.06 TCGA.EE.A2MH.06
#> "0131" "0131" "022" "022" "0411" "0111"
#> TCGA.D3.A2J6.06 TCGA.EE.A29Q.06 TCGA.BF.A1PZ.01 TCGA.D3.A3BZ.06 TCGA.D3.A2JO.06 TCGA.GN.A267.06
#> "0423" "03" "03" "0131" "04422" "0432"
#> TCGA.EE.A2MN.06 TCGA.GN.A264.06 TCGA.ER.A197.06 TCGA.DA.A1IB.06 TCGA.D3.A3CC.06 TCGA.ER.A19T.01
#> "0513" "023" "014" "014" "0423" "0523"
#> TCGA.GN.A261.06 TCGA.FS.A1YW.06 TCGA.BF.A1PU.01 TCGA.D3.A1QB.06 TCGA.D3.A1Q6.06 TCGA.D3.A3C8.06
#> "0122" "023" "0443" "0124" "0441" "014"
#> TCGA.ER.A19A.06 TCGA.EE.A2GN.06 TCGA.EE.A29M.06 TCGA.D3.A2J7.06 TCGA.EB.A24C.01 TCGA.GN.A262.06
#> "0131" "0522" "0121" "0113" "0432" "0212"
#> TCGA.EE.A2GD.06 TCGA.D3.A2J9.06 TCGA.EE.A29B.06 TCGA.D9.A1JX.06 TCGA.EE.A29A.06 TCGA.D3.A2JL.06
#> "014" "0113" "0511" "03" "022" "0412"
#> TCGA.D3.A1Q4.06 TCGA.FS.A1ZS.06 TCGA.D3.A3C3.06 TCGA.D3.A2J8.06 TCGA.FS.A1ZF.06 TCGA.FS.A1ZC.06
#> "0122" "0423" "0413" "0131" "03" "0212"
#> TCGA.EE.A20H.06 TCGA.EE.A29W.06 TCGA.D3.A1QA.07 TCGA.BF.A1PV.01 TCGA.EE.A29S.06 TCGA.DA.A1HV.06
#> "0522" "03" "0413" "0512" "04424" "03"
#> TCGA.FS.A1Z0.06 TCGA.EE.A2GO.06 TCGA.EB.A1NK.01 TCGA.GN.A26D.06 TCGA.EE.A2MJ.06 TCGA.ER.A198.06
#> "0122" "023" "0133" "0422" "0113" "0512"
#> TCGA.EE.A17X.06 TCGA.EE.A2M5.06 TCGA.GN.A266.06 TCGA.D3.A3C1.06 TCGA.D3.A2JH.06 TCGA.EE.A20F.06
#> "03" "0412" "0443" "04421" "0112" "0411"
#> TCGA.EE.A29E.06 TCGA.ER.A2NG.06 TCGA.ER.A193.06 TCGA.FS.A1ZW.06 TCGA.ER.A19O.06 TCGA.EE.A2ME.06
#> "0133" "014" "0421" "0413" "04421" "0111"
#> TCGA.EE.A20B.06 TCGA.EE.A3AF.06 TCGA.GN.A265.06 TCGA.FS.A1YX.06 TCGA.FS.A1ZJ.06 TCGA.ER.A19H.06
#> "0411" "03" "0113" "0441" "0523" "03"
#> TCGA.EE.A3AC.06 TCGA.EE.A2MU.06 TCGA.ER.A194.01 TCGA.EE.A2MS.06 TCGA.EE.A29R.06 TCGA.D9.A1X3.06
#> "0521" "0113" "04423" "0433" "023" "022"
#> TCGA.EE.A29X.06 TCGA.EE.A2GK.06 TCGA.EE.A3AA.06 TCGA.ER.A2NE.06 TCGA.EE.A2GR.06 TCGA.FS.A1ZD.06
#> "04421" "0123" "0111" "0212" "0521" "0523"
#> TCGA.ER.A19P.06 TCGA.D3.A1Q8.06 TCGA.ER.A2NC.06 TCGA.BF.A1Q0.01 TCGA.FS.A1ZP.06 TCGA.EE.A182.06
#> "014" "0112" "0443" "0421" "0522" "0432"
#> TCGA.D9.A1JW.06 TCGA.D3.A1Q7.06 TCGA.EE.A185.06 TCGA.EE.A2GJ.06 TCGA.D3.A3CB.06 TCGA.EE.A2GU.06
#> "0421" "014" "0212" "0431" "0111" "0421"
#> TCGA.ER.A195.06 TCGA.FS.A1Z7.06 TCGA.EE.A2M6.06 TCGA.ER.A19K.01 TCGA.DA.A1HY.06 TCGA.D3.A3C7.06
#> "0132" "0423" "0212" "04421" "03" "03"
#> TCGA.EE.A2MP.06 TCGA.EE.A29H.06 TCGA.FR.A3YO.06 TCGA.XV.AB01.01 TCGA.RP.A694.06 TCGA.EB.A5SF.01
#> "03" "03" "04421" "03" "04423" "0122"
#> TCGA.ER.A19G.06 TCGA.EE.A2GE.06 TCGA.GF.A3OT.06 TCGA.ER.A2NF.06 TCGA.RP.A695.06 TCGA.BF.AAP7.01
#> "03" "0112" "014" "0132" "0512" "0121"
#> TCGA.EB.A3Y7.01 TCGA.EB.A3XC.01 TCGA.ER.A19W.06 TCGA.FR.A69P.06 TCGA.RP.A693.06 TCGA.FW.A3TV.06
#> "0423" "03" "014" "03" "0111" "0124"
#> TCGA.FW.A3R5.11 TCGA.FW.A3TU.06 TCGA.BF.AAP8.01 TCGA.EE.A2MM.06 TCGA.DA.A1HW.06 TCGA.DA.A1IC.06
#> "0132" "0511" "0422" "0513" "0441" "0521"
#> TCGA.XV.AAZV.01 TCGA.D3.A3C6.06 TCGA.EE.A29C.06 TCGA.BF.AAP2.01 TCGA.EE.A2A2.06 TCGA.GF.A6C8.06
#> "0121" "03" "0132" "0212" "03" "0443"
#> TCGA.RP.A690.06 TCGA.FW.A5DY.06 TCGA.DA.A1I4.06 TCGA.EE.A29V.06 TCGA.GF.A6C9.06 TCGA.EE.A2GT.06
#> "0122" "014" "0132" "0412" "0113" "0131"
#> TCGA.GN.A9SD.06 TCGA.EE.A3AB.06 TCGA.BF.AAP6.01 TCGA.EB.A5SH.06 TCGA.D9.A6E9.06 TCGA.BF.AAP4.01
#> "014" "0413" "03" "0431" "04421" "04421"
#> TCGA.EE.A2GM.06 TCGA.D3.A3CF.06 TCGA.D9.A6EC.06 TCGA.DA.A1I1.06 TCGA.HR.A2OH.06 TCGA.EE.A2MT.06
#> "0212" "0121" "023" "0413" "014" "0422"
#> TCGA.ER.A19M.06 TCGA.GN.A26C.01 TCGA.FS.A1ZA.06 TCGA.EB.A5SE.01 TCGA.ER.A3PL.06 TCGA.FR.A3R1.01
#> "0411" "0111" "04422" "022" "0521" "03"
#> TCGA.EE.A2MI.06 TCGA.D3.A3CE.06 TCGA.D3.A5GT.01 TCGA.ER.A2NB.01 TCGA.D3.A1Q5.06 TCGA.EB.A5UN.06
#> "0443" "0441" "0511" "0421" "0422" "0111"
#> TCGA.EB.A299.01 TCGA.DA.A1IA.06 TCGA.EB.A5SG.06 TCGA.D9.A6EA.06 TCGA.XV.AAZY.01 TCGA.EB.A57M.01
#> "03" "0511" "014" "022" "014" "0412"
#> TCGA.EE.A2A6.06 TCGA.D3.A2JA.06 TCGA.D3.A1Q1.06 TCGA.EB.A3XF.01 TCGA.D3.A2JF.06 TCGA.XV.AAZW.01
#> "0421" "0132" "0422" "03" "03" "03"
#> TCGA.EB.A3Y6.01 TCGA.EB.A3XE.01 TCGA.D9.A3Z4.01 TCGA.FW.A3R5.06 TCGA.EE.A2GI.06 TCGA.EE.A2GL.06
#> "0441" "0432" "0523" "0432" "0411" "014"
#> TCGA.EB.A3XB.01 TCGA.BF.AAOU.01 TCGA.EB.A3XD.01 TCGA.EE.A2MD.06 TCGA.YD.A9TB.06 TCGA.W3.AA1V.06
#> "04421" "014" "0124" "04421" "0521" "0441"
#> TCGA.ER.A2ND.06 TCGA.D3.A2JK.06 TCGA.FS.A1ZB.06 TCGA.EE.A29D.06 TCGA.EB.A5UM.01 TCGA.QB.A6FS.06
#> "0521" "0412" "0112" "022" "0432" "0132"
#> TCGA.D9.A3Z1.06 TCGA.D3.A2JN.06 TCGA.FR.A3YN.06 TCGA.FS.A1ZT.06 TCGA.D9.A148.06 TCGA.HR.A2OG.06
#> "0113" "014" "03" "0132" "0412" "0125"
#> TCGA.EE.A2ML.06 TCGA.EB.A5UL.06 TCGA.EE.A29T.06 TCGA.D9.A3Z3.06 TCGA.D9.A4Z3.01 TCGA.ER.A3ES.06
#> "0413" "0412" "0432" "0124" "0522" "0422"
#> TCGA.XV.A9VZ.01 TCGA.QB.AA9O.06 TCGA.EB.A44Q.06 TCGA.EB.A44R.06 TCGA.BF.A3DJ.01 TCGA.EE.A3JD.06
#> "0122" "03" "04421" "0433" "03" "0131"
#> TCGA.D3.A51N.06 TCGA.EB.A44N.01 TCGA.EE.A3J3.06 TCGA.XV.A9W5.01 TCGA.D3.A51G.06 TCGA.EB.A4P0.01
#> "0413" "0113" "03" "0412" "03" "03"
#> TCGA.BF.AAP1.01 TCGA.EE.A3J4.06 TCGA.Z2.AA3V.06 TCGA.LH.A9QB.06 TCGA.D3.A51J.06 TCGA.3N.A9WC.06
#> "023" "0511" "0121" "023" "04421" "0421"
#> TCGA.DA.A3F8.06 TCGA.D9.A4Z6.06 TCGA.D3.A51R.06 TCGA.EB.A4OZ.01 TCGA.FS.A4FB.06 TCGA.EE.A3JE.06
#> "0113" "0412" "03" "0121" "03" "0113"
#> TCGA.W3.AA1W.06 TCGA.DA.A1I0.06 TCGA.D3.A51F.06 TCGA.IH.A3EA.01 TCGA.EB.A431.01 TCGA.EB.A97M.01
#> "0111" "0412" "0131" "0512" "0412" "022"
#> TCGA.BF.AAOX.01 TCGA.DA.A3F5.06 TCGA.YD.A9TA.06 TCGA.DA.A3F2.06 TCGA.EB.A44O.01 TCGA.EB.A4IQ.01
#> "0412" "0423" "0411" "0131" "0521" "0421"
#> TCGA.EB.A4IS.01 TCGA.YG.AA3O.06 TCGA.ER.A3EV.06 TCGA.3N.A9WD.06 TCGA.BF.A3DM.01 TCGA.XV.A9W2.01
#> "0112" "0512" "0433" "0113" "03" "0423"
#> TCGA.W3.AA1Q.06 TCGA.WE.AAA0.06 TCGA.W3.AA1R.06 TCGA.EE.A3J5.06 TCGA.EB.A4OY.01 TCGA.FS.A4FD.06
#> "0512" "0412" "03" "0412" "0122" "0422"
#> TCGA.BF.AAP0.06 TCGA.YG.AA3P.06 TCGA.EE.A3JA.06 TCGA.W3.AA21.06 TCGA.WE.AAA3.06 TCGA.FS.A4F4.06
#> "0123" "0523" "03" "0211" "0423" "03"
#> TCGA.BF.A3DN.01 TCGA.ER.A3ET.06 TCGA.W3.AA1O.06 TCGA.D3.A51E.06 TCGA.Z2.AA3S.06 TCGA.YG.AA3N.01
#> "03" "0423" "0513" "03" "022" "04421"
#> TCGA.WE.AA9Y.06 TCGA.FS.A4F5.06 TCGA.EE.A3J7.06 TCGA.FS.A4F8.06 TCGA.DA.A3F3.06 TCGA.D3.A51H.06
#> "0111" "023" "0511" "0111" "03" "0131"
#> TCGA.BF.A3DL.01 TCGA.D3.A51T.06 TCGA.D3.A51K.06 TCGA.EB.A44P.01 TCGA.D9.A4Z5.01 TCGA.WE.AAA4.06
#> "0124" "03" "0522" "0521" "023" "014"
#> TCGA.3N.A9WB.06 TCGA.EE.A3J8.06
#> "022" "0211"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 2780))
#> TCGA.FR.A728.01 TCGA.GN.A4U8.11 TCGA.GN.A8LL.06 TCGA.FR.A8YC.06 TCGA.DA.A95X.06 TCGA.ER.A42K.06
#> "014" "0113" "03" "022" "0211" "03"
#> TCGA.D3.A8GO.06 TCGA.D3.A8GK.06 TCGA.WE.A8JZ.06 TCGA.WE.A8ZO.06 TCGA.D3.A8GI.06 TCGA.FS.A4FC.06
#> "0124" "0524" "0212" "0511" "0512" "0421"
#> TCGA.FS.A4F2.06 TCGA.WE.A8ZM.06 TCGA.WE.A8ZT.06 TCGA.D3.A8GQ.06 TCGA.D3.A8GB.06 TCGA.DA.A95Y.06
#> "03" "0522" "03" "0411" "0131" "03"
#> TCGA.EE.A3JI.06 TCGA.OD.A75X.06 TCGA.DA.A960.01 TCGA.D3.A8GV.06 TCGA.WE.A8ZN.06 TCGA.D3.A8GN.06
#> "022" "023" "0211" "0212" "0112" "014"
#> TCGA.EB.A550.01 TCGA.BF.A5EQ.01 TCGA.EB.A3HV.01 TCGA.HR.A5NC.01 TCGA.DA.A95Z.06 TCGA.EB.A6QZ.01
#> "0122" "0421" "0521" "0523" "022" "0212"
#> TCGA.FW.A3I3.06 TCGA.WE.A8K6.06 TCGA.D3.A8GP.06 TCGA.EB.A42Z.01 TCGA.GN.A4U4.06 TCGA.GF.A4EO.06
#> "023" "03" "022" "023" "0212" "014"
#> TCGA.GN.A8LK.06 TCGA.WE.A8K4.01 TCGA.DA.A95W.06 TCGA.FW.A5DX.01 TCGA.GN.A4U3.06 TCGA.EB.A6QY.01
#> "0521" "0112" "022" "0212" "03" "0133"
#> TCGA.EB.A5VU.01 TCGA.Z2.A8RT.06 TCGA.WE.A8K1.06 TCGA.EB.A41B.01 TCGA.WE.A8ZY.06 TCGA.D9.A6EG.06
#> "0443" "03" "0112" "03" "0212" "022"
#> TCGA.BF.A5ER.01 TCGA.FR.A8YD.06 TCGA.FS.A4F9.06 TCGA.EB.A6R0.01 TCGA.ER.A42L.06 TCGA.D3.A8GJ.06
#> "0512" "0511" "0511" "03" "0113" "04423"
#> TCGA.FR.A8YE.06 TCGA.WE.A8ZR.06 TCGA.BF.A9VF.01 TCGA.EE.A3JH.06 TCGA.DA.A95V.06 TCGA.GF.A769.01
#> "0113" "043" "0521" "0112" "0412" "0212"
#> TCGA.D9.A4Z2.01 TCGA.FR.A44A.06 TCGA.EB.A5VV.06 TCGA.EE.A180.06 TCGA.D3.A8GC.06 TCGA.WE.A8K5.06
#> "03" "014" "0123" "022" "0513" "023"
#> TCGA.GN.A8LN.01 TCGA.EE.A3JB.06 TCGA.D3.A3MO.06 TCGA.ER.A42H.01 TCGA.WE.A8ZX.06 TCGA.GN.A4U5.01
#> "0212" "0411" "0522" "0511" "0412" "014"
#> TCGA.D3.A8GS.06 TCGA.WE.A8ZQ.06 TCGA.EE.A2MF.06 TCGA.D3.A5GU.06 TCGA.GN.A4U8.06 TCGA.EB.A42Y.01
#> "0441" "0523" "022" "0511" "0413" "0212"
#> TCGA.D3.A3ML.06 TCGA.EB.A551.01 TCGA.D3.A8GM.06 TCGA.D3.A8GL.06 TCGA.D3.A3MU.06 TCGA.FS.A4F0.06
#> "0511" "04422" "0412" "022" "022" "022"
#> TCGA.D3.A3MV.06 TCGA.GN.A4U7.06 TCGA.FR.A2OS.01 TCGA.D3.A2JE.06 TCGA.YD.A89C.06 TCGA.FR.A726.01
#> "03" "03" "0523" "0522" "0411" "0411"
#> TCGA.BF.A5EP.01 TCGA.D3.A3MR.06 TCGA.D3.A8GR.06 TCGA.GN.A4U9.06 TCGA.EB.A6L9.06 TCGA.D3.A5GL.06
#> "03" "0112" "0511" "0522" "0131" "03"
#> TCGA.EB.A430.01 TCGA.D3.A8GE.06 TCGA.D3.A8GD.06 TCGA.EB.A41A.01 TCGA.W3.A825.06 TCGA.EE.A183.06
#> "0133" "0132" "014" "022" "0443" "0111"
#> TCGA.ER.A2NH.06 TCGA.D3.A5GR.06 TCGA.FR.A729.06 TCGA.D3.A1QA.06 TCGA.FS.A1YY.06 TCGA.EE.A2MK.06
#> "0112" "0441" "0441" "0211" "03" "03"
#> TCGA.EE.A2M8.06 TCGA.EB.A5KH.06 TCGA.FS.A1ZR.06 TCGA.EE.A3AE.06 TCGA.EE.A29P.06 TCGA.EB.A553.01
#> "0123" "0212" "0521" "03" "04424" "0513"
#> TCGA.EE.A2MR.06 TCGA.GN.A26A.06 TCGA.FS.A1ZY.06 TCGA.EE.A20I.06 TCGA.DA.A1I5.06 TCGA.EE.A184.06
#> "0111" "0411" "0212" "0412" "0125" "023"
#> TCGA.EB.A85J.01 TCGA.RP.A6K9.06 TCGA.EE.A17Y.06 TCGA.D9.A149.06 TCGA.ER.A19D.06 TCGA.FS.A1ZZ.06
#> "043" "0423" "0411" "0421" "0122" "023"
#> TCGA.EE.A2GP.06 TCGA.EE.A3AD.06 TCGA.D3.A1Q9.06 TCGA.GF.A2C7.01 TCGA.BF.A5ES.01 TCGA.ER.A199.06
#> "0524" "0212" "0412" "0511" "0511" "014"
#> TCGA.EE.A3AH.06 TCGA.W3.A828.06 TCGA.EE.A2A5.06 TCGA.ER.A19L.06 TCGA.BF.A1PX.01 TCGA.ER.A19T.06
#> "0212" "0133" "0522" "043" "0111" "043"
#> TCGA.EB.A51B.01 TCGA.FS.A1ZQ.06 TCGA.D3.A2JG.06 TCGA.EE.A2GH.06 TCGA.ER.A19F.06 TCGA.ER.A196.01
#> "03" "03" "03" "0112" "03" "0124"
#> TCGA.D3.A2JC.06 TCGA.EE.A3AG.06 TCGA.ER.A19S.06 TCGA.EE.A2GC.06 TCGA.EE.A29N.06 TCGA.FR.A7U8.06
#> "0441" "03" "014" "0524" "0113" "023"
#> TCGA.BF.A5EO.01 TCGA.ER.A19B.06 TCGA.D3.A5GN.06 TCGA.D3.A2JB.06 TCGA.ER.A19J.06 TCGA.D3.A2JD.06
#> "0412" "03" "03" "0123" "023" "0112"
#> TCGA.FS.A1Z4.06 TCGA.FR.A7UA.06 TCGA.EE.A2M7.06 TCGA.D3.A1Q3.06 TCGA.EB.A85I.01 TCGA.EB.A82C.01
#> "0131" "014" "0441" "043" "0421" "023"
#> TCGA.ER.A19E.06 TCGA.FS.A1ZK.06 TCGA.FS.A1ZU.06 TCGA.EB.A5FP.01 TCGA.EB.A4XL.01 TCGA.DA.A1I2.06
#> "0522" "0524" "0522" "0212" "03" "0441"
#> TCGA.EE.A29L.06 TCGA.FS.A1ZN.01 TCGA.EB.A24D.01 TCGA.EE.A2GB.06 TCGA.DA.A1I7.06 TCGA.ER.A2NF.01
#> "0211" "0212" "0511" "03" "0441" "0132"
#> TCGA.GN.A263.01 TCGA.EE.A20C.06 TCGA.EE.A2MQ.06 TCGA.ER.A19N.06 TCGA.FS.A1Z3.06 TCGA.DA.A1I8.06
#> "0132" "023" "0512" "0112" "03" "03"
#> TCGA.D3.A5GS.06 TCGA.EE.A181.06 TCGA.GN.A268.06 TCGA.W3.A824.06 TCGA.EE.A2GS.06 TCGA.FR.A7U9.06
#> "03" "0412" "022" "0511" "03" "0121"
#> TCGA.ER.A19Q.06 TCGA.FS.A1ZM.06 TCGA.EE.A2MG.06 TCGA.EE.A2MC.06 TCGA.EE.A17Z.06 TCGA.D3.A2JP.06
#> "0125" "0441" "0131" "0131" "0522" "0412"
#> TCGA.ER.A19C.06 TCGA.EB.A82B.01 TCGA.EE.A2A0.06 TCGA.EE.A29G.06 TCGA.D3.A5GO.06 TCGA.GN.A269.01
#> "0443" "0423" "014" "0113" "03" "0111"
#> TCGA.EE.A2A1.06 TCGA.ER.A1A1.06 TCGA.FS.A1ZG.06 TCGA.FS.A1ZE.06 TCGA.FS.A1ZH.06 TCGA.EE.A2MH.06
#> "0131" "0131" "022" "022" "0411" "0111"
#> TCGA.D3.A2J6.06 TCGA.EE.A29Q.06 TCGA.BF.A1PZ.01 TCGA.D3.A3BZ.06 TCGA.D3.A2JO.06 TCGA.GN.A267.06
#> "0423" "03" "03" "0131" "04422" "043"
#> TCGA.EE.A2MN.06 TCGA.GN.A264.06 TCGA.ER.A197.06 TCGA.DA.A1IB.06 TCGA.D3.A3CC.06 TCGA.ER.A19T.01
#> "0513" "023" "014" "014" "0423" "0523"
#> TCGA.GN.A261.06 TCGA.FS.A1YW.06 TCGA.BF.A1PU.01 TCGA.D3.A1QB.06 TCGA.D3.A1Q6.06 TCGA.D3.A3C8.06
#> "0122" "023" "0443" "0124" "0441" "014"
#> TCGA.ER.A19A.06 TCGA.EE.A2GN.06 TCGA.EE.A29M.06 TCGA.D3.A2J7.06 TCGA.EB.A24C.01 TCGA.GN.A262.06
#> "0131" "0522" "0121" "0113" "043" "0212"
#> TCGA.EE.A2GD.06 TCGA.D3.A2J9.06 TCGA.EE.A29B.06 TCGA.D9.A1JX.06 TCGA.EE.A29A.06 TCGA.D3.A2JL.06
#> "014" "0113" "0511" "03" "022" "0412"
#> TCGA.D3.A1Q4.06 TCGA.FS.A1ZS.06 TCGA.D3.A3C3.06 TCGA.D3.A2J8.06 TCGA.FS.A1ZF.06 TCGA.FS.A1ZC.06
#> "0122" "0423" "0413" "0131" "03" "0212"
#> TCGA.EE.A20H.06 TCGA.EE.A29W.06 TCGA.D3.A1QA.07 TCGA.BF.A1PV.01 TCGA.EE.A29S.06 TCGA.DA.A1HV.06
#> "0522" "03" "0413" "0512" "04424" "03"
#> TCGA.FS.A1Z0.06 TCGA.EE.A2GO.06 TCGA.EB.A1NK.01 TCGA.GN.A26D.06 TCGA.EE.A2MJ.06 TCGA.ER.A198.06
#> "0122" "023" "0133" "0422" "0113" "0512"
#> TCGA.EE.A17X.06 TCGA.EE.A2M5.06 TCGA.GN.A266.06 TCGA.D3.A3C1.06 TCGA.D3.A2JH.06 TCGA.EE.A20F.06
#> "03" "0412" "0443" "04421" "0112" "0411"
#> TCGA.EE.A29E.06 TCGA.ER.A2NG.06 TCGA.ER.A193.06 TCGA.FS.A1ZW.06 TCGA.ER.A19O.06 TCGA.EE.A2ME.06
#> "0133" "014" "0421" "0413" "04421" "0111"
#> TCGA.EE.A20B.06 TCGA.EE.A3AF.06 TCGA.GN.A265.06 TCGA.FS.A1YX.06 TCGA.FS.A1ZJ.06 TCGA.ER.A19H.06
#> "0411" "03" "0113" "0441" "0523" "03"
#> TCGA.EE.A3AC.06 TCGA.EE.A2MU.06 TCGA.ER.A194.01 TCGA.EE.A2MS.06 TCGA.EE.A29R.06 TCGA.D9.A1X3.06
#> "0521" "0113" "04423" "043" "023" "022"
#> TCGA.EE.A29X.06 TCGA.EE.A2GK.06 TCGA.EE.A3AA.06 TCGA.ER.A2NE.06 TCGA.EE.A2GR.06 TCGA.FS.A1ZD.06
#> "04421" "0123" "0111" "0212" "0521" "0523"
#> TCGA.ER.A19P.06 TCGA.D3.A1Q8.06 TCGA.ER.A2NC.06 TCGA.BF.A1Q0.01 TCGA.FS.A1ZP.06 TCGA.EE.A182.06
#> "014" "0112" "0443" "0421" "0522" "043"
#> TCGA.D9.A1JW.06 TCGA.D3.A1Q7.06 TCGA.EE.A185.06 TCGA.EE.A2GJ.06 TCGA.D3.A3CB.06 TCGA.EE.A2GU.06
#> "0421" "014" "0212" "043" "0111" "0421"
#> TCGA.ER.A195.06 TCGA.FS.A1Z7.06 TCGA.EE.A2M6.06 TCGA.ER.A19K.01 TCGA.DA.A1HY.06 TCGA.D3.A3C7.06
#> "0132" "0423" "0212" "04421" "03" "03"
#> TCGA.EE.A2MP.06 TCGA.EE.A29H.06 TCGA.FR.A3YO.06 TCGA.XV.AB01.01 TCGA.RP.A694.06 TCGA.EB.A5SF.01
#> "03" "03" "04421" "03" "04423" "0122"
#> TCGA.ER.A19G.06 TCGA.EE.A2GE.06 TCGA.GF.A3OT.06 TCGA.ER.A2NF.06 TCGA.RP.A695.06 TCGA.BF.AAP7.01
#> "03" "0112" "014" "0132" "0512" "0121"
#> TCGA.EB.A3Y7.01 TCGA.EB.A3XC.01 TCGA.ER.A19W.06 TCGA.FR.A69P.06 TCGA.RP.A693.06 TCGA.FW.A3TV.06
#> "0423" "03" "014" "03" "0111" "0124"
#> TCGA.FW.A3R5.11 TCGA.FW.A3TU.06 TCGA.BF.AAP8.01 TCGA.EE.A2MM.06 TCGA.DA.A1HW.06 TCGA.DA.A1IC.06
#> "0132" "0511" "0422" "0513" "0441" "0521"
#> TCGA.XV.AAZV.01 TCGA.D3.A3C6.06 TCGA.EE.A29C.06 TCGA.BF.AAP2.01 TCGA.EE.A2A2.06 TCGA.GF.A6C8.06
#> "0121" "03" "0132" "0212" "03" "0443"
#> TCGA.RP.A690.06 TCGA.FW.A5DY.06 TCGA.DA.A1I4.06 TCGA.EE.A29V.06 TCGA.GF.A6C9.06 TCGA.EE.A2GT.06
#> "0122" "014" "0132" "0412" "0113" "0131"
#> TCGA.GN.A9SD.06 TCGA.EE.A3AB.06 TCGA.BF.AAP6.01 TCGA.EB.A5SH.06 TCGA.D9.A6E9.06 TCGA.BF.AAP4.01
#> "014" "0413" "03" "043" "04421" "04421"
#> TCGA.EE.A2GM.06 TCGA.D3.A3CF.06 TCGA.D9.A6EC.06 TCGA.DA.A1I1.06 TCGA.HR.A2OH.06 TCGA.EE.A2MT.06
#> "0212" "0121" "023" "0413" "014" "0422"
#> TCGA.ER.A19M.06 TCGA.GN.A26C.01 TCGA.FS.A1ZA.06 TCGA.EB.A5SE.01 TCGA.ER.A3PL.06 TCGA.FR.A3R1.01
#> "0411" "0111" "04422" "022" "0521" "03"
#> TCGA.EE.A2MI.06 TCGA.D3.A3CE.06 TCGA.D3.A5GT.01 TCGA.ER.A2NB.01 TCGA.D3.A1Q5.06 TCGA.EB.A5UN.06
#> "0443" "0441" "0511" "0421" "0422" "0111"
#> TCGA.EB.A299.01 TCGA.DA.A1IA.06 TCGA.EB.A5SG.06 TCGA.D9.A6EA.06 TCGA.XV.AAZY.01 TCGA.EB.A57M.01
#> "03" "0511" "014" "022" "014" "0412"
#> TCGA.EE.A2A6.06 TCGA.D3.A2JA.06 TCGA.D3.A1Q1.06 TCGA.EB.A3XF.01 TCGA.D3.A2JF.06 TCGA.XV.AAZW.01
#> "0421" "0132" "0422" "03" "03" "03"
#> TCGA.EB.A3Y6.01 TCGA.EB.A3XE.01 TCGA.D9.A3Z4.01 TCGA.FW.A3R5.06 TCGA.EE.A2GI.06 TCGA.EE.A2GL.06
#> "0441" "043" "0523" "043" "0411" "014"
#> TCGA.EB.A3XB.01 TCGA.BF.AAOU.01 TCGA.EB.A3XD.01 TCGA.EE.A2MD.06 TCGA.YD.A9TB.06 TCGA.W3.AA1V.06
#> "04421" "014" "0124" "04421" "0521" "0441"
#> TCGA.ER.A2ND.06 TCGA.D3.A2JK.06 TCGA.FS.A1ZB.06 TCGA.EE.A29D.06 TCGA.EB.A5UM.01 TCGA.QB.A6FS.06
#> "0521" "0412" "0112" "022" "043" "0132"
#> TCGA.D9.A3Z1.06 TCGA.D3.A2JN.06 TCGA.FR.A3YN.06 TCGA.FS.A1ZT.06 TCGA.D9.A148.06 TCGA.HR.A2OG.06
#> "0113" "014" "03" "0132" "0412" "0125"
#> TCGA.EE.A2ML.06 TCGA.EB.A5UL.06 TCGA.EE.A29T.06 TCGA.D9.A3Z3.06 TCGA.D9.A4Z3.01 TCGA.ER.A3ES.06
#> "0413" "0412" "043" "0124" "0522" "0422"
#> TCGA.XV.A9VZ.01 TCGA.QB.AA9O.06 TCGA.EB.A44Q.06 TCGA.EB.A44R.06 TCGA.BF.A3DJ.01 TCGA.EE.A3JD.06
#> "0122" "03" "04421" "043" "03" "0131"
#> TCGA.D3.A51N.06 TCGA.EB.A44N.01 TCGA.EE.A3J3.06 TCGA.XV.A9W5.01 TCGA.D3.A51G.06 TCGA.EB.A4P0.01
#> "0413" "0113" "03" "0412" "03" "03"
#> TCGA.BF.AAP1.01 TCGA.EE.A3J4.06 TCGA.Z2.AA3V.06 TCGA.LH.A9QB.06 TCGA.D3.A51J.06 TCGA.3N.A9WC.06
#> "023" "0511" "0121" "023" "04421" "0421"
#> TCGA.DA.A3F8.06 TCGA.D9.A4Z6.06 TCGA.D3.A51R.06 TCGA.EB.A4OZ.01 TCGA.FS.A4FB.06 TCGA.EE.A3JE.06
#> "0113" "0412" "03" "0121" "03" "0113"
#> TCGA.W3.AA1W.06 TCGA.DA.A1I0.06 TCGA.D3.A51F.06 TCGA.IH.A3EA.01 TCGA.EB.A431.01 TCGA.EB.A97M.01
#> "0111" "0412" "0131" "0512" "0412" "022"
#> TCGA.BF.AAOX.01 TCGA.DA.A3F5.06 TCGA.YD.A9TA.06 TCGA.DA.A3F2.06 TCGA.EB.A44O.01 TCGA.EB.A4IQ.01
#> "0412" "0423" "0411" "0131" "0521" "0421"
#> TCGA.EB.A4IS.01 TCGA.YG.AA3O.06 TCGA.ER.A3EV.06 TCGA.3N.A9WD.06 TCGA.BF.A3DM.01 TCGA.XV.A9W2.01
#> "0112" "0512" "043" "0113" "03" "0423"
#> TCGA.W3.AA1Q.06 TCGA.WE.AAA0.06 TCGA.W3.AA1R.06 TCGA.EE.A3J5.06 TCGA.EB.A4OY.01 TCGA.FS.A4FD.06
#> "0512" "0412" "03" "0412" "0122" "0422"
#> TCGA.BF.AAP0.06 TCGA.YG.AA3P.06 TCGA.EE.A3JA.06 TCGA.W3.AA21.06 TCGA.WE.AAA3.06 TCGA.FS.A4F4.06
#> "0123" "0523" "03" "0211" "0423" "03"
#> TCGA.BF.A3DN.01 TCGA.ER.A3ET.06 TCGA.W3.AA1O.06 TCGA.D3.A51E.06 TCGA.Z2.AA3S.06 TCGA.YG.AA3N.01
#> "03" "0423" "0513" "03" "022" "04421"
#> TCGA.WE.AA9Y.06 TCGA.FS.A4F5.06 TCGA.EE.A3J7.06 TCGA.FS.A4F8.06 TCGA.DA.A3F3.06 TCGA.D3.A51H.06
#> "0111" "023" "0511" "0111" "03" "0131"
#> TCGA.BF.A3DL.01 TCGA.D3.A51T.06 TCGA.D3.A51K.06 TCGA.EB.A44P.01 TCGA.D9.A4Z5.01 TCGA.WE.AAA4.06
#> "0124" "03" "0522" "0521" "023" "014"
#> TCGA.3N.A9WB.06 TCGA.EE.A3J8.06
#> "022" "0211"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 3485))
#> TCGA.FR.A728.01 TCGA.GN.A4U8.11 TCGA.GN.A8LL.06 TCGA.FR.A8YC.06 TCGA.DA.A95X.06 TCGA.ER.A42K.06
#> "014" "011" "03" "022" "0211" "03"
#> TCGA.D3.A8GO.06 TCGA.D3.A8GK.06 TCGA.WE.A8JZ.06 TCGA.WE.A8ZO.06 TCGA.D3.A8GI.06 TCGA.FS.A4FC.06
#> "0124" "0524" "0212" "0511" "0512" "0421"
#> TCGA.FS.A4F2.06 TCGA.WE.A8ZM.06 TCGA.WE.A8ZT.06 TCGA.D3.A8GQ.06 TCGA.D3.A8GB.06 TCGA.DA.A95Y.06
#> "03" "0522" "03" "0411" "0131" "03"
#> TCGA.EE.A3JI.06 TCGA.OD.A75X.06 TCGA.DA.A960.01 TCGA.D3.A8GV.06 TCGA.WE.A8ZN.06 TCGA.D3.A8GN.06
#> "022" "023" "0211" "0212" "011" "014"
#> TCGA.EB.A550.01 TCGA.BF.A5EQ.01 TCGA.EB.A3HV.01 TCGA.HR.A5NC.01 TCGA.DA.A95Z.06 TCGA.EB.A6QZ.01
#> "0122" "0421" "0521" "0523" "022" "0212"
#> TCGA.FW.A3I3.06 TCGA.WE.A8K6.06 TCGA.D3.A8GP.06 TCGA.EB.A42Z.01 TCGA.GN.A4U4.06 TCGA.GF.A4EO.06
#> "023" "03" "022" "023" "0212" "014"
#> TCGA.GN.A8LK.06 TCGA.WE.A8K4.01 TCGA.DA.A95W.06 TCGA.FW.A5DX.01 TCGA.GN.A4U3.06 TCGA.EB.A6QY.01
#> "0521" "011" "022" "0212" "03" "0133"
#> TCGA.EB.A5VU.01 TCGA.Z2.A8RT.06 TCGA.WE.A8K1.06 TCGA.EB.A41B.01 TCGA.WE.A8ZY.06 TCGA.D9.A6EG.06
#> "0443" "03" "011" "03" "0212" "022"
#> TCGA.BF.A5ER.01 TCGA.FR.A8YD.06 TCGA.FS.A4F9.06 TCGA.EB.A6R0.01 TCGA.ER.A42L.06 TCGA.D3.A8GJ.06
#> "0512" "0511" "0511" "03" "011" "04423"
#> TCGA.FR.A8YE.06 TCGA.WE.A8ZR.06 TCGA.BF.A9VF.01 TCGA.EE.A3JH.06 TCGA.DA.A95V.06 TCGA.GF.A769.01
#> "011" "043" "0521" "011" "0412" "0212"
#> TCGA.D9.A4Z2.01 TCGA.FR.A44A.06 TCGA.EB.A5VV.06 TCGA.EE.A180.06 TCGA.D3.A8GC.06 TCGA.WE.A8K5.06
#> "03" "014" "0123" "022" "0513" "023"
#> TCGA.GN.A8LN.01 TCGA.EE.A3JB.06 TCGA.D3.A3MO.06 TCGA.ER.A42H.01 TCGA.WE.A8ZX.06 TCGA.GN.A4U5.01
#> "0212" "0411" "0522" "0511" "0412" "014"
#> TCGA.D3.A8GS.06 TCGA.WE.A8ZQ.06 TCGA.EE.A2MF.06 TCGA.D3.A5GU.06 TCGA.GN.A4U8.06 TCGA.EB.A42Y.01
#> "0441" "0523" "022" "0511" "0413" "0212"
#> TCGA.D3.A3ML.06 TCGA.EB.A551.01 TCGA.D3.A8GM.06 TCGA.D3.A8GL.06 TCGA.D3.A3MU.06 TCGA.FS.A4F0.06
#> "0511" "04422" "0412" "022" "022" "022"
#> TCGA.D3.A3MV.06 TCGA.GN.A4U7.06 TCGA.FR.A2OS.01 TCGA.D3.A2JE.06 TCGA.YD.A89C.06 TCGA.FR.A726.01
#> "03" "03" "0523" "0522" "0411" "0411"
#> TCGA.BF.A5EP.01 TCGA.D3.A3MR.06 TCGA.D3.A8GR.06 TCGA.GN.A4U9.06 TCGA.EB.A6L9.06 TCGA.D3.A5GL.06
#> "03" "011" "0511" "0522" "0131" "03"
#> TCGA.EB.A430.01 TCGA.D3.A8GE.06 TCGA.D3.A8GD.06 TCGA.EB.A41A.01 TCGA.W3.A825.06 TCGA.EE.A183.06
#> "0133" "0132" "014" "022" "0443" "011"
#> TCGA.ER.A2NH.06 TCGA.D3.A5GR.06 TCGA.FR.A729.06 TCGA.D3.A1QA.06 TCGA.FS.A1YY.06 TCGA.EE.A2MK.06
#> "011" "0441" "0441" "0211" "03" "03"
#> TCGA.EE.A2M8.06 TCGA.EB.A5KH.06 TCGA.FS.A1ZR.06 TCGA.EE.A3AE.06 TCGA.EE.A29P.06 TCGA.EB.A553.01
#> "0123" "0212" "0521" "03" "04424" "0513"
#> TCGA.EE.A2MR.06 TCGA.GN.A26A.06 TCGA.FS.A1ZY.06 TCGA.EE.A20I.06 TCGA.DA.A1I5.06 TCGA.EE.A184.06
#> "011" "0411" "0212" "0412" "0125" "023"
#> TCGA.EB.A85J.01 TCGA.RP.A6K9.06 TCGA.EE.A17Y.06 TCGA.D9.A149.06 TCGA.ER.A19D.06 TCGA.FS.A1ZZ.06
#> "043" "0423" "0411" "0421" "0122" "023"
#> TCGA.EE.A2GP.06 TCGA.EE.A3AD.06 TCGA.D3.A1Q9.06 TCGA.GF.A2C7.01 TCGA.BF.A5ES.01 TCGA.ER.A199.06
#> "0524" "0212" "0412" "0511" "0511" "014"
#> TCGA.EE.A3AH.06 TCGA.W3.A828.06 TCGA.EE.A2A5.06 TCGA.ER.A19L.06 TCGA.BF.A1PX.01 TCGA.ER.A19T.06
#> "0212" "0133" "0522" "043" "011" "043"
#> TCGA.EB.A51B.01 TCGA.FS.A1ZQ.06 TCGA.D3.A2JG.06 TCGA.EE.A2GH.06 TCGA.ER.A19F.06 TCGA.ER.A196.01
#> "03" "03" "03" "011" "03" "0124"
#> TCGA.D3.A2JC.06 TCGA.EE.A3AG.06 TCGA.ER.A19S.06 TCGA.EE.A2GC.06 TCGA.EE.A29N.06 TCGA.FR.A7U8.06
#> "0441" "03" "014" "0524" "011" "023"
#> TCGA.BF.A5EO.01 TCGA.ER.A19B.06 TCGA.D3.A5GN.06 TCGA.D3.A2JB.06 TCGA.ER.A19J.06 TCGA.D3.A2JD.06
#> "0412" "03" "03" "0123" "023" "011"
#> TCGA.FS.A1Z4.06 TCGA.FR.A7UA.06 TCGA.EE.A2M7.06 TCGA.D3.A1Q3.06 TCGA.EB.A85I.01 TCGA.EB.A82C.01
#> "0131" "014" "0441" "043" "0421" "023"
#> TCGA.ER.A19E.06 TCGA.FS.A1ZK.06 TCGA.FS.A1ZU.06 TCGA.EB.A5FP.01 TCGA.EB.A4XL.01 TCGA.DA.A1I2.06
#> "0522" "0524" "0522" "0212" "03" "0441"
#> TCGA.EE.A29L.06 TCGA.FS.A1ZN.01 TCGA.EB.A24D.01 TCGA.EE.A2GB.06 TCGA.DA.A1I7.06 TCGA.ER.A2NF.01
#> "0211" "0212" "0511" "03" "0441" "0132"
#> TCGA.GN.A263.01 TCGA.EE.A20C.06 TCGA.EE.A2MQ.06 TCGA.ER.A19N.06 TCGA.FS.A1Z3.06 TCGA.DA.A1I8.06
#> "0132" "023" "0512" "011" "03" "03"
#> TCGA.D3.A5GS.06 TCGA.EE.A181.06 TCGA.GN.A268.06 TCGA.W3.A824.06 TCGA.EE.A2GS.06 TCGA.FR.A7U9.06
#> "03" "0412" "022" "0511" "03" "0121"
#> TCGA.ER.A19Q.06 TCGA.FS.A1ZM.06 TCGA.EE.A2MG.06 TCGA.EE.A2MC.06 TCGA.EE.A17Z.06 TCGA.D3.A2JP.06
#> "0125" "0441" "0131" "0131" "0522" "0412"
#> TCGA.ER.A19C.06 TCGA.EB.A82B.01 TCGA.EE.A2A0.06 TCGA.EE.A29G.06 TCGA.D3.A5GO.06 TCGA.GN.A269.01
#> "0443" "0423" "014" "011" "03" "011"
#> TCGA.EE.A2A1.06 TCGA.ER.A1A1.06 TCGA.FS.A1ZG.06 TCGA.FS.A1ZE.06 TCGA.FS.A1ZH.06 TCGA.EE.A2MH.06
#> "0131" "0131" "022" "022" "0411" "011"
#> TCGA.D3.A2J6.06 TCGA.EE.A29Q.06 TCGA.BF.A1PZ.01 TCGA.D3.A3BZ.06 TCGA.D3.A2JO.06 TCGA.GN.A267.06
#> "0423" "03" "03" "0131" "04422" "043"
#> TCGA.EE.A2MN.06 TCGA.GN.A264.06 TCGA.ER.A197.06 TCGA.DA.A1IB.06 TCGA.D3.A3CC.06 TCGA.ER.A19T.01
#> "0513" "023" "014" "014" "0423" "0523"
#> TCGA.GN.A261.06 TCGA.FS.A1YW.06 TCGA.BF.A1PU.01 TCGA.D3.A1QB.06 TCGA.D3.A1Q6.06 TCGA.D3.A3C8.06
#> "0122" "023" "0443" "0124" "0441" "014"
#> TCGA.ER.A19A.06 TCGA.EE.A2GN.06 TCGA.EE.A29M.06 TCGA.D3.A2J7.06 TCGA.EB.A24C.01 TCGA.GN.A262.06
#> "0131" "0522" "0121" "011" "043" "0212"
#> TCGA.EE.A2GD.06 TCGA.D3.A2J9.06 TCGA.EE.A29B.06 TCGA.D9.A1JX.06 TCGA.EE.A29A.06 TCGA.D3.A2JL.06
#> "014" "011" "0511" "03" "022" "0412"
#> TCGA.D3.A1Q4.06 TCGA.FS.A1ZS.06 TCGA.D3.A3C3.06 TCGA.D3.A2J8.06 TCGA.FS.A1ZF.06 TCGA.FS.A1ZC.06
#> "0122" "0423" "0413" "0131" "03" "0212"
#> TCGA.EE.A20H.06 TCGA.EE.A29W.06 TCGA.D3.A1QA.07 TCGA.BF.A1PV.01 TCGA.EE.A29S.06 TCGA.DA.A1HV.06
#> "0522" "03" "0413" "0512" "04424" "03"
#> TCGA.FS.A1Z0.06 TCGA.EE.A2GO.06 TCGA.EB.A1NK.01 TCGA.GN.A26D.06 TCGA.EE.A2MJ.06 TCGA.ER.A198.06
#> "0122" "023" "0133" "0422" "011" "0512"
#> TCGA.EE.A17X.06 TCGA.EE.A2M5.06 TCGA.GN.A266.06 TCGA.D3.A3C1.06 TCGA.D3.A2JH.06 TCGA.EE.A20F.06
#> "03" "0412" "0443" "04421" "011" "0411"
#> TCGA.EE.A29E.06 TCGA.ER.A2NG.06 TCGA.ER.A193.06 TCGA.FS.A1ZW.06 TCGA.ER.A19O.06 TCGA.EE.A2ME.06
#> "0133" "014" "0421" "0413" "04421" "011"
#> TCGA.EE.A20B.06 TCGA.EE.A3AF.06 TCGA.GN.A265.06 TCGA.FS.A1YX.06 TCGA.FS.A1ZJ.06 TCGA.ER.A19H.06
#> "0411" "03" "011" "0441" "0523" "03"
#> TCGA.EE.A3AC.06 TCGA.EE.A2MU.06 TCGA.ER.A194.01 TCGA.EE.A2MS.06 TCGA.EE.A29R.06 TCGA.D9.A1X3.06
#> "0521" "011" "04423" "043" "023" "022"
#> TCGA.EE.A29X.06 TCGA.EE.A2GK.06 TCGA.EE.A3AA.06 TCGA.ER.A2NE.06 TCGA.EE.A2GR.06 TCGA.FS.A1ZD.06
#> "04421" "0123" "011" "0212" "0521" "0523"
#> TCGA.ER.A19P.06 TCGA.D3.A1Q8.06 TCGA.ER.A2NC.06 TCGA.BF.A1Q0.01 TCGA.FS.A1ZP.06 TCGA.EE.A182.06
#> "014" "011" "0443" "0421" "0522" "043"
#> TCGA.D9.A1JW.06 TCGA.D3.A1Q7.06 TCGA.EE.A185.06 TCGA.EE.A2GJ.06 TCGA.D3.A3CB.06 TCGA.EE.A2GU.06
#> "0421" "014" "0212" "043" "011" "0421"
#> TCGA.ER.A195.06 TCGA.FS.A1Z7.06 TCGA.EE.A2M6.06 TCGA.ER.A19K.01 TCGA.DA.A1HY.06 TCGA.D3.A3C7.06
#> "0132" "0423" "0212" "04421" "03" "03"
#> TCGA.EE.A2MP.06 TCGA.EE.A29H.06 TCGA.FR.A3YO.06 TCGA.XV.AB01.01 TCGA.RP.A694.06 TCGA.EB.A5SF.01
#> "03" "03" "04421" "03" "04423" "0122"
#> TCGA.ER.A19G.06 TCGA.EE.A2GE.06 TCGA.GF.A3OT.06 TCGA.ER.A2NF.06 TCGA.RP.A695.06 TCGA.BF.AAP7.01
#> "03" "011" "014" "0132" "0512" "0121"
#> TCGA.EB.A3Y7.01 TCGA.EB.A3XC.01 TCGA.ER.A19W.06 TCGA.FR.A69P.06 TCGA.RP.A693.06 TCGA.FW.A3TV.06
#> "0423" "03" "014" "03" "011" "0124"
#> TCGA.FW.A3R5.11 TCGA.FW.A3TU.06 TCGA.BF.AAP8.01 TCGA.EE.A2MM.06 TCGA.DA.A1HW.06 TCGA.DA.A1IC.06
#> "0132" "0511" "0422" "0513" "0441" "0521"
#> TCGA.XV.AAZV.01 TCGA.D3.A3C6.06 TCGA.EE.A29C.06 TCGA.BF.AAP2.01 TCGA.EE.A2A2.06 TCGA.GF.A6C8.06
#> "0121" "03" "0132" "0212" "03" "0443"
#> TCGA.RP.A690.06 TCGA.FW.A5DY.06 TCGA.DA.A1I4.06 TCGA.EE.A29V.06 TCGA.GF.A6C9.06 TCGA.EE.A2GT.06
#> "0122" "014" "0132" "0412" "011" "0131"
#> TCGA.GN.A9SD.06 TCGA.EE.A3AB.06 TCGA.BF.AAP6.01 TCGA.EB.A5SH.06 TCGA.D9.A6E9.06 TCGA.BF.AAP4.01
#> "014" "0413" "03" "043" "04421" "04421"
#> TCGA.EE.A2GM.06 TCGA.D3.A3CF.06 TCGA.D9.A6EC.06 TCGA.DA.A1I1.06 TCGA.HR.A2OH.06 TCGA.EE.A2MT.06
#> "0212" "0121" "023" "0413" "014" "0422"
#> TCGA.ER.A19M.06 TCGA.GN.A26C.01 TCGA.FS.A1ZA.06 TCGA.EB.A5SE.01 TCGA.ER.A3PL.06 TCGA.FR.A3R1.01
#> "0411" "011" "04422" "022" "0521" "03"
#> TCGA.EE.A2MI.06 TCGA.D3.A3CE.06 TCGA.D3.A5GT.01 TCGA.ER.A2NB.01 TCGA.D3.A1Q5.06 TCGA.EB.A5UN.06
#> "0443" "0441" "0511" "0421" "0422" "011"
#> TCGA.EB.A299.01 TCGA.DA.A1IA.06 TCGA.EB.A5SG.06 TCGA.D9.A6EA.06 TCGA.XV.AAZY.01 TCGA.EB.A57M.01
#> "03" "0511" "014" "022" "014" "0412"
#> TCGA.EE.A2A6.06 TCGA.D3.A2JA.06 TCGA.D3.A1Q1.06 TCGA.EB.A3XF.01 TCGA.D3.A2JF.06 TCGA.XV.AAZW.01
#> "0421" "0132" "0422" "03" "03" "03"
#> TCGA.EB.A3Y6.01 TCGA.EB.A3XE.01 TCGA.D9.A3Z4.01 TCGA.FW.A3R5.06 TCGA.EE.A2GI.06 TCGA.EE.A2GL.06
#> "0441" "043" "0523" "043" "0411" "014"
#> TCGA.EB.A3XB.01 TCGA.BF.AAOU.01 TCGA.EB.A3XD.01 TCGA.EE.A2MD.06 TCGA.YD.A9TB.06 TCGA.W3.AA1V.06
#> "04421" "014" "0124" "04421" "0521" "0441"
#> TCGA.ER.A2ND.06 TCGA.D3.A2JK.06 TCGA.FS.A1ZB.06 TCGA.EE.A29D.06 TCGA.EB.A5UM.01 TCGA.QB.A6FS.06
#> "0521" "0412" "011" "022" "043" "0132"
#> TCGA.D9.A3Z1.06 TCGA.D3.A2JN.06 TCGA.FR.A3YN.06 TCGA.FS.A1ZT.06 TCGA.D9.A148.06 TCGA.HR.A2OG.06
#> "011" "014" "03" "0132" "0412" "0125"
#> TCGA.EE.A2ML.06 TCGA.EB.A5UL.06 TCGA.EE.A29T.06 TCGA.D9.A3Z3.06 TCGA.D9.A4Z3.01 TCGA.ER.A3ES.06
#> "0413" "0412" "043" "0124" "0522" "0422"
#> TCGA.XV.A9VZ.01 TCGA.QB.AA9O.06 TCGA.EB.A44Q.06 TCGA.EB.A44R.06 TCGA.BF.A3DJ.01 TCGA.EE.A3JD.06
#> "0122" "03" "04421" "043" "03" "0131"
#> TCGA.D3.A51N.06 TCGA.EB.A44N.01 TCGA.EE.A3J3.06 TCGA.XV.A9W5.01 TCGA.D3.A51G.06 TCGA.EB.A4P0.01
#> "0413" "011" "03" "0412" "03" "03"
#> TCGA.BF.AAP1.01 TCGA.EE.A3J4.06 TCGA.Z2.AA3V.06 TCGA.LH.A9QB.06 TCGA.D3.A51J.06 TCGA.3N.A9WC.06
#> "023" "0511" "0121" "023" "04421" "0421"
#> TCGA.DA.A3F8.06 TCGA.D9.A4Z6.06 TCGA.D3.A51R.06 TCGA.EB.A4OZ.01 TCGA.FS.A4FB.06 TCGA.EE.A3JE.06
#> "011" "0412" "03" "0121" "03" "011"
#> TCGA.W3.AA1W.06 TCGA.DA.A1I0.06 TCGA.D3.A51F.06 TCGA.IH.A3EA.01 TCGA.EB.A431.01 TCGA.EB.A97M.01
#> "011" "0412" "0131" "0512" "0412" "022"
#> TCGA.BF.AAOX.01 TCGA.DA.A3F5.06 TCGA.YD.A9TA.06 TCGA.DA.A3F2.06 TCGA.EB.A44O.01 TCGA.EB.A4IQ.01
#> "0412" "0423" "0411" "0131" "0521" "0421"
#> TCGA.EB.A4IS.01 TCGA.YG.AA3O.06 TCGA.ER.A3EV.06 TCGA.3N.A9WD.06 TCGA.BF.A3DM.01 TCGA.XV.A9W2.01
#> "011" "0512" "043" "011" "03" "0423"
#> TCGA.W3.AA1Q.06 TCGA.WE.AAA0.06 TCGA.W3.AA1R.06 TCGA.EE.A3J5.06 TCGA.EB.A4OY.01 TCGA.FS.A4FD.06
#> "0512" "0412" "03" "0412" "0122" "0422"
#> TCGA.BF.AAP0.06 TCGA.YG.AA3P.06 TCGA.EE.A3JA.06 TCGA.W3.AA21.06 TCGA.WE.AAA3.06 TCGA.FS.A4F4.06
#> "0123" "0523" "03" "0211" "0423" "03"
#> TCGA.BF.A3DN.01 TCGA.ER.A3ET.06 TCGA.W3.AA1O.06 TCGA.D3.A51E.06 TCGA.Z2.AA3S.06 TCGA.YG.AA3N.01
#> "03" "0423" "0513" "03" "022" "04421"
#> TCGA.WE.AA9Y.06 TCGA.FS.A4F5.06 TCGA.EE.A3J7.06 TCGA.FS.A4F8.06 TCGA.DA.A3F3.06 TCGA.D3.A51H.06
#> "011" "023" "0511" "011" "03" "0131"
#> TCGA.BF.A3DL.01 TCGA.D3.A51T.06 TCGA.D3.A51K.06 TCGA.EB.A44P.01 TCGA.D9.A4Z5.01 TCGA.WE.AAA4.06
#> "0124" "03" "0522" "0521" "023" "014"
#> TCGA.3N.A9WB.06 TCGA.EE.A3J8.06
#> "022" "0211"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 4070))
#> TCGA.FR.A728.01 TCGA.GN.A4U8.11 TCGA.GN.A8LL.06 TCGA.FR.A8YC.06 TCGA.DA.A95X.06 TCGA.ER.A42K.06
#> "014" "011" "03" "022" "0211" "03"
#> TCGA.D3.A8GO.06 TCGA.D3.A8GK.06 TCGA.WE.A8JZ.06 TCGA.WE.A8ZO.06 TCGA.D3.A8GI.06 TCGA.FS.A4FC.06
#> "0124" "0524" "0212" "0511" "0512" "0421"
#> TCGA.FS.A4F2.06 TCGA.WE.A8ZM.06 TCGA.WE.A8ZT.06 TCGA.D3.A8GQ.06 TCGA.D3.A8GB.06 TCGA.DA.A95Y.06
#> "03" "0522" "03" "041" "0131" "03"
#> TCGA.EE.A3JI.06 TCGA.OD.A75X.06 TCGA.DA.A960.01 TCGA.D3.A8GV.06 TCGA.WE.A8ZN.06 TCGA.D3.A8GN.06
#> "022" "023" "0211" "0212" "011" "014"
#> TCGA.EB.A550.01 TCGA.BF.A5EQ.01 TCGA.EB.A3HV.01 TCGA.HR.A5NC.01 TCGA.DA.A95Z.06 TCGA.EB.A6QZ.01
#> "0122" "0421" "0521" "0523" "022" "0212"
#> TCGA.FW.A3I3.06 TCGA.WE.A8K6.06 TCGA.D3.A8GP.06 TCGA.EB.A42Z.01 TCGA.GN.A4U4.06 TCGA.GF.A4EO.06
#> "023" "03" "022" "023" "0212" "014"
#> TCGA.GN.A8LK.06 TCGA.WE.A8K4.01 TCGA.DA.A95W.06 TCGA.FW.A5DX.01 TCGA.GN.A4U3.06 TCGA.EB.A6QY.01
#> "0521" "011" "022" "0212" "03" "0133"
#> TCGA.EB.A5VU.01 TCGA.Z2.A8RT.06 TCGA.WE.A8K1.06 TCGA.EB.A41B.01 TCGA.WE.A8ZY.06 TCGA.D9.A6EG.06
#> "0443" "03" "011" "03" "0212" "022"
#> TCGA.BF.A5ER.01 TCGA.FR.A8YD.06 TCGA.FS.A4F9.06 TCGA.EB.A6R0.01 TCGA.ER.A42L.06 TCGA.D3.A8GJ.06
#> "0512" "0511" "0511" "03" "011" "04423"
#> TCGA.FR.A8YE.06 TCGA.WE.A8ZR.06 TCGA.BF.A9VF.01 TCGA.EE.A3JH.06 TCGA.DA.A95V.06 TCGA.GF.A769.01
#> "011" "043" "0521" "011" "041" "0212"
#> TCGA.D9.A4Z2.01 TCGA.FR.A44A.06 TCGA.EB.A5VV.06 TCGA.EE.A180.06 TCGA.D3.A8GC.06 TCGA.WE.A8K5.06
#> "03" "014" "0123" "022" "0513" "023"
#> TCGA.GN.A8LN.01 TCGA.EE.A3JB.06 TCGA.D3.A3MO.06 TCGA.ER.A42H.01 TCGA.WE.A8ZX.06 TCGA.GN.A4U5.01
#> "0212" "041" "0522" "0511" "041" "014"
#> TCGA.D3.A8GS.06 TCGA.WE.A8ZQ.06 TCGA.EE.A2MF.06 TCGA.D3.A5GU.06 TCGA.GN.A4U8.06 TCGA.EB.A42Y.01
#> "0441" "0523" "022" "0511" "041" "0212"
#> TCGA.D3.A3ML.06 TCGA.EB.A551.01 TCGA.D3.A8GM.06 TCGA.D3.A8GL.06 TCGA.D3.A3MU.06 TCGA.FS.A4F0.06
#> "0511" "04422" "041" "022" "022" "022"
#> TCGA.D3.A3MV.06 TCGA.GN.A4U7.06 TCGA.FR.A2OS.01 TCGA.D3.A2JE.06 TCGA.YD.A89C.06 TCGA.FR.A726.01
#> "03" "03" "0523" "0522" "041" "041"
#> TCGA.BF.A5EP.01 TCGA.D3.A3MR.06 TCGA.D3.A8GR.06 TCGA.GN.A4U9.06 TCGA.EB.A6L9.06 TCGA.D3.A5GL.06
#> "03" "011" "0511" "0522" "0131" "03"
#> TCGA.EB.A430.01 TCGA.D3.A8GE.06 TCGA.D3.A8GD.06 TCGA.EB.A41A.01 TCGA.W3.A825.06 TCGA.EE.A183.06
#> "0133" "0132" "014" "022" "0443" "011"
#> TCGA.ER.A2NH.06 TCGA.D3.A5GR.06 TCGA.FR.A729.06 TCGA.D3.A1QA.06 TCGA.FS.A1YY.06 TCGA.EE.A2MK.06
#> "011" "0441" "0441" "0211" "03" "03"
#> TCGA.EE.A2M8.06 TCGA.EB.A5KH.06 TCGA.FS.A1ZR.06 TCGA.EE.A3AE.06 TCGA.EE.A29P.06 TCGA.EB.A553.01
#> "0123" "0212" "0521" "03" "04424" "0513"
#> TCGA.EE.A2MR.06 TCGA.GN.A26A.06 TCGA.FS.A1ZY.06 TCGA.EE.A20I.06 TCGA.DA.A1I5.06 TCGA.EE.A184.06
#> "011" "041" "0212" "041" "0125" "023"
#> TCGA.EB.A85J.01 TCGA.RP.A6K9.06 TCGA.EE.A17Y.06 TCGA.D9.A149.06 TCGA.ER.A19D.06 TCGA.FS.A1ZZ.06
#> "043" "0423" "041" "0421" "0122" "023"
#> TCGA.EE.A2GP.06 TCGA.EE.A3AD.06 TCGA.D3.A1Q9.06 TCGA.GF.A2C7.01 TCGA.BF.A5ES.01 TCGA.ER.A199.06
#> "0524" "0212" "041" "0511" "0511" "014"
#> TCGA.EE.A3AH.06 TCGA.W3.A828.06 TCGA.EE.A2A5.06 TCGA.ER.A19L.06 TCGA.BF.A1PX.01 TCGA.ER.A19T.06
#> "0212" "0133" "0522" "043" "011" "043"
#> TCGA.EB.A51B.01 TCGA.FS.A1ZQ.06 TCGA.D3.A2JG.06 TCGA.EE.A2GH.06 TCGA.ER.A19F.06 TCGA.ER.A196.01
#> "03" "03" "03" "011" "03" "0124"
#> TCGA.D3.A2JC.06 TCGA.EE.A3AG.06 TCGA.ER.A19S.06 TCGA.EE.A2GC.06 TCGA.EE.A29N.06 TCGA.FR.A7U8.06
#> "0441" "03" "014" "0524" "011" "023"
#> TCGA.BF.A5EO.01 TCGA.ER.A19B.06 TCGA.D3.A5GN.06 TCGA.D3.A2JB.06 TCGA.ER.A19J.06 TCGA.D3.A2JD.06
#> "041" "03" "03" "0123" "023" "011"
#> TCGA.FS.A1Z4.06 TCGA.FR.A7UA.06 TCGA.EE.A2M7.06 TCGA.D3.A1Q3.06 TCGA.EB.A85I.01 TCGA.EB.A82C.01
#> "0131" "014" "0441" "043" "0421" "023"
#> TCGA.ER.A19E.06 TCGA.FS.A1ZK.06 TCGA.FS.A1ZU.06 TCGA.EB.A5FP.01 TCGA.EB.A4XL.01 TCGA.DA.A1I2.06
#> "0522" "0524" "0522" "0212" "03" "0441"
#> TCGA.EE.A29L.06 TCGA.FS.A1ZN.01 TCGA.EB.A24D.01 TCGA.EE.A2GB.06 TCGA.DA.A1I7.06 TCGA.ER.A2NF.01
#> "0211" "0212" "0511" "03" "0441" "0132"
#> TCGA.GN.A263.01 TCGA.EE.A20C.06 TCGA.EE.A2MQ.06 TCGA.ER.A19N.06 TCGA.FS.A1Z3.06 TCGA.DA.A1I8.06
#> "0132" "023" "0512" "011" "03" "03"
#> TCGA.D3.A5GS.06 TCGA.EE.A181.06 TCGA.GN.A268.06 TCGA.W3.A824.06 TCGA.EE.A2GS.06 TCGA.FR.A7U9.06
#> "03" "041" "022" "0511" "03" "0121"
#> TCGA.ER.A19Q.06 TCGA.FS.A1ZM.06 TCGA.EE.A2MG.06 TCGA.EE.A2MC.06 TCGA.EE.A17Z.06 TCGA.D3.A2JP.06
#> "0125" "0441" "0131" "0131" "0522" "041"
#> TCGA.ER.A19C.06 TCGA.EB.A82B.01 TCGA.EE.A2A0.06 TCGA.EE.A29G.06 TCGA.D3.A5GO.06 TCGA.GN.A269.01
#> "0443" "0423" "014" "011" "03" "011"
#> TCGA.EE.A2A1.06 TCGA.ER.A1A1.06 TCGA.FS.A1ZG.06 TCGA.FS.A1ZE.06 TCGA.FS.A1ZH.06 TCGA.EE.A2MH.06
#> "0131" "0131" "022" "022" "041" "011"
#> TCGA.D3.A2J6.06 TCGA.EE.A29Q.06 TCGA.BF.A1PZ.01 TCGA.D3.A3BZ.06 TCGA.D3.A2JO.06 TCGA.GN.A267.06
#> "0423" "03" "03" "0131" "04422" "043"
#> TCGA.EE.A2MN.06 TCGA.GN.A264.06 TCGA.ER.A197.06 TCGA.DA.A1IB.06 TCGA.D3.A3CC.06 TCGA.ER.A19T.01
#> "0513" "023" "014" "014" "0423" "0523"
#> TCGA.GN.A261.06 TCGA.FS.A1YW.06 TCGA.BF.A1PU.01 TCGA.D3.A1QB.06 TCGA.D3.A1Q6.06 TCGA.D3.A3C8.06
#> "0122" "023" "0443" "0124" "0441" "014"
#> TCGA.ER.A19A.06 TCGA.EE.A2GN.06 TCGA.EE.A29M.06 TCGA.D3.A2J7.06 TCGA.EB.A24C.01 TCGA.GN.A262.06
#> "0131" "0522" "0121" "011" "043" "0212"
#> TCGA.EE.A2GD.06 TCGA.D3.A2J9.06 TCGA.EE.A29B.06 TCGA.D9.A1JX.06 TCGA.EE.A29A.06 TCGA.D3.A2JL.06
#> "014" "011" "0511" "03" "022" "041"
#> TCGA.D3.A1Q4.06 TCGA.FS.A1ZS.06 TCGA.D3.A3C3.06 TCGA.D3.A2J8.06 TCGA.FS.A1ZF.06 TCGA.FS.A1ZC.06
#> "0122" "0423" "041" "0131" "03" "0212"
#> TCGA.EE.A20H.06 TCGA.EE.A29W.06 TCGA.D3.A1QA.07 TCGA.BF.A1PV.01 TCGA.EE.A29S.06 TCGA.DA.A1HV.06
#> "0522" "03" "041" "0512" "04424" "03"
#> TCGA.FS.A1Z0.06 TCGA.EE.A2GO.06 TCGA.EB.A1NK.01 TCGA.GN.A26D.06 TCGA.EE.A2MJ.06 TCGA.ER.A198.06
#> "0122" "023" "0133" "0422" "011" "0512"
#> TCGA.EE.A17X.06 TCGA.EE.A2M5.06 TCGA.GN.A266.06 TCGA.D3.A3C1.06 TCGA.D3.A2JH.06 TCGA.EE.A20F.06
#> "03" "041" "0443" "04421" "011" "041"
#> TCGA.EE.A29E.06 TCGA.ER.A2NG.06 TCGA.ER.A193.06 TCGA.FS.A1ZW.06 TCGA.ER.A19O.06 TCGA.EE.A2ME.06
#> "0133" "014" "0421" "041" "04421" "011"
#> TCGA.EE.A20B.06 TCGA.EE.A3AF.06 TCGA.GN.A265.06 TCGA.FS.A1YX.06 TCGA.FS.A1ZJ.06 TCGA.ER.A19H.06
#> "041" "03" "011" "0441" "0523" "03"
#> TCGA.EE.A3AC.06 TCGA.EE.A2MU.06 TCGA.ER.A194.01 TCGA.EE.A2MS.06 TCGA.EE.A29R.06 TCGA.D9.A1X3.06
#> "0521" "011" "04423" "043" "023" "022"
#> TCGA.EE.A29X.06 TCGA.EE.A2GK.06 TCGA.EE.A3AA.06 TCGA.ER.A2NE.06 TCGA.EE.A2GR.06 TCGA.FS.A1ZD.06
#> "04421" "0123" "011" "0212" "0521" "0523"
#> TCGA.ER.A19P.06 TCGA.D3.A1Q8.06 TCGA.ER.A2NC.06 TCGA.BF.A1Q0.01 TCGA.FS.A1ZP.06 TCGA.EE.A182.06
#> "014" "011" "0443" "0421" "0522" "043"
#> TCGA.D9.A1JW.06 TCGA.D3.A1Q7.06 TCGA.EE.A185.06 TCGA.EE.A2GJ.06 TCGA.D3.A3CB.06 TCGA.EE.A2GU.06
#> "0421" "014" "0212" "043" "011" "0421"
#> TCGA.ER.A195.06 TCGA.FS.A1Z7.06 TCGA.EE.A2M6.06 TCGA.ER.A19K.01 TCGA.DA.A1HY.06 TCGA.D3.A3C7.06
#> "0132" "0423" "0212" "04421" "03" "03"
#> TCGA.EE.A2MP.06 TCGA.EE.A29H.06 TCGA.FR.A3YO.06 TCGA.XV.AB01.01 TCGA.RP.A694.06 TCGA.EB.A5SF.01
#> "03" "03" "04421" "03" "04423" "0122"
#> TCGA.ER.A19G.06 TCGA.EE.A2GE.06 TCGA.GF.A3OT.06 TCGA.ER.A2NF.06 TCGA.RP.A695.06 TCGA.BF.AAP7.01
#> "03" "011" "014" "0132" "0512" "0121"
#> TCGA.EB.A3Y7.01 TCGA.EB.A3XC.01 TCGA.ER.A19W.06 TCGA.FR.A69P.06 TCGA.RP.A693.06 TCGA.FW.A3TV.06
#> "0423" "03" "014" "03" "011" "0124"
#> TCGA.FW.A3R5.11 TCGA.FW.A3TU.06 TCGA.BF.AAP8.01 TCGA.EE.A2MM.06 TCGA.DA.A1HW.06 TCGA.DA.A1IC.06
#> "0132" "0511" "0422" "0513" "0441" "0521"
#> TCGA.XV.AAZV.01 TCGA.D3.A3C6.06 TCGA.EE.A29C.06 TCGA.BF.AAP2.01 TCGA.EE.A2A2.06 TCGA.GF.A6C8.06
#> "0121" "03" "0132" "0212" "03" "0443"
#> TCGA.RP.A690.06 TCGA.FW.A5DY.06 TCGA.DA.A1I4.06 TCGA.EE.A29V.06 TCGA.GF.A6C9.06 TCGA.EE.A2GT.06
#> "0122" "014" "0132" "041" "011" "0131"
#> TCGA.GN.A9SD.06 TCGA.EE.A3AB.06 TCGA.BF.AAP6.01 TCGA.EB.A5SH.06 TCGA.D9.A6E9.06 TCGA.BF.AAP4.01
#> "014" "041" "03" "043" "04421" "04421"
#> TCGA.EE.A2GM.06 TCGA.D3.A3CF.06 TCGA.D9.A6EC.06 TCGA.DA.A1I1.06 TCGA.HR.A2OH.06 TCGA.EE.A2MT.06
#> "0212" "0121" "023" "041" "014" "0422"
#> TCGA.ER.A19M.06 TCGA.GN.A26C.01 TCGA.FS.A1ZA.06 TCGA.EB.A5SE.01 TCGA.ER.A3PL.06 TCGA.FR.A3R1.01
#> "041" "011" "04422" "022" "0521" "03"
#> TCGA.EE.A2MI.06 TCGA.D3.A3CE.06 TCGA.D3.A5GT.01 TCGA.ER.A2NB.01 TCGA.D3.A1Q5.06 TCGA.EB.A5UN.06
#> "0443" "0441" "0511" "0421" "0422" "011"
#> TCGA.EB.A299.01 TCGA.DA.A1IA.06 TCGA.EB.A5SG.06 TCGA.D9.A6EA.06 TCGA.XV.AAZY.01 TCGA.EB.A57M.01
#> "03" "0511" "014" "022" "014" "041"
#> TCGA.EE.A2A6.06 TCGA.D3.A2JA.06 TCGA.D3.A1Q1.06 TCGA.EB.A3XF.01 TCGA.D3.A2JF.06 TCGA.XV.AAZW.01
#> "0421" "0132" "0422" "03" "03" "03"
#> TCGA.EB.A3Y6.01 TCGA.EB.A3XE.01 TCGA.D9.A3Z4.01 TCGA.FW.A3R5.06 TCGA.EE.A2GI.06 TCGA.EE.A2GL.06
#> "0441" "043" "0523" "043" "041" "014"
#> TCGA.EB.A3XB.01 TCGA.BF.AAOU.01 TCGA.EB.A3XD.01 TCGA.EE.A2MD.06 TCGA.YD.A9TB.06 TCGA.W3.AA1V.06
#> "04421" "014" "0124" "04421" "0521" "0441"
#> TCGA.ER.A2ND.06 TCGA.D3.A2JK.06 TCGA.FS.A1ZB.06 TCGA.EE.A29D.06 TCGA.EB.A5UM.01 TCGA.QB.A6FS.06
#> "0521" "041" "011" "022" "043" "0132"
#> TCGA.D9.A3Z1.06 TCGA.D3.A2JN.06 TCGA.FR.A3YN.06 TCGA.FS.A1ZT.06 TCGA.D9.A148.06 TCGA.HR.A2OG.06
#> "011" "014" "03" "0132" "041" "0125"
#> TCGA.EE.A2ML.06 TCGA.EB.A5UL.06 TCGA.EE.A29T.06 TCGA.D9.A3Z3.06 TCGA.D9.A4Z3.01 TCGA.ER.A3ES.06
#> "041" "041" "043" "0124" "0522" "0422"
#> TCGA.XV.A9VZ.01 TCGA.QB.AA9O.06 TCGA.EB.A44Q.06 TCGA.EB.A44R.06 TCGA.BF.A3DJ.01 TCGA.EE.A3JD.06
#> "0122" "03" "04421" "043" "03" "0131"
#> TCGA.D3.A51N.06 TCGA.EB.A44N.01 TCGA.EE.A3J3.06 TCGA.XV.A9W5.01 TCGA.D3.A51G.06 TCGA.EB.A4P0.01
#> "041" "011" "03" "041" "03" "03"
#> TCGA.BF.AAP1.01 TCGA.EE.A3J4.06 TCGA.Z2.AA3V.06 TCGA.LH.A9QB.06 TCGA.D3.A51J.06 TCGA.3N.A9WC.06
#> "023" "0511" "0121" "023" "04421" "0421"
#> TCGA.DA.A3F8.06 TCGA.D9.A4Z6.06 TCGA.D3.A51R.06 TCGA.EB.A4OZ.01 TCGA.FS.A4FB.06 TCGA.EE.A3JE.06
#> "011" "041" "03" "0121" "03" "011"
#> TCGA.W3.AA1W.06 TCGA.DA.A1I0.06 TCGA.D3.A51F.06 TCGA.IH.A3EA.01 TCGA.EB.A431.01 TCGA.EB.A97M.01
#> "011" "041" "0131" "0512" "041" "022"
#> TCGA.BF.AAOX.01 TCGA.DA.A3F5.06 TCGA.YD.A9TA.06 TCGA.DA.A3F2.06 TCGA.EB.A44O.01 TCGA.EB.A4IQ.01
#> "041" "0423" "041" "0131" "0521" "0421"
#> TCGA.EB.A4IS.01 TCGA.YG.AA3O.06 TCGA.ER.A3EV.06 TCGA.3N.A9WD.06 TCGA.BF.A3DM.01 TCGA.XV.A9W2.01
#> "011" "0512" "043" "011" "03" "0423"
#> TCGA.W3.AA1Q.06 TCGA.WE.AAA0.06 TCGA.W3.AA1R.06 TCGA.EE.A3J5.06 TCGA.EB.A4OY.01 TCGA.FS.A4FD.06
#> "0512" "041" "03" "041" "0122" "0422"
#> TCGA.BF.AAP0.06 TCGA.YG.AA3P.06 TCGA.EE.A3JA.06 TCGA.W3.AA21.06 TCGA.WE.AAA3.06 TCGA.FS.A4F4.06
#> "0123" "0523" "03" "0211" "0423" "03"
#> TCGA.BF.A3DN.01 TCGA.ER.A3ET.06 TCGA.W3.AA1O.06 TCGA.D3.A51E.06 TCGA.Z2.AA3S.06 TCGA.YG.AA3N.01
#> "03" "0423" "0513" "03" "022" "04421"
#> TCGA.WE.AA9Y.06 TCGA.FS.A4F5.06 TCGA.EE.A3J7.06 TCGA.FS.A4F8.06 TCGA.DA.A3F3.06 TCGA.D3.A51H.06
#> "011" "023" "0511" "011" "03" "0131"
#> TCGA.BF.A3DL.01 TCGA.D3.A51T.06 TCGA.D3.A51K.06 TCGA.EB.A44P.01 TCGA.D9.A4Z5.01 TCGA.WE.AAA4.06
#> "0124" "03" "0522" "0521" "023" "014"
#> TCGA.3N.A9WB.06 TCGA.EE.A3J8.06
#> "022" "0211"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 4105))
#> TCGA.FR.A728.01 TCGA.GN.A4U8.11 TCGA.GN.A8LL.06 TCGA.FR.A8YC.06 TCGA.DA.A95X.06 TCGA.ER.A42K.06
#> "014" "011" "03" "022" "021" "03"
#> TCGA.D3.A8GO.06 TCGA.D3.A8GK.06 TCGA.WE.A8JZ.06 TCGA.WE.A8ZO.06 TCGA.D3.A8GI.06 TCGA.FS.A4FC.06
#> "0124" "0524" "021" "0511" "0512" "0421"
#> TCGA.FS.A4F2.06 TCGA.WE.A8ZM.06 TCGA.WE.A8ZT.06 TCGA.D3.A8GQ.06 TCGA.D3.A8GB.06 TCGA.DA.A95Y.06
#> "03" "0522" "03" "041" "0131" "03"
#> TCGA.EE.A3JI.06 TCGA.OD.A75X.06 TCGA.DA.A960.01 TCGA.D3.A8GV.06 TCGA.WE.A8ZN.06 TCGA.D3.A8GN.06
#> "022" "023" "021" "021" "011" "014"
#> TCGA.EB.A550.01 TCGA.BF.A5EQ.01 TCGA.EB.A3HV.01 TCGA.HR.A5NC.01 TCGA.DA.A95Z.06 TCGA.EB.A6QZ.01
#> "0122" "0421" "0521" "0523" "022" "021"
#> TCGA.FW.A3I3.06 TCGA.WE.A8K6.06 TCGA.D3.A8GP.06 TCGA.EB.A42Z.01 TCGA.GN.A4U4.06 TCGA.GF.A4EO.06
#> "023" "03" "022" "023" "021" "014"
#> TCGA.GN.A8LK.06 TCGA.WE.A8K4.01 TCGA.DA.A95W.06 TCGA.FW.A5DX.01 TCGA.GN.A4U3.06 TCGA.EB.A6QY.01
#> "0521" "011" "022" "021" "03" "0133"
#> TCGA.EB.A5VU.01 TCGA.Z2.A8RT.06 TCGA.WE.A8K1.06 TCGA.EB.A41B.01 TCGA.WE.A8ZY.06 TCGA.D9.A6EG.06
#> "0443" "03" "011" "03" "021" "022"
#> TCGA.BF.A5ER.01 TCGA.FR.A8YD.06 TCGA.FS.A4F9.06 TCGA.EB.A6R0.01 TCGA.ER.A42L.06 TCGA.D3.A8GJ.06
#> "0512" "0511" "0511" "03" "011" "04423"
#> TCGA.FR.A8YE.06 TCGA.WE.A8ZR.06 TCGA.BF.A9VF.01 TCGA.EE.A3JH.06 TCGA.DA.A95V.06 TCGA.GF.A769.01
#> "011" "043" "0521" "011" "041" "021"
#> TCGA.D9.A4Z2.01 TCGA.FR.A44A.06 TCGA.EB.A5VV.06 TCGA.EE.A180.06 TCGA.D3.A8GC.06 TCGA.WE.A8K5.06
#> "03" "014" "0123" "022" "0513" "023"
#> TCGA.GN.A8LN.01 TCGA.EE.A3JB.06 TCGA.D3.A3MO.06 TCGA.ER.A42H.01 TCGA.WE.A8ZX.06 TCGA.GN.A4U5.01
#> "021" "041" "0522" "0511" "041" "014"
#> TCGA.D3.A8GS.06 TCGA.WE.A8ZQ.06 TCGA.EE.A2MF.06 TCGA.D3.A5GU.06 TCGA.GN.A4U8.06 TCGA.EB.A42Y.01
#> "0441" "0523" "022" "0511" "041" "021"
#> TCGA.D3.A3ML.06 TCGA.EB.A551.01 TCGA.D3.A8GM.06 TCGA.D3.A8GL.06 TCGA.D3.A3MU.06 TCGA.FS.A4F0.06
#> "0511" "04422" "041" "022" "022" "022"
#> TCGA.D3.A3MV.06 TCGA.GN.A4U7.06 TCGA.FR.A2OS.01 TCGA.D3.A2JE.06 TCGA.YD.A89C.06 TCGA.FR.A726.01
#> "03" "03" "0523" "0522" "041" "041"
#> TCGA.BF.A5EP.01 TCGA.D3.A3MR.06 TCGA.D3.A8GR.06 TCGA.GN.A4U9.06 TCGA.EB.A6L9.06 TCGA.D3.A5GL.06
#> "03" "011" "0511" "0522" "0131" "03"
#> TCGA.EB.A430.01 TCGA.D3.A8GE.06 TCGA.D3.A8GD.06 TCGA.EB.A41A.01 TCGA.W3.A825.06 TCGA.EE.A183.06
#> "0133" "0132" "014" "022" "0443" "011"
#> TCGA.ER.A2NH.06 TCGA.D3.A5GR.06 TCGA.FR.A729.06 TCGA.D3.A1QA.06 TCGA.FS.A1YY.06 TCGA.EE.A2MK.06
#> "011" "0441" "0441" "021" "03" "03"
#> TCGA.EE.A2M8.06 TCGA.EB.A5KH.06 TCGA.FS.A1ZR.06 TCGA.EE.A3AE.06 TCGA.EE.A29P.06 TCGA.EB.A553.01
#> "0123" "021" "0521" "03" "04424" "0513"
#> TCGA.EE.A2MR.06 TCGA.GN.A26A.06 TCGA.FS.A1ZY.06 TCGA.EE.A20I.06 TCGA.DA.A1I5.06 TCGA.EE.A184.06
#> "011" "041" "021" "041" "0125" "023"
#> TCGA.EB.A85J.01 TCGA.RP.A6K9.06 TCGA.EE.A17Y.06 TCGA.D9.A149.06 TCGA.ER.A19D.06 TCGA.FS.A1ZZ.06
#> "043" "0423" "041" "0421" "0122" "023"
#> TCGA.EE.A2GP.06 TCGA.EE.A3AD.06 TCGA.D3.A1Q9.06 TCGA.GF.A2C7.01 TCGA.BF.A5ES.01 TCGA.ER.A199.06
#> "0524" "021" "041" "0511" "0511" "014"
#> TCGA.EE.A3AH.06 TCGA.W3.A828.06 TCGA.EE.A2A5.06 TCGA.ER.A19L.06 TCGA.BF.A1PX.01 TCGA.ER.A19T.06
#> "021" "0133" "0522" "043" "011" "043"
#> TCGA.EB.A51B.01 TCGA.FS.A1ZQ.06 TCGA.D3.A2JG.06 TCGA.EE.A2GH.06 TCGA.ER.A19F.06 TCGA.ER.A196.01
#> "03" "03" "03" "011" "03" "0124"
#> TCGA.D3.A2JC.06 TCGA.EE.A3AG.06 TCGA.ER.A19S.06 TCGA.EE.A2GC.06 TCGA.EE.A29N.06 TCGA.FR.A7U8.06
#> "0441" "03" "014" "0524" "011" "023"
#> TCGA.BF.A5EO.01 TCGA.ER.A19B.06 TCGA.D3.A5GN.06 TCGA.D3.A2JB.06 TCGA.ER.A19J.06 TCGA.D3.A2JD.06
#> "041" "03" "03" "0123" "023" "011"
#> TCGA.FS.A1Z4.06 TCGA.FR.A7UA.06 TCGA.EE.A2M7.06 TCGA.D3.A1Q3.06 TCGA.EB.A85I.01 TCGA.EB.A82C.01
#> "0131" "014" "0441" "043" "0421" "023"
#> TCGA.ER.A19E.06 TCGA.FS.A1ZK.06 TCGA.FS.A1ZU.06 TCGA.EB.A5FP.01 TCGA.EB.A4XL.01 TCGA.DA.A1I2.06
#> "0522" "0524" "0522" "021" "03" "0441"
#> TCGA.EE.A29L.06 TCGA.FS.A1ZN.01 TCGA.EB.A24D.01 TCGA.EE.A2GB.06 TCGA.DA.A1I7.06 TCGA.ER.A2NF.01
#> "021" "021" "0511" "03" "0441" "0132"
#> TCGA.GN.A263.01 TCGA.EE.A20C.06 TCGA.EE.A2MQ.06 TCGA.ER.A19N.06 TCGA.FS.A1Z3.06 TCGA.DA.A1I8.06
#> "0132" "023" "0512" "011" "03" "03"
#> TCGA.D3.A5GS.06 TCGA.EE.A181.06 TCGA.GN.A268.06 TCGA.W3.A824.06 TCGA.EE.A2GS.06 TCGA.FR.A7U9.06
#> "03" "041" "022" "0511" "03" "0121"
#> TCGA.ER.A19Q.06 TCGA.FS.A1ZM.06 TCGA.EE.A2MG.06 TCGA.EE.A2MC.06 TCGA.EE.A17Z.06 TCGA.D3.A2JP.06
#> "0125" "0441" "0131" "0131" "0522" "041"
#> TCGA.ER.A19C.06 TCGA.EB.A82B.01 TCGA.EE.A2A0.06 TCGA.EE.A29G.06 TCGA.D3.A5GO.06 TCGA.GN.A269.01
#> "0443" "0423" "014" "011" "03" "011"
#> TCGA.EE.A2A1.06 TCGA.ER.A1A1.06 TCGA.FS.A1ZG.06 TCGA.FS.A1ZE.06 TCGA.FS.A1ZH.06 TCGA.EE.A2MH.06
#> "0131" "0131" "022" "022" "041" "011"
#> TCGA.D3.A2J6.06 TCGA.EE.A29Q.06 TCGA.BF.A1PZ.01 TCGA.D3.A3BZ.06 TCGA.D3.A2JO.06 TCGA.GN.A267.06
#> "0423" "03" "03" "0131" "04422" "043"
#> TCGA.EE.A2MN.06 TCGA.GN.A264.06 TCGA.ER.A197.06 TCGA.DA.A1IB.06 TCGA.D3.A3CC.06 TCGA.ER.A19T.01
#> "0513" "023" "014" "014" "0423" "0523"
#> TCGA.GN.A261.06 TCGA.FS.A1YW.06 TCGA.BF.A1PU.01 TCGA.D3.A1QB.06 TCGA.D3.A1Q6.06 TCGA.D3.A3C8.06
#> "0122" "023" "0443" "0124" "0441" "014"
#> TCGA.ER.A19A.06 TCGA.EE.A2GN.06 TCGA.EE.A29M.06 TCGA.D3.A2J7.06 TCGA.EB.A24C.01 TCGA.GN.A262.06
#> "0131" "0522" "0121" "011" "043" "021"
#> TCGA.EE.A2GD.06 TCGA.D3.A2J9.06 TCGA.EE.A29B.06 TCGA.D9.A1JX.06 TCGA.EE.A29A.06 TCGA.D3.A2JL.06
#> "014" "011" "0511" "03" "022" "041"
#> TCGA.D3.A1Q4.06 TCGA.FS.A1ZS.06 TCGA.D3.A3C3.06 TCGA.D3.A2J8.06 TCGA.FS.A1ZF.06 TCGA.FS.A1ZC.06
#> "0122" "0423" "041" "0131" "03" "021"
#> TCGA.EE.A20H.06 TCGA.EE.A29W.06 TCGA.D3.A1QA.07 TCGA.BF.A1PV.01 TCGA.EE.A29S.06 TCGA.DA.A1HV.06
#> "0522" "03" "041" "0512" "04424" "03"
#> TCGA.FS.A1Z0.06 TCGA.EE.A2GO.06 TCGA.EB.A1NK.01 TCGA.GN.A26D.06 TCGA.EE.A2MJ.06 TCGA.ER.A198.06
#> "0122" "023" "0133" "0422" "011" "0512"
#> TCGA.EE.A17X.06 TCGA.EE.A2M5.06 TCGA.GN.A266.06 TCGA.D3.A3C1.06 TCGA.D3.A2JH.06 TCGA.EE.A20F.06
#> "03" "041" "0443" "04421" "011" "041"
#> TCGA.EE.A29E.06 TCGA.ER.A2NG.06 TCGA.ER.A193.06 TCGA.FS.A1ZW.06 TCGA.ER.A19O.06 TCGA.EE.A2ME.06
#> "0133" "014" "0421" "041" "04421" "011"
#> TCGA.EE.A20B.06 TCGA.EE.A3AF.06 TCGA.GN.A265.06 TCGA.FS.A1YX.06 TCGA.FS.A1ZJ.06 TCGA.ER.A19H.06
#> "041" "03" "011" "0441" "0523" "03"
#> TCGA.EE.A3AC.06 TCGA.EE.A2MU.06 TCGA.ER.A194.01 TCGA.EE.A2MS.06 TCGA.EE.A29R.06 TCGA.D9.A1X3.06
#> "0521" "011" "04423" "043" "023" "022"
#> TCGA.EE.A29X.06 TCGA.EE.A2GK.06 TCGA.EE.A3AA.06 TCGA.ER.A2NE.06 TCGA.EE.A2GR.06 TCGA.FS.A1ZD.06
#> "04421" "0123" "011" "021" "0521" "0523"
#> TCGA.ER.A19P.06 TCGA.D3.A1Q8.06 TCGA.ER.A2NC.06 TCGA.BF.A1Q0.01 TCGA.FS.A1ZP.06 TCGA.EE.A182.06
#> "014" "011" "0443" "0421" "0522" "043"
#> TCGA.D9.A1JW.06 TCGA.D3.A1Q7.06 TCGA.EE.A185.06 TCGA.EE.A2GJ.06 TCGA.D3.A3CB.06 TCGA.EE.A2GU.06
#> "0421" "014" "021" "043" "011" "0421"
#> TCGA.ER.A195.06 TCGA.FS.A1Z7.06 TCGA.EE.A2M6.06 TCGA.ER.A19K.01 TCGA.DA.A1HY.06 TCGA.D3.A3C7.06
#> "0132" "0423" "021" "04421" "03" "03"
#> TCGA.EE.A2MP.06 TCGA.EE.A29H.06 TCGA.FR.A3YO.06 TCGA.XV.AB01.01 TCGA.RP.A694.06 TCGA.EB.A5SF.01
#> "03" "03" "04421" "03" "04423" "0122"
#> TCGA.ER.A19G.06 TCGA.EE.A2GE.06 TCGA.GF.A3OT.06 TCGA.ER.A2NF.06 TCGA.RP.A695.06 TCGA.BF.AAP7.01
#> "03" "011" "014" "0132" "0512" "0121"
#> TCGA.EB.A3Y7.01 TCGA.EB.A3XC.01 TCGA.ER.A19W.06 TCGA.FR.A69P.06 TCGA.RP.A693.06 TCGA.FW.A3TV.06
#> "0423" "03" "014" "03" "011" "0124"
#> TCGA.FW.A3R5.11 TCGA.FW.A3TU.06 TCGA.BF.AAP8.01 TCGA.EE.A2MM.06 TCGA.DA.A1HW.06 TCGA.DA.A1IC.06
#> "0132" "0511" "0422" "0513" "0441" "0521"
#> TCGA.XV.AAZV.01 TCGA.D3.A3C6.06 TCGA.EE.A29C.06 TCGA.BF.AAP2.01 TCGA.EE.A2A2.06 TCGA.GF.A6C8.06
#> "0121" "03" "0132" "021" "03" "0443"
#> TCGA.RP.A690.06 TCGA.FW.A5DY.06 TCGA.DA.A1I4.06 TCGA.EE.A29V.06 TCGA.GF.A6C9.06 TCGA.EE.A2GT.06
#> "0122" "014" "0132" "041" "011" "0131"
#> TCGA.GN.A9SD.06 TCGA.EE.A3AB.06 TCGA.BF.AAP6.01 TCGA.EB.A5SH.06 TCGA.D9.A6E9.06 TCGA.BF.AAP4.01
#> "014" "041" "03" "043" "04421" "04421"
#> TCGA.EE.A2GM.06 TCGA.D3.A3CF.06 TCGA.D9.A6EC.06 TCGA.DA.A1I1.06 TCGA.HR.A2OH.06 TCGA.EE.A2MT.06
#> "021" "0121" "023" "041" "014" "0422"
#> TCGA.ER.A19M.06 TCGA.GN.A26C.01 TCGA.FS.A1ZA.06 TCGA.EB.A5SE.01 TCGA.ER.A3PL.06 TCGA.FR.A3R1.01
#> "041" "011" "04422" "022" "0521" "03"
#> TCGA.EE.A2MI.06 TCGA.D3.A3CE.06 TCGA.D3.A5GT.01 TCGA.ER.A2NB.01 TCGA.D3.A1Q5.06 TCGA.EB.A5UN.06
#> "0443" "0441" "0511" "0421" "0422" "011"
#> TCGA.EB.A299.01 TCGA.DA.A1IA.06 TCGA.EB.A5SG.06 TCGA.D9.A6EA.06 TCGA.XV.AAZY.01 TCGA.EB.A57M.01
#> "03" "0511" "014" "022" "014" "041"
#> TCGA.EE.A2A6.06 TCGA.D3.A2JA.06 TCGA.D3.A1Q1.06 TCGA.EB.A3XF.01 TCGA.D3.A2JF.06 TCGA.XV.AAZW.01
#> "0421" "0132" "0422" "03" "03" "03"
#> TCGA.EB.A3Y6.01 TCGA.EB.A3XE.01 TCGA.D9.A3Z4.01 TCGA.FW.A3R5.06 TCGA.EE.A2GI.06 TCGA.EE.A2GL.06
#> "0441" "043" "0523" "043" "041" "014"
#> TCGA.EB.A3XB.01 TCGA.BF.AAOU.01 TCGA.EB.A3XD.01 TCGA.EE.A2MD.06 TCGA.YD.A9TB.06 TCGA.W3.AA1V.06
#> "04421" "014" "0124" "04421" "0521" "0441"
#> TCGA.ER.A2ND.06 TCGA.D3.A2JK.06 TCGA.FS.A1ZB.06 TCGA.EE.A29D.06 TCGA.EB.A5UM.01 TCGA.QB.A6FS.06
#> "0521" "041" "011" "022" "043" "0132"
#> TCGA.D9.A3Z1.06 TCGA.D3.A2JN.06 TCGA.FR.A3YN.06 TCGA.FS.A1ZT.06 TCGA.D9.A148.06 TCGA.HR.A2OG.06
#> "011" "014" "03" "0132" "041" "0125"
#> TCGA.EE.A2ML.06 TCGA.EB.A5UL.06 TCGA.EE.A29T.06 TCGA.D9.A3Z3.06 TCGA.D9.A4Z3.01 TCGA.ER.A3ES.06
#> "041" "041" "043" "0124" "0522" "0422"
#> TCGA.XV.A9VZ.01 TCGA.QB.AA9O.06 TCGA.EB.A44Q.06 TCGA.EB.A44R.06 TCGA.BF.A3DJ.01 TCGA.EE.A3JD.06
#> "0122" "03" "04421" "043" "03" "0131"
#> TCGA.D3.A51N.06 TCGA.EB.A44N.01 TCGA.EE.A3J3.06 TCGA.XV.A9W5.01 TCGA.D3.A51G.06 TCGA.EB.A4P0.01
#> "041" "011" "03" "041" "03" "03"
#> TCGA.BF.AAP1.01 TCGA.EE.A3J4.06 TCGA.Z2.AA3V.06 TCGA.LH.A9QB.06 TCGA.D3.A51J.06 TCGA.3N.A9WC.06
#> "023" "0511" "0121" "023" "04421" "0421"
#> TCGA.DA.A3F8.06 TCGA.D9.A4Z6.06 TCGA.D3.A51R.06 TCGA.EB.A4OZ.01 TCGA.FS.A4FB.06 TCGA.EE.A3JE.06
#> "011" "041" "03" "0121" "03" "011"
#> TCGA.W3.AA1W.06 TCGA.DA.A1I0.06 TCGA.D3.A51F.06 TCGA.IH.A3EA.01 TCGA.EB.A431.01 TCGA.EB.A97M.01
#> "011" "041" "0131" "0512" "041" "022"
#> TCGA.BF.AAOX.01 TCGA.DA.A3F5.06 TCGA.YD.A9TA.06 TCGA.DA.A3F2.06 TCGA.EB.A44O.01 TCGA.EB.A4IQ.01
#> "041" "0423" "041" "0131" "0521" "0421"
#> TCGA.EB.A4IS.01 TCGA.YG.AA3O.06 TCGA.ER.A3EV.06 TCGA.3N.A9WD.06 TCGA.BF.A3DM.01 TCGA.XV.A9W2.01
#> "011" "0512" "043" "011" "03" "0423"
#> TCGA.W3.AA1Q.06 TCGA.WE.AAA0.06 TCGA.W3.AA1R.06 TCGA.EE.A3J5.06 TCGA.EB.A4OY.01 TCGA.FS.A4FD.06
#> "0512" "041" "03" "041" "0122" "0422"
#> TCGA.BF.AAP0.06 TCGA.YG.AA3P.06 TCGA.EE.A3JA.06 TCGA.W3.AA21.06 TCGA.WE.AAA3.06 TCGA.FS.A4F4.06
#> "0123" "0523" "03" "021" "0423" "03"
#> TCGA.BF.A3DN.01 TCGA.ER.A3ET.06 TCGA.W3.AA1O.06 TCGA.D3.A51E.06 TCGA.Z2.AA3S.06 TCGA.YG.AA3N.01
#> "03" "0423" "0513" "03" "022" "04421"
#> TCGA.WE.AA9Y.06 TCGA.FS.A4F5.06 TCGA.EE.A3J7.06 TCGA.FS.A4F8.06 TCGA.DA.A3F3.06 TCGA.D3.A51H.06
#> "011" "023" "0511" "011" "03" "0131"
#> TCGA.BF.A3DL.01 TCGA.D3.A51T.06 TCGA.D3.A51K.06 TCGA.EB.A44P.01 TCGA.D9.A4Z5.01 TCGA.WE.AAA4.06
#> "0124" "03" "0522" "0521" "023" "014"
#> TCGA.3N.A9WB.06 TCGA.EE.A3J8.06
#> "022" "021"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 6230))
#> TCGA.FR.A728.01 TCGA.GN.A4U8.11 TCGA.GN.A8LL.06 TCGA.FR.A8YC.06 TCGA.DA.A95X.06 TCGA.ER.A42K.06
#> "01" "01" "03" "022" "021" "03"
#> TCGA.D3.A8GO.06 TCGA.D3.A8GK.06 TCGA.WE.A8JZ.06 TCGA.WE.A8ZO.06 TCGA.D3.A8GI.06 TCGA.FS.A4FC.06
#> "01" "0524" "021" "0511" "0512" "0421"
#> TCGA.FS.A4F2.06 TCGA.WE.A8ZM.06 TCGA.WE.A8ZT.06 TCGA.D3.A8GQ.06 TCGA.D3.A8GB.06 TCGA.DA.A95Y.06
#> "03" "0522" "03" "041" "01" "03"
#> TCGA.EE.A3JI.06 TCGA.OD.A75X.06 TCGA.DA.A960.01 TCGA.D3.A8GV.06 TCGA.WE.A8ZN.06 TCGA.D3.A8GN.06
#> "022" "023" "021" "021" "01" "01"
#> TCGA.EB.A550.01 TCGA.BF.A5EQ.01 TCGA.EB.A3HV.01 TCGA.HR.A5NC.01 TCGA.DA.A95Z.06 TCGA.EB.A6QZ.01
#> "01" "0421" "0521" "0523" "022" "021"
#> TCGA.FW.A3I3.06 TCGA.WE.A8K6.06 TCGA.D3.A8GP.06 TCGA.EB.A42Z.01 TCGA.GN.A4U4.06 TCGA.GF.A4EO.06
#> "023" "03" "022" "023" "021" "01"
#> TCGA.GN.A8LK.06 TCGA.WE.A8K4.01 TCGA.DA.A95W.06 TCGA.FW.A5DX.01 TCGA.GN.A4U3.06 TCGA.EB.A6QY.01
#> "0521" "01" "022" "021" "03" "01"
#> TCGA.EB.A5VU.01 TCGA.Z2.A8RT.06 TCGA.WE.A8K1.06 TCGA.EB.A41B.01 TCGA.WE.A8ZY.06 TCGA.D9.A6EG.06
#> "0443" "03" "01" "03" "021" "022"
#> TCGA.BF.A5ER.01 TCGA.FR.A8YD.06 TCGA.FS.A4F9.06 TCGA.EB.A6R0.01 TCGA.ER.A42L.06 TCGA.D3.A8GJ.06
#> "0512" "0511" "0511" "03" "01" "04423"
#> TCGA.FR.A8YE.06 TCGA.WE.A8ZR.06 TCGA.BF.A9VF.01 TCGA.EE.A3JH.06 TCGA.DA.A95V.06 TCGA.GF.A769.01
#> "01" "043" "0521" "01" "041" "021"
#> TCGA.D9.A4Z2.01 TCGA.FR.A44A.06 TCGA.EB.A5VV.06 TCGA.EE.A180.06 TCGA.D3.A8GC.06 TCGA.WE.A8K5.06
#> "03" "01" "01" "022" "0513" "023"
#> TCGA.GN.A8LN.01 TCGA.EE.A3JB.06 TCGA.D3.A3MO.06 TCGA.ER.A42H.01 TCGA.WE.A8ZX.06 TCGA.GN.A4U5.01
#> "021" "041" "0522" "0511" "041" "01"
#> TCGA.D3.A8GS.06 TCGA.WE.A8ZQ.06 TCGA.EE.A2MF.06 TCGA.D3.A5GU.06 TCGA.GN.A4U8.06 TCGA.EB.A42Y.01
#> "0441" "0523" "022" "0511" "041" "021"
#> TCGA.D3.A3ML.06 TCGA.EB.A551.01 TCGA.D3.A8GM.06 TCGA.D3.A8GL.06 TCGA.D3.A3MU.06 TCGA.FS.A4F0.06
#> "0511" "04422" "041" "022" "022" "022"
#> TCGA.D3.A3MV.06 TCGA.GN.A4U7.06 TCGA.FR.A2OS.01 TCGA.D3.A2JE.06 TCGA.YD.A89C.06 TCGA.FR.A726.01
#> "03" "03" "0523" "0522" "041" "041"
#> TCGA.BF.A5EP.01 TCGA.D3.A3MR.06 TCGA.D3.A8GR.06 TCGA.GN.A4U9.06 TCGA.EB.A6L9.06 TCGA.D3.A5GL.06
#> "03" "01" "0511" "0522" "01" "03"
#> TCGA.EB.A430.01 TCGA.D3.A8GE.06 TCGA.D3.A8GD.06 TCGA.EB.A41A.01 TCGA.W3.A825.06 TCGA.EE.A183.06
#> "01" "01" "01" "022" "0443" "01"
#> TCGA.ER.A2NH.06 TCGA.D3.A5GR.06 TCGA.FR.A729.06 TCGA.D3.A1QA.06 TCGA.FS.A1YY.06 TCGA.EE.A2MK.06
#> "01" "0441" "0441" "021" "03" "03"
#> TCGA.EE.A2M8.06 TCGA.EB.A5KH.06 TCGA.FS.A1ZR.06 TCGA.EE.A3AE.06 TCGA.EE.A29P.06 TCGA.EB.A553.01
#> "01" "021" "0521" "03" "04424" "0513"
#> TCGA.EE.A2MR.06 TCGA.GN.A26A.06 TCGA.FS.A1ZY.06 TCGA.EE.A20I.06 TCGA.DA.A1I5.06 TCGA.EE.A184.06
#> "01" "041" "021" "041" "01" "023"
#> TCGA.EB.A85J.01 TCGA.RP.A6K9.06 TCGA.EE.A17Y.06 TCGA.D9.A149.06 TCGA.ER.A19D.06 TCGA.FS.A1ZZ.06
#> "043" "0423" "041" "0421" "01" "023"
#> TCGA.EE.A2GP.06 TCGA.EE.A3AD.06 TCGA.D3.A1Q9.06 TCGA.GF.A2C7.01 TCGA.BF.A5ES.01 TCGA.ER.A199.06
#> "0524" "021" "041" "0511" "0511" "01"
#> TCGA.EE.A3AH.06 TCGA.W3.A828.06 TCGA.EE.A2A5.06 TCGA.ER.A19L.06 TCGA.BF.A1PX.01 TCGA.ER.A19T.06
#> "021" "01" "0522" "043" "01" "043"
#> TCGA.EB.A51B.01 TCGA.FS.A1ZQ.06 TCGA.D3.A2JG.06 TCGA.EE.A2GH.06 TCGA.ER.A19F.06 TCGA.ER.A196.01
#> "03" "03" "03" "01" "03" "01"
#> TCGA.D3.A2JC.06 TCGA.EE.A3AG.06 TCGA.ER.A19S.06 TCGA.EE.A2GC.06 TCGA.EE.A29N.06 TCGA.FR.A7U8.06
#> "0441" "03" "01" "0524" "01" "023"
#> TCGA.BF.A5EO.01 TCGA.ER.A19B.06 TCGA.D3.A5GN.06 TCGA.D3.A2JB.06 TCGA.ER.A19J.06 TCGA.D3.A2JD.06
#> "041" "03" "03" "01" "023" "01"
#> TCGA.FS.A1Z4.06 TCGA.FR.A7UA.06 TCGA.EE.A2M7.06 TCGA.D3.A1Q3.06 TCGA.EB.A85I.01 TCGA.EB.A82C.01
#> "01" "01" "0441" "043" "0421" "023"
#> TCGA.ER.A19E.06 TCGA.FS.A1ZK.06 TCGA.FS.A1ZU.06 TCGA.EB.A5FP.01 TCGA.EB.A4XL.01 TCGA.DA.A1I2.06
#> "0522" "0524" "0522" "021" "03" "0441"
#> TCGA.EE.A29L.06 TCGA.FS.A1ZN.01 TCGA.EB.A24D.01 TCGA.EE.A2GB.06 TCGA.DA.A1I7.06 TCGA.ER.A2NF.01
#> "021" "021" "0511" "03" "0441" "01"
#> TCGA.GN.A263.01 TCGA.EE.A20C.06 TCGA.EE.A2MQ.06 TCGA.ER.A19N.06 TCGA.FS.A1Z3.06 TCGA.DA.A1I8.06
#> "01" "023" "0512" "01" "03" "03"
#> TCGA.D3.A5GS.06 TCGA.EE.A181.06 TCGA.GN.A268.06 TCGA.W3.A824.06 TCGA.EE.A2GS.06 TCGA.FR.A7U9.06
#> "03" "041" "022" "0511" "03" "01"
#> TCGA.ER.A19Q.06 TCGA.FS.A1ZM.06 TCGA.EE.A2MG.06 TCGA.EE.A2MC.06 TCGA.EE.A17Z.06 TCGA.D3.A2JP.06
#> "01" "0441" "01" "01" "0522" "041"
#> TCGA.ER.A19C.06 TCGA.EB.A82B.01 TCGA.EE.A2A0.06 TCGA.EE.A29G.06 TCGA.D3.A5GO.06 TCGA.GN.A269.01
#> "0443" "0423" "01" "01" "03" "01"
#> TCGA.EE.A2A1.06 TCGA.ER.A1A1.06 TCGA.FS.A1ZG.06 TCGA.FS.A1ZE.06 TCGA.FS.A1ZH.06 TCGA.EE.A2MH.06
#> "01" "01" "022" "022" "041" "01"
#> TCGA.D3.A2J6.06 TCGA.EE.A29Q.06 TCGA.BF.A1PZ.01 TCGA.D3.A3BZ.06 TCGA.D3.A2JO.06 TCGA.GN.A267.06
#> "0423" "03" "03" "01" "04422" "043"
#> TCGA.EE.A2MN.06 TCGA.GN.A264.06 TCGA.ER.A197.06 TCGA.DA.A1IB.06 TCGA.D3.A3CC.06 TCGA.ER.A19T.01
#> "0513" "023" "01" "01" "0423" "0523"
#> TCGA.GN.A261.06 TCGA.FS.A1YW.06 TCGA.BF.A1PU.01 TCGA.D3.A1QB.06 TCGA.D3.A1Q6.06 TCGA.D3.A3C8.06
#> "01" "023" "0443" "01" "0441" "01"
#> TCGA.ER.A19A.06 TCGA.EE.A2GN.06 TCGA.EE.A29M.06 TCGA.D3.A2J7.06 TCGA.EB.A24C.01 TCGA.GN.A262.06
#> "01" "0522" "01" "01" "043" "021"
#> TCGA.EE.A2GD.06 TCGA.D3.A2J9.06 TCGA.EE.A29B.06 TCGA.D9.A1JX.06 TCGA.EE.A29A.06 TCGA.D3.A2JL.06
#> "01" "01" "0511" "03" "022" "041"
#> TCGA.D3.A1Q4.06 TCGA.FS.A1ZS.06 TCGA.D3.A3C3.06 TCGA.D3.A2J8.06 TCGA.FS.A1ZF.06 TCGA.FS.A1ZC.06
#> "01" "0423" "041" "01" "03" "021"
#> TCGA.EE.A20H.06 TCGA.EE.A29W.06 TCGA.D3.A1QA.07 TCGA.BF.A1PV.01 TCGA.EE.A29S.06 TCGA.DA.A1HV.06
#> "0522" "03" "041" "0512" "04424" "03"
#> TCGA.FS.A1Z0.06 TCGA.EE.A2GO.06 TCGA.EB.A1NK.01 TCGA.GN.A26D.06 TCGA.EE.A2MJ.06 TCGA.ER.A198.06
#> "01" "023" "01" "0422" "01" "0512"
#> TCGA.EE.A17X.06 TCGA.EE.A2M5.06 TCGA.GN.A266.06 TCGA.D3.A3C1.06 TCGA.D3.A2JH.06 TCGA.EE.A20F.06
#> "03" "041" "0443" "04421" "01" "041"
#> TCGA.EE.A29E.06 TCGA.ER.A2NG.06 TCGA.ER.A193.06 TCGA.FS.A1ZW.06 TCGA.ER.A19O.06 TCGA.EE.A2ME.06
#> "01" "01" "0421" "041" "04421" "01"
#> TCGA.EE.A20B.06 TCGA.EE.A3AF.06 TCGA.GN.A265.06 TCGA.FS.A1YX.06 TCGA.FS.A1ZJ.06 TCGA.ER.A19H.06
#> "041" "03" "01" "0441" "0523" "03"
#> TCGA.EE.A3AC.06 TCGA.EE.A2MU.06 TCGA.ER.A194.01 TCGA.EE.A2MS.06 TCGA.EE.A29R.06 TCGA.D9.A1X3.06
#> "0521" "01" "04423" "043" "023" "022"
#> TCGA.EE.A29X.06 TCGA.EE.A2GK.06 TCGA.EE.A3AA.06 TCGA.ER.A2NE.06 TCGA.EE.A2GR.06 TCGA.FS.A1ZD.06
#> "04421" "01" "01" "021" "0521" "0523"
#> TCGA.ER.A19P.06 TCGA.D3.A1Q8.06 TCGA.ER.A2NC.06 TCGA.BF.A1Q0.01 TCGA.FS.A1ZP.06 TCGA.EE.A182.06
#> "01" "01" "0443" "0421" "0522" "043"
#> TCGA.D9.A1JW.06 TCGA.D3.A1Q7.06 TCGA.EE.A185.06 TCGA.EE.A2GJ.06 TCGA.D3.A3CB.06 TCGA.EE.A2GU.06
#> "0421" "01" "021" "043" "01" "0421"
#> TCGA.ER.A195.06 TCGA.FS.A1Z7.06 TCGA.EE.A2M6.06 TCGA.ER.A19K.01 TCGA.DA.A1HY.06 TCGA.D3.A3C7.06
#> "01" "0423" "021" "04421" "03" "03"
#> TCGA.EE.A2MP.06 TCGA.EE.A29H.06 TCGA.FR.A3YO.06 TCGA.XV.AB01.01 TCGA.RP.A694.06 TCGA.EB.A5SF.01
#> "03" "03" "04421" "03" "04423" "01"
#> TCGA.ER.A19G.06 TCGA.EE.A2GE.06 TCGA.GF.A3OT.06 TCGA.ER.A2NF.06 TCGA.RP.A695.06 TCGA.BF.AAP7.01
#> "03" "01" "01" "01" "0512" "01"
#> TCGA.EB.A3Y7.01 TCGA.EB.A3XC.01 TCGA.ER.A19W.06 TCGA.FR.A69P.06 TCGA.RP.A693.06 TCGA.FW.A3TV.06
#> "0423" "03" "01" "03" "01" "01"
#> TCGA.FW.A3R5.11 TCGA.FW.A3TU.06 TCGA.BF.AAP8.01 TCGA.EE.A2MM.06 TCGA.DA.A1HW.06 TCGA.DA.A1IC.06
#> "01" "0511" "0422" "0513" "0441" "0521"
#> TCGA.XV.AAZV.01 TCGA.D3.A3C6.06 TCGA.EE.A29C.06 TCGA.BF.AAP2.01 TCGA.EE.A2A2.06 TCGA.GF.A6C8.06
#> "01" "03" "01" "021" "03" "0443"
#> TCGA.RP.A690.06 TCGA.FW.A5DY.06 TCGA.DA.A1I4.06 TCGA.EE.A29V.06 TCGA.GF.A6C9.06 TCGA.EE.A2GT.06
#> "01" "01" "01" "041" "01" "01"
#> TCGA.GN.A9SD.06 TCGA.EE.A3AB.06 TCGA.BF.AAP6.01 TCGA.EB.A5SH.06 TCGA.D9.A6E9.06 TCGA.BF.AAP4.01
#> "01" "041" "03" "043" "04421" "04421"
#> TCGA.EE.A2GM.06 TCGA.D3.A3CF.06 TCGA.D9.A6EC.06 TCGA.DA.A1I1.06 TCGA.HR.A2OH.06 TCGA.EE.A2MT.06
#> "021" "01" "023" "041" "01" "0422"
#> TCGA.ER.A19M.06 TCGA.GN.A26C.01 TCGA.FS.A1ZA.06 TCGA.EB.A5SE.01 TCGA.ER.A3PL.06 TCGA.FR.A3R1.01
#> "041" "01" "04422" "022" "0521" "03"
#> TCGA.EE.A2MI.06 TCGA.D3.A3CE.06 TCGA.D3.A5GT.01 TCGA.ER.A2NB.01 TCGA.D3.A1Q5.06 TCGA.EB.A5UN.06
#> "0443" "0441" "0511" "0421" "0422" "01"
#> TCGA.EB.A299.01 TCGA.DA.A1IA.06 TCGA.EB.A5SG.06 TCGA.D9.A6EA.06 TCGA.XV.AAZY.01 TCGA.EB.A57M.01
#> "03" "0511" "01" "022" "01" "041"
#> TCGA.EE.A2A6.06 TCGA.D3.A2JA.06 TCGA.D3.A1Q1.06 TCGA.EB.A3XF.01 TCGA.D3.A2JF.06 TCGA.XV.AAZW.01
#> "0421" "01" "0422" "03" "03" "03"
#> TCGA.EB.A3Y6.01 TCGA.EB.A3XE.01 TCGA.D9.A3Z4.01 TCGA.FW.A3R5.06 TCGA.EE.A2GI.06 TCGA.EE.A2GL.06
#> "0441" "043" "0523" "043" "041" "01"
#> TCGA.EB.A3XB.01 TCGA.BF.AAOU.01 TCGA.EB.A3XD.01 TCGA.EE.A2MD.06 TCGA.YD.A9TB.06 TCGA.W3.AA1V.06
#> "04421" "01" "01" "04421" "0521" "0441"
#> TCGA.ER.A2ND.06 TCGA.D3.A2JK.06 TCGA.FS.A1ZB.06 TCGA.EE.A29D.06 TCGA.EB.A5UM.01 TCGA.QB.A6FS.06
#> "0521" "041" "01" "022" "043" "01"
#> TCGA.D9.A3Z1.06 TCGA.D3.A2JN.06 TCGA.FR.A3YN.06 TCGA.FS.A1ZT.06 TCGA.D9.A148.06 TCGA.HR.A2OG.06
#> "01" "01" "03" "01" "041" "01"
#> TCGA.EE.A2ML.06 TCGA.EB.A5UL.06 TCGA.EE.A29T.06 TCGA.D9.A3Z3.06 TCGA.D9.A4Z3.01 TCGA.ER.A3ES.06
#> "041" "041" "043" "01" "0522" "0422"
#> TCGA.XV.A9VZ.01 TCGA.QB.AA9O.06 TCGA.EB.A44Q.06 TCGA.EB.A44R.06 TCGA.BF.A3DJ.01 TCGA.EE.A3JD.06
#> "01" "03" "04421" "043" "03" "01"
#> TCGA.D3.A51N.06 TCGA.EB.A44N.01 TCGA.EE.A3J3.06 TCGA.XV.A9W5.01 TCGA.D3.A51G.06 TCGA.EB.A4P0.01
#> "041" "01" "03" "041" "03" "03"
#> TCGA.BF.AAP1.01 TCGA.EE.A3J4.06 TCGA.Z2.AA3V.06 TCGA.LH.A9QB.06 TCGA.D3.A51J.06 TCGA.3N.A9WC.06
#> "023" "0511" "01" "023" "04421" "0421"
#> TCGA.DA.A3F8.06 TCGA.D9.A4Z6.06 TCGA.D3.A51R.06 TCGA.EB.A4OZ.01 TCGA.FS.A4FB.06 TCGA.EE.A3JE.06
#> "01" "041" "03" "01" "03" "01"
#> TCGA.W3.AA1W.06 TCGA.DA.A1I0.06 TCGA.D3.A51F.06 TCGA.IH.A3EA.01 TCGA.EB.A431.01 TCGA.EB.A97M.01
#> "01" "041" "01" "0512" "041" "022"
#> TCGA.BF.AAOX.01 TCGA.DA.A3F5.06 TCGA.YD.A9TA.06 TCGA.DA.A3F2.06 TCGA.EB.A44O.01 TCGA.EB.A4IQ.01
#> "041" "0423" "041" "01" "0521" "0421"
#> TCGA.EB.A4IS.01 TCGA.YG.AA3O.06 TCGA.ER.A3EV.06 TCGA.3N.A9WD.06 TCGA.BF.A3DM.01 TCGA.XV.A9W2.01
#> "01" "0512" "043" "01" "03" "0423"
#> TCGA.W3.AA1Q.06 TCGA.WE.AAA0.06 TCGA.W3.AA1R.06 TCGA.EE.A3J5.06 TCGA.EB.A4OY.01 TCGA.FS.A4FD.06
#> "0512" "041" "03" "041" "01" "0422"
#> TCGA.BF.AAP0.06 TCGA.YG.AA3P.06 TCGA.EE.A3JA.06 TCGA.W3.AA21.06 TCGA.WE.AAA3.06 TCGA.FS.A4F4.06
#> "01" "0523" "03" "021" "0423" "03"
#> TCGA.BF.A3DN.01 TCGA.ER.A3ET.06 TCGA.W3.AA1O.06 TCGA.D3.A51E.06 TCGA.Z2.AA3S.06 TCGA.YG.AA3N.01
#> "03" "0423" "0513" "03" "022" "04421"
#> TCGA.WE.AA9Y.06 TCGA.FS.A4F5.06 TCGA.EE.A3J7.06 TCGA.FS.A4F8.06 TCGA.DA.A3F3.06 TCGA.D3.A51H.06
#> "01" "023" "0511" "01" "03" "01"
#> TCGA.BF.A3DL.01 TCGA.D3.A51T.06 TCGA.D3.A51K.06 TCGA.EB.A44P.01 TCGA.D9.A4Z5.01 TCGA.WE.AAA4.06
#> "01" "03" "0522" "0521" "023" "01"
#> TCGA.3N.A9WB.06 TCGA.EE.A3J8.06
#> "022" "021"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 8228))
#> TCGA.FR.A728.01 TCGA.GN.A4U8.11 TCGA.GN.A8LL.06 TCGA.FR.A8YC.06 TCGA.DA.A95X.06 TCGA.ER.A42K.06
#> "01" "01" "03" "022" "021" "03"
#> TCGA.D3.A8GO.06 TCGA.D3.A8GK.06 TCGA.WE.A8JZ.06 TCGA.WE.A8ZO.06 TCGA.D3.A8GI.06 TCGA.FS.A4FC.06
#> "01" "0524" "021" "0511" "0512" "0421"
#> TCGA.FS.A4F2.06 TCGA.WE.A8ZM.06 TCGA.WE.A8ZT.06 TCGA.D3.A8GQ.06 TCGA.D3.A8GB.06 TCGA.DA.A95Y.06
#> "03" "0522" "03" "041" "01" "03"
#> TCGA.EE.A3JI.06 TCGA.OD.A75X.06 TCGA.DA.A960.01 TCGA.D3.A8GV.06 TCGA.WE.A8ZN.06 TCGA.D3.A8GN.06
#> "022" "023" "021" "021" "01" "01"
#> TCGA.EB.A550.01 TCGA.BF.A5EQ.01 TCGA.EB.A3HV.01 TCGA.HR.A5NC.01 TCGA.DA.A95Z.06 TCGA.EB.A6QZ.01
#> "01" "0421" "0521" "0523" "022" "021"
#> TCGA.FW.A3I3.06 TCGA.WE.A8K6.06 TCGA.D3.A8GP.06 TCGA.EB.A42Z.01 TCGA.GN.A4U4.06 TCGA.GF.A4EO.06
#> "023" "03" "022" "023" "021" "01"
#> TCGA.GN.A8LK.06 TCGA.WE.A8K4.01 TCGA.DA.A95W.06 TCGA.FW.A5DX.01 TCGA.GN.A4U3.06 TCGA.EB.A6QY.01
#> "0521" "01" "022" "021" "03" "01"
#> TCGA.EB.A5VU.01 TCGA.Z2.A8RT.06 TCGA.WE.A8K1.06 TCGA.EB.A41B.01 TCGA.WE.A8ZY.06 TCGA.D9.A6EG.06
#> "0443" "03" "01" "03" "021" "022"
#> TCGA.BF.A5ER.01 TCGA.FR.A8YD.06 TCGA.FS.A4F9.06 TCGA.EB.A6R0.01 TCGA.ER.A42L.06 TCGA.D3.A8GJ.06
#> "0512" "0511" "0511" "03" "01" "0442"
#> TCGA.FR.A8YE.06 TCGA.WE.A8ZR.06 TCGA.BF.A9VF.01 TCGA.EE.A3JH.06 TCGA.DA.A95V.06 TCGA.GF.A769.01
#> "01" "043" "0521" "01" "041" "021"
#> TCGA.D9.A4Z2.01 TCGA.FR.A44A.06 TCGA.EB.A5VV.06 TCGA.EE.A180.06 TCGA.D3.A8GC.06 TCGA.WE.A8K5.06
#> "03" "01" "01" "022" "0513" "023"
#> TCGA.GN.A8LN.01 TCGA.EE.A3JB.06 TCGA.D3.A3MO.06 TCGA.ER.A42H.01 TCGA.WE.A8ZX.06 TCGA.GN.A4U5.01
#> "021" "041" "0522" "0511" "041" "01"
#> TCGA.D3.A8GS.06 TCGA.WE.A8ZQ.06 TCGA.EE.A2MF.06 TCGA.D3.A5GU.06 TCGA.GN.A4U8.06 TCGA.EB.A42Y.01
#> "0441" "0523" "022" "0511" "041" "021"
#> TCGA.D3.A3ML.06 TCGA.EB.A551.01 TCGA.D3.A8GM.06 TCGA.D3.A8GL.06 TCGA.D3.A3MU.06 TCGA.FS.A4F0.06
#> "0511" "0442" "041" "022" "022" "022"
#> TCGA.D3.A3MV.06 TCGA.GN.A4U7.06 TCGA.FR.A2OS.01 TCGA.D3.A2JE.06 TCGA.YD.A89C.06 TCGA.FR.A726.01
#> "03" "03" "0523" "0522" "041" "041"
#> TCGA.BF.A5EP.01 TCGA.D3.A3MR.06 TCGA.D3.A8GR.06 TCGA.GN.A4U9.06 TCGA.EB.A6L9.06 TCGA.D3.A5GL.06
#> "03" "01" "0511" "0522" "01" "03"
#> TCGA.EB.A430.01 TCGA.D3.A8GE.06 TCGA.D3.A8GD.06 TCGA.EB.A41A.01 TCGA.W3.A825.06 TCGA.EE.A183.06
#> "01" "01" "01" "022" "0443" "01"
#> TCGA.ER.A2NH.06 TCGA.D3.A5GR.06 TCGA.FR.A729.06 TCGA.D3.A1QA.06 TCGA.FS.A1YY.06 TCGA.EE.A2MK.06
#> "01" "0441" "0441" "021" "03" "03"
#> TCGA.EE.A2M8.06 TCGA.EB.A5KH.06 TCGA.FS.A1ZR.06 TCGA.EE.A3AE.06 TCGA.EE.A29P.06 TCGA.EB.A553.01
#> "01" "021" "0521" "03" "0442" "0513"
#> TCGA.EE.A2MR.06 TCGA.GN.A26A.06 TCGA.FS.A1ZY.06 TCGA.EE.A20I.06 TCGA.DA.A1I5.06 TCGA.EE.A184.06
#> "01" "041" "021" "041" "01" "023"
#> TCGA.EB.A85J.01 TCGA.RP.A6K9.06 TCGA.EE.A17Y.06 TCGA.D9.A149.06 TCGA.ER.A19D.06 TCGA.FS.A1ZZ.06
#> "043" "0423" "041" "0421" "01" "023"
#> TCGA.EE.A2GP.06 TCGA.EE.A3AD.06 TCGA.D3.A1Q9.06 TCGA.GF.A2C7.01 TCGA.BF.A5ES.01 TCGA.ER.A199.06
#> "0524" "021" "041" "0511" "0511" "01"
#> TCGA.EE.A3AH.06 TCGA.W3.A828.06 TCGA.EE.A2A5.06 TCGA.ER.A19L.06 TCGA.BF.A1PX.01 TCGA.ER.A19T.06
#> "021" "01" "0522" "043" "01" "043"
#> TCGA.EB.A51B.01 TCGA.FS.A1ZQ.06 TCGA.D3.A2JG.06 TCGA.EE.A2GH.06 TCGA.ER.A19F.06 TCGA.ER.A196.01
#> "03" "03" "03" "01" "03" "01"
#> TCGA.D3.A2JC.06 TCGA.EE.A3AG.06 TCGA.ER.A19S.06 TCGA.EE.A2GC.06 TCGA.EE.A29N.06 TCGA.FR.A7U8.06
#> "0441" "03" "01" "0524" "01" "023"
#> TCGA.BF.A5EO.01 TCGA.ER.A19B.06 TCGA.D3.A5GN.06 TCGA.D3.A2JB.06 TCGA.ER.A19J.06 TCGA.D3.A2JD.06
#> "041" "03" "03" "01" "023" "01"
#> TCGA.FS.A1Z4.06 TCGA.FR.A7UA.06 TCGA.EE.A2M7.06 TCGA.D3.A1Q3.06 TCGA.EB.A85I.01 TCGA.EB.A82C.01
#> "01" "01" "0441" "043" "0421" "023"
#> TCGA.ER.A19E.06 TCGA.FS.A1ZK.06 TCGA.FS.A1ZU.06 TCGA.EB.A5FP.01 TCGA.EB.A4XL.01 TCGA.DA.A1I2.06
#> "0522" "0524" "0522" "021" "03" "0441"
#> TCGA.EE.A29L.06 TCGA.FS.A1ZN.01 TCGA.EB.A24D.01 TCGA.EE.A2GB.06 TCGA.DA.A1I7.06 TCGA.ER.A2NF.01
#> "021" "021" "0511" "03" "0441" "01"
#> TCGA.GN.A263.01 TCGA.EE.A20C.06 TCGA.EE.A2MQ.06 TCGA.ER.A19N.06 TCGA.FS.A1Z3.06 TCGA.DA.A1I8.06
#> "01" "023" "0512" "01" "03" "03"
#> TCGA.D3.A5GS.06 TCGA.EE.A181.06 TCGA.GN.A268.06 TCGA.W3.A824.06 TCGA.EE.A2GS.06 TCGA.FR.A7U9.06
#> "03" "041" "022" "0511" "03" "01"
#> TCGA.ER.A19Q.06 TCGA.FS.A1ZM.06 TCGA.EE.A2MG.06 TCGA.EE.A2MC.06 TCGA.EE.A17Z.06 TCGA.D3.A2JP.06
#> "01" "0441" "01" "01" "0522" "041"
#> TCGA.ER.A19C.06 TCGA.EB.A82B.01 TCGA.EE.A2A0.06 TCGA.EE.A29G.06 TCGA.D3.A5GO.06 TCGA.GN.A269.01
#> "0443" "0423" "01" "01" "03" "01"
#> TCGA.EE.A2A1.06 TCGA.ER.A1A1.06 TCGA.FS.A1ZG.06 TCGA.FS.A1ZE.06 TCGA.FS.A1ZH.06 TCGA.EE.A2MH.06
#> "01" "01" "022" "022" "041" "01"
#> TCGA.D3.A2J6.06 TCGA.EE.A29Q.06 TCGA.BF.A1PZ.01 TCGA.D3.A3BZ.06 TCGA.D3.A2JO.06 TCGA.GN.A267.06
#> "0423" "03" "03" "01" "0442" "043"
#> TCGA.EE.A2MN.06 TCGA.GN.A264.06 TCGA.ER.A197.06 TCGA.DA.A1IB.06 TCGA.D3.A3CC.06 TCGA.ER.A19T.01
#> "0513" "023" "01" "01" "0423" "0523"
#> TCGA.GN.A261.06 TCGA.FS.A1YW.06 TCGA.BF.A1PU.01 TCGA.D3.A1QB.06 TCGA.D3.A1Q6.06 TCGA.D3.A3C8.06
#> "01" "023" "0443" "01" "0441" "01"
#> TCGA.ER.A19A.06 TCGA.EE.A2GN.06 TCGA.EE.A29M.06 TCGA.D3.A2J7.06 TCGA.EB.A24C.01 TCGA.GN.A262.06
#> "01" "0522" "01" "01" "043" "021"
#> TCGA.EE.A2GD.06 TCGA.D3.A2J9.06 TCGA.EE.A29B.06 TCGA.D9.A1JX.06 TCGA.EE.A29A.06 TCGA.D3.A2JL.06
#> "01" "01" "0511" "03" "022" "041"
#> TCGA.D3.A1Q4.06 TCGA.FS.A1ZS.06 TCGA.D3.A3C3.06 TCGA.D3.A2J8.06 TCGA.FS.A1ZF.06 TCGA.FS.A1ZC.06
#> "01" "0423" "041" "01" "03" "021"
#> TCGA.EE.A20H.06 TCGA.EE.A29W.06 TCGA.D3.A1QA.07 TCGA.BF.A1PV.01 TCGA.EE.A29S.06 TCGA.DA.A1HV.06
#> "0522" "03" "041" "0512" "0442" "03"
#> TCGA.FS.A1Z0.06 TCGA.EE.A2GO.06 TCGA.EB.A1NK.01 TCGA.GN.A26D.06 TCGA.EE.A2MJ.06 TCGA.ER.A198.06
#> "01" "023" "01" "0422" "01" "0512"
#> TCGA.EE.A17X.06 TCGA.EE.A2M5.06 TCGA.GN.A266.06 TCGA.D3.A3C1.06 TCGA.D3.A2JH.06 TCGA.EE.A20F.06
#> "03" "041" "0443" "0442" "01" "041"
#> TCGA.EE.A29E.06 TCGA.ER.A2NG.06 TCGA.ER.A193.06 TCGA.FS.A1ZW.06 TCGA.ER.A19O.06 TCGA.EE.A2ME.06
#> "01" "01" "0421" "041" "0442" "01"
#> TCGA.EE.A20B.06 TCGA.EE.A3AF.06 TCGA.GN.A265.06 TCGA.FS.A1YX.06 TCGA.FS.A1ZJ.06 TCGA.ER.A19H.06
#> "041" "03" "01" "0441" "0523" "03"
#> TCGA.EE.A3AC.06 TCGA.EE.A2MU.06 TCGA.ER.A194.01 TCGA.EE.A2MS.06 TCGA.EE.A29R.06 TCGA.D9.A1X3.06
#> "0521" "01" "0442" "043" "023" "022"
#> TCGA.EE.A29X.06 TCGA.EE.A2GK.06 TCGA.EE.A3AA.06 TCGA.ER.A2NE.06 TCGA.EE.A2GR.06 TCGA.FS.A1ZD.06
#> "0442" "01" "01" "021" "0521" "0523"
#> TCGA.ER.A19P.06 TCGA.D3.A1Q8.06 TCGA.ER.A2NC.06 TCGA.BF.A1Q0.01 TCGA.FS.A1ZP.06 TCGA.EE.A182.06
#> "01" "01" "0443" "0421" "0522" "043"
#> TCGA.D9.A1JW.06 TCGA.D3.A1Q7.06 TCGA.EE.A185.06 TCGA.EE.A2GJ.06 TCGA.D3.A3CB.06 TCGA.EE.A2GU.06
#> "0421" "01" "021" "043" "01" "0421"
#> TCGA.ER.A195.06 TCGA.FS.A1Z7.06 TCGA.EE.A2M6.06 TCGA.ER.A19K.01 TCGA.DA.A1HY.06 TCGA.D3.A3C7.06
#> "01" "0423" "021" "0442" "03" "03"
#> TCGA.EE.A2MP.06 TCGA.EE.A29H.06 TCGA.FR.A3YO.06 TCGA.XV.AB01.01 TCGA.RP.A694.06 TCGA.EB.A5SF.01
#> "03" "03" "0442" "03" "0442" "01"
#> TCGA.ER.A19G.06 TCGA.EE.A2GE.06 TCGA.GF.A3OT.06 TCGA.ER.A2NF.06 TCGA.RP.A695.06 TCGA.BF.AAP7.01
#> "03" "01" "01" "01" "0512" "01"
#> TCGA.EB.A3Y7.01 TCGA.EB.A3XC.01 TCGA.ER.A19W.06 TCGA.FR.A69P.06 TCGA.RP.A693.06 TCGA.FW.A3TV.06
#> "0423" "03" "01" "03" "01" "01"
#> TCGA.FW.A3R5.11 TCGA.FW.A3TU.06 TCGA.BF.AAP8.01 TCGA.EE.A2MM.06 TCGA.DA.A1HW.06 TCGA.DA.A1IC.06
#> "01" "0511" "0422" "0513" "0441" "0521"
#> TCGA.XV.AAZV.01 TCGA.D3.A3C6.06 TCGA.EE.A29C.06 TCGA.BF.AAP2.01 TCGA.EE.A2A2.06 TCGA.GF.A6C8.06
#> "01" "03" "01" "021" "03" "0443"
#> TCGA.RP.A690.06 TCGA.FW.A5DY.06 TCGA.DA.A1I4.06 TCGA.EE.A29V.06 TCGA.GF.A6C9.06 TCGA.EE.A2GT.06
#> "01" "01" "01" "041" "01" "01"
#> TCGA.GN.A9SD.06 TCGA.EE.A3AB.06 TCGA.BF.AAP6.01 TCGA.EB.A5SH.06 TCGA.D9.A6E9.06 TCGA.BF.AAP4.01
#> "01" "041" "03" "043" "0442" "0442"
#> TCGA.EE.A2GM.06 TCGA.D3.A3CF.06 TCGA.D9.A6EC.06 TCGA.DA.A1I1.06 TCGA.HR.A2OH.06 TCGA.EE.A2MT.06
#> "021" "01" "023" "041" "01" "0422"
#> TCGA.ER.A19M.06 TCGA.GN.A26C.01 TCGA.FS.A1ZA.06 TCGA.EB.A5SE.01 TCGA.ER.A3PL.06 TCGA.FR.A3R1.01
#> "041" "01" "0442" "022" "0521" "03"
#> TCGA.EE.A2MI.06 TCGA.D3.A3CE.06 TCGA.D3.A5GT.01 TCGA.ER.A2NB.01 TCGA.D3.A1Q5.06 TCGA.EB.A5UN.06
#> "0443" "0441" "0511" "0421" "0422" "01"
#> TCGA.EB.A299.01 TCGA.DA.A1IA.06 TCGA.EB.A5SG.06 TCGA.D9.A6EA.06 TCGA.XV.AAZY.01 TCGA.EB.A57M.01
#> "03" "0511" "01" "022" "01" "041"
#> TCGA.EE.A2A6.06 TCGA.D3.A2JA.06 TCGA.D3.A1Q1.06 TCGA.EB.A3XF.01 TCGA.D3.A2JF.06 TCGA.XV.AAZW.01
#> "0421" "01" "0422" "03" "03" "03"
#> TCGA.EB.A3Y6.01 TCGA.EB.A3XE.01 TCGA.D9.A3Z4.01 TCGA.FW.A3R5.06 TCGA.EE.A2GI.06 TCGA.EE.A2GL.06
#> "0441" "043" "0523" "043" "041" "01"
#> TCGA.EB.A3XB.01 TCGA.BF.AAOU.01 TCGA.EB.A3XD.01 TCGA.EE.A2MD.06 TCGA.YD.A9TB.06 TCGA.W3.AA1V.06
#> "0442" "01" "01" "0442" "0521" "0441"
#> TCGA.ER.A2ND.06 TCGA.D3.A2JK.06 TCGA.FS.A1ZB.06 TCGA.EE.A29D.06 TCGA.EB.A5UM.01 TCGA.QB.A6FS.06
#> "0521" "041" "01" "022" "043" "01"
#> TCGA.D9.A3Z1.06 TCGA.D3.A2JN.06 TCGA.FR.A3YN.06 TCGA.FS.A1ZT.06 TCGA.D9.A148.06 TCGA.HR.A2OG.06
#> "01" "01" "03" "01" "041" "01"
#> TCGA.EE.A2ML.06 TCGA.EB.A5UL.06 TCGA.EE.A29T.06 TCGA.D9.A3Z3.06 TCGA.D9.A4Z3.01 TCGA.ER.A3ES.06
#> "041" "041" "043" "01" "0522" "0422"
#> TCGA.XV.A9VZ.01 TCGA.QB.AA9O.06 TCGA.EB.A44Q.06 TCGA.EB.A44R.06 TCGA.BF.A3DJ.01 TCGA.EE.A3JD.06
#> "01" "03" "0442" "043" "03" "01"
#> TCGA.D3.A51N.06 TCGA.EB.A44N.01 TCGA.EE.A3J3.06 TCGA.XV.A9W5.01 TCGA.D3.A51G.06 TCGA.EB.A4P0.01
#> "041" "01" "03" "041" "03" "03"
#> TCGA.BF.AAP1.01 TCGA.EE.A3J4.06 TCGA.Z2.AA3V.06 TCGA.LH.A9QB.06 TCGA.D3.A51J.06 TCGA.3N.A9WC.06
#> "023" "0511" "01" "023" "0442" "0421"
#> TCGA.DA.A3F8.06 TCGA.D9.A4Z6.06 TCGA.D3.A51R.06 TCGA.EB.A4OZ.01 TCGA.FS.A4FB.06 TCGA.EE.A3JE.06
#> "01" "041" "03" "01" "03" "01"
#> TCGA.W3.AA1W.06 TCGA.DA.A1I0.06 TCGA.D3.A51F.06 TCGA.IH.A3EA.01 TCGA.EB.A431.01 TCGA.EB.A97M.01
#> "01" "041" "01" "0512" "041" "022"
#> TCGA.BF.AAOX.01 TCGA.DA.A3F5.06 TCGA.YD.A9TA.06 TCGA.DA.A3F2.06 TCGA.EB.A44O.01 TCGA.EB.A4IQ.01
#> "041" "0423" "041" "01" "0521" "0421"
#> TCGA.EB.A4IS.01 TCGA.YG.AA3O.06 TCGA.ER.A3EV.06 TCGA.3N.A9WD.06 TCGA.BF.A3DM.01 TCGA.XV.A9W2.01
#> "01" "0512" "043" "01" "03" "0423"
#> TCGA.W3.AA1Q.06 TCGA.WE.AAA0.06 TCGA.W3.AA1R.06 TCGA.EE.A3J5.06 TCGA.EB.A4OY.01 TCGA.FS.A4FD.06
#> "0512" "041" "03" "041" "01" "0422"
#> TCGA.BF.AAP0.06 TCGA.YG.AA3P.06 TCGA.EE.A3JA.06 TCGA.W3.AA21.06 TCGA.WE.AAA3.06 TCGA.FS.A4F4.06
#> "01" "0523" "03" "021" "0423" "03"
#> TCGA.BF.A3DN.01 TCGA.ER.A3ET.06 TCGA.W3.AA1O.06 TCGA.D3.A51E.06 TCGA.Z2.AA3S.06 TCGA.YG.AA3N.01
#> "03" "0423" "0513" "03" "022" "0442"
#> TCGA.WE.AA9Y.06 TCGA.FS.A4F5.06 TCGA.EE.A3J7.06 TCGA.FS.A4F8.06 TCGA.DA.A3F3.06 TCGA.D3.A51H.06
#> "01" "023" "0511" "01" "03" "01"
#> TCGA.BF.A3DL.01 TCGA.D3.A51T.06 TCGA.D3.A51K.06 TCGA.EB.A44P.01 TCGA.D9.A4Z5.01 TCGA.WE.AAA4.06
#> "01" "03" "0522" "0521" "023" "01"
#> TCGA.3N.A9WB.06 TCGA.EE.A3J8.06
#> "022" "021"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 10240))
#> TCGA.FR.A728.01 TCGA.GN.A4U8.11 TCGA.GN.A8LL.06 TCGA.FR.A8YC.06 TCGA.DA.A95X.06 TCGA.ER.A42K.06
#> "01" "01" "03" "022" "021" "03"
#> TCGA.D3.A8GO.06 TCGA.D3.A8GK.06 TCGA.WE.A8JZ.06 TCGA.WE.A8ZO.06 TCGA.D3.A8GI.06 TCGA.FS.A4FC.06
#> "01" "0524" "021" "0511" "0512" "0421"
#> TCGA.FS.A4F2.06 TCGA.WE.A8ZM.06 TCGA.WE.A8ZT.06 TCGA.D3.A8GQ.06 TCGA.D3.A8GB.06 TCGA.DA.A95Y.06
#> "03" "0522" "03" "041" "01" "03"
#> TCGA.EE.A3JI.06 TCGA.OD.A75X.06 TCGA.DA.A960.01 TCGA.D3.A8GV.06 TCGA.WE.A8ZN.06 TCGA.D3.A8GN.06
#> "022" "023" "021" "021" "01" "01"
#> TCGA.EB.A550.01 TCGA.BF.A5EQ.01 TCGA.EB.A3HV.01 TCGA.HR.A5NC.01 TCGA.DA.A95Z.06 TCGA.EB.A6QZ.01
#> "01" "0421" "0521" "0523" "022" "021"
#> TCGA.FW.A3I3.06 TCGA.WE.A8K6.06 TCGA.D3.A8GP.06 TCGA.EB.A42Z.01 TCGA.GN.A4U4.06 TCGA.GF.A4EO.06
#> "023" "03" "022" "023" "021" "01"
#> TCGA.GN.A8LK.06 TCGA.WE.A8K4.01 TCGA.DA.A95W.06 TCGA.FW.A5DX.01 TCGA.GN.A4U3.06 TCGA.EB.A6QY.01
#> "0521" "01" "022" "021" "03" "01"
#> TCGA.EB.A5VU.01 TCGA.Z2.A8RT.06 TCGA.WE.A8K1.06 TCGA.EB.A41B.01 TCGA.WE.A8ZY.06 TCGA.D9.A6EG.06
#> "044" "03" "01" "03" "021" "022"
#> TCGA.BF.A5ER.01 TCGA.FR.A8YD.06 TCGA.FS.A4F9.06 TCGA.EB.A6R0.01 TCGA.ER.A42L.06 TCGA.D3.A8GJ.06
#> "0512" "0511" "0511" "03" "01" "044"
#> TCGA.FR.A8YE.06 TCGA.WE.A8ZR.06 TCGA.BF.A9VF.01 TCGA.EE.A3JH.06 TCGA.DA.A95V.06 TCGA.GF.A769.01
#> "01" "043" "0521" "01" "041" "021"
#> TCGA.D9.A4Z2.01 TCGA.FR.A44A.06 TCGA.EB.A5VV.06 TCGA.EE.A180.06 TCGA.D3.A8GC.06 TCGA.WE.A8K5.06
#> "03" "01" "01" "022" "0513" "023"
#> TCGA.GN.A8LN.01 TCGA.EE.A3JB.06 TCGA.D3.A3MO.06 TCGA.ER.A42H.01 TCGA.WE.A8ZX.06 TCGA.GN.A4U5.01
#> "021" "041" "0522" "0511" "041" "01"
#> TCGA.D3.A8GS.06 TCGA.WE.A8ZQ.06 TCGA.EE.A2MF.06 TCGA.D3.A5GU.06 TCGA.GN.A4U8.06 TCGA.EB.A42Y.01
#> "044" "0523" "022" "0511" "041" "021"
#> TCGA.D3.A3ML.06 TCGA.EB.A551.01 TCGA.D3.A8GM.06 TCGA.D3.A8GL.06 TCGA.D3.A3MU.06 TCGA.FS.A4F0.06
#> "0511" "044" "041" "022" "022" "022"
#> TCGA.D3.A3MV.06 TCGA.GN.A4U7.06 TCGA.FR.A2OS.01 TCGA.D3.A2JE.06 TCGA.YD.A89C.06 TCGA.FR.A726.01
#> "03" "03" "0523" "0522" "041" "041"
#> TCGA.BF.A5EP.01 TCGA.D3.A3MR.06 TCGA.D3.A8GR.06 TCGA.GN.A4U9.06 TCGA.EB.A6L9.06 TCGA.D3.A5GL.06
#> "03" "01" "0511" "0522" "01" "03"
#> TCGA.EB.A430.01 TCGA.D3.A8GE.06 TCGA.D3.A8GD.06 TCGA.EB.A41A.01 TCGA.W3.A825.06 TCGA.EE.A183.06
#> "01" "01" "01" "022" "044" "01"
#> TCGA.ER.A2NH.06 TCGA.D3.A5GR.06 TCGA.FR.A729.06 TCGA.D3.A1QA.06 TCGA.FS.A1YY.06 TCGA.EE.A2MK.06
#> "01" "044" "044" "021" "03" "03"
#> TCGA.EE.A2M8.06 TCGA.EB.A5KH.06 TCGA.FS.A1ZR.06 TCGA.EE.A3AE.06 TCGA.EE.A29P.06 TCGA.EB.A553.01
#> "01" "021" "0521" "03" "044" "0513"
#> TCGA.EE.A2MR.06 TCGA.GN.A26A.06 TCGA.FS.A1ZY.06 TCGA.EE.A20I.06 TCGA.DA.A1I5.06 TCGA.EE.A184.06
#> "01" "041" "021" "041" "01" "023"
#> TCGA.EB.A85J.01 TCGA.RP.A6K9.06 TCGA.EE.A17Y.06 TCGA.D9.A149.06 TCGA.ER.A19D.06 TCGA.FS.A1ZZ.06
#> "043" "0423" "041" "0421" "01" "023"
#> TCGA.EE.A2GP.06 TCGA.EE.A3AD.06 TCGA.D3.A1Q9.06 TCGA.GF.A2C7.01 TCGA.BF.A5ES.01 TCGA.ER.A199.06
#> "0524" "021" "041" "0511" "0511" "01"
#> TCGA.EE.A3AH.06 TCGA.W3.A828.06 TCGA.EE.A2A5.06 TCGA.ER.A19L.06 TCGA.BF.A1PX.01 TCGA.ER.A19T.06
#> "021" "01" "0522" "043" "01" "043"
#> TCGA.EB.A51B.01 TCGA.FS.A1ZQ.06 TCGA.D3.A2JG.06 TCGA.EE.A2GH.06 TCGA.ER.A19F.06 TCGA.ER.A196.01
#> "03" "03" "03" "01" "03" "01"
#> TCGA.D3.A2JC.06 TCGA.EE.A3AG.06 TCGA.ER.A19S.06 TCGA.EE.A2GC.06 TCGA.EE.A29N.06 TCGA.FR.A7U8.06
#> "044" "03" "01" "0524" "01" "023"
#> TCGA.BF.A5EO.01 TCGA.ER.A19B.06 TCGA.D3.A5GN.06 TCGA.D3.A2JB.06 TCGA.ER.A19J.06 TCGA.D3.A2JD.06
#> "041" "03" "03" "01" "023" "01"
#> TCGA.FS.A1Z4.06 TCGA.FR.A7UA.06 TCGA.EE.A2M7.06 TCGA.D3.A1Q3.06 TCGA.EB.A85I.01 TCGA.EB.A82C.01
#> "01" "01" "044" "043" "0421" "023"
#> TCGA.ER.A19E.06 TCGA.FS.A1ZK.06 TCGA.FS.A1ZU.06 TCGA.EB.A5FP.01 TCGA.EB.A4XL.01 TCGA.DA.A1I2.06
#> "0522" "0524" "0522" "021" "03" "044"
#> TCGA.EE.A29L.06 TCGA.FS.A1ZN.01 TCGA.EB.A24D.01 TCGA.EE.A2GB.06 TCGA.DA.A1I7.06 TCGA.ER.A2NF.01
#> "021" "021" "0511" "03" "044" "01"
#> TCGA.GN.A263.01 TCGA.EE.A20C.06 TCGA.EE.A2MQ.06 TCGA.ER.A19N.06 TCGA.FS.A1Z3.06 TCGA.DA.A1I8.06
#> "01" "023" "0512" "01" "03" "03"
#> TCGA.D3.A5GS.06 TCGA.EE.A181.06 TCGA.GN.A268.06 TCGA.W3.A824.06 TCGA.EE.A2GS.06 TCGA.FR.A7U9.06
#> "03" "041" "022" "0511" "03" "01"
#> TCGA.ER.A19Q.06 TCGA.FS.A1ZM.06 TCGA.EE.A2MG.06 TCGA.EE.A2MC.06 TCGA.EE.A17Z.06 TCGA.D3.A2JP.06
#> "01" "044" "01" "01" "0522" "041"
#> TCGA.ER.A19C.06 TCGA.EB.A82B.01 TCGA.EE.A2A0.06 TCGA.EE.A29G.06 TCGA.D3.A5GO.06 TCGA.GN.A269.01
#> "044" "0423" "01" "01" "03" "01"
#> TCGA.EE.A2A1.06 TCGA.ER.A1A1.06 TCGA.FS.A1ZG.06 TCGA.FS.A1ZE.06 TCGA.FS.A1ZH.06 TCGA.EE.A2MH.06
#> "01" "01" "022" "022" "041" "01"
#> TCGA.D3.A2J6.06 TCGA.EE.A29Q.06 TCGA.BF.A1PZ.01 TCGA.D3.A3BZ.06 TCGA.D3.A2JO.06 TCGA.GN.A267.06
#> "0423" "03" "03" "01" "044" "043"
#> TCGA.EE.A2MN.06 TCGA.GN.A264.06 TCGA.ER.A197.06 TCGA.DA.A1IB.06 TCGA.D3.A3CC.06 TCGA.ER.A19T.01
#> "0513" "023" "01" "01" "0423" "0523"
#> TCGA.GN.A261.06 TCGA.FS.A1YW.06 TCGA.BF.A1PU.01 TCGA.D3.A1QB.06 TCGA.D3.A1Q6.06 TCGA.D3.A3C8.06
#> "01" "023" "044" "01" "044" "01"
#> TCGA.ER.A19A.06 TCGA.EE.A2GN.06 TCGA.EE.A29M.06 TCGA.D3.A2J7.06 TCGA.EB.A24C.01 TCGA.GN.A262.06
#> "01" "0522" "01" "01" "043" "021"
#> TCGA.EE.A2GD.06 TCGA.D3.A2J9.06 TCGA.EE.A29B.06 TCGA.D9.A1JX.06 TCGA.EE.A29A.06 TCGA.D3.A2JL.06
#> "01" "01" "0511" "03" "022" "041"
#> TCGA.D3.A1Q4.06 TCGA.FS.A1ZS.06 TCGA.D3.A3C3.06 TCGA.D3.A2J8.06 TCGA.FS.A1ZF.06 TCGA.FS.A1ZC.06
#> "01" "0423" "041" "01" "03" "021"
#> TCGA.EE.A20H.06 TCGA.EE.A29W.06 TCGA.D3.A1QA.07 TCGA.BF.A1PV.01 TCGA.EE.A29S.06 TCGA.DA.A1HV.06
#> "0522" "03" "041" "0512" "044" "03"
#> TCGA.FS.A1Z0.06 TCGA.EE.A2GO.06 TCGA.EB.A1NK.01 TCGA.GN.A26D.06 TCGA.EE.A2MJ.06 TCGA.ER.A198.06
#> "01" "023" "01" "0422" "01" "0512"
#> TCGA.EE.A17X.06 TCGA.EE.A2M5.06 TCGA.GN.A266.06 TCGA.D3.A3C1.06 TCGA.D3.A2JH.06 TCGA.EE.A20F.06
#> "03" "041" "044" "044" "01" "041"
#> TCGA.EE.A29E.06 TCGA.ER.A2NG.06 TCGA.ER.A193.06 TCGA.FS.A1ZW.06 TCGA.ER.A19O.06 TCGA.EE.A2ME.06
#> "01" "01" "0421" "041" "044" "01"
#> TCGA.EE.A20B.06 TCGA.EE.A3AF.06 TCGA.GN.A265.06 TCGA.FS.A1YX.06 TCGA.FS.A1ZJ.06 TCGA.ER.A19H.06
#> "041" "03" "01" "044" "0523" "03"
#> TCGA.EE.A3AC.06 TCGA.EE.A2MU.06 TCGA.ER.A194.01 TCGA.EE.A2MS.06 TCGA.EE.A29R.06 TCGA.D9.A1X3.06
#> "0521" "01" "044" "043" "023" "022"
#> TCGA.EE.A29X.06 TCGA.EE.A2GK.06 TCGA.EE.A3AA.06 TCGA.ER.A2NE.06 TCGA.EE.A2GR.06 TCGA.FS.A1ZD.06
#> "044" "01" "01" "021" "0521" "0523"
#> TCGA.ER.A19P.06 TCGA.D3.A1Q8.06 TCGA.ER.A2NC.06 TCGA.BF.A1Q0.01 TCGA.FS.A1ZP.06 TCGA.EE.A182.06
#> "01" "01" "044" "0421" "0522" "043"
#> TCGA.D9.A1JW.06 TCGA.D3.A1Q7.06 TCGA.EE.A185.06 TCGA.EE.A2GJ.06 TCGA.D3.A3CB.06 TCGA.EE.A2GU.06
#> "0421" "01" "021" "043" "01" "0421"
#> TCGA.ER.A195.06 TCGA.FS.A1Z7.06 TCGA.EE.A2M6.06 TCGA.ER.A19K.01 TCGA.DA.A1HY.06 TCGA.D3.A3C7.06
#> "01" "0423" "021" "044" "03" "03"
#> TCGA.EE.A2MP.06 TCGA.EE.A29H.06 TCGA.FR.A3YO.06 TCGA.XV.AB01.01 TCGA.RP.A694.06 TCGA.EB.A5SF.01
#> "03" "03" "044" "03" "044" "01"
#> TCGA.ER.A19G.06 TCGA.EE.A2GE.06 TCGA.GF.A3OT.06 TCGA.ER.A2NF.06 TCGA.RP.A695.06 TCGA.BF.AAP7.01
#> "03" "01" "01" "01" "0512" "01"
#> TCGA.EB.A3Y7.01 TCGA.EB.A3XC.01 TCGA.ER.A19W.06 TCGA.FR.A69P.06 TCGA.RP.A693.06 TCGA.FW.A3TV.06
#> "0423" "03" "01" "03" "01" "01"
#> TCGA.FW.A3R5.11 TCGA.FW.A3TU.06 TCGA.BF.AAP8.01 TCGA.EE.A2MM.06 TCGA.DA.A1HW.06 TCGA.DA.A1IC.06
#> "01" "0511" "0422" "0513" "044" "0521"
#> TCGA.XV.AAZV.01 TCGA.D3.A3C6.06 TCGA.EE.A29C.06 TCGA.BF.AAP2.01 TCGA.EE.A2A2.06 TCGA.GF.A6C8.06
#> "01" "03" "01" "021" "03" "044"
#> TCGA.RP.A690.06 TCGA.FW.A5DY.06 TCGA.DA.A1I4.06 TCGA.EE.A29V.06 TCGA.GF.A6C9.06 TCGA.EE.A2GT.06
#> "01" "01" "01" "041" "01" "01"
#> TCGA.GN.A9SD.06 TCGA.EE.A3AB.06 TCGA.BF.AAP6.01 TCGA.EB.A5SH.06 TCGA.D9.A6E9.06 TCGA.BF.AAP4.01
#> "01" "041" "03" "043" "044" "044"
#> TCGA.EE.A2GM.06 TCGA.D3.A3CF.06 TCGA.D9.A6EC.06 TCGA.DA.A1I1.06 TCGA.HR.A2OH.06 TCGA.EE.A2MT.06
#> "021" "01" "023" "041" "01" "0422"
#> TCGA.ER.A19M.06 TCGA.GN.A26C.01 TCGA.FS.A1ZA.06 TCGA.EB.A5SE.01 TCGA.ER.A3PL.06 TCGA.FR.A3R1.01
#> "041" "01" "044" "022" "0521" "03"
#> TCGA.EE.A2MI.06 TCGA.D3.A3CE.06 TCGA.D3.A5GT.01 TCGA.ER.A2NB.01 TCGA.D3.A1Q5.06 TCGA.EB.A5UN.06
#> "044" "044" "0511" "0421" "0422" "01"
#> TCGA.EB.A299.01 TCGA.DA.A1IA.06 TCGA.EB.A5SG.06 TCGA.D9.A6EA.06 TCGA.XV.AAZY.01 TCGA.EB.A57M.01
#> "03" "0511" "01" "022" "01" "041"
#> TCGA.EE.A2A6.06 TCGA.D3.A2JA.06 TCGA.D3.A1Q1.06 TCGA.EB.A3XF.01 TCGA.D3.A2JF.06 TCGA.XV.AAZW.01
#> "0421" "01" "0422" "03" "03" "03"
#> TCGA.EB.A3Y6.01 TCGA.EB.A3XE.01 TCGA.D9.A3Z4.01 TCGA.FW.A3R5.06 TCGA.EE.A2GI.06 TCGA.EE.A2GL.06
#> "044" "043" "0523" "043" "041" "01"
#> TCGA.EB.A3XB.01 TCGA.BF.AAOU.01 TCGA.EB.A3XD.01 TCGA.EE.A2MD.06 TCGA.YD.A9TB.06 TCGA.W3.AA1V.06
#> "044" "01" "01" "044" "0521" "044"
#> TCGA.ER.A2ND.06 TCGA.D3.A2JK.06 TCGA.FS.A1ZB.06 TCGA.EE.A29D.06 TCGA.EB.A5UM.01 TCGA.QB.A6FS.06
#> "0521" "041" "01" "022" "043" "01"
#> TCGA.D9.A3Z1.06 TCGA.D3.A2JN.06 TCGA.FR.A3YN.06 TCGA.FS.A1ZT.06 TCGA.D9.A148.06 TCGA.HR.A2OG.06
#> "01" "01" "03" "01" "041" "01"
#> TCGA.EE.A2ML.06 TCGA.EB.A5UL.06 TCGA.EE.A29T.06 TCGA.D9.A3Z3.06 TCGA.D9.A4Z3.01 TCGA.ER.A3ES.06
#> "041" "041" "043" "01" "0522" "0422"
#> TCGA.XV.A9VZ.01 TCGA.QB.AA9O.06 TCGA.EB.A44Q.06 TCGA.EB.A44R.06 TCGA.BF.A3DJ.01 TCGA.EE.A3JD.06
#> "01" "03" "044" "043" "03" "01"
#> TCGA.D3.A51N.06 TCGA.EB.A44N.01 TCGA.EE.A3J3.06 TCGA.XV.A9W5.01 TCGA.D3.A51G.06 TCGA.EB.A4P0.01
#> "041" "01" "03" "041" "03" "03"
#> TCGA.BF.AAP1.01 TCGA.EE.A3J4.06 TCGA.Z2.AA3V.06 TCGA.LH.A9QB.06 TCGA.D3.A51J.06 TCGA.3N.A9WC.06
#> "023" "0511" "01" "023" "044" "0421"
#> TCGA.DA.A3F8.06 TCGA.D9.A4Z6.06 TCGA.D3.A51R.06 TCGA.EB.A4OZ.01 TCGA.FS.A4FB.06 TCGA.EE.A3JE.06
#> "01" "041" "03" "01" "03" "01"
#> TCGA.W3.AA1W.06 TCGA.DA.A1I0.06 TCGA.D3.A51F.06 TCGA.IH.A3EA.01 TCGA.EB.A431.01 TCGA.EB.A97M.01
#> "01" "041" "01" "0512" "041" "022"
#> TCGA.BF.AAOX.01 TCGA.DA.A3F5.06 TCGA.YD.A9TA.06 TCGA.DA.A3F2.06 TCGA.EB.A44O.01 TCGA.EB.A4IQ.01
#> "041" "0423" "041" "01" "0521" "0421"
#> TCGA.EB.A4IS.01 TCGA.YG.AA3O.06 TCGA.ER.A3EV.06 TCGA.3N.A9WD.06 TCGA.BF.A3DM.01 TCGA.XV.A9W2.01
#> "01" "0512" "043" "01" "03" "0423"
#> TCGA.W3.AA1Q.06 TCGA.WE.AAA0.06 TCGA.W3.AA1R.06 TCGA.EE.A3J5.06 TCGA.EB.A4OY.01 TCGA.FS.A4FD.06
#> "0512" "041" "03" "041" "01" "0422"
#> TCGA.BF.AAP0.06 TCGA.YG.AA3P.06 TCGA.EE.A3JA.06 TCGA.W3.AA21.06 TCGA.WE.AAA3.06 TCGA.FS.A4F4.06
#> "01" "0523" "03" "021" "0423" "03"
#> TCGA.BF.A3DN.01 TCGA.ER.A3ET.06 TCGA.W3.AA1O.06 TCGA.D3.A51E.06 TCGA.Z2.AA3S.06 TCGA.YG.AA3N.01
#> "03" "0423" "0513" "03" "022" "044"
#> TCGA.WE.AA9Y.06 TCGA.FS.A4F5.06 TCGA.EE.A3J7.06 TCGA.FS.A4F8.06 TCGA.DA.A3F3.06 TCGA.D3.A51H.06
#> "01" "023" "0511" "01" "03" "01"
#> TCGA.BF.A3DL.01 TCGA.D3.A51T.06 TCGA.D3.A51K.06 TCGA.EB.A44P.01 TCGA.D9.A4Z5.01 TCGA.WE.AAA4.06
#> "01" "03" "0522" "0521" "023" "01"
#> TCGA.3N.A9WB.06 TCGA.EE.A3J8.06
#> "022" "021"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 11354))
#> TCGA.FR.A728.01 TCGA.GN.A4U8.11 TCGA.GN.A8LL.06 TCGA.FR.A8YC.06 TCGA.DA.A95X.06 TCGA.ER.A42K.06
#> "01" "01" "03" "022" "021" "03"
#> TCGA.D3.A8GO.06 TCGA.D3.A8GK.06 TCGA.WE.A8JZ.06 TCGA.WE.A8ZO.06 TCGA.D3.A8GI.06 TCGA.FS.A4FC.06
#> "01" "05" "021" "05" "05" "0421"
#> TCGA.FS.A4F2.06 TCGA.WE.A8ZM.06 TCGA.WE.A8ZT.06 TCGA.D3.A8GQ.06 TCGA.D3.A8GB.06 TCGA.DA.A95Y.06
#> "03" "05" "03" "041" "01" "03"
#> TCGA.EE.A3JI.06 TCGA.OD.A75X.06 TCGA.DA.A960.01 TCGA.D3.A8GV.06 TCGA.WE.A8ZN.06 TCGA.D3.A8GN.06
#> "022" "023" "021" "021" "01" "01"
#> TCGA.EB.A550.01 TCGA.BF.A5EQ.01 TCGA.EB.A3HV.01 TCGA.HR.A5NC.01 TCGA.DA.A95Z.06 TCGA.EB.A6QZ.01
#> "01" "0421" "05" "05" "022" "021"
#> TCGA.FW.A3I3.06 TCGA.WE.A8K6.06 TCGA.D3.A8GP.06 TCGA.EB.A42Z.01 TCGA.GN.A4U4.06 TCGA.GF.A4EO.06
#> "023" "03" "022" "023" "021" "01"
#> TCGA.GN.A8LK.06 TCGA.WE.A8K4.01 TCGA.DA.A95W.06 TCGA.FW.A5DX.01 TCGA.GN.A4U3.06 TCGA.EB.A6QY.01
#> "05" "01" "022" "021" "03" "01"
#> TCGA.EB.A5VU.01 TCGA.Z2.A8RT.06 TCGA.WE.A8K1.06 TCGA.EB.A41B.01 TCGA.WE.A8ZY.06 TCGA.D9.A6EG.06
#> "044" "03" "01" "03" "021" "022"
#> TCGA.BF.A5ER.01 TCGA.FR.A8YD.06 TCGA.FS.A4F9.06 TCGA.EB.A6R0.01 TCGA.ER.A42L.06 TCGA.D3.A8GJ.06
#> "05" "05" "05" "03" "01" "044"
#> TCGA.FR.A8YE.06 TCGA.WE.A8ZR.06 TCGA.BF.A9VF.01 TCGA.EE.A3JH.06 TCGA.DA.A95V.06 TCGA.GF.A769.01
#> "01" "043" "05" "01" "041" "021"
#> TCGA.D9.A4Z2.01 TCGA.FR.A44A.06 TCGA.EB.A5VV.06 TCGA.EE.A180.06 TCGA.D3.A8GC.06 TCGA.WE.A8K5.06
#> "03" "01" "01" "022" "05" "023"
#> TCGA.GN.A8LN.01 TCGA.EE.A3JB.06 TCGA.D3.A3MO.06 TCGA.ER.A42H.01 TCGA.WE.A8ZX.06 TCGA.GN.A4U5.01
#> "021" "041" "05" "05" "041" "01"
#> TCGA.D3.A8GS.06 TCGA.WE.A8ZQ.06 TCGA.EE.A2MF.06 TCGA.D3.A5GU.06 TCGA.GN.A4U8.06 TCGA.EB.A42Y.01
#> "044" "05" "022" "05" "041" "021"
#> TCGA.D3.A3ML.06 TCGA.EB.A551.01 TCGA.D3.A8GM.06 TCGA.D3.A8GL.06 TCGA.D3.A3MU.06 TCGA.FS.A4F0.06
#> "05" "044" "041" "022" "022" "022"
#> TCGA.D3.A3MV.06 TCGA.GN.A4U7.06 TCGA.FR.A2OS.01 TCGA.D3.A2JE.06 TCGA.YD.A89C.06 TCGA.FR.A726.01
#> "03" "03" "05" "05" "041" "041"
#> TCGA.BF.A5EP.01 TCGA.D3.A3MR.06 TCGA.D3.A8GR.06 TCGA.GN.A4U9.06 TCGA.EB.A6L9.06 TCGA.D3.A5GL.06
#> "03" "01" "05" "05" "01" "03"
#> TCGA.EB.A430.01 TCGA.D3.A8GE.06 TCGA.D3.A8GD.06 TCGA.EB.A41A.01 TCGA.W3.A825.06 TCGA.EE.A183.06
#> "01" "01" "01" "022" "044" "01"
#> TCGA.ER.A2NH.06 TCGA.D3.A5GR.06 TCGA.FR.A729.06 TCGA.D3.A1QA.06 TCGA.FS.A1YY.06 TCGA.EE.A2MK.06
#> "01" "044" "044" "021" "03" "03"
#> TCGA.EE.A2M8.06 TCGA.EB.A5KH.06 TCGA.FS.A1ZR.06 TCGA.EE.A3AE.06 TCGA.EE.A29P.06 TCGA.EB.A553.01
#> "01" "021" "05" "03" "044" "05"
#> TCGA.EE.A2MR.06 TCGA.GN.A26A.06 TCGA.FS.A1ZY.06 TCGA.EE.A20I.06 TCGA.DA.A1I5.06 TCGA.EE.A184.06
#> "01" "041" "021" "041" "01" "023"
#> TCGA.EB.A85J.01 TCGA.RP.A6K9.06 TCGA.EE.A17Y.06 TCGA.D9.A149.06 TCGA.ER.A19D.06 TCGA.FS.A1ZZ.06
#> "043" "0423" "041" "0421" "01" "023"
#> TCGA.EE.A2GP.06 TCGA.EE.A3AD.06 TCGA.D3.A1Q9.06 TCGA.GF.A2C7.01 TCGA.BF.A5ES.01 TCGA.ER.A199.06
#> "05" "021" "041" "05" "05" "01"
#> TCGA.EE.A3AH.06 TCGA.W3.A828.06 TCGA.EE.A2A5.06 TCGA.ER.A19L.06 TCGA.BF.A1PX.01 TCGA.ER.A19T.06
#> "021" "01" "05" "043" "01" "043"
#> TCGA.EB.A51B.01 TCGA.FS.A1ZQ.06 TCGA.D3.A2JG.06 TCGA.EE.A2GH.06 TCGA.ER.A19F.06 TCGA.ER.A196.01
#> "03" "03" "03" "01" "03" "01"
#> TCGA.D3.A2JC.06 TCGA.EE.A3AG.06 TCGA.ER.A19S.06 TCGA.EE.A2GC.06 TCGA.EE.A29N.06 TCGA.FR.A7U8.06
#> "044" "03" "01" "05" "01" "023"
#> TCGA.BF.A5EO.01 TCGA.ER.A19B.06 TCGA.D3.A5GN.06 TCGA.D3.A2JB.06 TCGA.ER.A19J.06 TCGA.D3.A2JD.06
#> "041" "03" "03" "01" "023" "01"
#> TCGA.FS.A1Z4.06 TCGA.FR.A7UA.06 TCGA.EE.A2M7.06 TCGA.D3.A1Q3.06 TCGA.EB.A85I.01 TCGA.EB.A82C.01
#> "01" "01" "044" "043" "0421" "023"
#> TCGA.ER.A19E.06 TCGA.FS.A1ZK.06 TCGA.FS.A1ZU.06 TCGA.EB.A5FP.01 TCGA.EB.A4XL.01 TCGA.DA.A1I2.06
#> "05" "05" "05" "021" "03" "044"
#> TCGA.EE.A29L.06 TCGA.FS.A1ZN.01 TCGA.EB.A24D.01 TCGA.EE.A2GB.06 TCGA.DA.A1I7.06 TCGA.ER.A2NF.01
#> "021" "021" "05" "03" "044" "01"
#> TCGA.GN.A263.01 TCGA.EE.A20C.06 TCGA.EE.A2MQ.06 TCGA.ER.A19N.06 TCGA.FS.A1Z3.06 TCGA.DA.A1I8.06
#> "01" "023" "05" "01" "03" "03"
#> TCGA.D3.A5GS.06 TCGA.EE.A181.06 TCGA.GN.A268.06 TCGA.W3.A824.06 TCGA.EE.A2GS.06 TCGA.FR.A7U9.06
#> "03" "041" "022" "05" "03" "01"
#> TCGA.ER.A19Q.06 TCGA.FS.A1ZM.06 TCGA.EE.A2MG.06 TCGA.EE.A2MC.06 TCGA.EE.A17Z.06 TCGA.D3.A2JP.06
#> "01" "044" "01" "01" "05" "041"
#> TCGA.ER.A19C.06 TCGA.EB.A82B.01 TCGA.EE.A2A0.06 TCGA.EE.A29G.06 TCGA.D3.A5GO.06 TCGA.GN.A269.01
#> "044" "0423" "01" "01" "03" "01"
#> TCGA.EE.A2A1.06 TCGA.ER.A1A1.06 TCGA.FS.A1ZG.06 TCGA.FS.A1ZE.06 TCGA.FS.A1ZH.06 TCGA.EE.A2MH.06
#> "01" "01" "022" "022" "041" "01"
#> TCGA.D3.A2J6.06 TCGA.EE.A29Q.06 TCGA.BF.A1PZ.01 TCGA.D3.A3BZ.06 TCGA.D3.A2JO.06 TCGA.GN.A267.06
#> "0423" "03" "03" "01" "044" "043"
#> TCGA.EE.A2MN.06 TCGA.GN.A264.06 TCGA.ER.A197.06 TCGA.DA.A1IB.06 TCGA.D3.A3CC.06 TCGA.ER.A19T.01
#> "05" "023" "01" "01" "0423" "05"
#> TCGA.GN.A261.06 TCGA.FS.A1YW.06 TCGA.BF.A1PU.01 TCGA.D3.A1QB.06 TCGA.D3.A1Q6.06 TCGA.D3.A3C8.06
#> "01" "023" "044" "01" "044" "01"
#> TCGA.ER.A19A.06 TCGA.EE.A2GN.06 TCGA.EE.A29M.06 TCGA.D3.A2J7.06 TCGA.EB.A24C.01 TCGA.GN.A262.06
#> "01" "05" "01" "01" "043" "021"
#> TCGA.EE.A2GD.06 TCGA.D3.A2J9.06 TCGA.EE.A29B.06 TCGA.D9.A1JX.06 TCGA.EE.A29A.06 TCGA.D3.A2JL.06
#> "01" "01" "05" "03" "022" "041"
#> TCGA.D3.A1Q4.06 TCGA.FS.A1ZS.06 TCGA.D3.A3C3.06 TCGA.D3.A2J8.06 TCGA.FS.A1ZF.06 TCGA.FS.A1ZC.06
#> "01" "0423" "041" "01" "03" "021"
#> TCGA.EE.A20H.06 TCGA.EE.A29W.06 TCGA.D3.A1QA.07 TCGA.BF.A1PV.01 TCGA.EE.A29S.06 TCGA.DA.A1HV.06
#> "05" "03" "041" "05" "044" "03"
#> TCGA.FS.A1Z0.06 TCGA.EE.A2GO.06 TCGA.EB.A1NK.01 TCGA.GN.A26D.06 TCGA.EE.A2MJ.06 TCGA.ER.A198.06
#> "01" "023" "01" "0422" "01" "05"
#> TCGA.EE.A17X.06 TCGA.EE.A2M5.06 TCGA.GN.A266.06 TCGA.D3.A3C1.06 TCGA.D3.A2JH.06 TCGA.EE.A20F.06
#> "03" "041" "044" "044" "01" "041"
#> TCGA.EE.A29E.06 TCGA.ER.A2NG.06 TCGA.ER.A193.06 TCGA.FS.A1ZW.06 TCGA.ER.A19O.06 TCGA.EE.A2ME.06
#> "01" "01" "0421" "041" "044" "01"
#> TCGA.EE.A20B.06 TCGA.EE.A3AF.06 TCGA.GN.A265.06 TCGA.FS.A1YX.06 TCGA.FS.A1ZJ.06 TCGA.ER.A19H.06
#> "041" "03" "01" "044" "05" "03"
#> TCGA.EE.A3AC.06 TCGA.EE.A2MU.06 TCGA.ER.A194.01 TCGA.EE.A2MS.06 TCGA.EE.A29R.06 TCGA.D9.A1X3.06
#> "05" "01" "044" "043" "023" "022"
#> TCGA.EE.A29X.06 TCGA.EE.A2GK.06 TCGA.EE.A3AA.06 TCGA.ER.A2NE.06 TCGA.EE.A2GR.06 TCGA.FS.A1ZD.06
#> "044" "01" "01" "021" "05" "05"
#> TCGA.ER.A19P.06 TCGA.D3.A1Q8.06 TCGA.ER.A2NC.06 TCGA.BF.A1Q0.01 TCGA.FS.A1ZP.06 TCGA.EE.A182.06
#> "01" "01" "044" "0421" "05" "043"
#> TCGA.D9.A1JW.06 TCGA.D3.A1Q7.06 TCGA.EE.A185.06 TCGA.EE.A2GJ.06 TCGA.D3.A3CB.06 TCGA.EE.A2GU.06
#> "0421" "01" "021" "043" "01" "0421"
#> TCGA.ER.A195.06 TCGA.FS.A1Z7.06 TCGA.EE.A2M6.06 TCGA.ER.A19K.01 TCGA.DA.A1HY.06 TCGA.D3.A3C7.06
#> "01" "0423" "021" "044" "03" "03"
#> TCGA.EE.A2MP.06 TCGA.EE.A29H.06 TCGA.FR.A3YO.06 TCGA.XV.AB01.01 TCGA.RP.A694.06 TCGA.EB.A5SF.01
#> "03" "03" "044" "03" "044" "01"
#> TCGA.ER.A19G.06 TCGA.EE.A2GE.06 TCGA.GF.A3OT.06 TCGA.ER.A2NF.06 TCGA.RP.A695.06 TCGA.BF.AAP7.01
#> "03" "01" "01" "01" "05" "01"
#> TCGA.EB.A3Y7.01 TCGA.EB.A3XC.01 TCGA.ER.A19W.06 TCGA.FR.A69P.06 TCGA.RP.A693.06 TCGA.FW.A3TV.06
#> "0423" "03" "01" "03" "01" "01"
#> TCGA.FW.A3R5.11 TCGA.FW.A3TU.06 TCGA.BF.AAP8.01 TCGA.EE.A2MM.06 TCGA.DA.A1HW.06 TCGA.DA.A1IC.06
#> "01" "05" "0422" "05" "044" "05"
#> TCGA.XV.AAZV.01 TCGA.D3.A3C6.06 TCGA.EE.A29C.06 TCGA.BF.AAP2.01 TCGA.EE.A2A2.06 TCGA.GF.A6C8.06
#> "01" "03" "01" "021" "03" "044"
#> TCGA.RP.A690.06 TCGA.FW.A5DY.06 TCGA.DA.A1I4.06 TCGA.EE.A29V.06 TCGA.GF.A6C9.06 TCGA.EE.A2GT.06
#> "01" "01" "01" "041" "01" "01"
#> TCGA.GN.A9SD.06 TCGA.EE.A3AB.06 TCGA.BF.AAP6.01 TCGA.EB.A5SH.06 TCGA.D9.A6E9.06 TCGA.BF.AAP4.01
#> "01" "041" "03" "043" "044" "044"
#> TCGA.EE.A2GM.06 TCGA.D3.A3CF.06 TCGA.D9.A6EC.06 TCGA.DA.A1I1.06 TCGA.HR.A2OH.06 TCGA.EE.A2MT.06
#> "021" "01" "023" "041" "01" "0422"
#> TCGA.ER.A19M.06 TCGA.GN.A26C.01 TCGA.FS.A1ZA.06 TCGA.EB.A5SE.01 TCGA.ER.A3PL.06 TCGA.FR.A3R1.01
#> "041" "01" "044" "022" "05" "03"
#> TCGA.EE.A2MI.06 TCGA.D3.A3CE.06 TCGA.D3.A5GT.01 TCGA.ER.A2NB.01 TCGA.D3.A1Q5.06 TCGA.EB.A5UN.06
#> "044" "044" "05" "0421" "0422" "01"
#> TCGA.EB.A299.01 TCGA.DA.A1IA.06 TCGA.EB.A5SG.06 TCGA.D9.A6EA.06 TCGA.XV.AAZY.01 TCGA.EB.A57M.01
#> "03" "05" "01" "022" "01" "041"
#> TCGA.EE.A2A6.06 TCGA.D3.A2JA.06 TCGA.D3.A1Q1.06 TCGA.EB.A3XF.01 TCGA.D3.A2JF.06 TCGA.XV.AAZW.01
#> "0421" "01" "0422" "03" "03" "03"
#> TCGA.EB.A3Y6.01 TCGA.EB.A3XE.01 TCGA.D9.A3Z4.01 TCGA.FW.A3R5.06 TCGA.EE.A2GI.06 TCGA.EE.A2GL.06
#> "044" "043" "05" "043" "041" "01"
#> TCGA.EB.A3XB.01 TCGA.BF.AAOU.01 TCGA.EB.A3XD.01 TCGA.EE.A2MD.06 TCGA.YD.A9TB.06 TCGA.W3.AA1V.06
#> "044" "01" "01" "044" "05" "044"
#> TCGA.ER.A2ND.06 TCGA.D3.A2JK.06 TCGA.FS.A1ZB.06 TCGA.EE.A29D.06 TCGA.EB.A5UM.01 TCGA.QB.A6FS.06
#> "05" "041" "01" "022" "043" "01"
#> TCGA.D9.A3Z1.06 TCGA.D3.A2JN.06 TCGA.FR.A3YN.06 TCGA.FS.A1ZT.06 TCGA.D9.A148.06 TCGA.HR.A2OG.06
#> "01" "01" "03" "01" "041" "01"
#> TCGA.EE.A2ML.06 TCGA.EB.A5UL.06 TCGA.EE.A29T.06 TCGA.D9.A3Z3.06 TCGA.D9.A4Z3.01 TCGA.ER.A3ES.06
#> "041" "041" "043" "01" "05" "0422"
#> TCGA.XV.A9VZ.01 TCGA.QB.AA9O.06 TCGA.EB.A44Q.06 TCGA.EB.A44R.06 TCGA.BF.A3DJ.01 TCGA.EE.A3JD.06
#> "01" "03" "044" "043" "03" "01"
#> TCGA.D3.A51N.06 TCGA.EB.A44N.01 TCGA.EE.A3J3.06 TCGA.XV.A9W5.01 TCGA.D3.A51G.06 TCGA.EB.A4P0.01
#> "041" "01" "03" "041" "03" "03"
#> TCGA.BF.AAP1.01 TCGA.EE.A3J4.06 TCGA.Z2.AA3V.06 TCGA.LH.A9QB.06 TCGA.D3.A51J.06 TCGA.3N.A9WC.06
#> "023" "05" "01" "023" "044" "0421"
#> TCGA.DA.A3F8.06 TCGA.D9.A4Z6.06 TCGA.D3.A51R.06 TCGA.EB.A4OZ.01 TCGA.FS.A4FB.06 TCGA.EE.A3JE.06
#> "01" "041" "03" "01" "03" "01"
#> TCGA.W3.AA1W.06 TCGA.DA.A1I0.06 TCGA.D3.A51F.06 TCGA.IH.A3EA.01 TCGA.EB.A431.01 TCGA.EB.A97M.01
#> "01" "041" "01" "05" "041" "022"
#> TCGA.BF.AAOX.01 TCGA.DA.A3F5.06 TCGA.YD.A9TA.06 TCGA.DA.A3F2.06 TCGA.EB.A44O.01 TCGA.EB.A4IQ.01
#> "041" "0423" "041" "01" "05" "0421"
#> TCGA.EB.A4IS.01 TCGA.YG.AA3O.06 TCGA.ER.A3EV.06 TCGA.3N.A9WD.06 TCGA.BF.A3DM.01 TCGA.XV.A9W2.01
#> "01" "05" "043" "01" "03" "0423"
#> TCGA.W3.AA1Q.06 TCGA.WE.AAA0.06 TCGA.W3.AA1R.06 TCGA.EE.A3J5.06 TCGA.EB.A4OY.01 TCGA.FS.A4FD.06
#> "05" "041" "03" "041" "01" "0422"
#> TCGA.BF.AAP0.06 TCGA.YG.AA3P.06 TCGA.EE.A3JA.06 TCGA.W3.AA21.06 TCGA.WE.AAA3.06 TCGA.FS.A4F4.06
#> "01" "05" "03" "021" "0423" "03"
#> TCGA.BF.A3DN.01 TCGA.ER.A3ET.06 TCGA.W3.AA1O.06 TCGA.D3.A51E.06 TCGA.Z2.AA3S.06 TCGA.YG.AA3N.01
#> "03" "0423" "05" "03" "022" "044"
#> TCGA.WE.AA9Y.06 TCGA.FS.A4F5.06 TCGA.EE.A3J7.06 TCGA.FS.A4F8.06 TCGA.DA.A3F3.06 TCGA.D3.A51H.06
#> "01" "023" "05" "01" "03" "01"
#> TCGA.BF.A3DL.01 TCGA.D3.A51T.06 TCGA.D3.A51K.06 TCGA.EB.A44P.01 TCGA.D9.A4Z5.01 TCGA.WE.AAA4.06
#> "01" "03" "05" "05" "023" "01"
#> TCGA.3N.A9WB.06 TCGA.EE.A3J8.06
#> "022" "021"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 12706))
#> TCGA.FR.A728.01 TCGA.GN.A4U8.11 TCGA.GN.A8LL.06 TCGA.FR.A8YC.06 TCGA.DA.A95X.06 TCGA.ER.A42K.06
#> "01" "01" "03" "022" "021" "03"
#> TCGA.D3.A8GO.06 TCGA.D3.A8GK.06 TCGA.WE.A8JZ.06 TCGA.WE.A8ZO.06 TCGA.D3.A8GI.06 TCGA.FS.A4FC.06
#> "01" "05" "021" "05" "05" "042"
#> TCGA.FS.A4F2.06 TCGA.WE.A8ZM.06 TCGA.WE.A8ZT.06 TCGA.D3.A8GQ.06 TCGA.D3.A8GB.06 TCGA.DA.A95Y.06
#> "03" "05" "03" "041" "01" "03"
#> TCGA.EE.A3JI.06 TCGA.OD.A75X.06 TCGA.DA.A960.01 TCGA.D3.A8GV.06 TCGA.WE.A8ZN.06 TCGA.D3.A8GN.06
#> "022" "023" "021" "021" "01" "01"
#> TCGA.EB.A550.01 TCGA.BF.A5EQ.01 TCGA.EB.A3HV.01 TCGA.HR.A5NC.01 TCGA.DA.A95Z.06 TCGA.EB.A6QZ.01
#> "01" "042" "05" "05" "022" "021"
#> TCGA.FW.A3I3.06 TCGA.WE.A8K6.06 TCGA.D3.A8GP.06 TCGA.EB.A42Z.01 TCGA.GN.A4U4.06 TCGA.GF.A4EO.06
#> "023" "03" "022" "023" "021" "01"
#> TCGA.GN.A8LK.06 TCGA.WE.A8K4.01 TCGA.DA.A95W.06 TCGA.FW.A5DX.01 TCGA.GN.A4U3.06 TCGA.EB.A6QY.01
#> "05" "01" "022" "021" "03" "01"
#> TCGA.EB.A5VU.01 TCGA.Z2.A8RT.06 TCGA.WE.A8K1.06 TCGA.EB.A41B.01 TCGA.WE.A8ZY.06 TCGA.D9.A6EG.06
#> "044" "03" "01" "03" "021" "022"
#> TCGA.BF.A5ER.01 TCGA.FR.A8YD.06 TCGA.FS.A4F9.06 TCGA.EB.A6R0.01 TCGA.ER.A42L.06 TCGA.D3.A8GJ.06
#> "05" "05" "05" "03" "01" "044"
#> TCGA.FR.A8YE.06 TCGA.WE.A8ZR.06 TCGA.BF.A9VF.01 TCGA.EE.A3JH.06 TCGA.DA.A95V.06 TCGA.GF.A769.01
#> "01" "043" "05" "01" "041" "021"
#> TCGA.D9.A4Z2.01 TCGA.FR.A44A.06 TCGA.EB.A5VV.06 TCGA.EE.A180.06 TCGA.D3.A8GC.06 TCGA.WE.A8K5.06
#> "03" "01" "01" "022" "05" "023"
#> TCGA.GN.A8LN.01 TCGA.EE.A3JB.06 TCGA.D3.A3MO.06 TCGA.ER.A42H.01 TCGA.WE.A8ZX.06 TCGA.GN.A4U5.01
#> "021" "041" "05" "05" "041" "01"
#> TCGA.D3.A8GS.06 TCGA.WE.A8ZQ.06 TCGA.EE.A2MF.06 TCGA.D3.A5GU.06 TCGA.GN.A4U8.06 TCGA.EB.A42Y.01
#> "044" "05" "022" "05" "041" "021"
#> TCGA.D3.A3ML.06 TCGA.EB.A551.01 TCGA.D3.A8GM.06 TCGA.D3.A8GL.06 TCGA.D3.A3MU.06 TCGA.FS.A4F0.06
#> "05" "044" "041" "022" "022" "022"
#> TCGA.D3.A3MV.06 TCGA.GN.A4U7.06 TCGA.FR.A2OS.01 TCGA.D3.A2JE.06 TCGA.YD.A89C.06 TCGA.FR.A726.01
#> "03" "03" "05" "05" "041" "041"
#> TCGA.BF.A5EP.01 TCGA.D3.A3MR.06 TCGA.D3.A8GR.06 TCGA.GN.A4U9.06 TCGA.EB.A6L9.06 TCGA.D3.A5GL.06
#> "03" "01" "05" "05" "01" "03"
#> TCGA.EB.A430.01 TCGA.D3.A8GE.06 TCGA.D3.A8GD.06 TCGA.EB.A41A.01 TCGA.W3.A825.06 TCGA.EE.A183.06
#> "01" "01" "01" "022" "044" "01"
#> TCGA.ER.A2NH.06 TCGA.D3.A5GR.06 TCGA.FR.A729.06 TCGA.D3.A1QA.06 TCGA.FS.A1YY.06 TCGA.EE.A2MK.06
#> "01" "044" "044" "021" "03" "03"
#> TCGA.EE.A2M8.06 TCGA.EB.A5KH.06 TCGA.FS.A1ZR.06 TCGA.EE.A3AE.06 TCGA.EE.A29P.06 TCGA.EB.A553.01
#> "01" "021" "05" "03" "044" "05"
#> TCGA.EE.A2MR.06 TCGA.GN.A26A.06 TCGA.FS.A1ZY.06 TCGA.EE.A20I.06 TCGA.DA.A1I5.06 TCGA.EE.A184.06
#> "01" "041" "021" "041" "01" "023"
#> TCGA.EB.A85J.01 TCGA.RP.A6K9.06 TCGA.EE.A17Y.06 TCGA.D9.A149.06 TCGA.ER.A19D.06 TCGA.FS.A1ZZ.06
#> "043" "042" "041" "042" "01" "023"
#> TCGA.EE.A2GP.06 TCGA.EE.A3AD.06 TCGA.D3.A1Q9.06 TCGA.GF.A2C7.01 TCGA.BF.A5ES.01 TCGA.ER.A199.06
#> "05" "021" "041" "05" "05" "01"
#> TCGA.EE.A3AH.06 TCGA.W3.A828.06 TCGA.EE.A2A5.06 TCGA.ER.A19L.06 TCGA.BF.A1PX.01 TCGA.ER.A19T.06
#> "021" "01" "05" "043" "01" "043"
#> TCGA.EB.A51B.01 TCGA.FS.A1ZQ.06 TCGA.D3.A2JG.06 TCGA.EE.A2GH.06 TCGA.ER.A19F.06 TCGA.ER.A196.01
#> "03" "03" "03" "01" "03" "01"
#> TCGA.D3.A2JC.06 TCGA.EE.A3AG.06 TCGA.ER.A19S.06 TCGA.EE.A2GC.06 TCGA.EE.A29N.06 TCGA.FR.A7U8.06
#> "044" "03" "01" "05" "01" "023"
#> TCGA.BF.A5EO.01 TCGA.ER.A19B.06 TCGA.D3.A5GN.06 TCGA.D3.A2JB.06 TCGA.ER.A19J.06 TCGA.D3.A2JD.06
#> "041" "03" "03" "01" "023" "01"
#> TCGA.FS.A1Z4.06 TCGA.FR.A7UA.06 TCGA.EE.A2M7.06 TCGA.D3.A1Q3.06 TCGA.EB.A85I.01 TCGA.EB.A82C.01
#> "01" "01" "044" "043" "042" "023"
#> TCGA.ER.A19E.06 TCGA.FS.A1ZK.06 TCGA.FS.A1ZU.06 TCGA.EB.A5FP.01 TCGA.EB.A4XL.01 TCGA.DA.A1I2.06
#> "05" "05" "05" "021" "03" "044"
#> TCGA.EE.A29L.06 TCGA.FS.A1ZN.01 TCGA.EB.A24D.01 TCGA.EE.A2GB.06 TCGA.DA.A1I7.06 TCGA.ER.A2NF.01
#> "021" "021" "05" "03" "044" "01"
#> TCGA.GN.A263.01 TCGA.EE.A20C.06 TCGA.EE.A2MQ.06 TCGA.ER.A19N.06 TCGA.FS.A1Z3.06 TCGA.DA.A1I8.06
#> "01" "023" "05" "01" "03" "03"
#> TCGA.D3.A5GS.06 TCGA.EE.A181.06 TCGA.GN.A268.06 TCGA.W3.A824.06 TCGA.EE.A2GS.06 TCGA.FR.A7U9.06
#> "03" "041" "022" "05" "03" "01"
#> TCGA.ER.A19Q.06 TCGA.FS.A1ZM.06 TCGA.EE.A2MG.06 TCGA.EE.A2MC.06 TCGA.EE.A17Z.06 TCGA.D3.A2JP.06
#> "01" "044" "01" "01" "05" "041"
#> TCGA.ER.A19C.06 TCGA.EB.A82B.01 TCGA.EE.A2A0.06 TCGA.EE.A29G.06 TCGA.D3.A5GO.06 TCGA.GN.A269.01
#> "044" "042" "01" "01" "03" "01"
#> TCGA.EE.A2A1.06 TCGA.ER.A1A1.06 TCGA.FS.A1ZG.06 TCGA.FS.A1ZE.06 TCGA.FS.A1ZH.06 TCGA.EE.A2MH.06
#> "01" "01" "022" "022" "041" "01"
#> TCGA.D3.A2J6.06 TCGA.EE.A29Q.06 TCGA.BF.A1PZ.01 TCGA.D3.A3BZ.06 TCGA.D3.A2JO.06 TCGA.GN.A267.06
#> "042" "03" "03" "01" "044" "043"
#> TCGA.EE.A2MN.06 TCGA.GN.A264.06 TCGA.ER.A197.06 TCGA.DA.A1IB.06 TCGA.D3.A3CC.06 TCGA.ER.A19T.01
#> "05" "023" "01" "01" "042" "05"
#> TCGA.GN.A261.06 TCGA.FS.A1YW.06 TCGA.BF.A1PU.01 TCGA.D3.A1QB.06 TCGA.D3.A1Q6.06 TCGA.D3.A3C8.06
#> "01" "023" "044" "01" "044" "01"
#> TCGA.ER.A19A.06 TCGA.EE.A2GN.06 TCGA.EE.A29M.06 TCGA.D3.A2J7.06 TCGA.EB.A24C.01 TCGA.GN.A262.06
#> "01" "05" "01" "01" "043" "021"
#> TCGA.EE.A2GD.06 TCGA.D3.A2J9.06 TCGA.EE.A29B.06 TCGA.D9.A1JX.06 TCGA.EE.A29A.06 TCGA.D3.A2JL.06
#> "01" "01" "05" "03" "022" "041"
#> TCGA.D3.A1Q4.06 TCGA.FS.A1ZS.06 TCGA.D3.A3C3.06 TCGA.D3.A2J8.06 TCGA.FS.A1ZF.06 TCGA.FS.A1ZC.06
#> "01" "042" "041" "01" "03" "021"
#> TCGA.EE.A20H.06 TCGA.EE.A29W.06 TCGA.D3.A1QA.07 TCGA.BF.A1PV.01 TCGA.EE.A29S.06 TCGA.DA.A1HV.06
#> "05" "03" "041" "05" "044" "03"
#> TCGA.FS.A1Z0.06 TCGA.EE.A2GO.06 TCGA.EB.A1NK.01 TCGA.GN.A26D.06 TCGA.EE.A2MJ.06 TCGA.ER.A198.06
#> "01" "023" "01" "042" "01" "05"
#> TCGA.EE.A17X.06 TCGA.EE.A2M5.06 TCGA.GN.A266.06 TCGA.D3.A3C1.06 TCGA.D3.A2JH.06 TCGA.EE.A20F.06
#> "03" "041" "044" "044" "01" "041"
#> TCGA.EE.A29E.06 TCGA.ER.A2NG.06 TCGA.ER.A193.06 TCGA.FS.A1ZW.06 TCGA.ER.A19O.06 TCGA.EE.A2ME.06
#> "01" "01" "042" "041" "044" "01"
#> TCGA.EE.A20B.06 TCGA.EE.A3AF.06 TCGA.GN.A265.06 TCGA.FS.A1YX.06 TCGA.FS.A1ZJ.06 TCGA.ER.A19H.06
#> "041" "03" "01" "044" "05" "03"
#> TCGA.EE.A3AC.06 TCGA.EE.A2MU.06 TCGA.ER.A194.01 TCGA.EE.A2MS.06 TCGA.EE.A29R.06 TCGA.D9.A1X3.06
#> "05" "01" "044" "043" "023" "022"
#> TCGA.EE.A29X.06 TCGA.EE.A2GK.06 TCGA.EE.A3AA.06 TCGA.ER.A2NE.06 TCGA.EE.A2GR.06 TCGA.FS.A1ZD.06
#> "044" "01" "01" "021" "05" "05"
#> TCGA.ER.A19P.06 TCGA.D3.A1Q8.06 TCGA.ER.A2NC.06 TCGA.BF.A1Q0.01 TCGA.FS.A1ZP.06 TCGA.EE.A182.06
#> "01" "01" "044" "042" "05" "043"
#> TCGA.D9.A1JW.06 TCGA.D3.A1Q7.06 TCGA.EE.A185.06 TCGA.EE.A2GJ.06 TCGA.D3.A3CB.06 TCGA.EE.A2GU.06
#> "042" "01" "021" "043" "01" "042"
#> TCGA.ER.A195.06 TCGA.FS.A1Z7.06 TCGA.EE.A2M6.06 TCGA.ER.A19K.01 TCGA.DA.A1HY.06 TCGA.D3.A3C7.06
#> "01" "042" "021" "044" "03" "03"
#> TCGA.EE.A2MP.06 TCGA.EE.A29H.06 TCGA.FR.A3YO.06 TCGA.XV.AB01.01 TCGA.RP.A694.06 TCGA.EB.A5SF.01
#> "03" "03" "044" "03" "044" "01"
#> TCGA.ER.A19G.06 TCGA.EE.A2GE.06 TCGA.GF.A3OT.06 TCGA.ER.A2NF.06 TCGA.RP.A695.06 TCGA.BF.AAP7.01
#> "03" "01" "01" "01" "05" "01"
#> TCGA.EB.A3Y7.01 TCGA.EB.A3XC.01 TCGA.ER.A19W.06 TCGA.FR.A69P.06 TCGA.RP.A693.06 TCGA.FW.A3TV.06
#> "042" "03" "01" "03" "01" "01"
#> TCGA.FW.A3R5.11 TCGA.FW.A3TU.06 TCGA.BF.AAP8.01 TCGA.EE.A2MM.06 TCGA.DA.A1HW.06 TCGA.DA.A1IC.06
#> "01" "05" "042" "05" "044" "05"
#> TCGA.XV.AAZV.01 TCGA.D3.A3C6.06 TCGA.EE.A29C.06 TCGA.BF.AAP2.01 TCGA.EE.A2A2.06 TCGA.GF.A6C8.06
#> "01" "03" "01" "021" "03" "044"
#> TCGA.RP.A690.06 TCGA.FW.A5DY.06 TCGA.DA.A1I4.06 TCGA.EE.A29V.06 TCGA.GF.A6C9.06 TCGA.EE.A2GT.06
#> "01" "01" "01" "041" "01" "01"
#> TCGA.GN.A9SD.06 TCGA.EE.A3AB.06 TCGA.BF.AAP6.01 TCGA.EB.A5SH.06 TCGA.D9.A6E9.06 TCGA.BF.AAP4.01
#> "01" "041" "03" "043" "044" "044"
#> TCGA.EE.A2GM.06 TCGA.D3.A3CF.06 TCGA.D9.A6EC.06 TCGA.DA.A1I1.06 TCGA.HR.A2OH.06 TCGA.EE.A2MT.06
#> "021" "01" "023" "041" "01" "042"
#> TCGA.ER.A19M.06 TCGA.GN.A26C.01 TCGA.FS.A1ZA.06 TCGA.EB.A5SE.01 TCGA.ER.A3PL.06 TCGA.FR.A3R1.01
#> "041" "01" "044" "022" "05" "03"
#> TCGA.EE.A2MI.06 TCGA.D3.A3CE.06 TCGA.D3.A5GT.01 TCGA.ER.A2NB.01 TCGA.D3.A1Q5.06 TCGA.EB.A5UN.06
#> "044" "044" "05" "042" "042" "01"
#> TCGA.EB.A299.01 TCGA.DA.A1IA.06 TCGA.EB.A5SG.06 TCGA.D9.A6EA.06 TCGA.XV.AAZY.01 TCGA.EB.A57M.01
#> "03" "05" "01" "022" "01" "041"
#> TCGA.EE.A2A6.06 TCGA.D3.A2JA.06 TCGA.D3.A1Q1.06 TCGA.EB.A3XF.01 TCGA.D3.A2JF.06 TCGA.XV.AAZW.01
#> "042" "01" "042" "03" "03" "03"
#> TCGA.EB.A3Y6.01 TCGA.EB.A3XE.01 TCGA.D9.A3Z4.01 TCGA.FW.A3R5.06 TCGA.EE.A2GI.06 TCGA.EE.A2GL.06
#> "044" "043" "05" "043" "041" "01"
#> TCGA.EB.A3XB.01 TCGA.BF.AAOU.01 TCGA.EB.A3XD.01 TCGA.EE.A2MD.06 TCGA.YD.A9TB.06 TCGA.W3.AA1V.06
#> "044" "01" "01" "044" "05" "044"
#> TCGA.ER.A2ND.06 TCGA.D3.A2JK.06 TCGA.FS.A1ZB.06 TCGA.EE.A29D.06 TCGA.EB.A5UM.01 TCGA.QB.A6FS.06
#> "05" "041" "01" "022" "043" "01"
#> TCGA.D9.A3Z1.06 TCGA.D3.A2JN.06 TCGA.FR.A3YN.06 TCGA.FS.A1ZT.06 TCGA.D9.A148.06 TCGA.HR.A2OG.06
#> "01" "01" "03" "01" "041" "01"
#> TCGA.EE.A2ML.06 TCGA.EB.A5UL.06 TCGA.EE.A29T.06 TCGA.D9.A3Z3.06 TCGA.D9.A4Z3.01 TCGA.ER.A3ES.06
#> "041" "041" "043" "01" "05" "042"
#> TCGA.XV.A9VZ.01 TCGA.QB.AA9O.06 TCGA.EB.A44Q.06 TCGA.EB.A44R.06 TCGA.BF.A3DJ.01 TCGA.EE.A3JD.06
#> "01" "03" "044" "043" "03" "01"
#> TCGA.D3.A51N.06 TCGA.EB.A44N.01 TCGA.EE.A3J3.06 TCGA.XV.A9W5.01 TCGA.D3.A51G.06 TCGA.EB.A4P0.01
#> "041" "01" "03" "041" "03" "03"
#> TCGA.BF.AAP1.01 TCGA.EE.A3J4.06 TCGA.Z2.AA3V.06 TCGA.LH.A9QB.06 TCGA.D3.A51J.06 TCGA.3N.A9WC.06
#> "023" "05" "01" "023" "044" "042"
#> TCGA.DA.A3F8.06 TCGA.D9.A4Z6.06 TCGA.D3.A51R.06 TCGA.EB.A4OZ.01 TCGA.FS.A4FB.06 TCGA.EE.A3JE.06
#> "01" "041" "03" "01" "03" "01"
#> TCGA.W3.AA1W.06 TCGA.DA.A1I0.06 TCGA.D3.A51F.06 TCGA.IH.A3EA.01 TCGA.EB.A431.01 TCGA.EB.A97M.01
#> "01" "041" "01" "05" "041" "022"
#> TCGA.BF.AAOX.01 TCGA.DA.A3F5.06 TCGA.YD.A9TA.06 TCGA.DA.A3F2.06 TCGA.EB.A44O.01 TCGA.EB.A4IQ.01
#> "041" "042" "041" "01" "05" "042"
#> TCGA.EB.A4IS.01 TCGA.YG.AA3O.06 TCGA.ER.A3EV.06 TCGA.3N.A9WD.06 TCGA.BF.A3DM.01 TCGA.XV.A9W2.01
#> "01" "05" "043" "01" "03" "042"
#> TCGA.W3.AA1Q.06 TCGA.WE.AAA0.06 TCGA.W3.AA1R.06 TCGA.EE.A3J5.06 TCGA.EB.A4OY.01 TCGA.FS.A4FD.06
#> "05" "041" "03" "041" "01" "042"
#> TCGA.BF.AAP0.06 TCGA.YG.AA3P.06 TCGA.EE.A3JA.06 TCGA.W3.AA21.06 TCGA.WE.AAA3.06 TCGA.FS.A4F4.06
#> "01" "05" "03" "021" "042" "03"
#> TCGA.BF.A3DN.01 TCGA.ER.A3ET.06 TCGA.W3.AA1O.06 TCGA.D3.A51E.06 TCGA.Z2.AA3S.06 TCGA.YG.AA3N.01
#> "03" "042" "05" "03" "022" "044"
#> TCGA.WE.AA9Y.06 TCGA.FS.A4F5.06 TCGA.EE.A3J7.06 TCGA.FS.A4F8.06 TCGA.DA.A3F3.06 TCGA.D3.A51H.06
#> "01" "023" "05" "01" "03" "01"
#> TCGA.BF.A3DL.01 TCGA.D3.A51T.06 TCGA.D3.A51K.06 TCGA.EB.A44P.01 TCGA.D9.A4Z5.01 TCGA.WE.AAA4.06
#> "01" "03" "05" "05" "023" "01"
#> TCGA.3N.A9WB.06 TCGA.EE.A3J8.06
#> "022" "021"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 17313))
#> TCGA.FR.A728.01 TCGA.GN.A4U8.11 TCGA.GN.A8LL.06 TCGA.FR.A8YC.06 TCGA.DA.A95X.06 TCGA.ER.A42K.06
#> "01" "01" "03" "022" "021" "03"
#> TCGA.D3.A8GO.06 TCGA.D3.A8GK.06 TCGA.WE.A8JZ.06 TCGA.WE.A8ZO.06 TCGA.D3.A8GI.06 TCGA.FS.A4FC.06
#> "01" "05" "021" "05" "05" "042"
#> TCGA.FS.A4F2.06 TCGA.WE.A8ZM.06 TCGA.WE.A8ZT.06 TCGA.D3.A8GQ.06 TCGA.D3.A8GB.06 TCGA.DA.A95Y.06
#> "03" "05" "03" "041" "01" "03"
#> TCGA.EE.A3JI.06 TCGA.OD.A75X.06 TCGA.DA.A960.01 TCGA.D3.A8GV.06 TCGA.WE.A8ZN.06 TCGA.D3.A8GN.06
#> "022" "023" "021" "021" "01" "01"
#> TCGA.EB.A550.01 TCGA.BF.A5EQ.01 TCGA.EB.A3HV.01 TCGA.HR.A5NC.01 TCGA.DA.A95Z.06 TCGA.EB.A6QZ.01
#> "01" "042" "05" "05" "022" "021"
#> TCGA.FW.A3I3.06 TCGA.WE.A8K6.06 TCGA.D3.A8GP.06 TCGA.EB.A42Z.01 TCGA.GN.A4U4.06 TCGA.GF.A4EO.06
#> "023" "03" "022" "023" "021" "01"
#> TCGA.GN.A8LK.06 TCGA.WE.A8K4.01 TCGA.DA.A95W.06 TCGA.FW.A5DX.01 TCGA.GN.A4U3.06 TCGA.EB.A6QY.01
#> "05" "01" "022" "021" "03" "01"
#> TCGA.EB.A5VU.01 TCGA.Z2.A8RT.06 TCGA.WE.A8K1.06 TCGA.EB.A41B.01 TCGA.WE.A8ZY.06 TCGA.D9.A6EG.06
#> "044" "03" "01" "03" "021" "022"
#> TCGA.BF.A5ER.01 TCGA.FR.A8YD.06 TCGA.FS.A4F9.06 TCGA.EB.A6R0.01 TCGA.ER.A42L.06 TCGA.D3.A8GJ.06
#> "05" "05" "05" "03" "01" "044"
#> TCGA.FR.A8YE.06 TCGA.WE.A8ZR.06 TCGA.BF.A9VF.01 TCGA.EE.A3JH.06 TCGA.DA.A95V.06 TCGA.GF.A769.01
#> "01" "043" "05" "01" "041" "021"
#> TCGA.D9.A4Z2.01 TCGA.FR.A44A.06 TCGA.EB.A5VV.06 TCGA.EE.A180.06 TCGA.D3.A8GC.06 TCGA.WE.A8K5.06
#> "03" "01" "01" "022" "05" "023"
#> TCGA.GN.A8LN.01 TCGA.EE.A3JB.06 TCGA.D3.A3MO.06 TCGA.ER.A42H.01 TCGA.WE.A8ZX.06 TCGA.GN.A4U5.01
#> "021" "041" "05" "05" "041" "01"
#> TCGA.D3.A8GS.06 TCGA.WE.A8ZQ.06 TCGA.EE.A2MF.06 TCGA.D3.A5GU.06 TCGA.GN.A4U8.06 TCGA.EB.A42Y.01
#> "044" "05" "022" "05" "041" "021"
#> TCGA.D3.A3ML.06 TCGA.EB.A551.01 TCGA.D3.A8GM.06 TCGA.D3.A8GL.06 TCGA.D3.A3MU.06 TCGA.FS.A4F0.06
#> "05" "044" "041" "022" "022" "022"
#> TCGA.D3.A3MV.06 TCGA.GN.A4U7.06 TCGA.FR.A2OS.01 TCGA.D3.A2JE.06 TCGA.YD.A89C.06 TCGA.FR.A726.01
#> "03" "03" "05" "05" "041" "041"
#> TCGA.BF.A5EP.01 TCGA.D3.A3MR.06 TCGA.D3.A8GR.06 TCGA.GN.A4U9.06 TCGA.EB.A6L9.06 TCGA.D3.A5GL.06
#> "03" "01" "05" "05" "01" "03"
#> TCGA.EB.A430.01 TCGA.D3.A8GE.06 TCGA.D3.A8GD.06 TCGA.EB.A41A.01 TCGA.W3.A825.06 TCGA.EE.A183.06
#> "01" "01" "01" "022" "044" "01"
#> TCGA.ER.A2NH.06 TCGA.D3.A5GR.06 TCGA.FR.A729.06 TCGA.D3.A1QA.06 TCGA.FS.A1YY.06 TCGA.EE.A2MK.06
#> "01" "044" "044" "021" "03" "03"
#> TCGA.EE.A2M8.06 TCGA.EB.A5KH.06 TCGA.FS.A1ZR.06 TCGA.EE.A3AE.06 TCGA.EE.A29P.06 TCGA.EB.A553.01
#> "01" "021" "05" "03" "044" "05"
#> TCGA.EE.A2MR.06 TCGA.GN.A26A.06 TCGA.FS.A1ZY.06 TCGA.EE.A20I.06 TCGA.DA.A1I5.06 TCGA.EE.A184.06
#> "01" "041" "021" "041" "01" "023"
#> TCGA.EB.A85J.01 TCGA.RP.A6K9.06 TCGA.EE.A17Y.06 TCGA.D9.A149.06 TCGA.ER.A19D.06 TCGA.FS.A1ZZ.06
#> "043" "042" "041" "042" "01" "023"
#> TCGA.EE.A2GP.06 TCGA.EE.A3AD.06 TCGA.D3.A1Q9.06 TCGA.GF.A2C7.01 TCGA.BF.A5ES.01 TCGA.ER.A199.06
#> "05" "021" "041" "05" "05" "01"
#> TCGA.EE.A3AH.06 TCGA.W3.A828.06 TCGA.EE.A2A5.06 TCGA.ER.A19L.06 TCGA.BF.A1PX.01 TCGA.ER.A19T.06
#> "021" "01" "05" "043" "01" "043"
#> TCGA.EB.A51B.01 TCGA.FS.A1ZQ.06 TCGA.D3.A2JG.06 TCGA.EE.A2GH.06 TCGA.ER.A19F.06 TCGA.ER.A196.01
#> "03" "03" "03" "01" "03" "01"
#> TCGA.D3.A2JC.06 TCGA.EE.A3AG.06 TCGA.ER.A19S.06 TCGA.EE.A2GC.06 TCGA.EE.A29N.06 TCGA.FR.A7U8.06
#> "044" "03" "01" "05" "01" "023"
#> TCGA.BF.A5EO.01 TCGA.ER.A19B.06 TCGA.D3.A5GN.06 TCGA.D3.A2JB.06 TCGA.ER.A19J.06 TCGA.D3.A2JD.06
#> "041" "03" "03" "01" "023" "01"
#> TCGA.FS.A1Z4.06 TCGA.FR.A7UA.06 TCGA.EE.A2M7.06 TCGA.D3.A1Q3.06 TCGA.EB.A85I.01 TCGA.EB.A82C.01
#> "01" "01" "044" "043" "042" "023"
#> TCGA.ER.A19E.06 TCGA.FS.A1ZK.06 TCGA.FS.A1ZU.06 TCGA.EB.A5FP.01 TCGA.EB.A4XL.01 TCGA.DA.A1I2.06
#> "05" "05" "05" "021" "03" "044"
#> TCGA.EE.A29L.06 TCGA.FS.A1ZN.01 TCGA.EB.A24D.01 TCGA.EE.A2GB.06 TCGA.DA.A1I7.06 TCGA.ER.A2NF.01
#> "021" "021" "05" "03" "044" "01"
#> TCGA.GN.A263.01 TCGA.EE.A20C.06 TCGA.EE.A2MQ.06 TCGA.ER.A19N.06 TCGA.FS.A1Z3.06 TCGA.DA.A1I8.06
#> "01" "023" "05" "01" "03" "03"
#> TCGA.D3.A5GS.06 TCGA.EE.A181.06 TCGA.GN.A268.06 TCGA.W3.A824.06 TCGA.EE.A2GS.06 TCGA.FR.A7U9.06
#> "03" "041" "022" "05" "03" "01"
#> TCGA.ER.A19Q.06 TCGA.FS.A1ZM.06 TCGA.EE.A2MG.06 TCGA.EE.A2MC.06 TCGA.EE.A17Z.06 TCGA.D3.A2JP.06
#> "01" "044" "01" "01" "05" "041"
#> TCGA.ER.A19C.06 TCGA.EB.A82B.01 TCGA.EE.A2A0.06 TCGA.EE.A29G.06 TCGA.D3.A5GO.06 TCGA.GN.A269.01
#> "044" "042" "01" "01" "03" "01"
#> TCGA.EE.A2A1.06 TCGA.ER.A1A1.06 TCGA.FS.A1ZG.06 TCGA.FS.A1ZE.06 TCGA.FS.A1ZH.06 TCGA.EE.A2MH.06
#> "01" "01" "022" "022" "041" "01"
#> TCGA.D3.A2J6.06 TCGA.EE.A29Q.06 TCGA.BF.A1PZ.01 TCGA.D3.A3BZ.06 TCGA.D3.A2JO.06 TCGA.GN.A267.06
#> "042" "03" "03" "01" "044" "043"
#> TCGA.EE.A2MN.06 TCGA.GN.A264.06 TCGA.ER.A197.06 TCGA.DA.A1IB.06 TCGA.D3.A3CC.06 TCGA.ER.A19T.01
#> "05" "023" "01" "01" "042" "05"
#> TCGA.GN.A261.06 TCGA.FS.A1YW.06 TCGA.BF.A1PU.01 TCGA.D3.A1QB.06 TCGA.D3.A1Q6.06 TCGA.D3.A3C8.06
#> "01" "023" "044" "01" "044" "01"
#> TCGA.ER.A19A.06 TCGA.EE.A2GN.06 TCGA.EE.A29M.06 TCGA.D3.A2J7.06 TCGA.EB.A24C.01 TCGA.GN.A262.06
#> "01" "05" "01" "01" "043" "021"
#> TCGA.EE.A2GD.06 TCGA.D3.A2J9.06 TCGA.EE.A29B.06 TCGA.D9.A1JX.06 TCGA.EE.A29A.06 TCGA.D3.A2JL.06
#> "01" "01" "05" "03" "022" "041"
#> TCGA.D3.A1Q4.06 TCGA.FS.A1ZS.06 TCGA.D3.A3C3.06 TCGA.D3.A2J8.06 TCGA.FS.A1ZF.06 TCGA.FS.A1ZC.06
#> "01" "042" "041" "01" "03" "021"
#> TCGA.EE.A20H.06 TCGA.EE.A29W.06 TCGA.D3.A1QA.07 TCGA.BF.A1PV.01 TCGA.EE.A29S.06 TCGA.DA.A1HV.06
#> "05" "03" "041" "05" "044" "03"
#> TCGA.FS.A1Z0.06 TCGA.EE.A2GO.06 TCGA.EB.A1NK.01 TCGA.GN.A26D.06 TCGA.EE.A2MJ.06 TCGA.ER.A198.06
#> "01" "023" "01" "042" "01" "05"
#> TCGA.EE.A17X.06 TCGA.EE.A2M5.06 TCGA.GN.A266.06 TCGA.D3.A3C1.06 TCGA.D3.A2JH.06 TCGA.EE.A20F.06
#> "03" "041" "044" "044" "01" "041"
#> TCGA.EE.A29E.06 TCGA.ER.A2NG.06 TCGA.ER.A193.06 TCGA.FS.A1ZW.06 TCGA.ER.A19O.06 TCGA.EE.A2ME.06
#> "01" "01" "042" "041" "044" "01"
#> TCGA.EE.A20B.06 TCGA.EE.A3AF.06 TCGA.GN.A265.06 TCGA.FS.A1YX.06 TCGA.FS.A1ZJ.06 TCGA.ER.A19H.06
#> "041" "03" "01" "044" "05" "03"
#> TCGA.EE.A3AC.06 TCGA.EE.A2MU.06 TCGA.ER.A194.01 TCGA.EE.A2MS.06 TCGA.EE.A29R.06 TCGA.D9.A1X3.06
#> "05" "01" "044" "043" "023" "022"
#> TCGA.EE.A29X.06 TCGA.EE.A2GK.06 TCGA.EE.A3AA.06 TCGA.ER.A2NE.06 TCGA.EE.A2GR.06 TCGA.FS.A1ZD.06
#> "044" "01" "01" "021" "05" "05"
#> TCGA.ER.A19P.06 TCGA.D3.A1Q8.06 TCGA.ER.A2NC.06 TCGA.BF.A1Q0.01 TCGA.FS.A1ZP.06 TCGA.EE.A182.06
#> "01" "01" "044" "042" "05" "043"
#> TCGA.D9.A1JW.06 TCGA.D3.A1Q7.06 TCGA.EE.A185.06 TCGA.EE.A2GJ.06 TCGA.D3.A3CB.06 TCGA.EE.A2GU.06
#> "042" "01" "021" "043" "01" "042"
#> TCGA.ER.A195.06 TCGA.FS.A1Z7.06 TCGA.EE.A2M6.06 TCGA.ER.A19K.01 TCGA.DA.A1HY.06 TCGA.D3.A3C7.06
#> "01" "042" "021" "044" "03" "03"
#> TCGA.EE.A2MP.06 TCGA.EE.A29H.06 TCGA.FR.A3YO.06 TCGA.XV.AB01.01 TCGA.RP.A694.06 TCGA.EB.A5SF.01
#> "03" "03" "044" "03" "044" "01"
#> TCGA.ER.A19G.06 TCGA.EE.A2GE.06 TCGA.GF.A3OT.06 TCGA.ER.A2NF.06 TCGA.RP.A695.06 TCGA.BF.AAP7.01
#> "03" "01" "01" "01" "05" "01"
#> TCGA.EB.A3Y7.01 TCGA.EB.A3XC.01 TCGA.ER.A19W.06 TCGA.FR.A69P.06 TCGA.RP.A693.06 TCGA.FW.A3TV.06
#> "042" "03" "01" "03" "01" "01"
#> TCGA.FW.A3R5.11 TCGA.FW.A3TU.06 TCGA.BF.AAP8.01 TCGA.EE.A2MM.06 TCGA.DA.A1HW.06 TCGA.DA.A1IC.06
#> "01" "05" "042" "05" "044" "05"
#> TCGA.XV.AAZV.01 TCGA.D3.A3C6.06 TCGA.EE.A29C.06 TCGA.BF.AAP2.01 TCGA.EE.A2A2.06 TCGA.GF.A6C8.06
#> "01" "03" "01" "021" "03" "044"
#> TCGA.RP.A690.06 TCGA.FW.A5DY.06 TCGA.DA.A1I4.06 TCGA.EE.A29V.06 TCGA.GF.A6C9.06 TCGA.EE.A2GT.06
#> "01" "01" "01" "041" "01" "01"
#> TCGA.GN.A9SD.06 TCGA.EE.A3AB.06 TCGA.BF.AAP6.01 TCGA.EB.A5SH.06 TCGA.D9.A6E9.06 TCGA.BF.AAP4.01
#> "01" "041" "03" "043" "044" "044"
#> TCGA.EE.A2GM.06 TCGA.D3.A3CF.06 TCGA.D9.A6EC.06 TCGA.DA.A1I1.06 TCGA.HR.A2OH.06 TCGA.EE.A2MT.06
#> "021" "01" "023" "041" "01" "042"
#> TCGA.ER.A19M.06 TCGA.GN.A26C.01 TCGA.FS.A1ZA.06 TCGA.EB.A5SE.01 TCGA.ER.A3PL.06 TCGA.FR.A3R1.01
#> "041" "01" "044" "022" "05" "03"
#> TCGA.EE.A2MI.06 TCGA.D3.A3CE.06 TCGA.D3.A5GT.01 TCGA.ER.A2NB.01 TCGA.D3.A1Q5.06 TCGA.EB.A5UN.06
#> "044" "044" "05" "042" "042" "01"
#> TCGA.EB.A299.01 TCGA.DA.A1IA.06 TCGA.EB.A5SG.06 TCGA.D9.A6EA.06 TCGA.XV.AAZY.01 TCGA.EB.A57M.01
#> "03" "05" "01" "022" "01" "041"
#> TCGA.EE.A2A6.06 TCGA.D3.A2JA.06 TCGA.D3.A1Q1.06 TCGA.EB.A3XF.01 TCGA.D3.A2JF.06 TCGA.XV.AAZW.01
#> "042" "01" "042" "03" "03" "03"
#> TCGA.EB.A3Y6.01 TCGA.EB.A3XE.01 TCGA.D9.A3Z4.01 TCGA.FW.A3R5.06 TCGA.EE.A2GI.06 TCGA.EE.A2GL.06
#> "044" "043" "05" "043" "041" "01"
#> TCGA.EB.A3XB.01 TCGA.BF.AAOU.01 TCGA.EB.A3XD.01 TCGA.EE.A2MD.06 TCGA.YD.A9TB.06 TCGA.W3.AA1V.06
#> "044" "01" "01" "044" "05" "044"
#> TCGA.ER.A2ND.06 TCGA.D3.A2JK.06 TCGA.FS.A1ZB.06 TCGA.EE.A29D.06 TCGA.EB.A5UM.01 TCGA.QB.A6FS.06
#> "05" "041" "01" "022" "043" "01"
#> TCGA.D9.A3Z1.06 TCGA.D3.A2JN.06 TCGA.FR.A3YN.06 TCGA.FS.A1ZT.06 TCGA.D9.A148.06 TCGA.HR.A2OG.06
#> "01" "01" "03" "01" "041" "01"
#> TCGA.EE.A2ML.06 TCGA.EB.A5UL.06 TCGA.EE.A29T.06 TCGA.D9.A3Z3.06 TCGA.D9.A4Z3.01 TCGA.ER.A3ES.06
#> "041" "041" "043" "01" "05" "042"
#> TCGA.XV.A9VZ.01 TCGA.QB.AA9O.06 TCGA.EB.A44Q.06 TCGA.EB.A44R.06 TCGA.BF.A3DJ.01 TCGA.EE.A3JD.06
#> "01" "03" "044" "043" "03" "01"
#> TCGA.D3.A51N.06 TCGA.EB.A44N.01 TCGA.EE.A3J3.06 TCGA.XV.A9W5.01 TCGA.D3.A51G.06 TCGA.EB.A4P0.01
#> "041" "01" "03" "041" "03" "03"
#> TCGA.BF.AAP1.01 TCGA.EE.A3J4.06 TCGA.Z2.AA3V.06 TCGA.LH.A9QB.06 TCGA.D3.A51J.06 TCGA.3N.A9WC.06
#> "023" "05" "01" "023" "044" "042"
#> TCGA.DA.A3F8.06 TCGA.D9.A4Z6.06 TCGA.D3.A51R.06 TCGA.EB.A4OZ.01 TCGA.FS.A4FB.06 TCGA.EE.A3JE.06
#> "01" "041" "03" "01" "03" "01"
#> TCGA.W3.AA1W.06 TCGA.DA.A1I0.06 TCGA.D3.A51F.06 TCGA.IH.A3EA.01 TCGA.EB.A431.01 TCGA.EB.A97M.01
#> "01" "041" "01" "05" "041" "022"
#> TCGA.BF.AAOX.01 TCGA.DA.A3F5.06 TCGA.YD.A9TA.06 TCGA.DA.A3F2.06 TCGA.EB.A44O.01 TCGA.EB.A4IQ.01
#> "041" "042" "041" "01" "05" "042"
#> TCGA.EB.A4IS.01 TCGA.YG.AA3O.06 TCGA.ER.A3EV.06 TCGA.3N.A9WD.06 TCGA.BF.A3DM.01 TCGA.XV.A9W2.01
#> "01" "05" "043" "01" "03" "042"
#> TCGA.W3.AA1Q.06 TCGA.WE.AAA0.06 TCGA.W3.AA1R.06 TCGA.EE.A3J5.06 TCGA.EB.A4OY.01 TCGA.FS.A4FD.06
#> "05" "041" "03" "041" "01" "042"
#> TCGA.BF.AAP0.06 TCGA.YG.AA3P.06 TCGA.EE.A3JA.06 TCGA.W3.AA21.06 TCGA.WE.AAA3.06 TCGA.FS.A4F4.06
#> "01" "05" "03" "021" "042" "03"
#> TCGA.BF.A3DN.01 TCGA.ER.A3ET.06 TCGA.W3.AA1O.06 TCGA.D3.A51E.06 TCGA.Z2.AA3S.06 TCGA.YG.AA3N.01
#> "03" "042" "05" "03" "022" "044"
#> TCGA.WE.AA9Y.06 TCGA.FS.A4F5.06 TCGA.EE.A3J7.06 TCGA.FS.A4F8.06 TCGA.DA.A3F3.06 TCGA.D3.A51H.06
#> "01" "023" "05" "01" "03" "01"
#> TCGA.BF.A3DL.01 TCGA.D3.A51T.06 TCGA.D3.A51K.06 TCGA.EB.A44P.01 TCGA.D9.A4Z5.01 TCGA.WE.AAA4.06
#> "01" "03" "05" "05" "023" "01"
#> TCGA.3N.A9WB.06 TCGA.EE.A3J8.06
#> "022" "021"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 22901))
#> TCGA.FR.A728.01 TCGA.GN.A4U8.11 TCGA.GN.A8LL.06 TCGA.FR.A8YC.06 TCGA.DA.A95X.06 TCGA.ER.A42K.06
#> "01" "01" "03" "022" "021" "03"
#> TCGA.D3.A8GO.06 TCGA.D3.A8GK.06 TCGA.WE.A8JZ.06 TCGA.WE.A8ZO.06 TCGA.D3.A8GI.06 TCGA.FS.A4FC.06
#> "01" "05" "021" "05" "05" "042"
#> TCGA.FS.A4F2.06 TCGA.WE.A8ZM.06 TCGA.WE.A8ZT.06 TCGA.D3.A8GQ.06 TCGA.D3.A8GB.06 TCGA.DA.A95Y.06
#> "03" "05" "03" "041" "01" "03"
#> TCGA.EE.A3JI.06 TCGA.OD.A75X.06 TCGA.DA.A960.01 TCGA.D3.A8GV.06 TCGA.WE.A8ZN.06 TCGA.D3.A8GN.06
#> "022" "023" "021" "021" "01" "01"
#> TCGA.EB.A550.01 TCGA.BF.A5EQ.01 TCGA.EB.A3HV.01 TCGA.HR.A5NC.01 TCGA.DA.A95Z.06 TCGA.EB.A6QZ.01
#> "01" "042" "05" "05" "022" "021"
#> TCGA.FW.A3I3.06 TCGA.WE.A8K6.06 TCGA.D3.A8GP.06 TCGA.EB.A42Z.01 TCGA.GN.A4U4.06 TCGA.GF.A4EO.06
#> "023" "03" "022" "023" "021" "01"
#> TCGA.GN.A8LK.06 TCGA.WE.A8K4.01 TCGA.DA.A95W.06 TCGA.FW.A5DX.01 TCGA.GN.A4U3.06 TCGA.EB.A6QY.01
#> "05" "01" "022" "021" "03" "01"
#> TCGA.EB.A5VU.01 TCGA.Z2.A8RT.06 TCGA.WE.A8K1.06 TCGA.EB.A41B.01 TCGA.WE.A8ZY.06 TCGA.D9.A6EG.06
#> "044" "03" "01" "03" "021" "022"
#> TCGA.BF.A5ER.01 TCGA.FR.A8YD.06 TCGA.FS.A4F9.06 TCGA.EB.A6R0.01 TCGA.ER.A42L.06 TCGA.D3.A8GJ.06
#> "05" "05" "05" "03" "01" "044"
#> TCGA.FR.A8YE.06 TCGA.WE.A8ZR.06 TCGA.BF.A9VF.01 TCGA.EE.A3JH.06 TCGA.DA.A95V.06 TCGA.GF.A769.01
#> "01" "043" "05" "01" "041" "021"
#> TCGA.D9.A4Z2.01 TCGA.FR.A44A.06 TCGA.EB.A5VV.06 TCGA.EE.A180.06 TCGA.D3.A8GC.06 TCGA.WE.A8K5.06
#> "03" "01" "01" "022" "05" "023"
#> TCGA.GN.A8LN.01 TCGA.EE.A3JB.06 TCGA.D3.A3MO.06 TCGA.ER.A42H.01 TCGA.WE.A8ZX.06 TCGA.GN.A4U5.01
#> "021" "041" "05" "05" "041" "01"
#> TCGA.D3.A8GS.06 TCGA.WE.A8ZQ.06 TCGA.EE.A2MF.06 TCGA.D3.A5GU.06 TCGA.GN.A4U8.06 TCGA.EB.A42Y.01
#> "044" "05" "022" "05" "041" "021"
#> TCGA.D3.A3ML.06 TCGA.EB.A551.01 TCGA.D3.A8GM.06 TCGA.D3.A8GL.06 TCGA.D3.A3MU.06 TCGA.FS.A4F0.06
#> "05" "044" "041" "022" "022" "022"
#> TCGA.D3.A3MV.06 TCGA.GN.A4U7.06 TCGA.FR.A2OS.01 TCGA.D3.A2JE.06 TCGA.YD.A89C.06 TCGA.FR.A726.01
#> "03" "03" "05" "05" "041" "041"
#> TCGA.BF.A5EP.01 TCGA.D3.A3MR.06 TCGA.D3.A8GR.06 TCGA.GN.A4U9.06 TCGA.EB.A6L9.06 TCGA.D3.A5GL.06
#> "03" "01" "05" "05" "01" "03"
#> TCGA.EB.A430.01 TCGA.D3.A8GE.06 TCGA.D3.A8GD.06 TCGA.EB.A41A.01 TCGA.W3.A825.06 TCGA.EE.A183.06
#> "01" "01" "01" "022" "044" "01"
#> TCGA.ER.A2NH.06 TCGA.D3.A5GR.06 TCGA.FR.A729.06 TCGA.D3.A1QA.06 TCGA.FS.A1YY.06 TCGA.EE.A2MK.06
#> "01" "044" "044" "021" "03" "03"
#> TCGA.EE.A2M8.06 TCGA.EB.A5KH.06 TCGA.FS.A1ZR.06 TCGA.EE.A3AE.06 TCGA.EE.A29P.06 TCGA.EB.A553.01
#> "01" "021" "05" "03" "044" "05"
#> TCGA.EE.A2MR.06 TCGA.GN.A26A.06 TCGA.FS.A1ZY.06 TCGA.EE.A20I.06 TCGA.DA.A1I5.06 TCGA.EE.A184.06
#> "01" "041" "021" "041" "01" "023"
#> TCGA.EB.A85J.01 TCGA.RP.A6K9.06 TCGA.EE.A17Y.06 TCGA.D9.A149.06 TCGA.ER.A19D.06 TCGA.FS.A1ZZ.06
#> "043" "042" "041" "042" "01" "023"
#> TCGA.EE.A2GP.06 TCGA.EE.A3AD.06 TCGA.D3.A1Q9.06 TCGA.GF.A2C7.01 TCGA.BF.A5ES.01 TCGA.ER.A199.06
#> "05" "021" "041" "05" "05" "01"
#> TCGA.EE.A3AH.06 TCGA.W3.A828.06 TCGA.EE.A2A5.06 TCGA.ER.A19L.06 TCGA.BF.A1PX.01 TCGA.ER.A19T.06
#> "021" "01" "05" "043" "01" "043"
#> TCGA.EB.A51B.01 TCGA.FS.A1ZQ.06 TCGA.D3.A2JG.06 TCGA.EE.A2GH.06 TCGA.ER.A19F.06 TCGA.ER.A196.01
#> "03" "03" "03" "01" "03" "01"
#> TCGA.D3.A2JC.06 TCGA.EE.A3AG.06 TCGA.ER.A19S.06 TCGA.EE.A2GC.06 TCGA.EE.A29N.06 TCGA.FR.A7U8.06
#> "044" "03" "01" "05" "01" "023"
#> TCGA.BF.A5EO.01 TCGA.ER.A19B.06 TCGA.D3.A5GN.06 TCGA.D3.A2JB.06 TCGA.ER.A19J.06 TCGA.D3.A2JD.06
#> "041" "03" "03" "01" "023" "01"
#> TCGA.FS.A1Z4.06 TCGA.FR.A7UA.06 TCGA.EE.A2M7.06 TCGA.D3.A1Q3.06 TCGA.EB.A85I.01 TCGA.EB.A82C.01
#> "01" "01" "044" "043" "042" "023"
#> TCGA.ER.A19E.06 TCGA.FS.A1ZK.06 TCGA.FS.A1ZU.06 TCGA.EB.A5FP.01 TCGA.EB.A4XL.01 TCGA.DA.A1I2.06
#> "05" "05" "05" "021" "03" "044"
#> TCGA.EE.A29L.06 TCGA.FS.A1ZN.01 TCGA.EB.A24D.01 TCGA.EE.A2GB.06 TCGA.DA.A1I7.06 TCGA.ER.A2NF.01
#> "021" "021" "05" "03" "044" "01"
#> TCGA.GN.A263.01 TCGA.EE.A20C.06 TCGA.EE.A2MQ.06 TCGA.ER.A19N.06 TCGA.FS.A1Z3.06 TCGA.DA.A1I8.06
#> "01" "023" "05" "01" "03" "03"
#> TCGA.D3.A5GS.06 TCGA.EE.A181.06 TCGA.GN.A268.06 TCGA.W3.A824.06 TCGA.EE.A2GS.06 TCGA.FR.A7U9.06
#> "03" "041" "022" "05" "03" "01"
#> TCGA.ER.A19Q.06 TCGA.FS.A1ZM.06 TCGA.EE.A2MG.06 TCGA.EE.A2MC.06 TCGA.EE.A17Z.06 TCGA.D3.A2JP.06
#> "01" "044" "01" "01" "05" "041"
#> TCGA.ER.A19C.06 TCGA.EB.A82B.01 TCGA.EE.A2A0.06 TCGA.EE.A29G.06 TCGA.D3.A5GO.06 TCGA.GN.A269.01
#> "044" "042" "01" "01" "03" "01"
#> TCGA.EE.A2A1.06 TCGA.ER.A1A1.06 TCGA.FS.A1ZG.06 TCGA.FS.A1ZE.06 TCGA.FS.A1ZH.06 TCGA.EE.A2MH.06
#> "01" "01" "022" "022" "041" "01"
#> TCGA.D3.A2J6.06 TCGA.EE.A29Q.06 TCGA.BF.A1PZ.01 TCGA.D3.A3BZ.06 TCGA.D3.A2JO.06 TCGA.GN.A267.06
#> "042" "03" "03" "01" "044" "043"
#> TCGA.EE.A2MN.06 TCGA.GN.A264.06 TCGA.ER.A197.06 TCGA.DA.A1IB.06 TCGA.D3.A3CC.06 TCGA.ER.A19T.01
#> "05" "023" "01" "01" "042" "05"
#> TCGA.GN.A261.06 TCGA.FS.A1YW.06 TCGA.BF.A1PU.01 TCGA.D3.A1QB.06 TCGA.D3.A1Q6.06 TCGA.D3.A3C8.06
#> "01" "023" "044" "01" "044" "01"
#> TCGA.ER.A19A.06 TCGA.EE.A2GN.06 TCGA.EE.A29M.06 TCGA.D3.A2J7.06 TCGA.EB.A24C.01 TCGA.GN.A262.06
#> "01" "05" "01" "01" "043" "021"
#> TCGA.EE.A2GD.06 TCGA.D3.A2J9.06 TCGA.EE.A29B.06 TCGA.D9.A1JX.06 TCGA.EE.A29A.06 TCGA.D3.A2JL.06
#> "01" "01" "05" "03" "022" "041"
#> TCGA.D3.A1Q4.06 TCGA.FS.A1ZS.06 TCGA.D3.A3C3.06 TCGA.D3.A2J8.06 TCGA.FS.A1ZF.06 TCGA.FS.A1ZC.06
#> "01" "042" "041" "01" "03" "021"
#> TCGA.EE.A20H.06 TCGA.EE.A29W.06 TCGA.D3.A1QA.07 TCGA.BF.A1PV.01 TCGA.EE.A29S.06 TCGA.DA.A1HV.06
#> "05" "03" "041" "05" "044" "03"
#> TCGA.FS.A1Z0.06 TCGA.EE.A2GO.06 TCGA.EB.A1NK.01 TCGA.GN.A26D.06 TCGA.EE.A2MJ.06 TCGA.ER.A198.06
#> "01" "023" "01" "042" "01" "05"
#> TCGA.EE.A17X.06 TCGA.EE.A2M5.06 TCGA.GN.A266.06 TCGA.D3.A3C1.06 TCGA.D3.A2JH.06 TCGA.EE.A20F.06
#> "03" "041" "044" "044" "01" "041"
#> TCGA.EE.A29E.06 TCGA.ER.A2NG.06 TCGA.ER.A193.06 TCGA.FS.A1ZW.06 TCGA.ER.A19O.06 TCGA.EE.A2ME.06
#> "01" "01" "042" "041" "044" "01"
#> TCGA.EE.A20B.06 TCGA.EE.A3AF.06 TCGA.GN.A265.06 TCGA.FS.A1YX.06 TCGA.FS.A1ZJ.06 TCGA.ER.A19H.06
#> "041" "03" "01" "044" "05" "03"
#> TCGA.EE.A3AC.06 TCGA.EE.A2MU.06 TCGA.ER.A194.01 TCGA.EE.A2MS.06 TCGA.EE.A29R.06 TCGA.D9.A1X3.06
#> "05" "01" "044" "043" "023" "022"
#> TCGA.EE.A29X.06 TCGA.EE.A2GK.06 TCGA.EE.A3AA.06 TCGA.ER.A2NE.06 TCGA.EE.A2GR.06 TCGA.FS.A1ZD.06
#> "044" "01" "01" "021" "05" "05"
#> TCGA.ER.A19P.06 TCGA.D3.A1Q8.06 TCGA.ER.A2NC.06 TCGA.BF.A1Q0.01 TCGA.FS.A1ZP.06 TCGA.EE.A182.06
#> "01" "01" "044" "042" "05" "043"
#> TCGA.D9.A1JW.06 TCGA.D3.A1Q7.06 TCGA.EE.A185.06 TCGA.EE.A2GJ.06 TCGA.D3.A3CB.06 TCGA.EE.A2GU.06
#> "042" "01" "021" "043" "01" "042"
#> TCGA.ER.A195.06 TCGA.FS.A1Z7.06 TCGA.EE.A2M6.06 TCGA.ER.A19K.01 TCGA.DA.A1HY.06 TCGA.D3.A3C7.06
#> "01" "042" "021" "044" "03" "03"
#> TCGA.EE.A2MP.06 TCGA.EE.A29H.06 TCGA.FR.A3YO.06 TCGA.XV.AB01.01 TCGA.RP.A694.06 TCGA.EB.A5SF.01
#> "03" "03" "044" "03" "044" "01"
#> TCGA.ER.A19G.06 TCGA.EE.A2GE.06 TCGA.GF.A3OT.06 TCGA.ER.A2NF.06 TCGA.RP.A695.06 TCGA.BF.AAP7.01
#> "03" "01" "01" "01" "05" "01"
#> TCGA.EB.A3Y7.01 TCGA.EB.A3XC.01 TCGA.ER.A19W.06 TCGA.FR.A69P.06 TCGA.RP.A693.06 TCGA.FW.A3TV.06
#> "042" "03" "01" "03" "01" "01"
#> TCGA.FW.A3R5.11 TCGA.FW.A3TU.06 TCGA.BF.AAP8.01 TCGA.EE.A2MM.06 TCGA.DA.A1HW.06 TCGA.DA.A1IC.06
#> "01" "05" "042" "05" "044" "05"
#> TCGA.XV.AAZV.01 TCGA.D3.A3C6.06 TCGA.EE.A29C.06 TCGA.BF.AAP2.01 TCGA.EE.A2A2.06 TCGA.GF.A6C8.06
#> "01" "03" "01" "021" "03" "044"
#> TCGA.RP.A690.06 TCGA.FW.A5DY.06 TCGA.DA.A1I4.06 TCGA.EE.A29V.06 TCGA.GF.A6C9.06 TCGA.EE.A2GT.06
#> "01" "01" "01" "041" "01" "01"
#> TCGA.GN.A9SD.06 TCGA.EE.A3AB.06 TCGA.BF.AAP6.01 TCGA.EB.A5SH.06 TCGA.D9.A6E9.06 TCGA.BF.AAP4.01
#> "01" "041" "03" "043" "044" "044"
#> TCGA.EE.A2GM.06 TCGA.D3.A3CF.06 TCGA.D9.A6EC.06 TCGA.DA.A1I1.06 TCGA.HR.A2OH.06 TCGA.EE.A2MT.06
#> "021" "01" "023" "041" "01" "042"
#> TCGA.ER.A19M.06 TCGA.GN.A26C.01 TCGA.FS.A1ZA.06 TCGA.EB.A5SE.01 TCGA.ER.A3PL.06 TCGA.FR.A3R1.01
#> "041" "01" "044" "022" "05" "03"
#> TCGA.EE.A2MI.06 TCGA.D3.A3CE.06 TCGA.D3.A5GT.01 TCGA.ER.A2NB.01 TCGA.D3.A1Q5.06 TCGA.EB.A5UN.06
#> "044" "044" "05" "042" "042" "01"
#> TCGA.EB.A299.01 TCGA.DA.A1IA.06 TCGA.EB.A5SG.06 TCGA.D9.A6EA.06 TCGA.XV.AAZY.01 TCGA.EB.A57M.01
#> "03" "05" "01" "022" "01" "041"
#> TCGA.EE.A2A6.06 TCGA.D3.A2JA.06 TCGA.D3.A1Q1.06 TCGA.EB.A3XF.01 TCGA.D3.A2JF.06 TCGA.XV.AAZW.01
#> "042" "01" "042" "03" "03" "03"
#> TCGA.EB.A3Y6.01 TCGA.EB.A3XE.01 TCGA.D9.A3Z4.01 TCGA.FW.A3R5.06 TCGA.EE.A2GI.06 TCGA.EE.A2GL.06
#> "044" "043" "05" "043" "041" "01"
#> TCGA.EB.A3XB.01 TCGA.BF.AAOU.01 TCGA.EB.A3XD.01 TCGA.EE.A2MD.06 TCGA.YD.A9TB.06 TCGA.W3.AA1V.06
#> "044" "01" "01" "044" "05" "044"
#> TCGA.ER.A2ND.06 TCGA.D3.A2JK.06 TCGA.FS.A1ZB.06 TCGA.EE.A29D.06 TCGA.EB.A5UM.01 TCGA.QB.A6FS.06
#> "05" "041" "01" "022" "043" "01"
#> TCGA.D9.A3Z1.06 TCGA.D3.A2JN.06 TCGA.FR.A3YN.06 TCGA.FS.A1ZT.06 TCGA.D9.A148.06 TCGA.HR.A2OG.06
#> "01" "01" "03" "01" "041" "01"
#> TCGA.EE.A2ML.06 TCGA.EB.A5UL.06 TCGA.EE.A29T.06 TCGA.D9.A3Z3.06 TCGA.D9.A4Z3.01 TCGA.ER.A3ES.06
#> "041" "041" "043" "01" "05" "042"
#> TCGA.XV.A9VZ.01 TCGA.QB.AA9O.06 TCGA.EB.A44Q.06 TCGA.EB.A44R.06 TCGA.BF.A3DJ.01 TCGA.EE.A3JD.06
#> "01" "03" "044" "043" "03" "01"
#> TCGA.D3.A51N.06 TCGA.EB.A44N.01 TCGA.EE.A3J3.06 TCGA.XV.A9W5.01 TCGA.D3.A51G.06 TCGA.EB.A4P0.01
#> "041" "01" "03" "041" "03" "03"
#> TCGA.BF.AAP1.01 TCGA.EE.A3J4.06 TCGA.Z2.AA3V.06 TCGA.LH.A9QB.06 TCGA.D3.A51J.06 TCGA.3N.A9WC.06
#> "023" "05" "01" "023" "044" "042"
#> TCGA.DA.A3F8.06 TCGA.D9.A4Z6.06 TCGA.D3.A51R.06 TCGA.EB.A4OZ.01 TCGA.FS.A4FB.06 TCGA.EE.A3JE.06
#> "01" "041" "03" "01" "03" "01"
#> TCGA.W3.AA1W.06 TCGA.DA.A1I0.06 TCGA.D3.A51F.06 TCGA.IH.A3EA.01 TCGA.EB.A431.01 TCGA.EB.A97M.01
#> "01" "041" "01" "05" "041" "022"
#> TCGA.BF.AAOX.01 TCGA.DA.A3F5.06 TCGA.YD.A9TA.06 TCGA.DA.A3F2.06 TCGA.EB.A44O.01 TCGA.EB.A4IQ.01
#> "041" "042" "041" "01" "05" "042"
#> TCGA.EB.A4IS.01 TCGA.YG.AA3O.06 TCGA.ER.A3EV.06 TCGA.3N.A9WD.06 TCGA.BF.A3DM.01 TCGA.XV.A9W2.01
#> "01" "05" "043" "01" "03" "042"
#> TCGA.W3.AA1Q.06 TCGA.WE.AAA0.06 TCGA.W3.AA1R.06 TCGA.EE.A3J5.06 TCGA.EB.A4OY.01 TCGA.FS.A4FD.06
#> "05" "041" "03" "041" "01" "042"
#> TCGA.BF.AAP0.06 TCGA.YG.AA3P.06 TCGA.EE.A3JA.06 TCGA.W3.AA21.06 TCGA.WE.AAA3.06 TCGA.FS.A4F4.06
#> "01" "05" "03" "021" "042" "03"
#> TCGA.BF.A3DN.01 TCGA.ER.A3ET.06 TCGA.W3.AA1O.06 TCGA.D3.A51E.06 TCGA.Z2.AA3S.06 TCGA.YG.AA3N.01
#> "03" "042" "05" "03" "022" "044"
#> TCGA.WE.AA9Y.06 TCGA.FS.A4F5.06 TCGA.EE.A3J7.06 TCGA.FS.A4F8.06 TCGA.DA.A3F3.06 TCGA.D3.A51H.06
#> "01" "023" "05" "01" "03" "01"
#> TCGA.BF.A3DL.01 TCGA.D3.A51T.06 TCGA.D3.A51K.06 TCGA.EB.A44P.01 TCGA.D9.A4Z5.01 TCGA.WE.AAA4.06
#> "01" "03" "05" "05" "023" "01"
#> TCGA.3N.A9WB.06 TCGA.EE.A3J8.06
#> "022" "021"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 23773))
#> TCGA.FR.A728.01 TCGA.GN.A4U8.11 TCGA.GN.A8LL.06 TCGA.FR.A8YC.06 TCGA.DA.A95X.06 TCGA.ER.A42K.06
#> "01" "01" "03" "02" "02" "03"
#> TCGA.D3.A8GO.06 TCGA.D3.A8GK.06 TCGA.WE.A8JZ.06 TCGA.WE.A8ZO.06 TCGA.D3.A8GI.06 TCGA.FS.A4FC.06
#> "01" "05" "02" "05" "05" "042"
#> TCGA.FS.A4F2.06 TCGA.WE.A8ZM.06 TCGA.WE.A8ZT.06 TCGA.D3.A8GQ.06 TCGA.D3.A8GB.06 TCGA.DA.A95Y.06
#> "03" "05" "03" "041" "01" "03"
#> TCGA.EE.A3JI.06 TCGA.OD.A75X.06 TCGA.DA.A960.01 TCGA.D3.A8GV.06 TCGA.WE.A8ZN.06 TCGA.D3.A8GN.06
#> "02" "02" "02" "02" "01" "01"
#> TCGA.EB.A550.01 TCGA.BF.A5EQ.01 TCGA.EB.A3HV.01 TCGA.HR.A5NC.01 TCGA.DA.A95Z.06 TCGA.EB.A6QZ.01
#> "01" "042" "05" "05" "02" "02"
#> TCGA.FW.A3I3.06 TCGA.WE.A8K6.06 TCGA.D3.A8GP.06 TCGA.EB.A42Z.01 TCGA.GN.A4U4.06 TCGA.GF.A4EO.06
#> "02" "03" "02" "02" "02" "01"
#> TCGA.GN.A8LK.06 TCGA.WE.A8K4.01 TCGA.DA.A95W.06 TCGA.FW.A5DX.01 TCGA.GN.A4U3.06 TCGA.EB.A6QY.01
#> "05" "01" "02" "02" "03" "01"
#> TCGA.EB.A5VU.01 TCGA.Z2.A8RT.06 TCGA.WE.A8K1.06 TCGA.EB.A41B.01 TCGA.WE.A8ZY.06 TCGA.D9.A6EG.06
#> "044" "03" "01" "03" "02" "02"
#> TCGA.BF.A5ER.01 TCGA.FR.A8YD.06 TCGA.FS.A4F9.06 TCGA.EB.A6R0.01 TCGA.ER.A42L.06 TCGA.D3.A8GJ.06
#> "05" "05" "05" "03" "01" "044"
#> TCGA.FR.A8YE.06 TCGA.WE.A8ZR.06 TCGA.BF.A9VF.01 TCGA.EE.A3JH.06 TCGA.DA.A95V.06 TCGA.GF.A769.01
#> "01" "043" "05" "01" "041" "02"
#> TCGA.D9.A4Z2.01 TCGA.FR.A44A.06 TCGA.EB.A5VV.06 TCGA.EE.A180.06 TCGA.D3.A8GC.06 TCGA.WE.A8K5.06
#> "03" "01" "01" "02" "05" "02"
#> TCGA.GN.A8LN.01 TCGA.EE.A3JB.06 TCGA.D3.A3MO.06 TCGA.ER.A42H.01 TCGA.WE.A8ZX.06 TCGA.GN.A4U5.01
#> "02" "041" "05" "05" "041" "01"
#> TCGA.D3.A8GS.06 TCGA.WE.A8ZQ.06 TCGA.EE.A2MF.06 TCGA.D3.A5GU.06 TCGA.GN.A4U8.06 TCGA.EB.A42Y.01
#> "044" "05" "02" "05" "041" "02"
#> TCGA.D3.A3ML.06 TCGA.EB.A551.01 TCGA.D3.A8GM.06 TCGA.D3.A8GL.06 TCGA.D3.A3MU.06 TCGA.FS.A4F0.06
#> "05" "044" "041" "02" "02" "02"
#> TCGA.D3.A3MV.06 TCGA.GN.A4U7.06 TCGA.FR.A2OS.01 TCGA.D3.A2JE.06 TCGA.YD.A89C.06 TCGA.FR.A726.01
#> "03" "03" "05" "05" "041" "041"
#> TCGA.BF.A5EP.01 TCGA.D3.A3MR.06 TCGA.D3.A8GR.06 TCGA.GN.A4U9.06 TCGA.EB.A6L9.06 TCGA.D3.A5GL.06
#> "03" "01" "05" "05" "01" "03"
#> TCGA.EB.A430.01 TCGA.D3.A8GE.06 TCGA.D3.A8GD.06 TCGA.EB.A41A.01 TCGA.W3.A825.06 TCGA.EE.A183.06
#> "01" "01" "01" "02" "044" "01"
#> TCGA.ER.A2NH.06 TCGA.D3.A5GR.06 TCGA.FR.A729.06 TCGA.D3.A1QA.06 TCGA.FS.A1YY.06 TCGA.EE.A2MK.06
#> "01" "044" "044" "02" "03" "03"
#> TCGA.EE.A2M8.06 TCGA.EB.A5KH.06 TCGA.FS.A1ZR.06 TCGA.EE.A3AE.06 TCGA.EE.A29P.06 TCGA.EB.A553.01
#> "01" "02" "05" "03" "044" "05"
#> TCGA.EE.A2MR.06 TCGA.GN.A26A.06 TCGA.FS.A1ZY.06 TCGA.EE.A20I.06 TCGA.DA.A1I5.06 TCGA.EE.A184.06
#> "01" "041" "02" "041" "01" "02"
#> TCGA.EB.A85J.01 TCGA.RP.A6K9.06 TCGA.EE.A17Y.06 TCGA.D9.A149.06 TCGA.ER.A19D.06 TCGA.FS.A1ZZ.06
#> "043" "042" "041" "042" "01" "02"
#> TCGA.EE.A2GP.06 TCGA.EE.A3AD.06 TCGA.D3.A1Q9.06 TCGA.GF.A2C7.01 TCGA.BF.A5ES.01 TCGA.ER.A199.06
#> "05" "02" "041" "05" "05" "01"
#> TCGA.EE.A3AH.06 TCGA.W3.A828.06 TCGA.EE.A2A5.06 TCGA.ER.A19L.06 TCGA.BF.A1PX.01 TCGA.ER.A19T.06
#> "02" "01" "05" "043" "01" "043"
#> TCGA.EB.A51B.01 TCGA.FS.A1ZQ.06 TCGA.D3.A2JG.06 TCGA.EE.A2GH.06 TCGA.ER.A19F.06 TCGA.ER.A196.01
#> "03" "03" "03" "01" "03" "01"
#> TCGA.D3.A2JC.06 TCGA.EE.A3AG.06 TCGA.ER.A19S.06 TCGA.EE.A2GC.06 TCGA.EE.A29N.06 TCGA.FR.A7U8.06
#> "044" "03" "01" "05" "01" "02"
#> TCGA.BF.A5EO.01 TCGA.ER.A19B.06 TCGA.D3.A5GN.06 TCGA.D3.A2JB.06 TCGA.ER.A19J.06 TCGA.D3.A2JD.06
#> "041" "03" "03" "01" "02" "01"
#> TCGA.FS.A1Z4.06 TCGA.FR.A7UA.06 TCGA.EE.A2M7.06 TCGA.D3.A1Q3.06 TCGA.EB.A85I.01 TCGA.EB.A82C.01
#> "01" "01" "044" "043" "042" "02"
#> TCGA.ER.A19E.06 TCGA.FS.A1ZK.06 TCGA.FS.A1ZU.06 TCGA.EB.A5FP.01 TCGA.EB.A4XL.01 TCGA.DA.A1I2.06
#> "05" "05" "05" "02" "03" "044"
#> TCGA.EE.A29L.06 TCGA.FS.A1ZN.01 TCGA.EB.A24D.01 TCGA.EE.A2GB.06 TCGA.DA.A1I7.06 TCGA.ER.A2NF.01
#> "02" "02" "05" "03" "044" "01"
#> TCGA.GN.A263.01 TCGA.EE.A20C.06 TCGA.EE.A2MQ.06 TCGA.ER.A19N.06 TCGA.FS.A1Z3.06 TCGA.DA.A1I8.06
#> "01" "02" "05" "01" "03" "03"
#> TCGA.D3.A5GS.06 TCGA.EE.A181.06 TCGA.GN.A268.06 TCGA.W3.A824.06 TCGA.EE.A2GS.06 TCGA.FR.A7U9.06
#> "03" "041" "02" "05" "03" "01"
#> TCGA.ER.A19Q.06 TCGA.FS.A1ZM.06 TCGA.EE.A2MG.06 TCGA.EE.A2MC.06 TCGA.EE.A17Z.06 TCGA.D3.A2JP.06
#> "01" "044" "01" "01" "05" "041"
#> TCGA.ER.A19C.06 TCGA.EB.A82B.01 TCGA.EE.A2A0.06 TCGA.EE.A29G.06 TCGA.D3.A5GO.06 TCGA.GN.A269.01
#> "044" "042" "01" "01" "03" "01"
#> TCGA.EE.A2A1.06 TCGA.ER.A1A1.06 TCGA.FS.A1ZG.06 TCGA.FS.A1ZE.06 TCGA.FS.A1ZH.06 TCGA.EE.A2MH.06
#> "01" "01" "02" "02" "041" "01"
#> TCGA.D3.A2J6.06 TCGA.EE.A29Q.06 TCGA.BF.A1PZ.01 TCGA.D3.A3BZ.06 TCGA.D3.A2JO.06 TCGA.GN.A267.06
#> "042" "03" "03" "01" "044" "043"
#> TCGA.EE.A2MN.06 TCGA.GN.A264.06 TCGA.ER.A197.06 TCGA.DA.A1IB.06 TCGA.D3.A3CC.06 TCGA.ER.A19T.01
#> "05" "02" "01" "01" "042" "05"
#> TCGA.GN.A261.06 TCGA.FS.A1YW.06 TCGA.BF.A1PU.01 TCGA.D3.A1QB.06 TCGA.D3.A1Q6.06 TCGA.D3.A3C8.06
#> "01" "02" "044" "01" "044" "01"
#> TCGA.ER.A19A.06 TCGA.EE.A2GN.06 TCGA.EE.A29M.06 TCGA.D3.A2J7.06 TCGA.EB.A24C.01 TCGA.GN.A262.06
#> "01" "05" "01" "01" "043" "02"
#> TCGA.EE.A2GD.06 TCGA.D3.A2J9.06 TCGA.EE.A29B.06 TCGA.D9.A1JX.06 TCGA.EE.A29A.06 TCGA.D3.A2JL.06
#> "01" "01" "05" "03" "02" "041"
#> TCGA.D3.A1Q4.06 TCGA.FS.A1ZS.06 TCGA.D3.A3C3.06 TCGA.D3.A2J8.06 TCGA.FS.A1ZF.06 TCGA.FS.A1ZC.06
#> "01" "042" "041" "01" "03" "02"
#> TCGA.EE.A20H.06 TCGA.EE.A29W.06 TCGA.D3.A1QA.07 TCGA.BF.A1PV.01 TCGA.EE.A29S.06 TCGA.DA.A1HV.06
#> "05" "03" "041" "05" "044" "03"
#> TCGA.FS.A1Z0.06 TCGA.EE.A2GO.06 TCGA.EB.A1NK.01 TCGA.GN.A26D.06 TCGA.EE.A2MJ.06 TCGA.ER.A198.06
#> "01" "02" "01" "042" "01" "05"
#> TCGA.EE.A17X.06 TCGA.EE.A2M5.06 TCGA.GN.A266.06 TCGA.D3.A3C1.06 TCGA.D3.A2JH.06 TCGA.EE.A20F.06
#> "03" "041" "044" "044" "01" "041"
#> TCGA.EE.A29E.06 TCGA.ER.A2NG.06 TCGA.ER.A193.06 TCGA.FS.A1ZW.06 TCGA.ER.A19O.06 TCGA.EE.A2ME.06
#> "01" "01" "042" "041" "044" "01"
#> TCGA.EE.A20B.06 TCGA.EE.A3AF.06 TCGA.GN.A265.06 TCGA.FS.A1YX.06 TCGA.FS.A1ZJ.06 TCGA.ER.A19H.06
#> "041" "03" "01" "044" "05" "03"
#> TCGA.EE.A3AC.06 TCGA.EE.A2MU.06 TCGA.ER.A194.01 TCGA.EE.A2MS.06 TCGA.EE.A29R.06 TCGA.D9.A1X3.06
#> "05" "01" "044" "043" "02" "02"
#> TCGA.EE.A29X.06 TCGA.EE.A2GK.06 TCGA.EE.A3AA.06 TCGA.ER.A2NE.06 TCGA.EE.A2GR.06 TCGA.FS.A1ZD.06
#> "044" "01" "01" "02" "05" "05"
#> TCGA.ER.A19P.06 TCGA.D3.A1Q8.06 TCGA.ER.A2NC.06 TCGA.BF.A1Q0.01 TCGA.FS.A1ZP.06 TCGA.EE.A182.06
#> "01" "01" "044" "042" "05" "043"
#> TCGA.D9.A1JW.06 TCGA.D3.A1Q7.06 TCGA.EE.A185.06 TCGA.EE.A2GJ.06 TCGA.D3.A3CB.06 TCGA.EE.A2GU.06
#> "042" "01" "02" "043" "01" "042"
#> TCGA.ER.A195.06 TCGA.FS.A1Z7.06 TCGA.EE.A2M6.06 TCGA.ER.A19K.01 TCGA.DA.A1HY.06 TCGA.D3.A3C7.06
#> "01" "042" "02" "044" "03" "03"
#> TCGA.EE.A2MP.06 TCGA.EE.A29H.06 TCGA.FR.A3YO.06 TCGA.XV.AB01.01 TCGA.RP.A694.06 TCGA.EB.A5SF.01
#> "03" "03" "044" "03" "044" "01"
#> TCGA.ER.A19G.06 TCGA.EE.A2GE.06 TCGA.GF.A3OT.06 TCGA.ER.A2NF.06 TCGA.RP.A695.06 TCGA.BF.AAP7.01
#> "03" "01" "01" "01" "05" "01"
#> TCGA.EB.A3Y7.01 TCGA.EB.A3XC.01 TCGA.ER.A19W.06 TCGA.FR.A69P.06 TCGA.RP.A693.06 TCGA.FW.A3TV.06
#> "042" "03" "01" "03" "01" "01"
#> TCGA.FW.A3R5.11 TCGA.FW.A3TU.06 TCGA.BF.AAP8.01 TCGA.EE.A2MM.06 TCGA.DA.A1HW.06 TCGA.DA.A1IC.06
#> "01" "05" "042" "05" "044" "05"
#> TCGA.XV.AAZV.01 TCGA.D3.A3C6.06 TCGA.EE.A29C.06 TCGA.BF.AAP2.01 TCGA.EE.A2A2.06 TCGA.GF.A6C8.06
#> "01" "03" "01" "02" "03" "044"
#> TCGA.RP.A690.06 TCGA.FW.A5DY.06 TCGA.DA.A1I4.06 TCGA.EE.A29V.06 TCGA.GF.A6C9.06 TCGA.EE.A2GT.06
#> "01" "01" "01" "041" "01" "01"
#> TCGA.GN.A9SD.06 TCGA.EE.A3AB.06 TCGA.BF.AAP6.01 TCGA.EB.A5SH.06 TCGA.D9.A6E9.06 TCGA.BF.AAP4.01
#> "01" "041" "03" "043" "044" "044"
#> TCGA.EE.A2GM.06 TCGA.D3.A3CF.06 TCGA.D9.A6EC.06 TCGA.DA.A1I1.06 TCGA.HR.A2OH.06 TCGA.EE.A2MT.06
#> "02" "01" "02" "041" "01" "042"
#> TCGA.ER.A19M.06 TCGA.GN.A26C.01 TCGA.FS.A1ZA.06 TCGA.EB.A5SE.01 TCGA.ER.A3PL.06 TCGA.FR.A3R1.01
#> "041" "01" "044" "02" "05" "03"
#> TCGA.EE.A2MI.06 TCGA.D3.A3CE.06 TCGA.D3.A5GT.01 TCGA.ER.A2NB.01 TCGA.D3.A1Q5.06 TCGA.EB.A5UN.06
#> "044" "044" "05" "042" "042" "01"
#> TCGA.EB.A299.01 TCGA.DA.A1IA.06 TCGA.EB.A5SG.06 TCGA.D9.A6EA.06 TCGA.XV.AAZY.01 TCGA.EB.A57M.01
#> "03" "05" "01" "02" "01" "041"
#> TCGA.EE.A2A6.06 TCGA.D3.A2JA.06 TCGA.D3.A1Q1.06 TCGA.EB.A3XF.01 TCGA.D3.A2JF.06 TCGA.XV.AAZW.01
#> "042" "01" "042" "03" "03" "03"
#> TCGA.EB.A3Y6.01 TCGA.EB.A3XE.01 TCGA.D9.A3Z4.01 TCGA.FW.A3R5.06 TCGA.EE.A2GI.06 TCGA.EE.A2GL.06
#> "044" "043" "05" "043" "041" "01"
#> TCGA.EB.A3XB.01 TCGA.BF.AAOU.01 TCGA.EB.A3XD.01 TCGA.EE.A2MD.06 TCGA.YD.A9TB.06 TCGA.W3.AA1V.06
#> "044" "01" "01" "044" "05" "044"
#> TCGA.ER.A2ND.06 TCGA.D3.A2JK.06 TCGA.FS.A1ZB.06 TCGA.EE.A29D.06 TCGA.EB.A5UM.01 TCGA.QB.A6FS.06
#> "05" "041" "01" "02" "043" "01"
#> TCGA.D9.A3Z1.06 TCGA.D3.A2JN.06 TCGA.FR.A3YN.06 TCGA.FS.A1ZT.06 TCGA.D9.A148.06 TCGA.HR.A2OG.06
#> "01" "01" "03" "01" "041" "01"
#> TCGA.EE.A2ML.06 TCGA.EB.A5UL.06 TCGA.EE.A29T.06 TCGA.D9.A3Z3.06 TCGA.D9.A4Z3.01 TCGA.ER.A3ES.06
#> "041" "041" "043" "01" "05" "042"
#> TCGA.XV.A9VZ.01 TCGA.QB.AA9O.06 TCGA.EB.A44Q.06 TCGA.EB.A44R.06 TCGA.BF.A3DJ.01 TCGA.EE.A3JD.06
#> "01" "03" "044" "043" "03" "01"
#> TCGA.D3.A51N.06 TCGA.EB.A44N.01 TCGA.EE.A3J3.06 TCGA.XV.A9W5.01 TCGA.D3.A51G.06 TCGA.EB.A4P0.01
#> "041" "01" "03" "041" "03" "03"
#> TCGA.BF.AAP1.01 TCGA.EE.A3J4.06 TCGA.Z2.AA3V.06 TCGA.LH.A9QB.06 TCGA.D3.A51J.06 TCGA.3N.A9WC.06
#> "02" "05" "01" "02" "044" "042"
#> TCGA.DA.A3F8.06 TCGA.D9.A4Z6.06 TCGA.D3.A51R.06 TCGA.EB.A4OZ.01 TCGA.FS.A4FB.06 TCGA.EE.A3JE.06
#> "01" "041" "03" "01" "03" "01"
#> TCGA.W3.AA1W.06 TCGA.DA.A1I0.06 TCGA.D3.A51F.06 TCGA.IH.A3EA.01 TCGA.EB.A431.01 TCGA.EB.A97M.01
#> "01" "041" "01" "05" "041" "02"
#> TCGA.BF.AAOX.01 TCGA.DA.A3F5.06 TCGA.YD.A9TA.06 TCGA.DA.A3F2.06 TCGA.EB.A44O.01 TCGA.EB.A4IQ.01
#> "041" "042" "041" "01" "05" "042"
#> TCGA.EB.A4IS.01 TCGA.YG.AA3O.06 TCGA.ER.A3EV.06 TCGA.3N.A9WD.06 TCGA.BF.A3DM.01 TCGA.XV.A9W2.01
#> "01" "05" "043" "01" "03" "042"
#> TCGA.W3.AA1Q.06 TCGA.WE.AAA0.06 TCGA.W3.AA1R.06 TCGA.EE.A3J5.06 TCGA.EB.A4OY.01 TCGA.FS.A4FD.06
#> "05" "041" "03" "041" "01" "042"
#> TCGA.BF.AAP0.06 TCGA.YG.AA3P.06 TCGA.EE.A3JA.06 TCGA.W3.AA21.06 TCGA.WE.AAA3.06 TCGA.FS.A4F4.06
#> "01" "05" "03" "02" "042" "03"
#> TCGA.BF.A3DN.01 TCGA.ER.A3ET.06 TCGA.W3.AA1O.06 TCGA.D3.A51E.06 TCGA.Z2.AA3S.06 TCGA.YG.AA3N.01
#> "03" "042" "05" "03" "02" "044"
#> TCGA.WE.AA9Y.06 TCGA.FS.A4F5.06 TCGA.EE.A3J7.06 TCGA.FS.A4F8.06 TCGA.DA.A3F3.06 TCGA.D3.A51H.06
#> "01" "02" "05" "01" "03" "01"
#> TCGA.BF.A3DL.01 TCGA.D3.A51T.06 TCGA.D3.A51K.06 TCGA.EB.A44P.01 TCGA.D9.A4Z5.01 TCGA.WE.AAA4.06
#> "01" "03" "05" "05" "02" "01"
#> TCGA.3N.A9WB.06 TCGA.EE.A3J8.06
#> "02" "02"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 29265))
#> TCGA.FR.A728.01 TCGA.GN.A4U8.11 TCGA.GN.A8LL.06 TCGA.FR.A8YC.06 TCGA.DA.A95X.06 TCGA.ER.A42K.06
#> "01" "01" "03" "02" "02" "03"
#> TCGA.D3.A8GO.06 TCGA.D3.A8GK.06 TCGA.WE.A8JZ.06 TCGA.WE.A8ZO.06 TCGA.D3.A8GI.06 TCGA.FS.A4FC.06
#> "01" "05" "02" "05" "05" "042"
#> TCGA.FS.A4F2.06 TCGA.WE.A8ZM.06 TCGA.WE.A8ZT.06 TCGA.D3.A8GQ.06 TCGA.D3.A8GB.06 TCGA.DA.A95Y.06
#> "03" "05" "03" "041" "01" "03"
#> TCGA.EE.A3JI.06 TCGA.OD.A75X.06 TCGA.DA.A960.01 TCGA.D3.A8GV.06 TCGA.WE.A8ZN.06 TCGA.D3.A8GN.06
#> "02" "02" "02" "02" "01" "01"
#> TCGA.EB.A550.01 TCGA.BF.A5EQ.01 TCGA.EB.A3HV.01 TCGA.HR.A5NC.01 TCGA.DA.A95Z.06 TCGA.EB.A6QZ.01
#> "01" "042" "05" "05" "02" "02"
#> TCGA.FW.A3I3.06 TCGA.WE.A8K6.06 TCGA.D3.A8GP.06 TCGA.EB.A42Z.01 TCGA.GN.A4U4.06 TCGA.GF.A4EO.06
#> "02" "03" "02" "02" "02" "01"
#> TCGA.GN.A8LK.06 TCGA.WE.A8K4.01 TCGA.DA.A95W.06 TCGA.FW.A5DX.01 TCGA.GN.A4U3.06 TCGA.EB.A6QY.01
#> "05" "01" "02" "02" "03" "01"
#> TCGA.EB.A5VU.01 TCGA.Z2.A8RT.06 TCGA.WE.A8K1.06 TCGA.EB.A41B.01 TCGA.WE.A8ZY.06 TCGA.D9.A6EG.06
#> "044" "03" "01" "03" "02" "02"
#> TCGA.BF.A5ER.01 TCGA.FR.A8YD.06 TCGA.FS.A4F9.06 TCGA.EB.A6R0.01 TCGA.ER.A42L.06 TCGA.D3.A8GJ.06
#> "05" "05" "05" "03" "01" "044"
#> TCGA.FR.A8YE.06 TCGA.WE.A8ZR.06 TCGA.BF.A9VF.01 TCGA.EE.A3JH.06 TCGA.DA.A95V.06 TCGA.GF.A769.01
#> "01" "043" "05" "01" "041" "02"
#> TCGA.D9.A4Z2.01 TCGA.FR.A44A.06 TCGA.EB.A5VV.06 TCGA.EE.A180.06 TCGA.D3.A8GC.06 TCGA.WE.A8K5.06
#> "03" "01" "01" "02" "05" "02"
#> TCGA.GN.A8LN.01 TCGA.EE.A3JB.06 TCGA.D3.A3MO.06 TCGA.ER.A42H.01 TCGA.WE.A8ZX.06 TCGA.GN.A4U5.01
#> "02" "041" "05" "05" "041" "01"
#> TCGA.D3.A8GS.06 TCGA.WE.A8ZQ.06 TCGA.EE.A2MF.06 TCGA.D3.A5GU.06 TCGA.GN.A4U8.06 TCGA.EB.A42Y.01
#> "044" "05" "02" "05" "041" "02"
#> TCGA.D3.A3ML.06 TCGA.EB.A551.01 TCGA.D3.A8GM.06 TCGA.D3.A8GL.06 TCGA.D3.A3MU.06 TCGA.FS.A4F0.06
#> "05" "044" "041" "02" "02" "02"
#> TCGA.D3.A3MV.06 TCGA.GN.A4U7.06 TCGA.FR.A2OS.01 TCGA.D3.A2JE.06 TCGA.YD.A89C.06 TCGA.FR.A726.01
#> "03" "03" "05" "05" "041" "041"
#> TCGA.BF.A5EP.01 TCGA.D3.A3MR.06 TCGA.D3.A8GR.06 TCGA.GN.A4U9.06 TCGA.EB.A6L9.06 TCGA.D3.A5GL.06
#> "03" "01" "05" "05" "01" "03"
#> TCGA.EB.A430.01 TCGA.D3.A8GE.06 TCGA.D3.A8GD.06 TCGA.EB.A41A.01 TCGA.W3.A825.06 TCGA.EE.A183.06
#> "01" "01" "01" "02" "044" "01"
#> TCGA.ER.A2NH.06 TCGA.D3.A5GR.06 TCGA.FR.A729.06 TCGA.D3.A1QA.06 TCGA.FS.A1YY.06 TCGA.EE.A2MK.06
#> "01" "044" "044" "02" "03" "03"
#> TCGA.EE.A2M8.06 TCGA.EB.A5KH.06 TCGA.FS.A1ZR.06 TCGA.EE.A3AE.06 TCGA.EE.A29P.06 TCGA.EB.A553.01
#> "01" "02" "05" "03" "044" "05"
#> TCGA.EE.A2MR.06 TCGA.GN.A26A.06 TCGA.FS.A1ZY.06 TCGA.EE.A20I.06 TCGA.DA.A1I5.06 TCGA.EE.A184.06
#> "01" "041" "02" "041" "01" "02"
#> TCGA.EB.A85J.01 TCGA.RP.A6K9.06 TCGA.EE.A17Y.06 TCGA.D9.A149.06 TCGA.ER.A19D.06 TCGA.FS.A1ZZ.06
#> "043" "042" "041" "042" "01" "02"
#> TCGA.EE.A2GP.06 TCGA.EE.A3AD.06 TCGA.D3.A1Q9.06 TCGA.GF.A2C7.01 TCGA.BF.A5ES.01 TCGA.ER.A199.06
#> "05" "02" "041" "05" "05" "01"
#> TCGA.EE.A3AH.06 TCGA.W3.A828.06 TCGA.EE.A2A5.06 TCGA.ER.A19L.06 TCGA.BF.A1PX.01 TCGA.ER.A19T.06
#> "02" "01" "05" "043" "01" "043"
#> TCGA.EB.A51B.01 TCGA.FS.A1ZQ.06 TCGA.D3.A2JG.06 TCGA.EE.A2GH.06 TCGA.ER.A19F.06 TCGA.ER.A196.01
#> "03" "03" "03" "01" "03" "01"
#> TCGA.D3.A2JC.06 TCGA.EE.A3AG.06 TCGA.ER.A19S.06 TCGA.EE.A2GC.06 TCGA.EE.A29N.06 TCGA.FR.A7U8.06
#> "044" "03" "01" "05" "01" "02"
#> TCGA.BF.A5EO.01 TCGA.ER.A19B.06 TCGA.D3.A5GN.06 TCGA.D3.A2JB.06 TCGA.ER.A19J.06 TCGA.D3.A2JD.06
#> "041" "03" "03" "01" "02" "01"
#> TCGA.FS.A1Z4.06 TCGA.FR.A7UA.06 TCGA.EE.A2M7.06 TCGA.D3.A1Q3.06 TCGA.EB.A85I.01 TCGA.EB.A82C.01
#> "01" "01" "044" "043" "042" "02"
#> TCGA.ER.A19E.06 TCGA.FS.A1ZK.06 TCGA.FS.A1ZU.06 TCGA.EB.A5FP.01 TCGA.EB.A4XL.01 TCGA.DA.A1I2.06
#> "05" "05" "05" "02" "03" "044"
#> TCGA.EE.A29L.06 TCGA.FS.A1ZN.01 TCGA.EB.A24D.01 TCGA.EE.A2GB.06 TCGA.DA.A1I7.06 TCGA.ER.A2NF.01
#> "02" "02" "05" "03" "044" "01"
#> TCGA.GN.A263.01 TCGA.EE.A20C.06 TCGA.EE.A2MQ.06 TCGA.ER.A19N.06 TCGA.FS.A1Z3.06 TCGA.DA.A1I8.06
#> "01" "02" "05" "01" "03" "03"
#> TCGA.D3.A5GS.06 TCGA.EE.A181.06 TCGA.GN.A268.06 TCGA.W3.A824.06 TCGA.EE.A2GS.06 TCGA.FR.A7U9.06
#> "03" "041" "02" "05" "03" "01"
#> TCGA.ER.A19Q.06 TCGA.FS.A1ZM.06 TCGA.EE.A2MG.06 TCGA.EE.A2MC.06 TCGA.EE.A17Z.06 TCGA.D3.A2JP.06
#> "01" "044" "01" "01" "05" "041"
#> TCGA.ER.A19C.06 TCGA.EB.A82B.01 TCGA.EE.A2A0.06 TCGA.EE.A29G.06 TCGA.D3.A5GO.06 TCGA.GN.A269.01
#> "044" "042" "01" "01" "03" "01"
#> TCGA.EE.A2A1.06 TCGA.ER.A1A1.06 TCGA.FS.A1ZG.06 TCGA.FS.A1ZE.06 TCGA.FS.A1ZH.06 TCGA.EE.A2MH.06
#> "01" "01" "02" "02" "041" "01"
#> TCGA.D3.A2J6.06 TCGA.EE.A29Q.06 TCGA.BF.A1PZ.01 TCGA.D3.A3BZ.06 TCGA.D3.A2JO.06 TCGA.GN.A267.06
#> "042" "03" "03" "01" "044" "043"
#> TCGA.EE.A2MN.06 TCGA.GN.A264.06 TCGA.ER.A197.06 TCGA.DA.A1IB.06 TCGA.D3.A3CC.06 TCGA.ER.A19T.01
#> "05" "02" "01" "01" "042" "05"
#> TCGA.GN.A261.06 TCGA.FS.A1YW.06 TCGA.BF.A1PU.01 TCGA.D3.A1QB.06 TCGA.D3.A1Q6.06 TCGA.D3.A3C8.06
#> "01" "02" "044" "01" "044" "01"
#> TCGA.ER.A19A.06 TCGA.EE.A2GN.06 TCGA.EE.A29M.06 TCGA.D3.A2J7.06 TCGA.EB.A24C.01 TCGA.GN.A262.06
#> "01" "05" "01" "01" "043" "02"
#> TCGA.EE.A2GD.06 TCGA.D3.A2J9.06 TCGA.EE.A29B.06 TCGA.D9.A1JX.06 TCGA.EE.A29A.06 TCGA.D3.A2JL.06
#> "01" "01" "05" "03" "02" "041"
#> TCGA.D3.A1Q4.06 TCGA.FS.A1ZS.06 TCGA.D3.A3C3.06 TCGA.D3.A2J8.06 TCGA.FS.A1ZF.06 TCGA.FS.A1ZC.06
#> "01" "042" "041" "01" "03" "02"
#> TCGA.EE.A20H.06 TCGA.EE.A29W.06 TCGA.D3.A1QA.07 TCGA.BF.A1PV.01 TCGA.EE.A29S.06 TCGA.DA.A1HV.06
#> "05" "03" "041" "05" "044" "03"
#> TCGA.FS.A1Z0.06 TCGA.EE.A2GO.06 TCGA.EB.A1NK.01 TCGA.GN.A26D.06 TCGA.EE.A2MJ.06 TCGA.ER.A198.06
#> "01" "02" "01" "042" "01" "05"
#> TCGA.EE.A17X.06 TCGA.EE.A2M5.06 TCGA.GN.A266.06 TCGA.D3.A3C1.06 TCGA.D3.A2JH.06 TCGA.EE.A20F.06
#> "03" "041" "044" "044" "01" "041"
#> TCGA.EE.A29E.06 TCGA.ER.A2NG.06 TCGA.ER.A193.06 TCGA.FS.A1ZW.06 TCGA.ER.A19O.06 TCGA.EE.A2ME.06
#> "01" "01" "042" "041" "044" "01"
#> TCGA.EE.A20B.06 TCGA.EE.A3AF.06 TCGA.GN.A265.06 TCGA.FS.A1YX.06 TCGA.FS.A1ZJ.06 TCGA.ER.A19H.06
#> "041" "03" "01" "044" "05" "03"
#> TCGA.EE.A3AC.06 TCGA.EE.A2MU.06 TCGA.ER.A194.01 TCGA.EE.A2MS.06 TCGA.EE.A29R.06 TCGA.D9.A1X3.06
#> "05" "01" "044" "043" "02" "02"
#> TCGA.EE.A29X.06 TCGA.EE.A2GK.06 TCGA.EE.A3AA.06 TCGA.ER.A2NE.06 TCGA.EE.A2GR.06 TCGA.FS.A1ZD.06
#> "044" "01" "01" "02" "05" "05"
#> TCGA.ER.A19P.06 TCGA.D3.A1Q8.06 TCGA.ER.A2NC.06 TCGA.BF.A1Q0.01 TCGA.FS.A1ZP.06 TCGA.EE.A182.06
#> "01" "01" "044" "042" "05" "043"
#> TCGA.D9.A1JW.06 TCGA.D3.A1Q7.06 TCGA.EE.A185.06 TCGA.EE.A2GJ.06 TCGA.D3.A3CB.06 TCGA.EE.A2GU.06
#> "042" "01" "02" "043" "01" "042"
#> TCGA.ER.A195.06 TCGA.FS.A1Z7.06 TCGA.EE.A2M6.06 TCGA.ER.A19K.01 TCGA.DA.A1HY.06 TCGA.D3.A3C7.06
#> "01" "042" "02" "044" "03" "03"
#> TCGA.EE.A2MP.06 TCGA.EE.A29H.06 TCGA.FR.A3YO.06 TCGA.XV.AB01.01 TCGA.RP.A694.06 TCGA.EB.A5SF.01
#> "03" "03" "044" "03" "044" "01"
#> TCGA.ER.A19G.06 TCGA.EE.A2GE.06 TCGA.GF.A3OT.06 TCGA.ER.A2NF.06 TCGA.RP.A695.06 TCGA.BF.AAP7.01
#> "03" "01" "01" "01" "05" "01"
#> TCGA.EB.A3Y7.01 TCGA.EB.A3XC.01 TCGA.ER.A19W.06 TCGA.FR.A69P.06 TCGA.RP.A693.06 TCGA.FW.A3TV.06
#> "042" "03" "01" "03" "01" "01"
#> TCGA.FW.A3R5.11 TCGA.FW.A3TU.06 TCGA.BF.AAP8.01 TCGA.EE.A2MM.06 TCGA.DA.A1HW.06 TCGA.DA.A1IC.06
#> "01" "05" "042" "05" "044" "05"
#> TCGA.XV.AAZV.01 TCGA.D3.A3C6.06 TCGA.EE.A29C.06 TCGA.BF.AAP2.01 TCGA.EE.A2A2.06 TCGA.GF.A6C8.06
#> "01" "03" "01" "02" "03" "044"
#> TCGA.RP.A690.06 TCGA.FW.A5DY.06 TCGA.DA.A1I4.06 TCGA.EE.A29V.06 TCGA.GF.A6C9.06 TCGA.EE.A2GT.06
#> "01" "01" "01" "041" "01" "01"
#> TCGA.GN.A9SD.06 TCGA.EE.A3AB.06 TCGA.BF.AAP6.01 TCGA.EB.A5SH.06 TCGA.D9.A6E9.06 TCGA.BF.AAP4.01
#> "01" "041" "03" "043" "044" "044"
#> TCGA.EE.A2GM.06 TCGA.D3.A3CF.06 TCGA.D9.A6EC.06 TCGA.DA.A1I1.06 TCGA.HR.A2OH.06 TCGA.EE.A2MT.06
#> "02" "01" "02" "041" "01" "042"
#> TCGA.ER.A19M.06 TCGA.GN.A26C.01 TCGA.FS.A1ZA.06 TCGA.EB.A5SE.01 TCGA.ER.A3PL.06 TCGA.FR.A3R1.01
#> "041" "01" "044" "02" "05" "03"
#> TCGA.EE.A2MI.06 TCGA.D3.A3CE.06 TCGA.D3.A5GT.01 TCGA.ER.A2NB.01 TCGA.D3.A1Q5.06 TCGA.EB.A5UN.06
#> "044" "044" "05" "042" "042" "01"
#> TCGA.EB.A299.01 TCGA.DA.A1IA.06 TCGA.EB.A5SG.06 TCGA.D9.A6EA.06 TCGA.XV.AAZY.01 TCGA.EB.A57M.01
#> "03" "05" "01" "02" "01" "041"
#> TCGA.EE.A2A6.06 TCGA.D3.A2JA.06 TCGA.D3.A1Q1.06 TCGA.EB.A3XF.01 TCGA.D3.A2JF.06 TCGA.XV.AAZW.01
#> "042" "01" "042" "03" "03" "03"
#> TCGA.EB.A3Y6.01 TCGA.EB.A3XE.01 TCGA.D9.A3Z4.01 TCGA.FW.A3R5.06 TCGA.EE.A2GI.06 TCGA.EE.A2GL.06
#> "044" "043" "05" "043" "041" "01"
#> TCGA.EB.A3XB.01 TCGA.BF.AAOU.01 TCGA.EB.A3XD.01 TCGA.EE.A2MD.06 TCGA.YD.A9TB.06 TCGA.W3.AA1V.06
#> "044" "01" "01" "044" "05" "044"
#> TCGA.ER.A2ND.06 TCGA.D3.A2JK.06 TCGA.FS.A1ZB.06 TCGA.EE.A29D.06 TCGA.EB.A5UM.01 TCGA.QB.A6FS.06
#> "05" "041" "01" "02" "043" "01"
#> TCGA.D9.A3Z1.06 TCGA.D3.A2JN.06 TCGA.FR.A3YN.06 TCGA.FS.A1ZT.06 TCGA.D9.A148.06 TCGA.HR.A2OG.06
#> "01" "01" "03" "01" "041" "01"
#> TCGA.EE.A2ML.06 TCGA.EB.A5UL.06 TCGA.EE.A29T.06 TCGA.D9.A3Z3.06 TCGA.D9.A4Z3.01 TCGA.ER.A3ES.06
#> "041" "041" "043" "01" "05" "042"
#> TCGA.XV.A9VZ.01 TCGA.QB.AA9O.06 TCGA.EB.A44Q.06 TCGA.EB.A44R.06 TCGA.BF.A3DJ.01 TCGA.EE.A3JD.06
#> "01" "03" "044" "043" "03" "01"
#> TCGA.D3.A51N.06 TCGA.EB.A44N.01 TCGA.EE.A3J3.06 TCGA.XV.A9W5.01 TCGA.D3.A51G.06 TCGA.EB.A4P0.01
#> "041" "01" "03" "041" "03" "03"
#> TCGA.BF.AAP1.01 TCGA.EE.A3J4.06 TCGA.Z2.AA3V.06 TCGA.LH.A9QB.06 TCGA.D3.A51J.06 TCGA.3N.A9WC.06
#> "02" "05" "01" "02" "044" "042"
#> TCGA.DA.A3F8.06 TCGA.D9.A4Z6.06 TCGA.D3.A51R.06 TCGA.EB.A4OZ.01 TCGA.FS.A4FB.06 TCGA.EE.A3JE.06
#> "01" "041" "03" "01" "03" "01"
#> TCGA.W3.AA1W.06 TCGA.DA.A1I0.06 TCGA.D3.A51F.06 TCGA.IH.A3EA.01 TCGA.EB.A431.01 TCGA.EB.A97M.01
#> "01" "041" "01" "05" "041" "02"
#> TCGA.BF.AAOX.01 TCGA.DA.A3F5.06 TCGA.YD.A9TA.06 TCGA.DA.A3F2.06 TCGA.EB.A44O.01 TCGA.EB.A4IQ.01
#> "041" "042" "041" "01" "05" "042"
#> TCGA.EB.A4IS.01 TCGA.YG.AA3O.06 TCGA.ER.A3EV.06 TCGA.3N.A9WD.06 TCGA.BF.A3DM.01 TCGA.XV.A9W2.01
#> "01" "05" "043" "01" "03" "042"
#> TCGA.W3.AA1Q.06 TCGA.WE.AAA0.06 TCGA.W3.AA1R.06 TCGA.EE.A3J5.06 TCGA.EB.A4OY.01 TCGA.FS.A4FD.06
#> "05" "041" "03" "041" "01" "042"
#> TCGA.BF.AAP0.06 TCGA.YG.AA3P.06 TCGA.EE.A3JA.06 TCGA.W3.AA21.06 TCGA.WE.AAA3.06 TCGA.FS.A4F4.06
#> "01" "05" "03" "02" "042" "03"
#> TCGA.BF.A3DN.01 TCGA.ER.A3ET.06 TCGA.W3.AA1O.06 TCGA.D3.A51E.06 TCGA.Z2.AA3S.06 TCGA.YG.AA3N.01
#> "03" "042" "05" "03" "02" "044"
#> TCGA.WE.AA9Y.06 TCGA.FS.A4F5.06 TCGA.EE.A3J7.06 TCGA.FS.A4F8.06 TCGA.DA.A3F3.06 TCGA.D3.A51H.06
#> "01" "02" "05" "01" "03" "01"
#> TCGA.BF.A3DL.01 TCGA.D3.A51T.06 TCGA.D3.A51K.06 TCGA.EB.A44P.01 TCGA.D9.A4Z5.01 TCGA.WE.AAA4.06
#> "01" "03" "05" "05" "02" "01"
#> TCGA.3N.A9WB.06 TCGA.EE.A3J8.06
#> "02" "02"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 41067))
#> TCGA.FR.A728.01 TCGA.GN.A4U8.11 TCGA.GN.A8LL.06 TCGA.FR.A8YC.06 TCGA.DA.A95X.06 TCGA.ER.A42K.06
#> "01" "01" "03" "02" "02" "03"
#> TCGA.D3.A8GO.06 TCGA.D3.A8GK.06 TCGA.WE.A8JZ.06 TCGA.WE.A8ZO.06 TCGA.D3.A8GI.06 TCGA.FS.A4FC.06
#> "01" "05" "02" "05" "05" "042"
#> TCGA.FS.A4F2.06 TCGA.WE.A8ZM.06 TCGA.WE.A8ZT.06 TCGA.D3.A8GQ.06 TCGA.D3.A8GB.06 TCGA.DA.A95Y.06
#> "03" "05" "03" "041" "01" "03"
#> TCGA.EE.A3JI.06 TCGA.OD.A75X.06 TCGA.DA.A960.01 TCGA.D3.A8GV.06 TCGA.WE.A8ZN.06 TCGA.D3.A8GN.06
#> "02" "02" "02" "02" "01" "01"
#> TCGA.EB.A550.01 TCGA.BF.A5EQ.01 TCGA.EB.A3HV.01 TCGA.HR.A5NC.01 TCGA.DA.A95Z.06 TCGA.EB.A6QZ.01
#> "01" "042" "05" "05" "02" "02"
#> TCGA.FW.A3I3.06 TCGA.WE.A8K6.06 TCGA.D3.A8GP.06 TCGA.EB.A42Z.01 TCGA.GN.A4U4.06 TCGA.GF.A4EO.06
#> "02" "03" "02" "02" "02" "01"
#> TCGA.GN.A8LK.06 TCGA.WE.A8K4.01 TCGA.DA.A95W.06 TCGA.FW.A5DX.01 TCGA.GN.A4U3.06 TCGA.EB.A6QY.01
#> "05" "01" "02" "02" "03" "01"
#> TCGA.EB.A5VU.01 TCGA.Z2.A8RT.06 TCGA.WE.A8K1.06 TCGA.EB.A41B.01 TCGA.WE.A8ZY.06 TCGA.D9.A6EG.06
#> "044" "03" "01" "03" "02" "02"
#> TCGA.BF.A5ER.01 TCGA.FR.A8YD.06 TCGA.FS.A4F9.06 TCGA.EB.A6R0.01 TCGA.ER.A42L.06 TCGA.D3.A8GJ.06
#> "05" "05" "05" "03" "01" "044"
#> TCGA.FR.A8YE.06 TCGA.WE.A8ZR.06 TCGA.BF.A9VF.01 TCGA.EE.A3JH.06 TCGA.DA.A95V.06 TCGA.GF.A769.01
#> "01" "043" "05" "01" "041" "02"
#> TCGA.D9.A4Z2.01 TCGA.FR.A44A.06 TCGA.EB.A5VV.06 TCGA.EE.A180.06 TCGA.D3.A8GC.06 TCGA.WE.A8K5.06
#> "03" "01" "01" "02" "05" "02"
#> TCGA.GN.A8LN.01 TCGA.EE.A3JB.06 TCGA.D3.A3MO.06 TCGA.ER.A42H.01 TCGA.WE.A8ZX.06 TCGA.GN.A4U5.01
#> "02" "041" "05" "05" "041" "01"
#> TCGA.D3.A8GS.06 TCGA.WE.A8ZQ.06 TCGA.EE.A2MF.06 TCGA.D3.A5GU.06 TCGA.GN.A4U8.06 TCGA.EB.A42Y.01
#> "044" "05" "02" "05" "041" "02"
#> TCGA.D3.A3ML.06 TCGA.EB.A551.01 TCGA.D3.A8GM.06 TCGA.D3.A8GL.06 TCGA.D3.A3MU.06 TCGA.FS.A4F0.06
#> "05" "044" "041" "02" "02" "02"
#> TCGA.D3.A3MV.06 TCGA.GN.A4U7.06 TCGA.FR.A2OS.01 TCGA.D3.A2JE.06 TCGA.YD.A89C.06 TCGA.FR.A726.01
#> "03" "03" "05" "05" "041" "041"
#> TCGA.BF.A5EP.01 TCGA.D3.A3MR.06 TCGA.D3.A8GR.06 TCGA.GN.A4U9.06 TCGA.EB.A6L9.06 TCGA.D3.A5GL.06
#> "03" "01" "05" "05" "01" "03"
#> TCGA.EB.A430.01 TCGA.D3.A8GE.06 TCGA.D3.A8GD.06 TCGA.EB.A41A.01 TCGA.W3.A825.06 TCGA.EE.A183.06
#> "01" "01" "01" "02" "044" "01"
#> TCGA.ER.A2NH.06 TCGA.D3.A5GR.06 TCGA.FR.A729.06 TCGA.D3.A1QA.06 TCGA.FS.A1YY.06 TCGA.EE.A2MK.06
#> "01" "044" "044" "02" "03" "03"
#> TCGA.EE.A2M8.06 TCGA.EB.A5KH.06 TCGA.FS.A1ZR.06 TCGA.EE.A3AE.06 TCGA.EE.A29P.06 TCGA.EB.A553.01
#> "01" "02" "05" "03" "044" "05"
#> TCGA.EE.A2MR.06 TCGA.GN.A26A.06 TCGA.FS.A1ZY.06 TCGA.EE.A20I.06 TCGA.DA.A1I5.06 TCGA.EE.A184.06
#> "01" "041" "02" "041" "01" "02"
#> TCGA.EB.A85J.01 TCGA.RP.A6K9.06 TCGA.EE.A17Y.06 TCGA.D9.A149.06 TCGA.ER.A19D.06 TCGA.FS.A1ZZ.06
#> "043" "042" "041" "042" "01" "02"
#> TCGA.EE.A2GP.06 TCGA.EE.A3AD.06 TCGA.D3.A1Q9.06 TCGA.GF.A2C7.01 TCGA.BF.A5ES.01 TCGA.ER.A199.06
#> "05" "02" "041" "05" "05" "01"
#> TCGA.EE.A3AH.06 TCGA.W3.A828.06 TCGA.EE.A2A5.06 TCGA.ER.A19L.06 TCGA.BF.A1PX.01 TCGA.ER.A19T.06
#> "02" "01" "05" "043" "01" "043"
#> TCGA.EB.A51B.01 TCGA.FS.A1ZQ.06 TCGA.D3.A2JG.06 TCGA.EE.A2GH.06 TCGA.ER.A19F.06 TCGA.ER.A196.01
#> "03" "03" "03" "01" "03" "01"
#> TCGA.D3.A2JC.06 TCGA.EE.A3AG.06 TCGA.ER.A19S.06 TCGA.EE.A2GC.06 TCGA.EE.A29N.06 TCGA.FR.A7U8.06
#> "044" "03" "01" "05" "01" "02"
#> TCGA.BF.A5EO.01 TCGA.ER.A19B.06 TCGA.D3.A5GN.06 TCGA.D3.A2JB.06 TCGA.ER.A19J.06 TCGA.D3.A2JD.06
#> "041" "03" "03" "01" "02" "01"
#> TCGA.FS.A1Z4.06 TCGA.FR.A7UA.06 TCGA.EE.A2M7.06 TCGA.D3.A1Q3.06 TCGA.EB.A85I.01 TCGA.EB.A82C.01
#> "01" "01" "044" "043" "042" "02"
#> TCGA.ER.A19E.06 TCGA.FS.A1ZK.06 TCGA.FS.A1ZU.06 TCGA.EB.A5FP.01 TCGA.EB.A4XL.01 TCGA.DA.A1I2.06
#> "05" "05" "05" "02" "03" "044"
#> TCGA.EE.A29L.06 TCGA.FS.A1ZN.01 TCGA.EB.A24D.01 TCGA.EE.A2GB.06 TCGA.DA.A1I7.06 TCGA.ER.A2NF.01
#> "02" "02" "05" "03" "044" "01"
#> TCGA.GN.A263.01 TCGA.EE.A20C.06 TCGA.EE.A2MQ.06 TCGA.ER.A19N.06 TCGA.FS.A1Z3.06 TCGA.DA.A1I8.06
#> "01" "02" "05" "01" "03" "03"
#> TCGA.D3.A5GS.06 TCGA.EE.A181.06 TCGA.GN.A268.06 TCGA.W3.A824.06 TCGA.EE.A2GS.06 TCGA.FR.A7U9.06
#> "03" "041" "02" "05" "03" "01"
#> TCGA.ER.A19Q.06 TCGA.FS.A1ZM.06 TCGA.EE.A2MG.06 TCGA.EE.A2MC.06 TCGA.EE.A17Z.06 TCGA.D3.A2JP.06
#> "01" "044" "01" "01" "05" "041"
#> TCGA.ER.A19C.06 TCGA.EB.A82B.01 TCGA.EE.A2A0.06 TCGA.EE.A29G.06 TCGA.D3.A5GO.06 TCGA.GN.A269.01
#> "044" "042" "01" "01" "03" "01"
#> TCGA.EE.A2A1.06 TCGA.ER.A1A1.06 TCGA.FS.A1ZG.06 TCGA.FS.A1ZE.06 TCGA.FS.A1ZH.06 TCGA.EE.A2MH.06
#> "01" "01" "02" "02" "041" "01"
#> TCGA.D3.A2J6.06 TCGA.EE.A29Q.06 TCGA.BF.A1PZ.01 TCGA.D3.A3BZ.06 TCGA.D3.A2JO.06 TCGA.GN.A267.06
#> "042" "03" "03" "01" "044" "043"
#> TCGA.EE.A2MN.06 TCGA.GN.A264.06 TCGA.ER.A197.06 TCGA.DA.A1IB.06 TCGA.D3.A3CC.06 TCGA.ER.A19T.01
#> "05" "02" "01" "01" "042" "05"
#> TCGA.GN.A261.06 TCGA.FS.A1YW.06 TCGA.BF.A1PU.01 TCGA.D3.A1QB.06 TCGA.D3.A1Q6.06 TCGA.D3.A3C8.06
#> "01" "02" "044" "01" "044" "01"
#> TCGA.ER.A19A.06 TCGA.EE.A2GN.06 TCGA.EE.A29M.06 TCGA.D3.A2J7.06 TCGA.EB.A24C.01 TCGA.GN.A262.06
#> "01" "05" "01" "01" "043" "02"
#> TCGA.EE.A2GD.06 TCGA.D3.A2J9.06 TCGA.EE.A29B.06 TCGA.D9.A1JX.06 TCGA.EE.A29A.06 TCGA.D3.A2JL.06
#> "01" "01" "05" "03" "02" "041"
#> TCGA.D3.A1Q4.06 TCGA.FS.A1ZS.06 TCGA.D3.A3C3.06 TCGA.D3.A2J8.06 TCGA.FS.A1ZF.06 TCGA.FS.A1ZC.06
#> "01" "042" "041" "01" "03" "02"
#> TCGA.EE.A20H.06 TCGA.EE.A29W.06 TCGA.D3.A1QA.07 TCGA.BF.A1PV.01 TCGA.EE.A29S.06 TCGA.DA.A1HV.06
#> "05" "03" "041" "05" "044" "03"
#> TCGA.FS.A1Z0.06 TCGA.EE.A2GO.06 TCGA.EB.A1NK.01 TCGA.GN.A26D.06 TCGA.EE.A2MJ.06 TCGA.ER.A198.06
#> "01" "02" "01" "042" "01" "05"
#> TCGA.EE.A17X.06 TCGA.EE.A2M5.06 TCGA.GN.A266.06 TCGA.D3.A3C1.06 TCGA.D3.A2JH.06 TCGA.EE.A20F.06
#> "03" "041" "044" "044" "01" "041"
#> TCGA.EE.A29E.06 TCGA.ER.A2NG.06 TCGA.ER.A193.06 TCGA.FS.A1ZW.06 TCGA.ER.A19O.06 TCGA.EE.A2ME.06
#> "01" "01" "042" "041" "044" "01"
#> TCGA.EE.A20B.06 TCGA.EE.A3AF.06 TCGA.GN.A265.06 TCGA.FS.A1YX.06 TCGA.FS.A1ZJ.06 TCGA.ER.A19H.06
#> "041" "03" "01" "044" "05" "03"
#> TCGA.EE.A3AC.06 TCGA.EE.A2MU.06 TCGA.ER.A194.01 TCGA.EE.A2MS.06 TCGA.EE.A29R.06 TCGA.D9.A1X3.06
#> "05" "01" "044" "043" "02" "02"
#> TCGA.EE.A29X.06 TCGA.EE.A2GK.06 TCGA.EE.A3AA.06 TCGA.ER.A2NE.06 TCGA.EE.A2GR.06 TCGA.FS.A1ZD.06
#> "044" "01" "01" "02" "05" "05"
#> TCGA.ER.A19P.06 TCGA.D3.A1Q8.06 TCGA.ER.A2NC.06 TCGA.BF.A1Q0.01 TCGA.FS.A1ZP.06 TCGA.EE.A182.06
#> "01" "01" "044" "042" "05" "043"
#> TCGA.D9.A1JW.06 TCGA.D3.A1Q7.06 TCGA.EE.A185.06 TCGA.EE.A2GJ.06 TCGA.D3.A3CB.06 TCGA.EE.A2GU.06
#> "042" "01" "02" "043" "01" "042"
#> TCGA.ER.A195.06 TCGA.FS.A1Z7.06 TCGA.EE.A2M6.06 TCGA.ER.A19K.01 TCGA.DA.A1HY.06 TCGA.D3.A3C7.06
#> "01" "042" "02" "044" "03" "03"
#> TCGA.EE.A2MP.06 TCGA.EE.A29H.06 TCGA.FR.A3YO.06 TCGA.XV.AB01.01 TCGA.RP.A694.06 TCGA.EB.A5SF.01
#> "03" "03" "044" "03" "044" "01"
#> TCGA.ER.A19G.06 TCGA.EE.A2GE.06 TCGA.GF.A3OT.06 TCGA.ER.A2NF.06 TCGA.RP.A695.06 TCGA.BF.AAP7.01
#> "03" "01" "01" "01" "05" "01"
#> TCGA.EB.A3Y7.01 TCGA.EB.A3XC.01 TCGA.ER.A19W.06 TCGA.FR.A69P.06 TCGA.RP.A693.06 TCGA.FW.A3TV.06
#> "042" "03" "01" "03" "01" "01"
#> TCGA.FW.A3R5.11 TCGA.FW.A3TU.06 TCGA.BF.AAP8.01 TCGA.EE.A2MM.06 TCGA.DA.A1HW.06 TCGA.DA.A1IC.06
#> "01" "05" "042" "05" "044" "05"
#> TCGA.XV.AAZV.01 TCGA.D3.A3C6.06 TCGA.EE.A29C.06 TCGA.BF.AAP2.01 TCGA.EE.A2A2.06 TCGA.GF.A6C8.06
#> "01" "03" "01" "02" "03" "044"
#> TCGA.RP.A690.06 TCGA.FW.A5DY.06 TCGA.DA.A1I4.06 TCGA.EE.A29V.06 TCGA.GF.A6C9.06 TCGA.EE.A2GT.06
#> "01" "01" "01" "041" "01" "01"
#> TCGA.GN.A9SD.06 TCGA.EE.A3AB.06 TCGA.BF.AAP6.01 TCGA.EB.A5SH.06 TCGA.D9.A6E9.06 TCGA.BF.AAP4.01
#> "01" "041" "03" "043" "044" "044"
#> TCGA.EE.A2GM.06 TCGA.D3.A3CF.06 TCGA.D9.A6EC.06 TCGA.DA.A1I1.06 TCGA.HR.A2OH.06 TCGA.EE.A2MT.06
#> "02" "01" "02" "041" "01" "042"
#> TCGA.ER.A19M.06 TCGA.GN.A26C.01 TCGA.FS.A1ZA.06 TCGA.EB.A5SE.01 TCGA.ER.A3PL.06 TCGA.FR.A3R1.01
#> "041" "01" "044" "02" "05" "03"
#> TCGA.EE.A2MI.06 TCGA.D3.A3CE.06 TCGA.D3.A5GT.01 TCGA.ER.A2NB.01 TCGA.D3.A1Q5.06 TCGA.EB.A5UN.06
#> "044" "044" "05" "042" "042" "01"
#> TCGA.EB.A299.01 TCGA.DA.A1IA.06 TCGA.EB.A5SG.06 TCGA.D9.A6EA.06 TCGA.XV.AAZY.01 TCGA.EB.A57M.01
#> "03" "05" "01" "02" "01" "041"
#> TCGA.EE.A2A6.06 TCGA.D3.A2JA.06 TCGA.D3.A1Q1.06 TCGA.EB.A3XF.01 TCGA.D3.A2JF.06 TCGA.XV.AAZW.01
#> "042" "01" "042" "03" "03" "03"
#> TCGA.EB.A3Y6.01 TCGA.EB.A3XE.01 TCGA.D9.A3Z4.01 TCGA.FW.A3R5.06 TCGA.EE.A2GI.06 TCGA.EE.A2GL.06
#> "044" "043" "05" "043" "041" "01"
#> TCGA.EB.A3XB.01 TCGA.BF.AAOU.01 TCGA.EB.A3XD.01 TCGA.EE.A2MD.06 TCGA.YD.A9TB.06 TCGA.W3.AA1V.06
#> "044" "01" "01" "044" "05" "044"
#> TCGA.ER.A2ND.06 TCGA.D3.A2JK.06 TCGA.FS.A1ZB.06 TCGA.EE.A29D.06 TCGA.EB.A5UM.01 TCGA.QB.A6FS.06
#> "05" "041" "01" "02" "043" "01"
#> TCGA.D9.A3Z1.06 TCGA.D3.A2JN.06 TCGA.FR.A3YN.06 TCGA.FS.A1ZT.06 TCGA.D9.A148.06 TCGA.HR.A2OG.06
#> "01" "01" "03" "01" "041" "01"
#> TCGA.EE.A2ML.06 TCGA.EB.A5UL.06 TCGA.EE.A29T.06 TCGA.D9.A3Z3.06 TCGA.D9.A4Z3.01 TCGA.ER.A3ES.06
#> "041" "041" "043" "01" "05" "042"
#> TCGA.XV.A9VZ.01 TCGA.QB.AA9O.06 TCGA.EB.A44Q.06 TCGA.EB.A44R.06 TCGA.BF.A3DJ.01 TCGA.EE.A3JD.06
#> "01" "03" "044" "043" "03" "01"
#> TCGA.D3.A51N.06 TCGA.EB.A44N.01 TCGA.EE.A3J3.06 TCGA.XV.A9W5.01 TCGA.D3.A51G.06 TCGA.EB.A4P0.01
#> "041" "01" "03" "041" "03" "03"
#> TCGA.BF.AAP1.01 TCGA.EE.A3J4.06 TCGA.Z2.AA3V.06 TCGA.LH.A9QB.06 TCGA.D3.A51J.06 TCGA.3N.A9WC.06
#> "02" "05" "01" "02" "044" "042"
#> TCGA.DA.A3F8.06 TCGA.D9.A4Z6.06 TCGA.D3.A51R.06 TCGA.EB.A4OZ.01 TCGA.FS.A4FB.06 TCGA.EE.A3JE.06
#> "01" "041" "03" "01" "03" "01"
#> TCGA.W3.AA1W.06 TCGA.DA.A1I0.06 TCGA.D3.A51F.06 TCGA.IH.A3EA.01 TCGA.EB.A431.01 TCGA.EB.A97M.01
#> "01" "041" "01" "05" "041" "02"
#> TCGA.BF.AAOX.01 TCGA.DA.A3F5.06 TCGA.YD.A9TA.06 TCGA.DA.A3F2.06 TCGA.EB.A44O.01 TCGA.EB.A4IQ.01
#> "041" "042" "041" "01" "05" "042"
#> TCGA.EB.A4IS.01 TCGA.YG.AA3O.06 TCGA.ER.A3EV.06 TCGA.3N.A9WD.06 TCGA.BF.A3DM.01 TCGA.XV.A9W2.01
#> "01" "05" "043" "01" "03" "042"
#> TCGA.W3.AA1Q.06 TCGA.WE.AAA0.06 TCGA.W3.AA1R.06 TCGA.EE.A3J5.06 TCGA.EB.A4OY.01 TCGA.FS.A4FD.06
#> "05" "041" "03" "041" "01" "042"
#> TCGA.BF.AAP0.06 TCGA.YG.AA3P.06 TCGA.EE.A3JA.06 TCGA.W3.AA21.06 TCGA.WE.AAA3.06 TCGA.FS.A4F4.06
#> "01" "05" "03" "02" "042" "03"
#> TCGA.BF.A3DN.01 TCGA.ER.A3ET.06 TCGA.W3.AA1O.06 TCGA.D3.A51E.06 TCGA.Z2.AA3S.06 TCGA.YG.AA3N.01
#> "03" "042" "05" "03" "02" "044"
#> TCGA.WE.AA9Y.06 TCGA.FS.A4F5.06 TCGA.EE.A3J7.06 TCGA.FS.A4F8.06 TCGA.DA.A3F3.06 TCGA.D3.A51H.06
#> "01" "02" "05" "01" "03" "01"
#> TCGA.BF.A3DL.01 TCGA.D3.A51T.06 TCGA.D3.A51K.06 TCGA.EB.A44P.01 TCGA.D9.A4Z5.01 TCGA.WE.AAA4.06
#> "01" "03" "05" "05" "02" "01"
#> TCGA.3N.A9WB.06 TCGA.EE.A3J8.06
#> "02" "02"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 52804))
#> TCGA.FR.A728.01 TCGA.GN.A4U8.11 TCGA.GN.A8LL.06 TCGA.FR.A8YC.06 TCGA.DA.A95X.06 TCGA.ER.A42K.06
#> "01" "01" "03" "02" "02" "03"
#> TCGA.D3.A8GO.06 TCGA.D3.A8GK.06 TCGA.WE.A8JZ.06 TCGA.WE.A8ZO.06 TCGA.D3.A8GI.06 TCGA.FS.A4FC.06
#> "01" "05" "02" "05" "05" "042"
#> TCGA.FS.A4F2.06 TCGA.WE.A8ZM.06 TCGA.WE.A8ZT.06 TCGA.D3.A8GQ.06 TCGA.D3.A8GB.06 TCGA.DA.A95Y.06
#> "03" "05" "03" "041" "01" "03"
#> TCGA.EE.A3JI.06 TCGA.OD.A75X.06 TCGA.DA.A960.01 TCGA.D3.A8GV.06 TCGA.WE.A8ZN.06 TCGA.D3.A8GN.06
#> "02" "02" "02" "02" "01" "01"
#> TCGA.EB.A550.01 TCGA.BF.A5EQ.01 TCGA.EB.A3HV.01 TCGA.HR.A5NC.01 TCGA.DA.A95Z.06 TCGA.EB.A6QZ.01
#> "01" "042" "05" "05" "02" "02"
#> TCGA.FW.A3I3.06 TCGA.WE.A8K6.06 TCGA.D3.A8GP.06 TCGA.EB.A42Z.01 TCGA.GN.A4U4.06 TCGA.GF.A4EO.06
#> "02" "03" "02" "02" "02" "01"
#> TCGA.GN.A8LK.06 TCGA.WE.A8K4.01 TCGA.DA.A95W.06 TCGA.FW.A5DX.01 TCGA.GN.A4U3.06 TCGA.EB.A6QY.01
#> "05" "01" "02" "02" "03" "01"
#> TCGA.EB.A5VU.01 TCGA.Z2.A8RT.06 TCGA.WE.A8K1.06 TCGA.EB.A41B.01 TCGA.WE.A8ZY.06 TCGA.D9.A6EG.06
#> "044" "03" "01" "03" "02" "02"
#> TCGA.BF.A5ER.01 TCGA.FR.A8YD.06 TCGA.FS.A4F9.06 TCGA.EB.A6R0.01 TCGA.ER.A42L.06 TCGA.D3.A8GJ.06
#> "05" "05" "05" "03" "01" "044"
#> TCGA.FR.A8YE.06 TCGA.WE.A8ZR.06 TCGA.BF.A9VF.01 TCGA.EE.A3JH.06 TCGA.DA.A95V.06 TCGA.GF.A769.01
#> "01" "043" "05" "01" "041" "02"
#> TCGA.D9.A4Z2.01 TCGA.FR.A44A.06 TCGA.EB.A5VV.06 TCGA.EE.A180.06 TCGA.D3.A8GC.06 TCGA.WE.A8K5.06
#> "03" "01" "01" "02" "05" "02"
#> TCGA.GN.A8LN.01 TCGA.EE.A3JB.06 TCGA.D3.A3MO.06 TCGA.ER.A42H.01 TCGA.WE.A8ZX.06 TCGA.GN.A4U5.01
#> "02" "041" "05" "05" "041" "01"
#> TCGA.D3.A8GS.06 TCGA.WE.A8ZQ.06 TCGA.EE.A2MF.06 TCGA.D3.A5GU.06 TCGA.GN.A4U8.06 TCGA.EB.A42Y.01
#> "044" "05" "02" "05" "041" "02"
#> TCGA.D3.A3ML.06 TCGA.EB.A551.01 TCGA.D3.A8GM.06 TCGA.D3.A8GL.06 TCGA.D3.A3MU.06 TCGA.FS.A4F0.06
#> "05" "044" "041" "02" "02" "02"
#> TCGA.D3.A3MV.06 TCGA.GN.A4U7.06 TCGA.FR.A2OS.01 TCGA.D3.A2JE.06 TCGA.YD.A89C.06 TCGA.FR.A726.01
#> "03" "03" "05" "05" "041" "041"
#> TCGA.BF.A5EP.01 TCGA.D3.A3MR.06 TCGA.D3.A8GR.06 TCGA.GN.A4U9.06 TCGA.EB.A6L9.06 TCGA.D3.A5GL.06
#> "03" "01" "05" "05" "01" "03"
#> TCGA.EB.A430.01 TCGA.D3.A8GE.06 TCGA.D3.A8GD.06 TCGA.EB.A41A.01 TCGA.W3.A825.06 TCGA.EE.A183.06
#> "01" "01" "01" "02" "044" "01"
#> TCGA.ER.A2NH.06 TCGA.D3.A5GR.06 TCGA.FR.A729.06 TCGA.D3.A1QA.06 TCGA.FS.A1YY.06 TCGA.EE.A2MK.06
#> "01" "044" "044" "02" "03" "03"
#> TCGA.EE.A2M8.06 TCGA.EB.A5KH.06 TCGA.FS.A1ZR.06 TCGA.EE.A3AE.06 TCGA.EE.A29P.06 TCGA.EB.A553.01
#> "01" "02" "05" "03" "044" "05"
#> TCGA.EE.A2MR.06 TCGA.GN.A26A.06 TCGA.FS.A1ZY.06 TCGA.EE.A20I.06 TCGA.DA.A1I5.06 TCGA.EE.A184.06
#> "01" "041" "02" "041" "01" "02"
#> TCGA.EB.A85J.01 TCGA.RP.A6K9.06 TCGA.EE.A17Y.06 TCGA.D9.A149.06 TCGA.ER.A19D.06 TCGA.FS.A1ZZ.06
#> "043" "042" "041" "042" "01" "02"
#> TCGA.EE.A2GP.06 TCGA.EE.A3AD.06 TCGA.D3.A1Q9.06 TCGA.GF.A2C7.01 TCGA.BF.A5ES.01 TCGA.ER.A199.06
#> "05" "02" "041" "05" "05" "01"
#> TCGA.EE.A3AH.06 TCGA.W3.A828.06 TCGA.EE.A2A5.06 TCGA.ER.A19L.06 TCGA.BF.A1PX.01 TCGA.ER.A19T.06
#> "02" "01" "05" "043" "01" "043"
#> TCGA.EB.A51B.01 TCGA.FS.A1ZQ.06 TCGA.D3.A2JG.06 TCGA.EE.A2GH.06 TCGA.ER.A19F.06 TCGA.ER.A196.01
#> "03" "03" "03" "01" "03" "01"
#> TCGA.D3.A2JC.06 TCGA.EE.A3AG.06 TCGA.ER.A19S.06 TCGA.EE.A2GC.06 TCGA.EE.A29N.06 TCGA.FR.A7U8.06
#> "044" "03" "01" "05" "01" "02"
#> TCGA.BF.A5EO.01 TCGA.ER.A19B.06 TCGA.D3.A5GN.06 TCGA.D3.A2JB.06 TCGA.ER.A19J.06 TCGA.D3.A2JD.06
#> "041" "03" "03" "01" "02" "01"
#> TCGA.FS.A1Z4.06 TCGA.FR.A7UA.06 TCGA.EE.A2M7.06 TCGA.D3.A1Q3.06 TCGA.EB.A85I.01 TCGA.EB.A82C.01
#> "01" "01" "044" "043" "042" "02"
#> TCGA.ER.A19E.06 TCGA.FS.A1ZK.06 TCGA.FS.A1ZU.06 TCGA.EB.A5FP.01 TCGA.EB.A4XL.01 TCGA.DA.A1I2.06
#> "05" "05" "05" "02" "03" "044"
#> TCGA.EE.A29L.06 TCGA.FS.A1ZN.01 TCGA.EB.A24D.01 TCGA.EE.A2GB.06 TCGA.DA.A1I7.06 TCGA.ER.A2NF.01
#> "02" "02" "05" "03" "044" "01"
#> TCGA.GN.A263.01 TCGA.EE.A20C.06 TCGA.EE.A2MQ.06 TCGA.ER.A19N.06 TCGA.FS.A1Z3.06 TCGA.DA.A1I8.06
#> "01" "02" "05" "01" "03" "03"
#> TCGA.D3.A5GS.06 TCGA.EE.A181.06 TCGA.GN.A268.06 TCGA.W3.A824.06 TCGA.EE.A2GS.06 TCGA.FR.A7U9.06
#> "03" "041" "02" "05" "03" "01"
#> TCGA.ER.A19Q.06 TCGA.FS.A1ZM.06 TCGA.EE.A2MG.06 TCGA.EE.A2MC.06 TCGA.EE.A17Z.06 TCGA.D3.A2JP.06
#> "01" "044" "01" "01" "05" "041"
#> TCGA.ER.A19C.06 TCGA.EB.A82B.01 TCGA.EE.A2A0.06 TCGA.EE.A29G.06 TCGA.D3.A5GO.06 TCGA.GN.A269.01
#> "044" "042" "01" "01" "03" "01"
#> TCGA.EE.A2A1.06 TCGA.ER.A1A1.06 TCGA.FS.A1ZG.06 TCGA.FS.A1ZE.06 TCGA.FS.A1ZH.06 TCGA.EE.A2MH.06
#> "01" "01" "02" "02" "041" "01"
#> TCGA.D3.A2J6.06 TCGA.EE.A29Q.06 TCGA.BF.A1PZ.01 TCGA.D3.A3BZ.06 TCGA.D3.A2JO.06 TCGA.GN.A267.06
#> "042" "03" "03" "01" "044" "043"
#> TCGA.EE.A2MN.06 TCGA.GN.A264.06 TCGA.ER.A197.06 TCGA.DA.A1IB.06 TCGA.D3.A3CC.06 TCGA.ER.A19T.01
#> "05" "02" "01" "01" "042" "05"
#> TCGA.GN.A261.06 TCGA.FS.A1YW.06 TCGA.BF.A1PU.01 TCGA.D3.A1QB.06 TCGA.D3.A1Q6.06 TCGA.D3.A3C8.06
#> "01" "02" "044" "01" "044" "01"
#> TCGA.ER.A19A.06 TCGA.EE.A2GN.06 TCGA.EE.A29M.06 TCGA.D3.A2J7.06 TCGA.EB.A24C.01 TCGA.GN.A262.06
#> "01" "05" "01" "01" "043" "02"
#> TCGA.EE.A2GD.06 TCGA.D3.A2J9.06 TCGA.EE.A29B.06 TCGA.D9.A1JX.06 TCGA.EE.A29A.06 TCGA.D3.A2JL.06
#> "01" "01" "05" "03" "02" "041"
#> TCGA.D3.A1Q4.06 TCGA.FS.A1ZS.06 TCGA.D3.A3C3.06 TCGA.D3.A2J8.06 TCGA.FS.A1ZF.06 TCGA.FS.A1ZC.06
#> "01" "042" "041" "01" "03" "02"
#> TCGA.EE.A20H.06 TCGA.EE.A29W.06 TCGA.D3.A1QA.07 TCGA.BF.A1PV.01 TCGA.EE.A29S.06 TCGA.DA.A1HV.06
#> "05" "03" "041" "05" "044" "03"
#> TCGA.FS.A1Z0.06 TCGA.EE.A2GO.06 TCGA.EB.A1NK.01 TCGA.GN.A26D.06 TCGA.EE.A2MJ.06 TCGA.ER.A198.06
#> "01" "02" "01" "042" "01" "05"
#> TCGA.EE.A17X.06 TCGA.EE.A2M5.06 TCGA.GN.A266.06 TCGA.D3.A3C1.06 TCGA.D3.A2JH.06 TCGA.EE.A20F.06
#> "03" "041" "044" "044" "01" "041"
#> TCGA.EE.A29E.06 TCGA.ER.A2NG.06 TCGA.ER.A193.06 TCGA.FS.A1ZW.06 TCGA.ER.A19O.06 TCGA.EE.A2ME.06
#> "01" "01" "042" "041" "044" "01"
#> TCGA.EE.A20B.06 TCGA.EE.A3AF.06 TCGA.GN.A265.06 TCGA.FS.A1YX.06 TCGA.FS.A1ZJ.06 TCGA.ER.A19H.06
#> "041" "03" "01" "044" "05" "03"
#> TCGA.EE.A3AC.06 TCGA.EE.A2MU.06 TCGA.ER.A194.01 TCGA.EE.A2MS.06 TCGA.EE.A29R.06 TCGA.D9.A1X3.06
#> "05" "01" "044" "043" "02" "02"
#> TCGA.EE.A29X.06 TCGA.EE.A2GK.06 TCGA.EE.A3AA.06 TCGA.ER.A2NE.06 TCGA.EE.A2GR.06 TCGA.FS.A1ZD.06
#> "044" "01" "01" "02" "05" "05"
#> TCGA.ER.A19P.06 TCGA.D3.A1Q8.06 TCGA.ER.A2NC.06 TCGA.BF.A1Q0.01 TCGA.FS.A1ZP.06 TCGA.EE.A182.06
#> "01" "01" "044" "042" "05" "043"
#> TCGA.D9.A1JW.06 TCGA.D3.A1Q7.06 TCGA.EE.A185.06 TCGA.EE.A2GJ.06 TCGA.D3.A3CB.06 TCGA.EE.A2GU.06
#> "042" "01" "02" "043" "01" "042"
#> TCGA.ER.A195.06 TCGA.FS.A1Z7.06 TCGA.EE.A2M6.06 TCGA.ER.A19K.01 TCGA.DA.A1HY.06 TCGA.D3.A3C7.06
#> "01" "042" "02" "044" "03" "03"
#> TCGA.EE.A2MP.06 TCGA.EE.A29H.06 TCGA.FR.A3YO.06 TCGA.XV.AB01.01 TCGA.RP.A694.06 TCGA.EB.A5SF.01
#> "03" "03" "044" "03" "044" "01"
#> TCGA.ER.A19G.06 TCGA.EE.A2GE.06 TCGA.GF.A3OT.06 TCGA.ER.A2NF.06 TCGA.RP.A695.06 TCGA.BF.AAP7.01
#> "03" "01" "01" "01" "05" "01"
#> TCGA.EB.A3Y7.01 TCGA.EB.A3XC.01 TCGA.ER.A19W.06 TCGA.FR.A69P.06 TCGA.RP.A693.06 TCGA.FW.A3TV.06
#> "042" "03" "01" "03" "01" "01"
#> TCGA.FW.A3R5.11 TCGA.FW.A3TU.06 TCGA.BF.AAP8.01 TCGA.EE.A2MM.06 TCGA.DA.A1HW.06 TCGA.DA.A1IC.06
#> "01" "05" "042" "05" "044" "05"
#> TCGA.XV.AAZV.01 TCGA.D3.A3C6.06 TCGA.EE.A29C.06 TCGA.BF.AAP2.01 TCGA.EE.A2A2.06 TCGA.GF.A6C8.06
#> "01" "03" "01" "02" "03" "044"
#> TCGA.RP.A690.06 TCGA.FW.A5DY.06 TCGA.DA.A1I4.06 TCGA.EE.A29V.06 TCGA.GF.A6C9.06 TCGA.EE.A2GT.06
#> "01" "01" "01" "041" "01" "01"
#> TCGA.GN.A9SD.06 TCGA.EE.A3AB.06 TCGA.BF.AAP6.01 TCGA.EB.A5SH.06 TCGA.D9.A6E9.06 TCGA.BF.AAP4.01
#> "01" "041" "03" "043" "044" "044"
#> TCGA.EE.A2GM.06 TCGA.D3.A3CF.06 TCGA.D9.A6EC.06 TCGA.DA.A1I1.06 TCGA.HR.A2OH.06 TCGA.EE.A2MT.06
#> "02" "01" "02" "041" "01" "042"
#> TCGA.ER.A19M.06 TCGA.GN.A26C.01 TCGA.FS.A1ZA.06 TCGA.EB.A5SE.01 TCGA.ER.A3PL.06 TCGA.FR.A3R1.01
#> "041" "01" "044" "02" "05" "03"
#> TCGA.EE.A2MI.06 TCGA.D3.A3CE.06 TCGA.D3.A5GT.01 TCGA.ER.A2NB.01 TCGA.D3.A1Q5.06 TCGA.EB.A5UN.06
#> "044" "044" "05" "042" "042" "01"
#> TCGA.EB.A299.01 TCGA.DA.A1IA.06 TCGA.EB.A5SG.06 TCGA.D9.A6EA.06 TCGA.XV.AAZY.01 TCGA.EB.A57M.01
#> "03" "05" "01" "02" "01" "041"
#> TCGA.EE.A2A6.06 TCGA.D3.A2JA.06 TCGA.D3.A1Q1.06 TCGA.EB.A3XF.01 TCGA.D3.A2JF.06 TCGA.XV.AAZW.01
#> "042" "01" "042" "03" "03" "03"
#> TCGA.EB.A3Y6.01 TCGA.EB.A3XE.01 TCGA.D9.A3Z4.01 TCGA.FW.A3R5.06 TCGA.EE.A2GI.06 TCGA.EE.A2GL.06
#> "044" "043" "05" "043" "041" "01"
#> TCGA.EB.A3XB.01 TCGA.BF.AAOU.01 TCGA.EB.A3XD.01 TCGA.EE.A2MD.06 TCGA.YD.A9TB.06 TCGA.W3.AA1V.06
#> "044" "01" "01" "044" "05" "044"
#> TCGA.ER.A2ND.06 TCGA.D3.A2JK.06 TCGA.FS.A1ZB.06 TCGA.EE.A29D.06 TCGA.EB.A5UM.01 TCGA.QB.A6FS.06
#> "05" "041" "01" "02" "043" "01"
#> TCGA.D9.A3Z1.06 TCGA.D3.A2JN.06 TCGA.FR.A3YN.06 TCGA.FS.A1ZT.06 TCGA.D9.A148.06 TCGA.HR.A2OG.06
#> "01" "01" "03" "01" "041" "01"
#> TCGA.EE.A2ML.06 TCGA.EB.A5UL.06 TCGA.EE.A29T.06 TCGA.D9.A3Z3.06 TCGA.D9.A4Z3.01 TCGA.ER.A3ES.06
#> "041" "041" "043" "01" "05" "042"
#> TCGA.XV.A9VZ.01 TCGA.QB.AA9O.06 TCGA.EB.A44Q.06 TCGA.EB.A44R.06 TCGA.BF.A3DJ.01 TCGA.EE.A3JD.06
#> "01" "03" "044" "043" "03" "01"
#> TCGA.D3.A51N.06 TCGA.EB.A44N.01 TCGA.EE.A3J3.06 TCGA.XV.A9W5.01 TCGA.D3.A51G.06 TCGA.EB.A4P0.01
#> "041" "01" "03" "041" "03" "03"
#> TCGA.BF.AAP1.01 TCGA.EE.A3J4.06 TCGA.Z2.AA3V.06 TCGA.LH.A9QB.06 TCGA.D3.A51J.06 TCGA.3N.A9WC.06
#> "02" "05" "01" "02" "044" "042"
#> TCGA.DA.A3F8.06 TCGA.D9.A4Z6.06 TCGA.D3.A51R.06 TCGA.EB.A4OZ.01 TCGA.FS.A4FB.06 TCGA.EE.A3JE.06
#> "01" "041" "03" "01" "03" "01"
#> TCGA.W3.AA1W.06 TCGA.DA.A1I0.06 TCGA.D3.A51F.06 TCGA.IH.A3EA.01 TCGA.EB.A431.01 TCGA.EB.A97M.01
#> "01" "041" "01" "05" "041" "02"
#> TCGA.BF.AAOX.01 TCGA.DA.A3F5.06 TCGA.YD.A9TA.06 TCGA.DA.A3F2.06 TCGA.EB.A44O.01 TCGA.EB.A4IQ.01
#> "041" "042" "041" "01" "05" "042"
#> TCGA.EB.A4IS.01 TCGA.YG.AA3O.06 TCGA.ER.A3EV.06 TCGA.3N.A9WD.06 TCGA.BF.A3DM.01 TCGA.XV.A9W2.01
#> "01" "05" "043" "01" "03" "042"
#> TCGA.W3.AA1Q.06 TCGA.WE.AAA0.06 TCGA.W3.AA1R.06 TCGA.EE.A3J5.06 TCGA.EB.A4OY.01 TCGA.FS.A4FD.06
#> "05" "041" "03" "041" "01" "042"
#> TCGA.BF.AAP0.06 TCGA.YG.AA3P.06 TCGA.EE.A3JA.06 TCGA.W3.AA21.06 TCGA.WE.AAA3.06 TCGA.FS.A4F4.06
#> "01" "05" "03" "02" "042" "03"
#> TCGA.BF.A3DN.01 TCGA.ER.A3ET.06 TCGA.W3.AA1O.06 TCGA.D3.A51E.06 TCGA.Z2.AA3S.06 TCGA.YG.AA3N.01
#> "03" "042" "05" "03" "02" "044"
#> TCGA.WE.AA9Y.06 TCGA.FS.A4F5.06 TCGA.EE.A3J7.06 TCGA.FS.A4F8.06 TCGA.DA.A3F3.06 TCGA.D3.A51H.06
#> "01" "02" "05" "01" "03" "01"
#> TCGA.BF.A3DL.01 TCGA.D3.A51T.06 TCGA.D3.A51K.06 TCGA.EB.A44P.01 TCGA.D9.A4Z5.01 TCGA.WE.AAA4.06
#> "01" "03" "05" "05" "02" "01"
#> TCGA.3N.A9WB.06 TCGA.EE.A3J8.06
#> "02" "02"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 57862))
#> TCGA.FR.A728.01 TCGA.GN.A4U8.11 TCGA.GN.A8LL.06 TCGA.FR.A8YC.06 TCGA.DA.A95X.06 TCGA.ER.A42K.06
#> "01" "01" "03" "02" "02" "03"
#> TCGA.D3.A8GO.06 TCGA.D3.A8GK.06 TCGA.WE.A8JZ.06 TCGA.WE.A8ZO.06 TCGA.D3.A8GI.06 TCGA.FS.A4FC.06
#> "01" "05" "02" "05" "05" "04"
#> TCGA.FS.A4F2.06 TCGA.WE.A8ZM.06 TCGA.WE.A8ZT.06 TCGA.D3.A8GQ.06 TCGA.D3.A8GB.06 TCGA.DA.A95Y.06
#> "03" "05" "03" "04" "01" "03"
#> TCGA.EE.A3JI.06 TCGA.OD.A75X.06 TCGA.DA.A960.01 TCGA.D3.A8GV.06 TCGA.WE.A8ZN.06 TCGA.D3.A8GN.06
#> "02" "02" "02" "02" "01" "01"
#> TCGA.EB.A550.01 TCGA.BF.A5EQ.01 TCGA.EB.A3HV.01 TCGA.HR.A5NC.01 TCGA.DA.A95Z.06 TCGA.EB.A6QZ.01
#> "01" "04" "05" "05" "02" "02"
#> TCGA.FW.A3I3.06 TCGA.WE.A8K6.06 TCGA.D3.A8GP.06 TCGA.EB.A42Z.01 TCGA.GN.A4U4.06 TCGA.GF.A4EO.06
#> "02" "03" "02" "02" "02" "01"
#> TCGA.GN.A8LK.06 TCGA.WE.A8K4.01 TCGA.DA.A95W.06 TCGA.FW.A5DX.01 TCGA.GN.A4U3.06 TCGA.EB.A6QY.01
#> "05" "01" "02" "02" "03" "01"
#> TCGA.EB.A5VU.01 TCGA.Z2.A8RT.06 TCGA.WE.A8K1.06 TCGA.EB.A41B.01 TCGA.WE.A8ZY.06 TCGA.D9.A6EG.06
#> "04" "03" "01" "03" "02" "02"
#> TCGA.BF.A5ER.01 TCGA.FR.A8YD.06 TCGA.FS.A4F9.06 TCGA.EB.A6R0.01 TCGA.ER.A42L.06 TCGA.D3.A8GJ.06
#> "05" "05" "05" "03" "01" "04"
#> TCGA.FR.A8YE.06 TCGA.WE.A8ZR.06 TCGA.BF.A9VF.01 TCGA.EE.A3JH.06 TCGA.DA.A95V.06 TCGA.GF.A769.01
#> "01" "04" "05" "01" "04" "02"
#> TCGA.D9.A4Z2.01 TCGA.FR.A44A.06 TCGA.EB.A5VV.06 TCGA.EE.A180.06 TCGA.D3.A8GC.06 TCGA.WE.A8K5.06
#> "03" "01" "01" "02" "05" "02"
#> TCGA.GN.A8LN.01 TCGA.EE.A3JB.06 TCGA.D3.A3MO.06 TCGA.ER.A42H.01 TCGA.WE.A8ZX.06 TCGA.GN.A4U5.01
#> "02" "04" "05" "05" "04" "01"
#> TCGA.D3.A8GS.06 TCGA.WE.A8ZQ.06 TCGA.EE.A2MF.06 TCGA.D3.A5GU.06 TCGA.GN.A4U8.06 TCGA.EB.A42Y.01
#> "04" "05" "02" "05" "04" "02"
#> TCGA.D3.A3ML.06 TCGA.EB.A551.01 TCGA.D3.A8GM.06 TCGA.D3.A8GL.06 TCGA.D3.A3MU.06 TCGA.FS.A4F0.06
#> "05" "04" "04" "02" "02" "02"
#> TCGA.D3.A3MV.06 TCGA.GN.A4U7.06 TCGA.FR.A2OS.01 TCGA.D3.A2JE.06 TCGA.YD.A89C.06 TCGA.FR.A726.01
#> "03" "03" "05" "05" "04" "04"
#> TCGA.BF.A5EP.01 TCGA.D3.A3MR.06 TCGA.D3.A8GR.06 TCGA.GN.A4U9.06 TCGA.EB.A6L9.06 TCGA.D3.A5GL.06
#> "03" "01" "05" "05" "01" "03"
#> TCGA.EB.A430.01 TCGA.D3.A8GE.06 TCGA.D3.A8GD.06 TCGA.EB.A41A.01 TCGA.W3.A825.06 TCGA.EE.A183.06
#> "01" "01" "01" "02" "04" "01"
#> TCGA.ER.A2NH.06 TCGA.D3.A5GR.06 TCGA.FR.A729.06 TCGA.D3.A1QA.06 TCGA.FS.A1YY.06 TCGA.EE.A2MK.06
#> "01" "04" "04" "02" "03" "03"
#> TCGA.EE.A2M8.06 TCGA.EB.A5KH.06 TCGA.FS.A1ZR.06 TCGA.EE.A3AE.06 TCGA.EE.A29P.06 TCGA.EB.A553.01
#> "01" "02" "05" "03" "04" "05"
#> TCGA.EE.A2MR.06 TCGA.GN.A26A.06 TCGA.FS.A1ZY.06 TCGA.EE.A20I.06 TCGA.DA.A1I5.06 TCGA.EE.A184.06
#> "01" "04" "02" "04" "01" "02"
#> TCGA.EB.A85J.01 TCGA.RP.A6K9.06 TCGA.EE.A17Y.06 TCGA.D9.A149.06 TCGA.ER.A19D.06 TCGA.FS.A1ZZ.06
#> "04" "04" "04" "04" "01" "02"
#> TCGA.EE.A2GP.06 TCGA.EE.A3AD.06 TCGA.D3.A1Q9.06 TCGA.GF.A2C7.01 TCGA.BF.A5ES.01 TCGA.ER.A199.06
#> "05" "02" "04" "05" "05" "01"
#> TCGA.EE.A3AH.06 TCGA.W3.A828.06 TCGA.EE.A2A5.06 TCGA.ER.A19L.06 TCGA.BF.A1PX.01 TCGA.ER.A19T.06
#> "02" "01" "05" "04" "01" "04"
#> TCGA.EB.A51B.01 TCGA.FS.A1ZQ.06 TCGA.D3.A2JG.06 TCGA.EE.A2GH.06 TCGA.ER.A19F.06 TCGA.ER.A196.01
#> "03" "03" "03" "01" "03" "01"
#> TCGA.D3.A2JC.06 TCGA.EE.A3AG.06 TCGA.ER.A19S.06 TCGA.EE.A2GC.06 TCGA.EE.A29N.06 TCGA.FR.A7U8.06
#> "04" "03" "01" "05" "01" "02"
#> TCGA.BF.A5EO.01 TCGA.ER.A19B.06 TCGA.D3.A5GN.06 TCGA.D3.A2JB.06 TCGA.ER.A19J.06 TCGA.D3.A2JD.06
#> "04" "03" "03" "01" "02" "01"
#> TCGA.FS.A1Z4.06 TCGA.FR.A7UA.06 TCGA.EE.A2M7.06 TCGA.D3.A1Q3.06 TCGA.EB.A85I.01 TCGA.EB.A82C.01
#> "01" "01" "04" "04" "04" "02"
#> TCGA.ER.A19E.06 TCGA.FS.A1ZK.06 TCGA.FS.A1ZU.06 TCGA.EB.A5FP.01 TCGA.EB.A4XL.01 TCGA.DA.A1I2.06
#> "05" "05" "05" "02" "03" "04"
#> TCGA.EE.A29L.06 TCGA.FS.A1ZN.01 TCGA.EB.A24D.01 TCGA.EE.A2GB.06 TCGA.DA.A1I7.06 TCGA.ER.A2NF.01
#> "02" "02" "05" "03" "04" "01"
#> TCGA.GN.A263.01 TCGA.EE.A20C.06 TCGA.EE.A2MQ.06 TCGA.ER.A19N.06 TCGA.FS.A1Z3.06 TCGA.DA.A1I8.06
#> "01" "02" "05" "01" "03" "03"
#> TCGA.D3.A5GS.06 TCGA.EE.A181.06 TCGA.GN.A268.06 TCGA.W3.A824.06 TCGA.EE.A2GS.06 TCGA.FR.A7U9.06
#> "03" "04" "02" "05" "03" "01"
#> TCGA.ER.A19Q.06 TCGA.FS.A1ZM.06 TCGA.EE.A2MG.06 TCGA.EE.A2MC.06 TCGA.EE.A17Z.06 TCGA.D3.A2JP.06
#> "01" "04" "01" "01" "05" "04"
#> TCGA.ER.A19C.06 TCGA.EB.A82B.01 TCGA.EE.A2A0.06 TCGA.EE.A29G.06 TCGA.D3.A5GO.06 TCGA.GN.A269.01
#> "04" "04" "01" "01" "03" "01"
#> TCGA.EE.A2A1.06 TCGA.ER.A1A1.06 TCGA.FS.A1ZG.06 TCGA.FS.A1ZE.06 TCGA.FS.A1ZH.06 TCGA.EE.A2MH.06
#> "01" "01" "02" "02" "04" "01"
#> TCGA.D3.A2J6.06 TCGA.EE.A29Q.06 TCGA.BF.A1PZ.01 TCGA.D3.A3BZ.06 TCGA.D3.A2JO.06 TCGA.GN.A267.06
#> "04" "03" "03" "01" "04" "04"
#> TCGA.EE.A2MN.06 TCGA.GN.A264.06 TCGA.ER.A197.06 TCGA.DA.A1IB.06 TCGA.D3.A3CC.06 TCGA.ER.A19T.01
#> "05" "02" "01" "01" "04" "05"
#> TCGA.GN.A261.06 TCGA.FS.A1YW.06 TCGA.BF.A1PU.01 TCGA.D3.A1QB.06 TCGA.D3.A1Q6.06 TCGA.D3.A3C8.06
#> "01" "02" "04" "01" "04" "01"
#> TCGA.ER.A19A.06 TCGA.EE.A2GN.06 TCGA.EE.A29M.06 TCGA.D3.A2J7.06 TCGA.EB.A24C.01 TCGA.GN.A262.06
#> "01" "05" "01" "01" "04" "02"
#> TCGA.EE.A2GD.06 TCGA.D3.A2J9.06 TCGA.EE.A29B.06 TCGA.D9.A1JX.06 TCGA.EE.A29A.06 TCGA.D3.A2JL.06
#> "01" "01" "05" "03" "02" "04"
#> TCGA.D3.A1Q4.06 TCGA.FS.A1ZS.06 TCGA.D3.A3C3.06 TCGA.D3.A2J8.06 TCGA.FS.A1ZF.06 TCGA.FS.A1ZC.06
#> "01" "04" "04" "01" "03" "02"
#> TCGA.EE.A20H.06 TCGA.EE.A29W.06 TCGA.D3.A1QA.07 TCGA.BF.A1PV.01 TCGA.EE.A29S.06 TCGA.DA.A1HV.06
#> "05" "03" "04" "05" "04" "03"
#> TCGA.FS.A1Z0.06 TCGA.EE.A2GO.06 TCGA.EB.A1NK.01 TCGA.GN.A26D.06 TCGA.EE.A2MJ.06 TCGA.ER.A198.06
#> "01" "02" "01" "04" "01" "05"
#> TCGA.EE.A17X.06 TCGA.EE.A2M5.06 TCGA.GN.A266.06 TCGA.D3.A3C1.06 TCGA.D3.A2JH.06 TCGA.EE.A20F.06
#> "03" "04" "04" "04" "01" "04"
#> TCGA.EE.A29E.06 TCGA.ER.A2NG.06 TCGA.ER.A193.06 TCGA.FS.A1ZW.06 TCGA.ER.A19O.06 TCGA.EE.A2ME.06
#> "01" "01" "04" "04" "04" "01"
#> TCGA.EE.A20B.06 TCGA.EE.A3AF.06 TCGA.GN.A265.06 TCGA.FS.A1YX.06 TCGA.FS.A1ZJ.06 TCGA.ER.A19H.06
#> "04" "03" "01" "04" "05" "03"
#> TCGA.EE.A3AC.06 TCGA.EE.A2MU.06 TCGA.ER.A194.01 TCGA.EE.A2MS.06 TCGA.EE.A29R.06 TCGA.D9.A1X3.06
#> "05" "01" "04" "04" "02" "02"
#> TCGA.EE.A29X.06 TCGA.EE.A2GK.06 TCGA.EE.A3AA.06 TCGA.ER.A2NE.06 TCGA.EE.A2GR.06 TCGA.FS.A1ZD.06
#> "04" "01" "01" "02" "05" "05"
#> TCGA.ER.A19P.06 TCGA.D3.A1Q8.06 TCGA.ER.A2NC.06 TCGA.BF.A1Q0.01 TCGA.FS.A1ZP.06 TCGA.EE.A182.06
#> "01" "01" "04" "04" "05" "04"
#> TCGA.D9.A1JW.06 TCGA.D3.A1Q7.06 TCGA.EE.A185.06 TCGA.EE.A2GJ.06 TCGA.D3.A3CB.06 TCGA.EE.A2GU.06
#> "04" "01" "02" "04" "01" "04"
#> TCGA.ER.A195.06 TCGA.FS.A1Z7.06 TCGA.EE.A2M6.06 TCGA.ER.A19K.01 TCGA.DA.A1HY.06 TCGA.D3.A3C7.06
#> "01" "04" "02" "04" "03" "03"
#> TCGA.EE.A2MP.06 TCGA.EE.A29H.06 TCGA.FR.A3YO.06 TCGA.XV.AB01.01 TCGA.RP.A694.06 TCGA.EB.A5SF.01
#> "03" "03" "04" "03" "04" "01"
#> TCGA.ER.A19G.06 TCGA.EE.A2GE.06 TCGA.GF.A3OT.06 TCGA.ER.A2NF.06 TCGA.RP.A695.06 TCGA.BF.AAP7.01
#> "03" "01" "01" "01" "05" "01"
#> TCGA.EB.A3Y7.01 TCGA.EB.A3XC.01 TCGA.ER.A19W.06 TCGA.FR.A69P.06 TCGA.RP.A693.06 TCGA.FW.A3TV.06
#> "04" "03" "01" "03" "01" "01"
#> TCGA.FW.A3R5.11 TCGA.FW.A3TU.06 TCGA.BF.AAP8.01 TCGA.EE.A2MM.06 TCGA.DA.A1HW.06 TCGA.DA.A1IC.06
#> "01" "05" "04" "05" "04" "05"
#> TCGA.XV.AAZV.01 TCGA.D3.A3C6.06 TCGA.EE.A29C.06 TCGA.BF.AAP2.01 TCGA.EE.A2A2.06 TCGA.GF.A6C8.06
#> "01" "03" "01" "02" "03" "04"
#> TCGA.RP.A690.06 TCGA.FW.A5DY.06 TCGA.DA.A1I4.06 TCGA.EE.A29V.06 TCGA.GF.A6C9.06 TCGA.EE.A2GT.06
#> "01" "01" "01" "04" "01" "01"
#> TCGA.GN.A9SD.06 TCGA.EE.A3AB.06 TCGA.BF.AAP6.01 TCGA.EB.A5SH.06 TCGA.D9.A6E9.06 TCGA.BF.AAP4.01
#> "01" "04" "03" "04" "04" "04"
#> TCGA.EE.A2GM.06 TCGA.D3.A3CF.06 TCGA.D9.A6EC.06 TCGA.DA.A1I1.06 TCGA.HR.A2OH.06 TCGA.EE.A2MT.06
#> "02" "01" "02" "04" "01" "04"
#> TCGA.ER.A19M.06 TCGA.GN.A26C.01 TCGA.FS.A1ZA.06 TCGA.EB.A5SE.01 TCGA.ER.A3PL.06 TCGA.FR.A3R1.01
#> "04" "01" "04" "02" "05" "03"
#> TCGA.EE.A2MI.06 TCGA.D3.A3CE.06 TCGA.D3.A5GT.01 TCGA.ER.A2NB.01 TCGA.D3.A1Q5.06 TCGA.EB.A5UN.06
#> "04" "04" "05" "04" "04" "01"
#> TCGA.EB.A299.01 TCGA.DA.A1IA.06 TCGA.EB.A5SG.06 TCGA.D9.A6EA.06 TCGA.XV.AAZY.01 TCGA.EB.A57M.01
#> "03" "05" "01" "02" "01" "04"
#> TCGA.EE.A2A6.06 TCGA.D3.A2JA.06 TCGA.D3.A1Q1.06 TCGA.EB.A3XF.01 TCGA.D3.A2JF.06 TCGA.XV.AAZW.01
#> "04" "01" "04" "03" "03" "03"
#> TCGA.EB.A3Y6.01 TCGA.EB.A3XE.01 TCGA.D9.A3Z4.01 TCGA.FW.A3R5.06 TCGA.EE.A2GI.06 TCGA.EE.A2GL.06
#> "04" "04" "05" "04" "04" "01"
#> TCGA.EB.A3XB.01 TCGA.BF.AAOU.01 TCGA.EB.A3XD.01 TCGA.EE.A2MD.06 TCGA.YD.A9TB.06 TCGA.W3.AA1V.06
#> "04" "01" "01" "04" "05" "04"
#> TCGA.ER.A2ND.06 TCGA.D3.A2JK.06 TCGA.FS.A1ZB.06 TCGA.EE.A29D.06 TCGA.EB.A5UM.01 TCGA.QB.A6FS.06
#> "05" "04" "01" "02" "04" "01"
#> TCGA.D9.A3Z1.06 TCGA.D3.A2JN.06 TCGA.FR.A3YN.06 TCGA.FS.A1ZT.06 TCGA.D9.A148.06 TCGA.HR.A2OG.06
#> "01" "01" "03" "01" "04" "01"
#> TCGA.EE.A2ML.06 TCGA.EB.A5UL.06 TCGA.EE.A29T.06 TCGA.D9.A3Z3.06 TCGA.D9.A4Z3.01 TCGA.ER.A3ES.06
#> "04" "04" "04" "01" "05" "04"
#> TCGA.XV.A9VZ.01 TCGA.QB.AA9O.06 TCGA.EB.A44Q.06 TCGA.EB.A44R.06 TCGA.BF.A3DJ.01 TCGA.EE.A3JD.06
#> "01" "03" "04" "04" "03" "01"
#> TCGA.D3.A51N.06 TCGA.EB.A44N.01 TCGA.EE.A3J3.06 TCGA.XV.A9W5.01 TCGA.D3.A51G.06 TCGA.EB.A4P0.01
#> "04" "01" "03" "04" "03" "03"
#> TCGA.BF.AAP1.01 TCGA.EE.A3J4.06 TCGA.Z2.AA3V.06 TCGA.LH.A9QB.06 TCGA.D3.A51J.06 TCGA.3N.A9WC.06
#> "02" "05" "01" "02" "04" "04"
#> TCGA.DA.A3F8.06 TCGA.D9.A4Z6.06 TCGA.D3.A51R.06 TCGA.EB.A4OZ.01 TCGA.FS.A4FB.06 TCGA.EE.A3JE.06
#> "01" "04" "03" "01" "03" "01"
#> TCGA.W3.AA1W.06 TCGA.DA.A1I0.06 TCGA.D3.A51F.06 TCGA.IH.A3EA.01 TCGA.EB.A431.01 TCGA.EB.A97M.01
#> "01" "04" "01" "05" "04" "02"
#> TCGA.BF.AAOX.01 TCGA.DA.A3F5.06 TCGA.YD.A9TA.06 TCGA.DA.A3F2.06 TCGA.EB.A44O.01 TCGA.EB.A4IQ.01
#> "04" "04" "04" "01" "05" "04"
#> TCGA.EB.A4IS.01 TCGA.YG.AA3O.06 TCGA.ER.A3EV.06 TCGA.3N.A9WD.06 TCGA.BF.A3DM.01 TCGA.XV.A9W2.01
#> "01" "05" "04" "01" "03" "04"
#> TCGA.W3.AA1Q.06 TCGA.WE.AAA0.06 TCGA.W3.AA1R.06 TCGA.EE.A3J5.06 TCGA.EB.A4OY.01 TCGA.FS.A4FD.06
#> "05" "04" "03" "04" "01" "04"
#> TCGA.BF.AAP0.06 TCGA.YG.AA3P.06 TCGA.EE.A3JA.06 TCGA.W3.AA21.06 TCGA.WE.AAA3.06 TCGA.FS.A4F4.06
#> "01" "05" "03" "02" "04" "03"
#> TCGA.BF.A3DN.01 TCGA.ER.A3ET.06 TCGA.W3.AA1O.06 TCGA.D3.A51E.06 TCGA.Z2.AA3S.06 TCGA.YG.AA3N.01
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#> TCGA.WE.AA9Y.06 TCGA.FS.A4F5.06 TCGA.EE.A3J7.06 TCGA.FS.A4F8.06 TCGA.DA.A3F3.06 TCGA.D3.A51H.06
#> "01" "02" "05" "01" "03" "01"
#> TCGA.BF.A3DL.01 TCGA.D3.A51T.06 TCGA.D3.A51K.06 TCGA.EB.A44P.01 TCGA.D9.A4Z5.01 TCGA.WE.AAA4.06
#> "01" "03" "05" "05" "02" "01"
#> TCGA.3N.A9WB.06 TCGA.EE.A3J8.06
#> "02" "02"
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 = 1034),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 1034),
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 = 1119),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 1119),
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 = 1144),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 1144),
method = "UMAP", top_value_method = "ATC", top_n = 40000, scale_rows = TRUE)
par(mfrow = c(1, 2))
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 1564),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 1564),
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 = 1831),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 1831),
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 = 1969),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 1969),
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 = 2117),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 2117),
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 = 2142),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 2142),
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 = 2164),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 2164),
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 = 2255),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 2255),
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 = 2328),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 2328),
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 = 2454),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 2454),
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 = 2616),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 2616),
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 = 2664),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 2664),
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 = 2780),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 2780),
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 = 3485),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 3485),
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 = 4070),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 4070),
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 = 4105),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 4105),
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 = 6230),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 6230),
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 = 8228),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 8228),
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 = 10240),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 10240),
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 = 11354),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 11354),
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 = 12706),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 12706),
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 = 17313),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 17313),
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 = 22901),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 22901),
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 = 23773),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 23773),
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 = 29265),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 29265),
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 = 41067),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 41067),
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 = 52804),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 52804),
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 = 57862),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 57862),
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 = 1034))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 1119))
#> Error in lt[[hierarchy[i, 1]]]$AddChildNode({: attempt to apply non-function
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 1144))
#> Error in lt[[hierarchy[i, 1]]]$AddChildNode({: attempt to apply non-function
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 1564))
#> Error in lt[[hierarchy[i, 1]]]$AddChildNode({: attempt to apply non-function
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 1831))
#> Error in lt[[hierarchy[i, 1]]]$AddChildNode({: attempt to apply non-function
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 1969))
#> Error in lt[[hierarchy[i, 1]]]$AddChildNode({: attempt to apply non-function
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 2117))
#> Error in lt[[hierarchy[i, 1]]]$AddChildNode({: attempt to apply non-function
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 2142))
#> Error in lt[[hierarchy[i, 1]]]$AddChildNode({: attempt to apply non-function
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 2164))
#> Error in lt[[hierarchy[i, 1]]]$AddChildNode({: attempt to apply non-function
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 2255))
#> Error in lt[[hierarchy[i, 1]]]$AddChildNode({: attempt to apply non-function
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 2328))
#> Error in lt[[hierarchy[i, 1]]]$AddChildNode({: attempt to apply non-function
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 2454))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 2616))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 2664))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 2780))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 3485))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 4070))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 4105))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 6230))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 8228))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 10240))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 11354))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 12706))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 17313))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 22901))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 23773))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 29265))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 41067))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 52804))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 57862))
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 , Node04 , Node05 .
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 476 columns.
#> Top rows (1000) are extracted by 'ATC' method.
#> Subgroups are detected by 'skmeans' method.
#> Performed in total 350 partitions by row resampling.
#> Best k for subgroups seems to be 7.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_partitions"
#> [7] "compare_signatures" "consensus_heatmap" "dimension_reduction"
#> [10] "functional_enrichment" "get_anno_col" "get_anno"
#> [13] "get_classes" "get_consensus" "get_matrix"
#> [16] "get_membership" "get_param" "get_signatures"
#> [19] "get_stats" "is_best_k" "is_stable_k"
#> [22] "membership_heatmap" "ncol" "nrow"
#> [25] "plot_ecdf" "predict_classes" "rownames"
#> [28] "select_partition_number" "show" "suggest_best_k"
#> [31] "test_to_known_factors" "top_rows_heatmap"
collect_plots() function collects all the plots made from res for all k (number of subgroups)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
The plots are:
k and the heatmap of
predicted classes for each k.k.k.k.All the plots in panels can be made by individual functions and they are plotted later in this section.
select_partition_number() produces several plots showing different
statistics for choosing “optimized” k. There are following statistics:
k;k, the area increased is defined as \(A_k - A_{k-1}\).The detailed explanations of these statistics can be found in the cola vignette.
Generally speaking, higher 1-PAC score, higher mean silhouette score or higher
concordance corresponds to better partition. Rand index and Jaccard index
measure how similar the current partition is compared to partition with k-1.
If they are too similar, we won't accept k is better than k-1.
select_partition_number(res)
The numeric values for all these statistics can be obtained by get_stats().
get_stats(res)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> 2 2 1.000 0.987 0.995 0.4970 0.504 0.504
#> 3 3 0.971 0.937 0.976 0.3095 0.728 0.517
#> 4 4 0.836 0.861 0.937 0.1429 0.790 0.485
#> 5 5 0.988 0.955 0.981 0.0499 0.916 0.698
#> 6 6 0.858 0.854 0.918 0.0410 0.896 0.591
#> 7 7 0.918 0.851 0.929 0.0303 0.926 0.651
#> 8 8 0.842 0.693 0.846 0.0216 0.980 0.880
suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:
suggest_best_k(res)
#> [1] 7
#> attr(,"optional")
#> [1] 2 3 5
There is also optional best \(k\) = 2 3 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.FR.A728.01 1 0.000 0.99464 1.00 0.00
#> TCGA.GN.A4U8.11 1 0.000 0.99464 1.00 0.00
#> TCGA.GN.A8LL.06 2 0.000 0.99501 0.00 1.00
#> TCGA.FR.A8YC.06 2 0.000 0.99501 0.00 1.00
#> TCGA.DA.A95X.06 2 0.000 0.99501 0.00 1.00
#> TCGA.ER.A42K.06 2 0.000 0.99501 0.00 1.00
#> TCGA.D3.A8GO.06 1 0.000 0.99464 1.00 0.00
#> TCGA.D3.A8GK.06 2 0.000 0.99501 0.00 1.00
#> TCGA.WE.A8JZ.06 2 0.000 0.99501 0.00 1.00
#> TCGA.WE.A8ZO.06 2 0.000 0.99501 0.00 1.00
#> TCGA.D3.A8GI.06 2 0.000 0.99501 0.00 1.00
#> TCGA.FS.A4FC.06 1 0.000 0.99464 1.00 0.00
#> TCGA.FS.A4F2.06 2 0.000 0.99501 0.00 1.00
#> TCGA.WE.A8ZM.06 2 0.000 0.99501 0.00 1.00
#> TCGA.WE.A8ZT.06 2 0.000 0.99501 0.00 1.00
#> TCGA.D3.A8GQ.06 1 0.000 0.99464 1.00 0.00
#> TCGA.D3.A8GB.06 1 0.000 0.99464 1.00 0.00
#> TCGA.DA.A95Y.06 2 0.000 0.99501 0.00 1.00
#> TCGA.EE.A3JI.06 2 0.000 0.99501 0.00 1.00
#> TCGA.OD.A75X.06 2 0.000 0.99501 0.00 1.00
#> TCGA.DA.A960.01 2 0.000 0.99501 0.00 1.00
#> TCGA.D3.A8GV.06 2 0.000 0.99501 0.00 1.00
#> TCGA.WE.A8ZN.06 1 0.000 0.99464 1.00 0.00
#> TCGA.D3.A8GN.06 1 0.000 0.99464 1.00 0.00
#> TCGA.EB.A550.01 1 0.000 0.99464 1.00 0.00
#> TCGA.BF.A5EQ.01 1 0.000 0.99464 1.00 0.00
#> TCGA.EB.A3HV.01 2 0.000 0.99501 0.00 1.00
#> TCGA.HR.A5NC.01 2 0.680 0.78225 0.18 0.82
#> TCGA.DA.A95Z.06 2 0.000 0.99501 0.00 1.00
#> TCGA.EB.A6QZ.01 2 0.000 0.99501 0.00 1.00
#> TCGA.FW.A3I3.06 2 0.000 0.99501 0.00 1.00
#> TCGA.WE.A8K6.06 2 0.000 0.99501 0.00 1.00
#> TCGA.D3.A8GP.06 2 0.000 0.99501 0.00 1.00
#> TCGA.EB.A42Z.01 2 0.000 0.99501 0.00 1.00
#> TCGA.GN.A4U4.06 2 0.000 0.99501 0.00 1.00
#> TCGA.GF.A4EO.06 1 0.000 0.99464 1.00 0.00
#> TCGA.GN.A8LK.06 2 0.000 0.99501 0.00 1.00
#> TCGA.WE.A8K4.01 1 0.000 0.99464 1.00 0.00
#> TCGA.DA.A95W.06 2 0.000 0.99501 0.00 1.00
#> TCGA.FW.A5DX.01 2 0.000 0.99501 0.00 1.00
#> TCGA.GN.A4U3.06 2 0.000 0.99501 0.00 1.00
#> TCGA.EB.A6QY.01 1 0.000 0.99464 1.00 0.00
#> TCGA.EB.A5VU.01 1 0.000 0.99464 1.00 0.00
#> TCGA.Z2.A8RT.06 2 0.000 0.99501 0.00 1.00
#> TCGA.WE.A8K1.06 1 0.000 0.99464 1.00 0.00
#> TCGA.EB.A41B.01 2 0.000 0.99501 0.00 1.00
#> TCGA.WE.A8ZY.06 2 0.000 0.99501 0.00 1.00
#> TCGA.D9.A6EG.06 2 0.000 0.99501 0.00 1.00
#> TCGA.BF.A5ER.01 2 0.000 0.99501 0.00 1.00
#> TCGA.FR.A8YD.06 2 0.000 0.99501 0.00 1.00
#> TCGA.FS.A4F9.06 2 0.000 0.99501 0.00 1.00
#> TCGA.EB.A6R0.01 2 0.000 0.99501 0.00 1.00
#> TCGA.ER.A42L.06 1 0.000 0.99464 1.00 0.00
#> TCGA.D3.A8GJ.06 1 0.000 0.99464 1.00 0.00
#> TCGA.FR.A8YE.06 1 0.000 0.99464 1.00 0.00
#> TCGA.WE.A8ZR.06 1 0.000 0.99464 1.00 0.00
#> TCGA.BF.A9VF.01 2 0.000 0.99501 0.00 1.00
#> TCGA.EE.A3JH.06 1 0.000 0.99464 1.00 0.00
#> TCGA.DA.A95V.06 1 0.000 0.99464 1.00 0.00
#> TCGA.GF.A769.01 2 0.000 0.99501 0.00 1.00
#> TCGA.D9.A4Z2.01 2 0.000 0.99501 0.00 1.00
#> TCGA.FR.A44A.06 1 0.000 0.99464 1.00 0.00
#> TCGA.EB.A5VV.06 1 0.000 0.99464 1.00 0.00
#> TCGA.EE.A180.06 2 0.000 0.99501 0.00 1.00
#> TCGA.D3.A8GC.06 2 0.000 0.99501 0.00 1.00
#> TCGA.WE.A8K5.06 2 0.000 0.99501 0.00 1.00
#> TCGA.GN.A8LN.01 2 0.000 0.99501 0.00 1.00
#> TCGA.EE.A3JB.06 1 0.000 0.99464 1.00 0.00
#> TCGA.D3.A3MO.06 2 0.000 0.99501 0.00 1.00
#> TCGA.ER.A42H.01 2 0.000 0.99501 0.00 1.00
#> TCGA.WE.A8ZX.06 1 0.000 0.99464 1.00 0.00
#> TCGA.GN.A4U5.01 1 0.000 0.99464 1.00 0.00
#> TCGA.D3.A8GS.06 1 0.000 0.99464 1.00 0.00
#> TCGA.WE.A8ZQ.06 2 0.000 0.99501 0.00 1.00
#> TCGA.EE.A2MF.06 2 0.000 0.99501 0.00 1.00
#> TCGA.D3.A5GU.06 2 0.000 0.99501 0.00 1.00
#> TCGA.GN.A4U8.06 1 0.000 0.99464 1.00 0.00
#> TCGA.EB.A42Y.01 2 0.000 0.99501 0.00 1.00
#> TCGA.D3.A3ML.06 2 0.000 0.99501 0.00 1.00
#> TCGA.EB.A551.01 1 0.000 0.99464 1.00 0.00
#> TCGA.D3.A8GM.06 1 0.000 0.99464 1.00 0.00
#> TCGA.D3.A8GL.06 2 0.000 0.99501 0.00 1.00
#> TCGA.D3.A3MU.06 2 0.000 0.99501 0.00 1.00
#> TCGA.FS.A4F0.06 2 0.000 0.99501 0.00 1.00
#> TCGA.D3.A3MV.06 2 0.000 0.99501 0.00 1.00
#> TCGA.GN.A4U7.06 2 0.000 0.99501 0.00 1.00
#> TCGA.FR.A2OS.01 2 0.000 0.99501 0.00 1.00
#> TCGA.D3.A2JE.06 2 0.000 0.99501 0.00 1.00
#> TCGA.YD.A89C.06 2 0.795 0.68662 0.24 0.76
#> TCGA.FR.A726.01 1 0.000 0.99464 1.00 0.00
#> TCGA.BF.A5EP.01 2 0.000 0.99501 0.00 1.00
#> TCGA.D3.A3MR.06 1 0.000 0.99464 1.00 0.00
#> TCGA.D3.A8GR.06 2 0.000 0.99501 0.00 1.00
#> TCGA.GN.A4U9.06 2 0.000 0.99501 0.00 1.00
#> TCGA.EB.A6L9.06 1 0.000 0.99464 1.00 0.00
#> TCGA.D3.A5GL.06 2 0.000 0.99501 0.00 1.00
#> TCGA.EB.A430.01 1 0.000 0.99464 1.00 0.00
#> TCGA.D3.A8GE.06 1 0.000 0.99464 1.00 0.00
#> TCGA.D3.A8GD.06 1 0.000 0.99464 1.00 0.00
#> TCGA.EB.A41A.01 2 0.000 0.99501 0.00 1.00
#> TCGA.W3.A825.06 1 0.000 0.99464 1.00 0.00
#> TCGA.EE.A183.06 1 0.000 0.99464 1.00 0.00
#> TCGA.ER.A2NH.06 1 0.000 0.99464 1.00 0.00
#> TCGA.D3.A5GR.06 1 0.000 0.99464 1.00 0.00
#> TCGA.FR.A729.06 1 0.000 0.99464 1.00 0.00
#> TCGA.D3.A1QA.06 2 0.000 0.99501 0.00 1.00
#> TCGA.FS.A1YY.06 2 0.000 0.99501 0.00 1.00
#> TCGA.EE.A2MK.06 2 0.000 0.99501 0.00 1.00
#> TCGA.EE.A2M8.06 1 0.000 0.99464 1.00 0.00
#> TCGA.EB.A5KH.06 2 0.000 0.99501 0.00 1.00
#> TCGA.FS.A1ZR.06 2 0.000 0.99501 0.00 1.00
#> TCGA.EE.A3AE.06 1 0.000 0.99464 1.00 0.00
#> TCGA.EE.A29P.06 1 0.000 0.99464 1.00 0.00
#> TCGA.EB.A553.01 1 0.000 0.99464 1.00 0.00
#> TCGA.EE.A2MR.06 1 0.000 0.99464 1.00 0.00
#> TCGA.GN.A26A.06 1 0.000 0.99464 1.00 0.00
#> TCGA.FS.A1ZY.06 2 0.000 0.99501 0.00 1.00
#> TCGA.EE.A20I.06 1 0.000 0.99464 1.00 0.00
#> TCGA.DA.A1I5.06 1 0.000 0.99464 1.00 0.00
#> TCGA.EE.A184.06 2 0.000 0.99501 0.00 1.00
#> TCGA.EB.A85J.01 1 0.000 0.99464 1.00 0.00
#> TCGA.RP.A6K9.06 1 0.000 0.99464 1.00 0.00
#> TCGA.EE.A17Y.06 1 0.000 0.99464 1.00 0.00
#> TCGA.D9.A149.06 1 0.000 0.99464 1.00 0.00
#> TCGA.ER.A19D.06 1 0.000 0.99464 1.00 0.00
#> TCGA.FS.A1ZZ.06 2 0.000 0.99501 0.00 1.00
#> TCGA.EE.A2GP.06 2 0.000 0.99501 0.00 1.00
#> TCGA.EE.A3AD.06 2 0.000 0.99501 0.00 1.00
#> TCGA.D3.A1Q9.06 1 0.000 0.99464 1.00 0.00
#> TCGA.GF.A2C7.01 2 0.000 0.99501 0.00 1.00
#> TCGA.BF.A5ES.01 2 0.000 0.99501 0.00 1.00
#> TCGA.ER.A199.06 1 0.000 0.99464 1.00 0.00
#> TCGA.EE.A3AH.06 2 0.000 0.99501 0.00 1.00
#> TCGA.W3.A828.06 1 0.000 0.99464 1.00 0.00
#> TCGA.EE.A2A5.06 2 0.000 0.99501 0.00 1.00
#> TCGA.ER.A19L.06 1 0.000 0.99464 1.00 0.00
#> TCGA.BF.A1PX.01 1 0.000 0.99464 1.00 0.00
#> TCGA.ER.A19T.06 1 0.000 0.99464 1.00 0.00
#> TCGA.EB.A51B.01 2 0.000 0.99501 0.00 1.00
#> TCGA.FS.A1ZQ.06 2 0.000 0.99501 0.00 1.00
#> TCGA.D3.A2JG.06 2 0.000 0.99501 0.00 1.00
#> TCGA.EE.A2GH.06 1 0.000 0.99464 1.00 0.00
#> TCGA.ER.A19F.06 2 0.000 0.99501 0.00 1.00
#> TCGA.ER.A196.01 1 0.000 0.99464 1.00 0.00
#> TCGA.D3.A2JC.06 1 0.000 0.99464 1.00 0.00
#> TCGA.EE.A3AG.06 2 0.000 0.99501 0.00 1.00
#> TCGA.ER.A19S.06 1 0.000 0.99464 1.00 0.00
#> TCGA.EE.A2GC.06 2 0.000 0.99501 0.00 1.00
#> TCGA.EE.A29N.06 1 0.000 0.99464 1.00 0.00
#> TCGA.FR.A7U8.06 2 0.000 0.99501 0.00 1.00
#> TCGA.BF.A5EO.01 1 0.000 0.99464 1.00 0.00
#> TCGA.ER.A19B.06 2 0.000 0.99501 0.00 1.00
#> TCGA.D3.A5GN.06 2 0.000 0.99501 0.00 1.00
#> TCGA.D3.A2JB.06 1 0.000 0.99464 1.00 0.00
#> TCGA.ER.A19J.06 2 0.000 0.99501 0.00 1.00
#> TCGA.D3.A2JD.06 1 0.000 0.99464 1.00 0.00
#> TCGA.FS.A1Z4.06 1 0.000 0.99464 1.00 0.00
#> TCGA.FR.A7UA.06 1 0.000 0.99464 1.00 0.00
#> TCGA.EE.A2M7.06 1 0.000 0.99464 1.00 0.00
#> TCGA.D3.A1Q3.06 1 0.000 0.99464 1.00 0.00
#> TCGA.EB.A85I.01 1 0.000 0.99464 1.00 0.00
#> TCGA.EB.A82C.01 2 0.000 0.99501 0.00 1.00
#> TCGA.ER.A19E.06 2 0.000 0.99501 0.00 1.00
#> TCGA.FS.A1ZK.06 2 0.000 0.99501 0.00 1.00
#> TCGA.FS.A1ZU.06 2 0.000 0.99501 0.00 1.00
#> TCGA.EB.A5FP.01 2 0.000 0.99501 0.00 1.00
#> TCGA.EB.A4XL.01 2 0.000 0.99501 0.00 1.00
#> TCGA.DA.A1I2.06 2 0.469 0.88826 0.10 0.90
#> TCGA.EE.A29L.06 2 0.000 0.99501 0.00 1.00
#> TCGA.FS.A1ZN.01 2 0.000 0.99501 0.00 1.00
#> TCGA.EB.A24D.01 2 0.000 0.99501 0.00 1.00
#> TCGA.EE.A2GB.06 2 0.000 0.99501 0.00 1.00
#> TCGA.DA.A1I7.06 1 0.000 0.99464 1.00 0.00
#> TCGA.ER.A2NF.01 1 0.000 0.99464 1.00 0.00
#> TCGA.GN.A263.01 1 0.000 0.99464 1.00 0.00
#> TCGA.EE.A20C.06 2 0.000 0.99501 0.00 1.00
#> TCGA.EE.A2MQ.06 2 0.000 0.99501 0.00 1.00
#> TCGA.ER.A19N.06 1 0.000 0.99464 1.00 0.00
#> TCGA.FS.A1Z3.06 2 0.000 0.99501 0.00 1.00
#> TCGA.DA.A1I8.06 2 0.000 0.99501 0.00 1.00
#> TCGA.D3.A5GS.06 2 0.000 0.99501 0.00 1.00
#> TCGA.EE.A181.06 1 0.000 0.99464 1.00 0.00
#> TCGA.GN.A268.06 2 0.000 0.99501 0.00 1.00
#> TCGA.W3.A824.06 2 0.000 0.99501 0.00 1.00
#> TCGA.EE.A2GS.06 2 0.000 0.99501 0.00 1.00
#> TCGA.FR.A7U9.06 1 0.000 0.99464 1.00 0.00
#> TCGA.ER.A19Q.06 1 0.000 0.99464 1.00 0.00
#> TCGA.FS.A1ZM.06 1 1.000 -0.00571 0.50 0.50
#> TCGA.EE.A2MG.06 1 0.000 0.99464 1.00 0.00
#> TCGA.EE.A2MC.06 1 0.000 0.99464 1.00 0.00
#> TCGA.EE.A17Z.06 2 0.000 0.99501 0.00 1.00
#> TCGA.D3.A2JP.06 1 0.000 0.99464 1.00 0.00
#> TCGA.ER.A19C.06 2 0.855 0.61341 0.28 0.72
#> TCGA.EB.A82B.01 1 0.000 0.99464 1.00 0.00
#> TCGA.EE.A2A0.06 1 0.000 0.99464 1.00 0.00
#> TCGA.EE.A29G.06 1 0.000 0.99464 1.00 0.00
#> TCGA.D3.A5GO.06 2 0.000 0.99501 0.00 1.00
#> TCGA.GN.A269.01 1 0.000 0.99464 1.00 0.00
#> TCGA.EE.A2A1.06 1 0.000 0.99464 1.00 0.00
#> TCGA.ER.A1A1.06 1 0.000 0.99464 1.00 0.00
#> TCGA.FS.A1ZG.06 2 0.000 0.99501 0.00 1.00
#> TCGA.FS.A1ZE.06 2 0.000 0.99501 0.00 1.00
#> TCGA.FS.A1ZH.06 1 0.000 0.99464 1.00 0.00
#> TCGA.EE.A2MH.06 1 0.000 0.99464 1.00 0.00
#> TCGA.D3.A2J6.06 1 0.000 0.99464 1.00 0.00
#> TCGA.EE.A29Q.06 2 0.000 0.99501 0.00 1.00
#> TCGA.BF.A1PZ.01 2 0.000 0.99501 0.00 1.00
#> TCGA.D3.A3BZ.06 1 0.000 0.99464 1.00 0.00
#> TCGA.D3.A2JO.06 1 0.000 0.99464 1.00 0.00
#> TCGA.GN.A267.06 1 0.000 0.99464 1.00 0.00
#> TCGA.EE.A2MN.06 2 0.000 0.99501 0.00 1.00
#> TCGA.GN.A264.06 2 0.000 0.99501 0.00 1.00
#> TCGA.ER.A197.06 1 0.000 0.99464 1.00 0.00
#> TCGA.DA.A1IB.06 1 0.000 0.99464 1.00 0.00
#> TCGA.D3.A3CC.06 1 0.000 0.99464 1.00 0.00
#> TCGA.ER.A19T.01 2 0.000 0.99501 0.00 1.00
#> TCGA.GN.A261.06 1 0.000 0.99464 1.00 0.00
#> TCGA.FS.A1YW.06 2 0.000 0.99501 0.00 1.00
#> TCGA.BF.A1PU.01 1 0.000 0.99464 1.00 0.00
#> TCGA.D3.A1QB.06 1 0.000 0.99464 1.00 0.00
#> TCGA.D3.A1Q6.06 1 0.000 0.99464 1.00 0.00
#> TCGA.D3.A3C8.06 1 0.000 0.99464 1.00 0.00
#> TCGA.ER.A19A.06 1 0.000 0.99464 1.00 0.00
#> TCGA.EE.A2GN.06 2 0.000 0.99501 0.00 1.00
#> TCGA.EE.A29M.06 1 0.000 0.99464 1.00 0.00
#> TCGA.D3.A2J7.06 1 0.000 0.99464 1.00 0.00
#> TCGA.EB.A24C.01 1 0.000 0.99464 1.00 0.00
#> TCGA.GN.A262.06 2 0.000 0.99501 0.00 1.00
#> TCGA.EE.A2GD.06 1 0.000 0.99464 1.00 0.00
#> TCGA.D3.A2J9.06 1 0.000 0.99464 1.00 0.00
#> TCGA.EE.A29B.06 2 0.000 0.99501 0.00 1.00
#> TCGA.D9.A1JX.06 2 0.000 0.99501 0.00 1.00
#> TCGA.EE.A29A.06 2 0.000 0.99501 0.00 1.00
#> TCGA.D3.A2JL.06 1 0.000 0.99464 1.00 0.00
#> TCGA.D3.A1Q4.06 1 0.000 0.99464 1.00 0.00
#> TCGA.FS.A1ZS.06 1 0.981 0.27249 0.58 0.42
#> TCGA.D3.A3C3.06 1 0.000 0.99464 1.00 0.00
#> TCGA.D3.A2J8.06 1 0.000 0.99464 1.00 0.00
#> TCGA.FS.A1ZF.06 2 0.000 0.99501 0.00 1.00
#> TCGA.FS.A1ZC.06 2 0.000 0.99501 0.00 1.00
#> TCGA.EE.A20H.06 2 0.000 0.99501 0.00 1.00
#> TCGA.EE.A29W.06 2 0.000 0.99501 0.00 1.00
#> TCGA.D3.A1QA.07 1 0.000 0.99464 1.00 0.00
#> TCGA.BF.A1PV.01 2 0.000 0.99501 0.00 1.00
#> TCGA.EE.A29S.06 2 0.000 0.99501 0.00 1.00
#> TCGA.DA.A1HV.06 2 0.000 0.99501 0.00 1.00
#> TCGA.FS.A1Z0.06 1 0.000 0.99464 1.00 0.00
#> TCGA.EE.A2GO.06 2 0.000 0.99501 0.00 1.00
#> TCGA.EB.A1NK.01 1 0.000 0.99464 1.00 0.00
#> TCGA.GN.A26D.06 1 0.000 0.99464 1.00 0.00
#> TCGA.EE.A2MJ.06 1 0.000 0.99464 1.00 0.00
#> TCGA.ER.A198.06 2 0.000 0.99501 0.00 1.00
#> TCGA.EE.A17X.06 2 0.000 0.99501 0.00 1.00
#> TCGA.EE.A2M5.06 1 0.000 0.99464 1.00 0.00
#> TCGA.GN.A266.06 1 0.000 0.99464 1.00 0.00
#> TCGA.D3.A3C1.06 1 0.000 0.99464 1.00 0.00
#> TCGA.D3.A2JH.06 1 0.000 0.99464 1.00 0.00
#> TCGA.EE.A20F.06 1 0.000 0.99464 1.00 0.00
#> TCGA.EE.A29E.06 1 0.000 0.99464 1.00 0.00
#> TCGA.ER.A2NG.06 1 0.000 0.99464 1.00 0.00
#> TCGA.ER.A193.06 1 0.000 0.99464 1.00 0.00
#> TCGA.FS.A1ZW.06 1 0.000 0.99464 1.00 0.00
#> TCGA.ER.A19O.06 1 0.000 0.99464 1.00 0.00
#> TCGA.EE.A2ME.06 1 0.000 0.99464 1.00 0.00
#> TCGA.EE.A20B.06 1 0.000 0.99464 1.00 0.00
#> TCGA.EE.A3AF.06 2 0.000 0.99501 0.00 1.00
#> TCGA.GN.A265.06 1 0.000 0.99464 1.00 0.00
#> TCGA.FS.A1YX.06 2 0.000 0.99501 0.00 1.00
#> TCGA.FS.A1ZJ.06 2 0.000 0.99501 0.00 1.00
#> TCGA.ER.A19H.06 1 0.000 0.99464 1.00 0.00
#> TCGA.EE.A3AC.06 2 0.000 0.99501 0.00 1.00
#> TCGA.EE.A2MU.06 1 0.000 0.99464 1.00 0.00
#> TCGA.ER.A194.01 1 0.000 0.99464 1.00 0.00
#> TCGA.EE.A2MS.06 1 0.000 0.99464 1.00 0.00
#> TCGA.EE.A29R.06 2 0.000 0.99501 0.00 1.00
#> TCGA.D9.A1X3.06 2 0.000 0.99501 0.00 1.00
#> TCGA.EE.A29X.06 2 0.000 0.99501 0.00 1.00
#> TCGA.EE.A2GK.06 1 0.000 0.99464 1.00 0.00
#> TCGA.EE.A3AA.06 1 0.000 0.99464 1.00 0.00
#> TCGA.ER.A2NE.06 2 0.000 0.99501 0.00 1.00
#> TCGA.EE.A2GR.06 2 0.000 0.99501 0.00 1.00
#> TCGA.FS.A1ZD.06 2 0.000 0.99501 0.00 1.00
#> TCGA.ER.A19P.06 1 0.000 0.99464 1.00 0.00
#> TCGA.D3.A1Q8.06 1 0.000 0.99464 1.00 0.00
#> TCGA.ER.A2NC.06 1 0.000 0.99464 1.00 0.00
#> TCGA.BF.A1Q0.01 1 0.000 0.99464 1.00 0.00
#> TCGA.FS.A1ZP.06 2 0.000 0.99501 0.00 1.00
#> TCGA.EE.A182.06 1 0.000 0.99464 1.00 0.00
#> TCGA.D9.A1JW.06 1 0.000 0.99464 1.00 0.00
#> TCGA.D3.A1Q7.06 1 0.000 0.99464 1.00 0.00
#> TCGA.EE.A185.06 2 0.000 0.99501 0.00 1.00
#> TCGA.EE.A2GJ.06 1 0.000 0.99464 1.00 0.00
#> TCGA.D3.A3CB.06 1 0.000 0.99464 1.00 0.00
#> TCGA.EE.A2GU.06 1 0.000 0.99464 1.00 0.00
#> TCGA.ER.A195.06 1 0.000 0.99464 1.00 0.00
#> TCGA.FS.A1Z7.06 1 0.000 0.99464 1.00 0.00
#> TCGA.EE.A2M6.06 2 0.000 0.99501 0.00 1.00
#> TCGA.ER.A19K.01 1 0.000 0.99464 1.00 0.00
#> TCGA.DA.A1HY.06 2 0.000 0.99501 0.00 1.00
#> TCGA.D3.A3C7.06 2 0.000 0.99501 0.00 1.00
#> TCGA.EE.A2MP.06 2 0.000 0.99501 0.00 1.00
#> TCGA.EE.A29H.06 2 0.000 0.99501 0.00 1.00
#> TCGA.FR.A3YO.06 1 0.000 0.99464 1.00 0.00
#> TCGA.XV.AB01.01 2 0.000 0.99501 0.00 1.00
#> TCGA.RP.A694.06 2 0.000 0.99501 0.00 1.00
#> TCGA.EB.A5SF.01 1 0.000 0.99464 1.00 0.00
#> TCGA.ER.A19G.06 2 0.000 0.99501 0.00 1.00
#> TCGA.EE.A2GE.06 1 0.000 0.99464 1.00 0.00
#> TCGA.GF.A3OT.06 1 0.000 0.99464 1.00 0.00
#> TCGA.ER.A2NF.06 1 0.000 0.99464 1.00 0.00
#> TCGA.RP.A695.06 2 0.000 0.99501 0.00 1.00
#> TCGA.BF.AAP7.01 1 0.000 0.99464 1.00 0.00
#> TCGA.EB.A3Y7.01 1 0.000 0.99464 1.00 0.00
#> TCGA.EB.A3XC.01 2 0.000 0.99501 0.00 1.00
#> TCGA.ER.A19W.06 1 0.000 0.99464 1.00 0.00
#> TCGA.FR.A69P.06 2 0.469 0.88832 0.10 0.90
#> TCGA.RP.A693.06 1 0.000 0.99464 1.00 0.00
#> TCGA.FW.A3TV.06 1 0.000 0.99464 1.00 0.00
#> TCGA.FW.A3R5.11 1 0.000 0.99464 1.00 0.00
#> TCGA.FW.A3TU.06 2 0.000 0.99501 0.00 1.00
#> TCGA.BF.AAP8.01 1 0.000 0.99464 1.00 0.00
#> TCGA.EE.A2MM.06 2 0.000 0.99501 0.00 1.00
#> TCGA.DA.A1HW.06 1 0.000 0.99464 1.00 0.00
#> TCGA.DA.A1IC.06 2 0.000 0.99501 0.00 1.00
#> TCGA.XV.AAZV.01 1 0.000 0.99464 1.00 0.00
#> TCGA.D3.A3C6.06 2 0.000 0.99501 0.00 1.00
#> TCGA.EE.A29C.06 1 0.000 0.99464 1.00 0.00
#> TCGA.BF.AAP2.01 2 0.000 0.99501 0.00 1.00
#> TCGA.EE.A2A2.06 2 0.000 0.99501 0.00 1.00
#> TCGA.GF.A6C8.06 1 0.000 0.99464 1.00 0.00
#> TCGA.RP.A690.06 1 0.000 0.99464 1.00 0.00
#> TCGA.FW.A5DY.06 1 0.000 0.99464 1.00 0.00
#> TCGA.DA.A1I4.06 1 0.000 0.99464 1.00 0.00
#> TCGA.EE.A29V.06 1 0.000 0.99464 1.00 0.00
#> TCGA.GF.A6C9.06 1 0.000 0.99464 1.00 0.00
#> TCGA.EE.A2GT.06 1 0.000 0.99464 1.00 0.00
#> TCGA.GN.A9SD.06 1 0.000 0.99464 1.00 0.00
#> TCGA.EE.A3AB.06 1 0.000 0.99464 1.00 0.00
#> TCGA.BF.AAP6.01 2 0.000 0.99501 0.00 1.00
#> TCGA.EB.A5SH.06 1 0.000 0.99464 1.00 0.00
#> TCGA.D9.A6E9.06 1 0.000 0.99464 1.00 0.00
#> TCGA.BF.AAP4.01 1 0.000 0.99464 1.00 0.00
#> TCGA.EE.A2GM.06 2 0.000 0.99501 0.00 1.00
#> TCGA.D3.A3CF.06 1 0.000 0.99464 1.00 0.00
#> TCGA.D9.A6EC.06 2 0.000 0.99501 0.00 1.00
#> TCGA.DA.A1I1.06 1 0.000 0.99464 1.00 0.00
#> TCGA.HR.A2OH.06 1 0.000 0.99464 1.00 0.00
#> TCGA.EE.A2MT.06 1 0.000 0.99464 1.00 0.00
#> TCGA.ER.A19M.06 1 0.000 0.99464 1.00 0.00
#> TCGA.GN.A26C.01 1 0.000 0.99464 1.00 0.00
#> TCGA.FS.A1ZA.06 2 0.000 0.99501 0.00 1.00
#> TCGA.EB.A5SE.01 2 0.000 0.99501 0.00 1.00
#> TCGA.ER.A3PL.06 2 0.000 0.99501 0.00 1.00
#> TCGA.FR.A3R1.01 2 0.000 0.99501 0.00 1.00
#> TCGA.EE.A2MI.06 1 0.000 0.99464 1.00 0.00
#> TCGA.D3.A3CE.06 2 0.000 0.99501 0.00 1.00
#> TCGA.D3.A5GT.01 2 0.000 0.99501 0.00 1.00
#> TCGA.ER.A2NB.01 1 0.000 0.99464 1.00 0.00
#> TCGA.D3.A1Q5.06 1 0.000 0.99464 1.00 0.00
#> TCGA.EB.A5UN.06 1 0.000 0.99464 1.00 0.00
#> TCGA.EB.A299.01 1 0.000 0.99464 1.00 0.00
#> TCGA.DA.A1IA.06 2 0.000 0.99501 0.00 1.00
#> TCGA.EB.A5SG.06 1 0.000 0.99464 1.00 0.00
#> TCGA.D9.A6EA.06 2 0.000 0.99501 0.00 1.00
#> TCGA.XV.AAZY.01 1 0.000 0.99464 1.00 0.00
#> TCGA.EB.A57M.01 1 0.000 0.99464 1.00 0.00
#> TCGA.EE.A2A6.06 1 0.000 0.99464 1.00 0.00
#> TCGA.D3.A2JA.06 1 0.000 0.99464 1.00 0.00
#> TCGA.D3.A1Q1.06 1 0.000 0.99464 1.00 0.00
#> TCGA.EB.A3XF.01 2 0.000 0.99501 0.00 1.00
#> TCGA.D3.A2JF.06 1 0.469 0.88482 0.90 0.10
#> TCGA.XV.AAZW.01 2 0.000 0.99501 0.00 1.00
#> TCGA.EB.A3Y6.01 1 0.000 0.99464 1.00 0.00
#> TCGA.EB.A3XE.01 1 0.000 0.99464 1.00 0.00
#> TCGA.D9.A3Z4.01 2 0.000 0.99501 0.00 1.00
#> TCGA.FW.A3R5.06 1 0.000 0.99464 1.00 0.00
#> TCGA.EE.A2GI.06 1 0.000 0.99464 1.00 0.00
#> TCGA.EE.A2GL.06 1 0.000 0.99464 1.00 0.00
#> TCGA.EB.A3XB.01 1 0.000 0.99464 1.00 0.00
#> TCGA.BF.AAOU.01 1 0.000 0.99464 1.00 0.00
#> TCGA.EB.A3XD.01 1 0.000 0.99464 1.00 0.00
#> TCGA.EE.A2MD.06 1 0.000 0.99464 1.00 0.00
#> TCGA.YD.A9TB.06 2 0.000 0.99501 0.00 1.00
#> TCGA.W3.AA1V.06 1 0.000 0.99464 1.00 0.00
#> TCGA.ER.A2ND.06 2 0.584 0.83790 0.14 0.86
#> TCGA.D3.A2JK.06 1 0.000 0.99464 1.00 0.00
#> TCGA.FS.A1ZB.06 1 0.000 0.99464 1.00 0.00
#> TCGA.EE.A29D.06 2 0.000 0.99501 0.00 1.00
#> TCGA.EB.A5UM.01 1 0.000 0.99464 1.00 0.00
#> TCGA.QB.A6FS.06 1 0.000 0.99464 1.00 0.00
#> TCGA.D9.A3Z1.06 1 0.000 0.99464 1.00 0.00
#> TCGA.D3.A2JN.06 1 0.000 0.99464 1.00 0.00
#> TCGA.FR.A3YN.06 2 0.000 0.99501 0.00 1.00
#> TCGA.FS.A1ZT.06 1 0.000 0.99464 1.00 0.00
#> TCGA.D9.A148.06 1 0.000 0.99464 1.00 0.00
#> TCGA.HR.A2OG.06 1 0.000 0.99464 1.00 0.00
#> TCGA.EE.A2ML.06 1 0.925 0.48210 0.66 0.34
#> TCGA.EB.A5UL.06 1 0.000 0.99464 1.00 0.00
#> TCGA.EE.A29T.06 1 0.000 0.99464 1.00 0.00
#> TCGA.D9.A3Z3.06 1 0.000 0.99464 1.00 0.00
#> TCGA.D9.A4Z3.01 2 0.000 0.99501 0.00 1.00
#> TCGA.ER.A3ES.06 1 0.000 0.99464 1.00 0.00
#> TCGA.XV.A9VZ.01 1 0.000 0.99464 1.00 0.00
#> TCGA.QB.AA9O.06 2 0.141 0.97549 0.02 0.98
#> TCGA.EB.A44Q.06 1 0.000 0.99464 1.00 0.00
#> TCGA.EB.A44R.06 1 0.000 0.99464 1.00 0.00
#> TCGA.BF.A3DJ.01 2 0.000 0.99501 0.00 1.00
#> TCGA.EE.A3JD.06 1 0.000 0.99464 1.00 0.00
#> TCGA.D3.A51N.06 1 0.000 0.99464 1.00 0.00
#> TCGA.EB.A44N.01 1 0.000 0.99464 1.00 0.00
#> TCGA.EE.A3J3.06 2 0.000 0.99501 0.00 1.00
#> TCGA.XV.A9W5.01 1 0.000 0.99464 1.00 0.00
#> TCGA.D3.A51G.06 2 0.000 0.99501 0.00 1.00
#> TCGA.EB.A4P0.01 2 0.000 0.99501 0.00 1.00
#> TCGA.BF.AAP1.01 2 0.000 0.99501 0.00 1.00
#> TCGA.EE.A3J4.06 2 0.000 0.99501 0.00 1.00
#> TCGA.Z2.AA3V.06 1 0.000 0.99464 1.00 0.00
#> TCGA.LH.A9QB.06 2 0.000 0.99501 0.00 1.00
#> TCGA.D3.A51J.06 1 0.000 0.99464 1.00 0.00
#> TCGA.3N.A9WC.06 1 0.000 0.99464 1.00 0.00
#> TCGA.DA.A3F8.06 1 0.000 0.99464 1.00 0.00
#> TCGA.D9.A4Z6.06 1 0.000 0.99464 1.00 0.00
#> TCGA.D3.A51R.06 2 0.000 0.99501 0.00 1.00
#> TCGA.EB.A4OZ.01 1 0.000 0.99464 1.00 0.00
#> TCGA.FS.A4FB.06 2 0.000 0.99501 0.00 1.00
#> TCGA.EE.A3JE.06 1 0.000 0.99464 1.00 0.00
#> TCGA.W3.AA1W.06 1 0.000 0.99464 1.00 0.00
#> TCGA.DA.A1I0.06 1 0.000 0.99464 1.00 0.00
#> TCGA.D3.A51F.06 1 0.000 0.99464 1.00 0.00
#> TCGA.IH.A3EA.01 2 0.000 0.99501 0.00 1.00
#> TCGA.EB.A431.01 1 0.000 0.99464 1.00 0.00
#> TCGA.EB.A97M.01 2 0.000 0.99501 0.00 1.00
#> TCGA.BF.AAOX.01 1 0.000 0.99464 1.00 0.00
#> TCGA.DA.A3F5.06 1 0.000 0.99464 1.00 0.00
#> TCGA.YD.A9TA.06 1 0.000 0.99464 1.00 0.00
#> TCGA.DA.A3F2.06 1 0.000 0.99464 1.00 0.00
#> TCGA.EB.A44O.01 2 0.000 0.99501 0.00 1.00
#> TCGA.EB.A4IQ.01 1 0.000 0.99464 1.00 0.00
#> TCGA.EB.A4IS.01 1 0.000 0.99464 1.00 0.00
#> TCGA.YG.AA3O.06 2 0.000 0.99501 0.00 1.00
#> TCGA.ER.A3EV.06 1 0.000 0.99464 1.00 0.00
#> TCGA.3N.A9WD.06 1 0.000 0.99464 1.00 0.00
#> TCGA.BF.A3DM.01 2 0.000 0.99501 0.00 1.00
#> TCGA.XV.A9W2.01 1 0.000 0.99464 1.00 0.00
#> TCGA.W3.AA1Q.06 2 0.000 0.99501 0.00 1.00
#> TCGA.WE.AAA0.06 1 0.000 0.99464 1.00 0.00
#> TCGA.W3.AA1R.06 2 0.000 0.99501 0.00 1.00
#> TCGA.EE.A3J5.06 1 0.000 0.99464 1.00 0.00
#> TCGA.EB.A4OY.01 1 0.000 0.99464 1.00 0.00
#> TCGA.FS.A4FD.06 1 0.000 0.99464 1.00 0.00
#> TCGA.BF.AAP0.06 1 0.000 0.99464 1.00 0.00
#> TCGA.YG.AA3P.06 2 0.000 0.99501 0.00 1.00
#> TCGA.EE.A3JA.06 2 0.000 0.99501 0.00 1.00
#> TCGA.W3.AA21.06 2 0.000 0.99501 0.00 1.00
#> TCGA.WE.AAA3.06 1 0.000 0.99464 1.00 0.00
#> TCGA.FS.A4F4.06 2 0.000 0.99501 0.00 1.00
#> TCGA.BF.A3DN.01 2 0.000 0.99501 0.00 1.00
#> TCGA.ER.A3ET.06 1 0.000 0.99464 1.00 0.00
#> TCGA.W3.AA1O.06 2 0.000 0.99501 0.00 1.00
#> TCGA.D3.A51E.06 1 0.141 0.97459 0.98 0.02
#> TCGA.Z2.AA3S.06 2 0.000 0.99501 0.00 1.00
#> TCGA.YG.AA3N.01 2 0.000 0.99501 0.00 1.00
#> TCGA.WE.AA9Y.06 1 0.000 0.99464 1.00 0.00
#> TCGA.FS.A4F5.06 2 0.000 0.99501 0.00 1.00
#> TCGA.EE.A3J7.06 2 0.000 0.99501 0.00 1.00
#> TCGA.FS.A4F8.06 1 0.000 0.99464 1.00 0.00
#> TCGA.DA.A3F3.06 2 0.000 0.99501 0.00 1.00
#> TCGA.D3.A51H.06 1 0.000 0.99464 1.00 0.00
#> TCGA.BF.A3DL.01 1 0.000 0.99464 1.00 0.00
#> TCGA.D3.A51T.06 2 0.000 0.99501 0.00 1.00
#> TCGA.D3.A51K.06 2 0.000 0.99501 0.00 1.00
#> TCGA.EB.A44P.01 2 0.000 0.99501 0.00 1.00
#> TCGA.D9.A4Z5.01 2 0.000 0.99501 0.00 1.00
#> TCGA.WE.AAA4.06 1 0.000 0.99464 1.00 0.00
#> TCGA.3N.A9WB.06 2 0.000 0.99501 0.00 1.00
#> TCGA.EE.A3J8.06 2 0.000 0.99501 0.00 1.00
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.FR.A728.01 1 0.0000 0.9746 1.00 0.00 0.00
#> TCGA.GN.A4U8.11 1 0.0000 0.9746 1.00 0.00 0.00
#> TCGA.GN.A8LL.06 3 0.0000 0.9695 0.00 0.00 1.00
#> TCGA.FR.A8YC.06 2 0.0000 0.9811 0.00 1.00 0.00
#> TCGA.DA.A95X.06 2 0.0000 0.9811 0.00 1.00 0.00
#> TCGA.ER.A42K.06 3 0.0000 0.9695 0.00 0.00 1.00
#> TCGA.D3.A8GO.06 1 0.0000 0.9746 1.00 0.00 0.00
#> TCGA.D3.A8GK.06 3 0.0000 0.9695 0.00 0.00 1.00
#> TCGA.WE.A8JZ.06 2 0.0000 0.9811 0.00 1.00 0.00
#> TCGA.WE.A8ZO.06 3 0.6302 0.0642 0.00 0.48 0.52
#> TCGA.D3.A8GI.06 2 0.0000 0.9811 0.00 1.00 0.00
#> TCGA.FS.A4FC.06 3 0.0000 0.9695 0.00 0.00 1.00
#> TCGA.FS.A4F2.06 3 0.0000 0.9695 0.00 0.00 1.00
#> TCGA.WE.A8ZM.06 3 0.0000 0.9695 0.00 0.00 1.00
#> TCGA.WE.A8ZT.06 3 0.0000 0.9695 0.00 0.00 1.00
#> TCGA.D3.A8GQ.06 1 0.6309 0.0389 0.50 0.00 0.50
#> TCGA.D3.A8GB.06 1 0.0000 0.9746 1.00 0.00 0.00
#> TCGA.DA.A95Y.06 2 0.0000 0.9811 0.00 1.00 0.00
#> TCGA.EE.A3JI.06 2 0.0000 0.9811 0.00 1.00 0.00
#> TCGA.OD.A75X.06 2 0.0000 0.9811 0.00 1.00 0.00
#> TCGA.DA.A960.01 2 0.0000 0.9811 0.00 1.00 0.00
#> TCGA.D3.A8GV.06 2 0.0000 0.9811 0.00 1.00 0.00
#> TCGA.WE.A8ZN.06 1 0.0000 0.9746 1.00 0.00 0.00
#> TCGA.D3.A8GN.06 1 0.0000 0.9746 1.00 0.00 0.00
#> TCGA.EB.A550.01 1 0.0000 0.9746 1.00 0.00 0.00
#> TCGA.BF.A5EQ.01 3 0.0000 0.9695 0.00 0.00 1.00
#> TCGA.EB.A3HV.01 3 0.0000 0.9695 0.00 0.00 1.00
#> TCGA.HR.A5NC.01 3 0.0000 0.9695 0.00 0.00 1.00
#> TCGA.DA.A95Z.06 2 0.0000 0.9811 0.00 1.00 0.00
#> TCGA.EB.A6QZ.01 2 0.0000 0.9811 0.00 1.00 0.00
#> TCGA.FW.A3I3.06 2 0.0000 0.9811 0.00 1.00 0.00
#> TCGA.WE.A8K6.06 3 0.0000 0.9695 0.00 0.00 1.00
#> TCGA.D3.A8GP.06 2 0.0000 0.9811 0.00 1.00 0.00
#> TCGA.EB.A42Z.01 2 0.0000 0.9811 0.00 1.00 0.00
#> TCGA.GN.A4U4.06 2 0.0000 0.9811 0.00 1.00 0.00
#> TCGA.GF.A4EO.06 1 0.0000 0.9746 1.00 0.00 0.00
#> TCGA.GN.A8LK.06 2 0.0000 0.9811 0.00 1.00 0.00
#> TCGA.WE.A8K4.01 1 0.0000 0.9746 1.00 0.00 0.00
#> TCGA.DA.A95W.06 2 0.0000 0.9811 0.00 1.00 0.00
#> TCGA.FW.A5DX.01 2 0.0000 0.9811 0.00 1.00 0.00
#> TCGA.GN.A4U3.06 2 0.0000 0.9811 0.00 1.00 0.00
#> TCGA.EB.A6QY.01 1 0.0000 0.9746 1.00 0.00 0.00
#> TCGA.EB.A5VU.01 3 0.0000 0.9695 0.00 0.00 1.00
#> TCGA.Z2.A8RT.06 3 0.0000 0.9695 0.00 0.00 1.00
#> TCGA.WE.A8K1.06 1 0.0000 0.9746 1.00 0.00 0.00
#> TCGA.EB.A41B.01 3 0.0892 0.9509 0.00 0.02 0.98
#> TCGA.WE.A8ZY.06 2 0.0000 0.9811 0.00 1.00 0.00
#> TCGA.D9.A6EG.06 2 0.0000 0.9811 0.00 1.00 0.00
#> TCGA.BF.A5ER.01 3 0.0000 0.9695 0.00 0.00 1.00
#> TCGA.FR.A8YD.06 2 0.0000 0.9811 0.00 1.00 0.00
#> TCGA.FS.A4F9.06 2 0.0000 0.9811 0.00 1.00 0.00
#> TCGA.EB.A6R0.01 3 0.0000 0.9695 0.00 0.00 1.00
#> TCGA.ER.A42L.06 1 0.0000 0.9746 1.00 0.00 0.00
#> TCGA.D3.A8GJ.06 1 0.0000 0.9746 1.00 0.00 0.00
#> TCGA.FR.A8YE.06 1 0.0000 0.9746 1.00 0.00 0.00
#> TCGA.WE.A8ZR.06 3 0.0000 0.9695 0.00 0.00 1.00
#> TCGA.BF.A9VF.01 2 0.2537 0.9022 0.00 0.92 0.08
#> TCGA.EE.A3JH.06 1 0.0000 0.9746 1.00 0.00 0.00
#> TCGA.DA.A95V.06 3 0.0000 0.9695 0.00 0.00 1.00
#> TCGA.GF.A769.01 2 0.0000 0.9811 0.00 1.00 0.00
#> TCGA.D9.A4Z2.01 2 0.0892 0.9631 0.00 0.98 0.02
#> TCGA.FR.A44A.06 1 0.0000 0.9746 1.00 0.00 0.00
#> TCGA.EB.A5VV.06 1 0.0000 0.9746 1.00 0.00 0.00
#> TCGA.EE.A180.06 2 0.0000 0.9811 0.00 1.00 0.00
#> TCGA.D3.A8GC.06 2 0.0000 0.9811 0.00 1.00 0.00
#> TCGA.WE.A8K5.06 2 0.0000 0.9811 0.00 1.00 0.00
#> TCGA.GN.A8LN.01 2 0.0000 0.9811 0.00 1.00 0.00
#> TCGA.EE.A3JB.06 1 0.0000 0.9746 1.00 0.00 0.00
#> TCGA.D3.A3MO.06 3 0.4002 0.7923 0.00 0.16 0.84
#> TCGA.ER.A42H.01 2 0.2959 0.8793 0.00 0.90 0.10
#> TCGA.WE.A8ZX.06 3 0.0000 0.9695 0.00 0.00 1.00
#> TCGA.GN.A4U5.01 1 0.0000 0.9746 1.00 0.00 0.00
#> TCGA.D3.A8GS.06 1 0.0000 0.9746 1.00 0.00 0.00
#> TCGA.WE.A8ZQ.06 2 0.0000 0.9811 0.00 1.00 0.00
#> TCGA.EE.A2MF.06 2 0.0000 0.9811 0.00 1.00 0.00
#> TCGA.D3.A5GU.06 3 0.0000 0.9695 0.00 0.00 1.00
#> TCGA.GN.A4U8.06 1 0.0000 0.9746 1.00 0.00 0.00
#> TCGA.EB.A42Y.01 2 0.0000 0.9811 0.00 1.00 0.00
#> TCGA.D3.A3ML.06 2 0.0000 0.9811 0.00 1.00 0.00
#> TCGA.EB.A551.01 1 0.0000 0.9746 1.00 0.00 0.00
#> TCGA.D3.A8GM.06 1 0.5216 0.6567 0.74 0.00 0.26
#> TCGA.D3.A8GL.06 2 0.0000 0.9811 0.00 1.00 0.00
#> TCGA.D3.A3MU.06 2 0.0000 0.9811 0.00 1.00 0.00
#> TCGA.FS.A4F0.06 2 0.0000 0.9811 0.00 1.00 0.00
#> TCGA.D3.A3MV.06 3 0.0000 0.9695 0.00 0.00 1.00
#> TCGA.GN.A4U7.06 3 0.0000 0.9695 0.00 0.00 1.00
#> TCGA.FR.A2OS.01 3 0.0000 0.9695 0.00 0.00 1.00
#> TCGA.D3.A2JE.06 2 0.0000 0.9811 0.00 1.00 0.00
#> TCGA.YD.A89C.06 3 0.0000 0.9695 0.00 0.00 1.00
#> TCGA.FR.A726.01 3 0.0000 0.9695 0.00 0.00 1.00
#> TCGA.BF.A5EP.01 2 0.0000 0.9811 0.00 1.00 0.00
#> TCGA.D3.A3MR.06 1 0.0000 0.9746 1.00 0.00 0.00
#> TCGA.D3.A8GR.06 3 0.0000 0.9695 0.00 0.00 1.00
#> TCGA.GN.A4U9.06 3 0.0000 0.9695 0.00 0.00 1.00
#> TCGA.EB.A6L9.06 1 0.0000 0.9746 1.00 0.00 0.00
#> TCGA.D3.A5GL.06 3 0.0000 0.9695 0.00 0.00 1.00
#> TCGA.EB.A430.01 1 0.0000 0.9746 1.00 0.00 0.00
#> TCGA.D3.A8GE.06 1 0.0000 0.9746 1.00 0.00 0.00
#> TCGA.D3.A8GD.06 1 0.0000 0.9746 1.00 0.00 0.00
#> TCGA.EB.A41A.01 2 0.0000 0.9811 0.00 1.00 0.00
#> TCGA.W3.A825.06 3 0.3686 0.8084 0.14 0.00 0.86
#> TCGA.EE.A183.06 1 0.0000 0.9746 1.00 0.00 0.00
#> TCGA.ER.A2NH.06 1 0.0000 0.9746 1.00 0.00 0.00
#> TCGA.D3.A5GR.06 1 0.0000 0.9746 1.00 0.00 0.00
#> TCGA.FR.A729.06 1 0.0000 0.9746 1.00 0.00 0.00
#> TCGA.D3.A1QA.06 2 0.0000 0.9811 0.00 1.00 0.00
#> TCGA.FS.A1YY.06 3 0.0000 0.9695 0.00 0.00 1.00
#> TCGA.EE.A2MK.06 3 0.0000 0.9695 0.00 0.00 1.00
#> TCGA.EE.A2M8.06 1 0.0000 0.9746 1.00 0.00 0.00
#> TCGA.EB.A5KH.06 2 0.0000 0.9811 0.00 1.00 0.00
#> TCGA.FS.A1ZR.06 3 0.0000 0.9695 0.00 0.00 1.00
#> TCGA.EE.A3AE.06 3 0.0000 0.9695 0.00 0.00 1.00
#> TCGA.EE.A29P.06 3 0.0000 0.9695 0.00 0.00 1.00
#> TCGA.EB.A553.01 3 0.0000 0.9695 0.00 0.00 1.00
#> TCGA.EE.A2MR.06 1 0.0000 0.9746 1.00 0.00 0.00
#> TCGA.GN.A26A.06 1 0.1529 0.9370 0.96 0.00 0.04
#> TCGA.FS.A1ZY.06 2 0.0000 0.9811 0.00 1.00 0.00
#> TCGA.EE.A20I.06 3 0.0000 0.9695 0.00 0.00 1.00
#> TCGA.DA.A1I5.06 1 0.0000 0.9746 1.00 0.00 0.00
#> TCGA.EE.A184.06 2 0.0000 0.9811 0.00 1.00 0.00
#> TCGA.EB.A85J.01 1 0.0000 0.9746 1.00 0.00 0.00
#> TCGA.RP.A6K9.06 3 0.2537 0.8819 0.08 0.00 0.92
#> TCGA.EE.A17Y.06 1 0.0000 0.9746 1.00 0.00 0.00
#> TCGA.D9.A149.06 1 0.0000 0.9746 1.00 0.00 0.00
#> TCGA.ER.A19D.06 1 0.0000 0.9746 1.00 0.00 0.00
#> TCGA.FS.A1ZZ.06 2 0.0000 0.9811 0.00 1.00 0.00
#> TCGA.EE.A2GP.06 3 0.0000 0.9695 0.00 0.00 1.00
#> TCGA.EE.A3AD.06 2 0.0000 0.9811 0.00 1.00 0.00
#> TCGA.D3.A1Q9.06 3 0.0000 0.9695 0.00 0.00 1.00
#> TCGA.GF.A2C7.01 2 0.0000 0.9811 0.00 1.00 0.00
#> TCGA.BF.A5ES.01 3 0.0000 0.9695 0.00 0.00 1.00
#> TCGA.ER.A199.06 1 0.0000 0.9746 1.00 0.00 0.00
#> TCGA.EE.A3AH.06 2 0.0000 0.9811 0.00 1.00 0.00
#> TCGA.W3.A828.06 1 0.0000 0.9746 1.00 0.00 0.00
#> TCGA.EE.A2A5.06 2 0.6244 0.2157 0.00 0.56 0.44
#> TCGA.ER.A19L.06 1 0.6302 0.1153 0.52 0.00 0.48
#> TCGA.BF.A1PX.01 1 0.0000 0.9746 1.00 0.00 0.00
#> TCGA.ER.A19T.06 3 0.0000 0.9695 0.00 0.00 1.00
#> TCGA.EB.A51B.01 3 0.0000 0.9695 0.00 0.00 1.00
#> TCGA.FS.A1ZQ.06 3 0.0000 0.9695 0.00 0.00 1.00
#> TCGA.D3.A2JG.06 2 0.2959 0.8786 0.00 0.90 0.10
#> TCGA.EE.A2GH.06 1 0.0000 0.9746 1.00 0.00 0.00
#> TCGA.ER.A19F.06 3 0.0000 0.9695 0.00 0.00 1.00
#> TCGA.ER.A196.01 1 0.0000 0.9746 1.00 0.00 0.00
#> TCGA.D3.A2JC.06 1 0.0000 0.9746 1.00 0.00 0.00
#> TCGA.EE.A3AG.06 3 0.0000 0.9695 0.00 0.00 1.00
#> TCGA.ER.A19S.06 1 0.0000 0.9746 1.00 0.00 0.00
#> TCGA.EE.A2GC.06 3 0.0000 0.9695 0.00 0.00 1.00
#> TCGA.EE.A29N.06 1 0.0000 0.9746 1.00 0.00 0.00
#> TCGA.FR.A7U8.06 2 0.0000 0.9811 0.00 1.00 0.00
#> TCGA.BF.A5EO.01 1 0.0000 0.9746 1.00 0.00 0.00
#> TCGA.ER.A19B.06 3 0.0000 0.9695 0.00 0.00 1.00
#> TCGA.D3.A5GN.06 3 0.0000 0.9695 0.00 0.00 1.00
#> TCGA.D3.A2JB.06 1 0.0000 0.9746 1.00 0.00 0.00
#> TCGA.ER.A19J.06 2 0.0000 0.9811 0.00 1.00 0.00
#> TCGA.D3.A2JD.06 1 0.0000 0.9746 1.00 0.00 0.00
#> TCGA.FS.A1Z4.06 1 0.0000 0.9746 1.00 0.00 0.00
#> TCGA.FR.A7UA.06 1 0.0000 0.9746 1.00 0.00 0.00
#> TCGA.EE.A2M7.06 3 0.6244 0.1736 0.44 0.00 0.56
#> TCGA.D3.A1Q3.06 1 0.0000 0.9746 1.00 0.00 0.00
#> TCGA.EB.A85I.01 1 0.0000 0.9746 1.00 0.00 0.00
#> TCGA.EB.A82C.01 2 0.0000 0.9811 0.00 1.00 0.00
#> TCGA.ER.A19E.06 3 0.0000 0.9695 0.00 0.00 1.00
#> TCGA.FS.A1ZK.06 3 0.6280 0.1383 0.00 0.46 0.54
#> TCGA.FS.A1ZU.06 3 0.0000 0.9695 0.00 0.00 1.00
#> TCGA.EB.A5FP.01 2 0.0000 0.9811 0.00 1.00 0.00
#> TCGA.EB.A4XL.01 3 0.0000 0.9695 0.00 0.00 1.00
#> TCGA.DA.A1I2.06 3 0.0000 0.9695 0.00 0.00 1.00
#> TCGA.EE.A29L.06 2 0.0000 0.9811 0.00 1.00 0.00
#> TCGA.FS.A1ZN.01 2 0.0000 0.9811 0.00 1.00 0.00
#> TCGA.EB.A24D.01 3 0.0000 0.9695 0.00 0.00 1.00
#> TCGA.EE.A2GB.06 3 0.0000 0.9695 0.00 0.00 1.00
#> TCGA.DA.A1I7.06 3 0.0000 0.9695 0.00 0.00 1.00
#> TCGA.ER.A2NF.01 1 0.0000 0.9746 1.00 0.00 0.00
#> TCGA.GN.A263.01 1 0.0000 0.9746 1.00 0.00 0.00
#> TCGA.EE.A20C.06 2 0.0000 0.9811 0.00 1.00 0.00
#> TCGA.EE.A2MQ.06 2 0.0000 0.9811 0.00 1.00 0.00
#> TCGA.ER.A19N.06 1 0.0000 0.9746 1.00 0.00 0.00
#> TCGA.FS.A1Z3.06 2 0.0000 0.9811 0.00 1.00 0.00
#> TCGA.DA.A1I8.06 3 0.0000 0.9695 0.00 0.00 1.00
#> TCGA.D3.A5GS.06 3 0.0000 0.9695 0.00 0.00 1.00
#> TCGA.EE.A181.06 3 0.0000 0.9695 0.00 0.00 1.00
#> TCGA.GN.A268.06 2 0.0000 0.9811 0.00 1.00 0.00
#> TCGA.W3.A824.06 3 0.0000 0.9695 0.00 0.00 1.00
#> TCGA.EE.A2GS.06 3 0.0000 0.9695 0.00 0.00 1.00
#> TCGA.FR.A7U9.06 1 0.0000 0.9746 1.00 0.00 0.00
#> TCGA.ER.A19Q.06 1 0.0000 0.9746 1.00 0.00 0.00
#> TCGA.FS.A1ZM.06 3 0.0000 0.9695 0.00 0.00 1.00
#> TCGA.EE.A2MG.06 1 0.0000 0.9746 1.00 0.00 0.00
#> TCGA.EE.A2MC.06 1 0.0000 0.9746 1.00 0.00 0.00
#> TCGA.EE.A17Z.06 3 0.0000 0.9695 0.00 0.00 1.00
#> TCGA.D3.A2JP.06 1 0.0000 0.9746 1.00 0.00 0.00
#> TCGA.ER.A19C.06 3 0.0000 0.9695 0.00 0.00 1.00
#> TCGA.EB.A82B.01 3 0.0000 0.9695 0.00 0.00 1.00
#> TCGA.EE.A2A0.06 1 0.0000 0.9746 1.00 0.00 0.00
#> TCGA.EE.A29G.06 1 0.0000 0.9746 1.00 0.00 0.00
#> TCGA.D3.A5GO.06 3 0.0000 0.9695 0.00 0.00 1.00
#> TCGA.GN.A269.01 1 0.0000 0.9746 1.00 0.00 0.00
#> TCGA.EE.A2A1.06 1 0.0000 0.9746 1.00 0.00 0.00
#> TCGA.ER.A1A1.06 1 0.0000 0.9746 1.00 0.00 0.00
#> TCGA.FS.A1ZG.06 2 0.0000 0.9811 0.00 1.00 0.00
#> TCGA.FS.A1ZE.06 2 0.0000 0.9811 0.00 1.00 0.00
#> TCGA.FS.A1ZH.06 1 0.0000 0.9746 1.00 0.00 0.00
#> TCGA.EE.A2MH.06 1 0.0000 0.9746 1.00 0.00 0.00
#> TCGA.D3.A2J6.06 1 0.0000 0.9746 1.00 0.00 0.00
#> TCGA.EE.A29Q.06 2 0.0000 0.9811 0.00 1.00 0.00
#> TCGA.BF.A1PZ.01 3 0.0000 0.9695 0.00 0.00 1.00
#> TCGA.D3.A3BZ.06 1 0.0000 0.9746 1.00 0.00 0.00
#> TCGA.D3.A2JO.06 1 0.0000 0.9746 1.00 0.00 0.00
#> TCGA.GN.A267.06 3 0.0000 0.9695 0.00 0.00 1.00
#> TCGA.EE.A2MN.06 3 0.6309 -0.0144 0.00 0.50 0.50
#> TCGA.GN.A264.06 2 0.0000 0.9811 0.00 1.00 0.00
#> TCGA.ER.A197.06 1 0.0000 0.9746 1.00 0.00 0.00
#> TCGA.DA.A1IB.06 1 0.0000 0.9746 1.00 0.00 0.00
#> TCGA.D3.A3CC.06 1 0.0000 0.9746 1.00 0.00 0.00
#> TCGA.ER.A19T.01 3 0.0000 0.9695 0.00 0.00 1.00
#> TCGA.GN.A261.06 1 0.0000 0.9746 1.00 0.00 0.00
#> TCGA.FS.A1YW.06 2 0.0000 0.9811 0.00 1.00 0.00
#> TCGA.BF.A1PU.01 1 0.0000 0.9746 1.00 0.00 0.00
#> TCGA.D3.A1QB.06 1 0.0000 0.9746 1.00 0.00 0.00
#> TCGA.D3.A1Q6.06 1 0.0000 0.9746 1.00 0.00 0.00
#> TCGA.D3.A3C8.06 1 0.0000 0.9746 1.00 0.00 0.00
#> TCGA.ER.A19A.06 1 0.0000 0.9746 1.00 0.00 0.00
#> TCGA.EE.A2GN.06 3 0.5948 0.4264 0.00 0.36 0.64
#> TCGA.EE.A29M.06 1 0.0000 0.9746 1.00 0.00 0.00
#> TCGA.D3.A2J7.06 1 0.0000 0.9746 1.00 0.00 0.00
#> TCGA.EB.A24C.01 3 0.0000 0.9695 0.00 0.00 1.00
#> TCGA.GN.A262.06 2 0.0000 0.9811 0.00 1.00 0.00
#> TCGA.EE.A2GD.06 1 0.0000 0.9746 1.00 0.00 0.00
#> TCGA.D3.A2J9.06 1 0.0000 0.9746 1.00 0.00 0.00
#> TCGA.EE.A29B.06 3 0.4291 0.7654 0.00 0.18 0.82
#> TCGA.D9.A1JX.06 2 0.0000 0.9811 0.00 1.00 0.00
#> TCGA.EE.A29A.06 2 0.0000 0.9811 0.00 1.00 0.00
#> TCGA.D3.A2JL.06 1 0.5397 0.6216 0.72 0.00 0.28
#> TCGA.D3.A1Q4.06 1 0.0000 0.9746 1.00 0.00 0.00
#> TCGA.FS.A1ZS.06 3 0.0000 0.9695 0.00 0.00 1.00
#> TCGA.D3.A3C3.06 1 0.6280 0.1835 0.54 0.00 0.46
#> TCGA.D3.A2J8.06 1 0.0000 0.9746 1.00 0.00 0.00
#> TCGA.FS.A1ZF.06 2 0.0000 0.9811 0.00 1.00 0.00
#> TCGA.FS.A1ZC.06 2 0.0000 0.9811 0.00 1.00 0.00
#> TCGA.EE.A20H.06 3 0.0000 0.9695 0.00 0.00 1.00
#> TCGA.EE.A29W.06 3 0.0000 0.9695 0.00 0.00 1.00
#> TCGA.D3.A1QA.07 3 0.0000 0.9695 0.00 0.00 1.00
#> TCGA.BF.A1PV.01 2 0.1529 0.9439 0.00 0.96 0.04
#> TCGA.EE.A29S.06 3 0.0000 0.9695 0.00 0.00 1.00
#> TCGA.DA.A1HV.06 3 0.0000 0.9695 0.00 0.00 1.00
#> TCGA.FS.A1Z0.06 1 0.0000 0.9746 1.00 0.00 0.00
#> TCGA.EE.A2GO.06 2 0.0000 0.9811 0.00 1.00 0.00
#> TCGA.EB.A1NK.01 1 0.0000 0.9746 1.00 0.00 0.00
#> TCGA.GN.A26D.06 3 0.0000 0.9695 0.00 0.00 1.00
#> TCGA.EE.A2MJ.06 1 0.0000 0.9746 1.00 0.00 0.00
#> TCGA.ER.A198.06 3 0.0000 0.9695 0.00 0.00 1.00
#> TCGA.EE.A17X.06 2 0.0000 0.9811 0.00 1.00 0.00
#> TCGA.EE.A2M5.06 1 0.0000 0.9746 1.00 0.00 0.00
#> TCGA.GN.A266.06 1 0.0000 0.9746 1.00 0.00 0.00
#> TCGA.D3.A3C1.06 3 0.0000 0.9695 0.00 0.00 1.00
#> TCGA.D3.A2JH.06 1 0.0000 0.9746 1.00 0.00 0.00
#> TCGA.EE.A20F.06 1 0.6244 0.2469 0.56 0.00 0.44
#> TCGA.EE.A29E.06 1 0.0000 0.9746 1.00 0.00 0.00
#> TCGA.ER.A2NG.06 1 0.0000 0.9746 1.00 0.00 0.00
#> TCGA.ER.A193.06 3 0.1529 0.9274 0.04 0.00 0.96
#> TCGA.FS.A1ZW.06 1 0.4291 0.7790 0.82 0.00 0.18
#> TCGA.ER.A19O.06 1 0.0000 0.9746 1.00 0.00 0.00
#> TCGA.EE.A2ME.06 1 0.0000 0.9746 1.00 0.00 0.00
#> TCGA.EE.A20B.06 3 0.0000 0.9695 0.00 0.00 1.00
#> TCGA.EE.A3AF.06 3 0.0000 0.9695 0.00 0.00 1.00
#> TCGA.GN.A265.06 1 0.0000 0.9746 1.00 0.00 0.00
#> TCGA.FS.A1YX.06 3 0.0000 0.9695 0.00 0.00 1.00
#> TCGA.FS.A1ZJ.06 3 0.0000 0.9695 0.00 0.00 1.00
#> TCGA.ER.A19H.06 3 0.0000 0.9695 0.00 0.00 1.00
#> TCGA.EE.A3AC.06 3 0.0000 0.9695 0.00 0.00 1.00
#> TCGA.EE.A2MU.06 1 0.0000 0.9746 1.00 0.00 0.00
#> TCGA.ER.A194.01 3 0.0000 0.9695 0.00 0.00 1.00
#> TCGA.EE.A2MS.06 1 0.0000 0.9746 1.00 0.00 0.00
#> TCGA.EE.A29R.06 2 0.0000 0.9811 0.00 1.00 0.00
#> TCGA.D9.A1X3.06 2 0.0000 0.9811 0.00 1.00 0.00
#> TCGA.EE.A29X.06 3 0.0000 0.9695 0.00 0.00 1.00
#> TCGA.EE.A2GK.06 1 0.0000 0.9746 1.00 0.00 0.00
#> TCGA.EE.A3AA.06 1 0.0000 0.9746 1.00 0.00 0.00
#> TCGA.ER.A2NE.06 2 0.0000 0.9811 0.00 1.00 0.00
#> TCGA.EE.A2GR.06 3 0.0000 0.9695 0.00 0.00 1.00
#> TCGA.FS.A1ZD.06 3 0.0000 0.9695 0.00 0.00 1.00
#> TCGA.ER.A19P.06 1 0.0000 0.9746 1.00 0.00 0.00
#> TCGA.D3.A1Q8.06 1 0.0000 0.9746 1.00 0.00 0.00
#> TCGA.ER.A2NC.06 3 0.0000 0.9695 0.00 0.00 1.00
#> TCGA.BF.A1Q0.01 3 0.0000 0.9695 0.00 0.00 1.00
#> TCGA.FS.A1ZP.06 3 0.5706 0.5183 0.00 0.32 0.68
#> TCGA.EE.A182.06 3 0.0000 0.9695 0.00 0.00 1.00
#> TCGA.D9.A1JW.06 1 0.4002 0.8058 0.84 0.00 0.16
#> TCGA.D3.A1Q7.06 1 0.0000 0.9746 1.00 0.00 0.00
#> TCGA.EE.A185.06 2 0.0000 0.9811 0.00 1.00 0.00
#> TCGA.EE.A2GJ.06 3 0.0000 0.9695 0.00 0.00 1.00
#> TCGA.D3.A3CB.06 1 0.0000 0.9746 1.00 0.00 0.00
#> TCGA.EE.A2GU.06 3 0.0000 0.9695 0.00 0.00 1.00
#> TCGA.ER.A195.06 1 0.0000 0.9746 1.00 0.00 0.00
#> TCGA.FS.A1Z7.06 3 0.0000 0.9695 0.00 0.00 1.00
#> TCGA.EE.A2M6.06 2 0.0000 0.9811 0.00 1.00 0.00
#> TCGA.ER.A19K.01 3 0.0000 0.9695 0.00 0.00 1.00
#> TCGA.DA.A1HY.06 3 0.0000 0.9695 0.00 0.00 1.00
#> TCGA.D3.A3C7.06 3 0.0000 0.9695 0.00 0.00 1.00
#> TCGA.EE.A2MP.06 3 0.0000 0.9695 0.00 0.00 1.00
#> TCGA.EE.A29H.06 2 0.0000 0.9811 0.00 1.00 0.00
#> TCGA.FR.A3YO.06 1 0.2537 0.8962 0.92 0.00 0.08
#> TCGA.XV.AB01.01 2 0.0000 0.9811 0.00 1.00 0.00
#> TCGA.RP.A694.06 3 0.0000 0.9695 0.00 0.00 1.00
#> TCGA.EB.A5SF.01 1 0.0000 0.9746 1.00 0.00 0.00
#> TCGA.ER.A19G.06 3 0.0000 0.9695 0.00 0.00 1.00
#> TCGA.EE.A2GE.06 1 0.0000 0.9746 1.00 0.00 0.00
#> TCGA.GF.A3OT.06 1 0.0000 0.9746 1.00 0.00 0.00
#> TCGA.ER.A2NF.06 1 0.0000 0.9746 1.00 0.00 0.00
#> TCGA.RP.A695.06 2 0.6244 0.2156 0.00 0.56 0.44
#> TCGA.BF.AAP7.01 1 0.0000 0.9746 1.00 0.00 0.00
#> TCGA.EB.A3Y7.01 1 0.0000 0.9746 1.00 0.00 0.00
#> TCGA.EB.A3XC.01 3 0.0000 0.9695 0.00 0.00 1.00
#> TCGA.ER.A19W.06 1 0.0000 0.9746 1.00 0.00 0.00
#> TCGA.FR.A69P.06 3 0.0000 0.9695 0.00 0.00 1.00
#> TCGA.RP.A693.06 1 0.0000 0.9746 1.00 0.00 0.00
#> TCGA.FW.A3TV.06 1 0.0000 0.9746 1.00 0.00 0.00
#> TCGA.FW.A3R5.11 1 0.0000 0.9746 1.00 0.00 0.00
#> TCGA.FW.A3TU.06 3 0.0000 0.9695 0.00 0.00 1.00
#> TCGA.BF.AAP8.01 1 0.0000 0.9746 1.00 0.00 0.00
#> TCGA.EE.A2MM.06 3 0.0000 0.9695 0.00 0.00 1.00
#> TCGA.DA.A1HW.06 1 0.0892 0.9564 0.98 0.00 0.02
#> TCGA.DA.A1IC.06 3 0.0000 0.9695 0.00 0.00 1.00
#> TCGA.XV.AAZV.01 1 0.0000 0.9746 1.00 0.00 0.00
#> TCGA.D3.A3C6.06 3 0.0000 0.9695 0.00 0.00 1.00
#> TCGA.EE.A29C.06 1 0.0000 0.9746 1.00 0.00 0.00
#> TCGA.BF.AAP2.01 2 0.0000 0.9811 0.00 1.00 0.00
#> TCGA.EE.A2A2.06 3 0.0000 0.9695 0.00 0.00 1.00
#> TCGA.GF.A6C8.06 3 0.0000 0.9695 0.00 0.00 1.00
#> TCGA.RP.A690.06 1 0.0000 0.9746 1.00 0.00 0.00
#> TCGA.FW.A5DY.06 1 0.0000 0.9746 1.00 0.00 0.00
#> TCGA.DA.A1I4.06 1 0.0000 0.9746 1.00 0.00 0.00
#> TCGA.EE.A29V.06 1 0.0000 0.9746 1.00 0.00 0.00
#> TCGA.GF.A6C9.06 1 0.0000 0.9746 1.00 0.00 0.00
#> TCGA.EE.A2GT.06 1 0.0000 0.9746 1.00 0.00 0.00
#> TCGA.GN.A9SD.06 1 0.0000 0.9746 1.00 0.00 0.00
#> TCGA.EE.A3AB.06 3 0.6302 0.0270 0.48 0.00 0.52
#> TCGA.BF.AAP6.01 3 0.0000 0.9695 0.00 0.00 1.00
#> TCGA.EB.A5SH.06 3 0.0000 0.9695 0.00 0.00 1.00
#> TCGA.D9.A6E9.06 1 0.0000 0.9746 1.00 0.00 0.00
#> TCGA.BF.AAP4.01 1 0.0000 0.9746 1.00 0.00 0.00
#> TCGA.EE.A2GM.06 2 0.0000 0.9811 0.00 1.00 0.00
#> TCGA.D3.A3CF.06 1 0.0000 0.9746 1.00 0.00 0.00
#> TCGA.D9.A6EC.06 2 0.0000 0.9811 0.00 1.00 0.00
#> TCGA.DA.A1I1.06 3 0.0000 0.9695 0.00 0.00 1.00
#> TCGA.HR.A2OH.06 1 0.0000 0.9746 1.00 0.00 0.00
#> TCGA.EE.A2MT.06 1 0.0000 0.9746 1.00 0.00 0.00
#> TCGA.ER.A19M.06 1 0.0000 0.9746 1.00 0.00 0.00
#> TCGA.GN.A26C.01 1 0.0000 0.9746 1.00 0.00 0.00
#> TCGA.FS.A1ZA.06 3 0.0000 0.9695 0.00 0.00 1.00
#> TCGA.EB.A5SE.01 2 0.0000 0.9811 0.00 1.00 0.00
#> TCGA.ER.A3PL.06 3 0.0000 0.9695 0.00 0.00 1.00
#> TCGA.FR.A3R1.01 3 0.0000 0.9695 0.00 0.00 1.00
#> TCGA.EE.A2MI.06 3 0.5216 0.6271 0.26 0.00 0.74
#> TCGA.D3.A3CE.06 3 0.0000 0.9695 0.00 0.00 1.00
#> TCGA.D3.A5GT.01 2 0.0000 0.9811 0.00 1.00 0.00
#> TCGA.ER.A2NB.01 1 0.0000 0.9746 1.00 0.00 0.00
#> TCGA.D3.A1Q5.06 3 0.0000 0.9695 0.00 0.00 1.00
#> TCGA.EB.A5UN.06 1 0.0000 0.9746 1.00 0.00 0.00
#> TCGA.EB.A299.01 3 0.0000 0.9695 0.00 0.00 1.00
#> TCGA.DA.A1IA.06 2 0.5216 0.6447 0.00 0.74 0.26
#> TCGA.EB.A5SG.06 1 0.0000 0.9746 1.00 0.00 0.00
#> TCGA.D9.A6EA.06 2 0.0000 0.9811 0.00 1.00 0.00
#> TCGA.XV.AAZY.01 1 0.0000 0.9746 1.00 0.00 0.00
#> TCGA.EB.A57M.01 3 0.0000 0.9695 0.00 0.00 1.00
#> TCGA.EE.A2A6.06 1 0.0892 0.9564 0.98 0.00 0.02
#> TCGA.D3.A2JA.06 1 0.0000 0.9746 1.00 0.00 0.00
#> TCGA.D3.A1Q1.06 3 0.0000 0.9695 0.00 0.00 1.00
#> TCGA.EB.A3XF.01 3 0.0000 0.9695 0.00 0.00 1.00
#> TCGA.D3.A2JF.06 3 0.0000 0.9695 0.00 0.00 1.00
#> TCGA.XV.AAZW.01 2 0.0000 0.9811 0.00 1.00 0.00
#> TCGA.EB.A3Y6.01 3 0.0000 0.9695 0.00 0.00 1.00
#> TCGA.EB.A3XE.01 3 0.0000 0.9695 0.00 0.00 1.00
#> TCGA.D9.A3Z4.01 3 0.0000 0.9695 0.00 0.00 1.00
#> TCGA.FW.A3R5.06 1 0.5016 0.6904 0.76 0.00 0.24
#> TCGA.EE.A2GI.06 3 0.0892 0.9488 0.02 0.00 0.98
#> TCGA.EE.A2GL.06 1 0.0000 0.9746 1.00 0.00 0.00
#> TCGA.EB.A3XB.01 1 0.6309 0.0409 0.50 0.00 0.50
#> TCGA.BF.AAOU.01 1 0.0000 0.9746 1.00 0.00 0.00
#> TCGA.EB.A3XD.01 1 0.0000 0.9746 1.00 0.00 0.00
#> TCGA.EE.A2MD.06 1 0.0892 0.9563 0.98 0.00 0.02
#> TCGA.YD.A9TB.06 3 0.0000 0.9695 0.00 0.00 1.00
#> TCGA.W3.AA1V.06 3 0.0000 0.9695 0.00 0.00 1.00
#> TCGA.ER.A2ND.06 3 0.0000 0.9695 0.00 0.00 1.00
#> TCGA.D3.A2JK.06 3 0.0000 0.9695 0.00 0.00 1.00
#> TCGA.FS.A1ZB.06 1 0.0000 0.9746 1.00 0.00 0.00
#> TCGA.EE.A29D.06 2 0.0000 0.9811 0.00 1.00 0.00
#> TCGA.EB.A5UM.01 3 0.0000 0.9695 0.00 0.00 1.00
#> TCGA.QB.A6FS.06 1 0.0000 0.9746 1.00 0.00 0.00
#> TCGA.D9.A3Z1.06 1 0.0000 0.9746 1.00 0.00 0.00
#> TCGA.D3.A2JN.06 1 0.0000 0.9746 1.00 0.00 0.00
#> TCGA.FR.A3YN.06 2 0.0000 0.9811 0.00 1.00 0.00
#> TCGA.FS.A1ZT.06 1 0.0000 0.9746 1.00 0.00 0.00
#> TCGA.D9.A148.06 1 0.0000 0.9746 1.00 0.00 0.00
#> TCGA.HR.A2OG.06 1 0.0000 0.9746 1.00 0.00 0.00
#> TCGA.EE.A2ML.06 3 0.0000 0.9695 0.00 0.00 1.00
#> TCGA.EB.A5UL.06 1 0.0000 0.9746 1.00 0.00 0.00
#> TCGA.EE.A29T.06 1 0.0000 0.9746 1.00 0.00 0.00
#> TCGA.D9.A3Z3.06 1 0.0000 0.9746 1.00 0.00 0.00
#> TCGA.D9.A4Z3.01 3 0.2959 0.8676 0.00 0.10 0.90
#> TCGA.ER.A3ES.06 3 0.0000 0.9695 0.00 0.00 1.00
#> TCGA.XV.A9VZ.01 1 0.0000 0.9746 1.00 0.00 0.00
#> TCGA.QB.AA9O.06 3 0.0000 0.9695 0.00 0.00 1.00
#> TCGA.EB.A44Q.06 3 0.0000 0.9695 0.00 0.00 1.00
#> TCGA.EB.A44R.06 1 0.0000 0.9746 1.00 0.00 0.00
#> TCGA.BF.A3DJ.01 3 0.0000 0.9695 0.00 0.00 1.00
#> TCGA.EE.A3JD.06 1 0.0000 0.9746 1.00 0.00 0.00
#> TCGA.D3.A51N.06 1 0.0892 0.9564 0.98 0.00 0.02
#> TCGA.EB.A44N.01 1 0.0000 0.9746 1.00 0.00 0.00
#> TCGA.EE.A3J3.06 3 0.0000 0.9695 0.00 0.00 1.00
#> TCGA.XV.A9W5.01 3 0.0000 0.9695 0.00 0.00 1.00
#> TCGA.D3.A51G.06 3 0.0000 0.9695 0.00 0.00 1.00
#> TCGA.EB.A4P0.01 2 0.0000 0.9811 0.00 1.00 0.00
#> TCGA.BF.AAP1.01 2 0.0000 0.9811 0.00 1.00 0.00
#> TCGA.EE.A3J4.06 2 0.0000 0.9811 0.00 1.00 0.00
#> TCGA.Z2.AA3V.06 1 0.0000 0.9746 1.00 0.00 0.00
#> TCGA.LH.A9QB.06 2 0.0000 0.9811 0.00 1.00 0.00
#> TCGA.D3.A51J.06 1 0.0000 0.9746 1.00 0.00 0.00
#> TCGA.3N.A9WC.06 1 0.3686 0.8311 0.86 0.00 0.14
#> TCGA.DA.A3F8.06 1 0.0000 0.9746 1.00 0.00 0.00
#> TCGA.D9.A4Z6.06 3 0.0000 0.9695 0.00 0.00 1.00
#> TCGA.D3.A51R.06 2 0.0000 0.9811 0.00 1.00 0.00
#> TCGA.EB.A4OZ.01 1 0.0000 0.9746 1.00 0.00 0.00
#> TCGA.FS.A4FB.06 3 0.0000 0.9695 0.00 0.00 1.00
#> TCGA.EE.A3JE.06 1 0.0000 0.9746 1.00 0.00 0.00
#> TCGA.W3.AA1W.06 1 0.0000 0.9746 1.00 0.00 0.00
#> TCGA.DA.A1I0.06 1 0.0000 0.9746 1.00 0.00 0.00
#> TCGA.D3.A51F.06 1 0.0000 0.9746 1.00 0.00 0.00
#> TCGA.IH.A3EA.01 3 0.0000 0.9695 0.00 0.00 1.00
#> TCGA.EB.A431.01 1 0.6280 0.1819 0.54 0.00 0.46
#> TCGA.EB.A97M.01 2 0.0000 0.9811 0.00 1.00 0.00
#> TCGA.BF.AAOX.01 3 0.0000 0.9695 0.00 0.00 1.00
#> TCGA.DA.A3F5.06 1 0.0892 0.9564 0.98 0.00 0.02
#> TCGA.YD.A9TA.06 1 0.0000 0.9746 1.00 0.00 0.00
#> TCGA.DA.A3F2.06 1 0.0000 0.9746 1.00 0.00 0.00
#> TCGA.EB.A44O.01 3 0.0000 0.9695 0.00 0.00 1.00
#> TCGA.EB.A4IQ.01 1 0.0000 0.9746 1.00 0.00 0.00
#> TCGA.EB.A4IS.01 1 0.0000 0.9746 1.00 0.00 0.00
#> TCGA.YG.AA3O.06 3 0.6126 0.3244 0.00 0.40 0.60
#> TCGA.ER.A3EV.06 1 0.5397 0.6216 0.72 0.00 0.28
#> TCGA.3N.A9WD.06 1 0.0000 0.9746 1.00 0.00 0.00
#> TCGA.BF.A3DM.01 3 0.0000 0.9695 0.00 0.00 1.00
#> TCGA.XV.A9W2.01 1 0.0000 0.9746 1.00 0.00 0.00
#> TCGA.W3.AA1Q.06 3 0.0000 0.9695 0.00 0.00 1.00
#> TCGA.WE.AAA0.06 1 0.0000 0.9746 1.00 0.00 0.00
#> TCGA.W3.AA1R.06 2 0.0892 0.9632 0.00 0.98 0.02
#> TCGA.EE.A3J5.06 1 0.0000 0.9746 1.00 0.00 0.00
#> TCGA.EB.A4OY.01 1 0.0000 0.9746 1.00 0.00 0.00
#> TCGA.FS.A4FD.06 3 0.0000 0.9695 0.00 0.00 1.00
#> TCGA.BF.AAP0.06 1 0.0000 0.9746 1.00 0.00 0.00
#> TCGA.YG.AA3P.06 3 0.0000 0.9695 0.00 0.00 1.00
#> TCGA.EE.A3JA.06 3 0.0000 0.9695 0.00 0.00 1.00
#> TCGA.W3.AA21.06 2 0.0000 0.9811 0.00 1.00 0.00
#> TCGA.WE.AAA3.06 3 0.0000 0.9695 0.00 0.00 1.00
#> TCGA.FS.A4F4.06 3 0.0000 0.9695 0.00 0.00 1.00
#> TCGA.BF.A3DN.01 3 0.4291 0.7649 0.00 0.18 0.82
#> TCGA.ER.A3ET.06 3 0.0000 0.9695 0.00 0.00 1.00
#> TCGA.W3.AA1O.06 3 0.0000 0.9695 0.00 0.00 1.00
#> TCGA.D3.A51E.06 3 0.0000 0.9695 0.00 0.00 1.00
#> TCGA.Z2.AA3S.06 2 0.0000 0.9811 0.00 1.00 0.00
#> TCGA.YG.AA3N.01 3 0.0000 0.9695 0.00 0.00 1.00
#> TCGA.WE.AA9Y.06 1 0.0000 0.9746 1.00 0.00 0.00
#> TCGA.FS.A4F5.06 2 0.0000 0.9811 0.00 1.00 0.00
#> TCGA.EE.A3J7.06 2 0.0000 0.9811 0.00 1.00 0.00
#> TCGA.FS.A4F8.06 1 0.0000 0.9746 1.00 0.00 0.00
#> TCGA.DA.A3F3.06 2 0.6280 0.1440 0.00 0.54 0.46
#> TCGA.D3.A51H.06 1 0.0000 0.9746 1.00 0.00 0.00
#> TCGA.BF.A3DL.01 1 0.0000 0.9746 1.00 0.00 0.00
#> TCGA.D3.A51T.06 2 0.0000 0.9811 0.00 1.00 0.00
#> TCGA.D3.A51K.06 3 0.2959 0.8674 0.00 0.10 0.90
#> TCGA.EB.A44P.01 3 0.0000 0.9695 0.00 0.00 1.00
#> TCGA.D9.A4Z5.01 2 0.0000 0.9811 0.00 1.00 0.00
#> TCGA.WE.AAA4.06 1 0.0000 0.9746 1.00 0.00 0.00
#> TCGA.3N.A9WB.06 2 0.0000 0.9811 0.00 1.00 0.00
#> TCGA.EE.A3J8.06 2 0.0000 0.9811 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.FR.A728.01 1 0.3975 0.6813 0.76 0.00 0.00 0.24
#> TCGA.GN.A4U8.11 1 0.0000 0.9823 1.00 0.00 0.00 0.00
#> TCGA.GN.A8LL.06 3 0.0000 0.8557 0.00 0.00 1.00 0.00
#> TCGA.FR.A8YC.06 2 0.0000 0.9392 0.00 1.00 0.00 0.00
#> TCGA.DA.A95X.06 2 0.3400 0.7922 0.00 0.82 0.18 0.00
#> TCGA.ER.A42K.06 3 0.0000 0.8557 0.00 0.00 1.00 0.00
#> TCGA.D3.A8GO.06 1 0.0000 0.9823 1.00 0.00 0.00 0.00
#> TCGA.D3.A8GK.06 3 0.3801 0.7600 0.00 0.00 0.78 0.22
#> TCGA.WE.A8JZ.06 2 0.3172 0.8130 0.00 0.84 0.16 0.00
#> TCGA.WE.A8ZO.06 3 0.3801 0.7289 0.00 0.22 0.78 0.00
#> TCGA.D3.A8GI.06 2 0.2011 0.8706 0.00 0.92 0.08 0.00
#> TCGA.FS.A4FC.06 4 0.0000 0.9278 0.00 0.00 0.00 1.00
#> TCGA.FS.A4F2.06 3 0.0000 0.8557 0.00 0.00 1.00 0.00
#> TCGA.WE.A8ZM.06 3 0.3172 0.7804 0.00 0.16 0.84 0.00
#> TCGA.WE.A8ZT.06 3 0.0000 0.8557 0.00 0.00 1.00 0.00
#> TCGA.D3.A8GQ.06 4 0.0000 0.9278 0.00 0.00 0.00 1.00
#> TCGA.D3.A8GB.06 1 0.0000 0.9823 1.00 0.00 0.00 0.00
#> TCGA.DA.A95Y.06 2 0.4994 0.2381 0.00 0.52 0.48 0.00
#> TCGA.EE.A3JI.06 2 0.0000 0.9392 0.00 1.00 0.00 0.00
#> TCGA.OD.A75X.06 2 0.0000 0.9392 0.00 1.00 0.00 0.00
#> TCGA.DA.A960.01 2 0.0000 0.9392 0.00 1.00 0.00 0.00
#> TCGA.D3.A8GV.06 2 0.2647 0.8488 0.00 0.88 0.12 0.00
#> TCGA.WE.A8ZN.06 1 0.0707 0.9633 0.98 0.00 0.00 0.02
#> TCGA.D3.A8GN.06 1 0.0000 0.9823 1.00 0.00 0.00 0.00
#> TCGA.EB.A550.01 1 0.0000 0.9823 1.00 0.00 0.00 0.00
#> TCGA.BF.A5EQ.01 4 0.0000 0.9278 0.00 0.00 0.00 1.00
#> TCGA.EB.A3HV.01 3 0.3801 0.7600 0.00 0.00 0.78 0.22
#> TCGA.HR.A5NC.01 4 0.4994 -0.1055 0.00 0.00 0.48 0.52
#> TCGA.DA.A95Z.06 2 0.0000 0.9392 0.00 1.00 0.00 0.00
#> TCGA.EB.A6QZ.01 2 0.0000 0.9392 0.00 1.00 0.00 0.00
#> TCGA.FW.A3I3.06 2 0.0000 0.9392 0.00 1.00 0.00 0.00
#> TCGA.WE.A8K6.06 3 0.0000 0.8557 0.00 0.00 1.00 0.00
#> TCGA.D3.A8GP.06 2 0.0000 0.9392 0.00 1.00 0.00 0.00
#> TCGA.EB.A42Z.01 2 0.0000 0.9392 0.00 1.00 0.00 0.00
#> TCGA.GN.A4U4.06 3 0.4907 0.3567 0.00 0.42 0.58 0.00
#> TCGA.GF.A4EO.06 1 0.0000 0.9823 1.00 0.00 0.00 0.00
#> TCGA.GN.A8LK.06 2 0.0000 0.9392 0.00 1.00 0.00 0.00
#> TCGA.WE.A8K4.01 1 0.4948 0.2004 0.56 0.00 0.00 0.44
#> TCGA.DA.A95W.06 2 0.0000 0.9392 0.00 1.00 0.00 0.00
#> TCGA.FW.A5DX.01 2 0.0000 0.9392 0.00 1.00 0.00 0.00
#> TCGA.GN.A4U3.06 2 0.3975 0.7263 0.00 0.76 0.24 0.00
#> TCGA.EB.A6QY.01 1 0.0000 0.9823 1.00 0.00 0.00 0.00
#> TCGA.EB.A5VU.01 4 0.0000 0.9278 0.00 0.00 0.00 1.00
#> TCGA.Z2.A8RT.06 3 0.0000 0.8557 0.00 0.00 1.00 0.00
#> TCGA.WE.A8K1.06 1 0.0707 0.9629 0.98 0.00 0.00 0.02
#> TCGA.EB.A41B.01 3 0.0000 0.8557 0.00 0.00 1.00 0.00
#> TCGA.WE.A8ZY.06 2 0.0000 0.9392 0.00 1.00 0.00 0.00
#> TCGA.D9.A6EG.06 2 0.0000 0.9392 0.00 1.00 0.00 0.00
#> TCGA.BF.A5ER.01 3 0.3172 0.7804 0.00 0.16 0.84 0.00
#> TCGA.FR.A8YD.06 2 0.0000 0.9392 0.00 1.00 0.00 0.00
#> TCGA.FS.A4F9.06 2 0.0000 0.9392 0.00 1.00 0.00 0.00
#> TCGA.EB.A6R0.01 3 0.0000 0.8557 0.00 0.00 1.00 0.00
#> TCGA.ER.A42L.06 1 0.0000 0.9823 1.00 0.00 0.00 0.00
#> TCGA.D3.A8GJ.06 4 0.0000 0.9278 0.00 0.00 0.00 1.00
#> TCGA.FR.A8YE.06 1 0.0000 0.9823 1.00 0.00 0.00 0.00
#> TCGA.WE.A8ZR.06 4 0.0000 0.9278 0.00 0.00 0.00 1.00
#> TCGA.BF.A9VF.01 3 0.3172 0.7804 0.00 0.16 0.84 0.00
#> TCGA.EE.A3JH.06 1 0.0000 0.9823 1.00 0.00 0.00 0.00
#> TCGA.DA.A95V.06 4 0.0000 0.9278 0.00 0.00 0.00 1.00
#> TCGA.GF.A769.01 2 0.2345 0.8522 0.00 0.90 0.10 0.00
#> TCGA.D9.A4Z2.01 3 0.0000 0.8557 0.00 0.00 1.00 0.00
#> TCGA.FR.A44A.06 1 0.0000 0.9823 1.00 0.00 0.00 0.00
#> TCGA.EB.A5VV.06 1 0.0000 0.9823 1.00 0.00 0.00 0.00
#> TCGA.EE.A180.06 2 0.0000 0.9392 0.00 1.00 0.00 0.00
#> TCGA.D3.A8GC.06 2 0.0000 0.9392 0.00 1.00 0.00 0.00
#> TCGA.WE.A8K5.06 2 0.0000 0.9392 0.00 1.00 0.00 0.00
#> TCGA.GN.A8LN.01 2 0.3610 0.7713 0.00 0.80 0.20 0.00
#> TCGA.EE.A3JB.06 4 0.2921 0.8028 0.14 0.00 0.00 0.86
#> TCGA.D3.A3MO.06 3 0.0000 0.8557 0.00 0.00 1.00 0.00
#> TCGA.ER.A42H.01 3 0.4277 0.6540 0.00 0.28 0.72 0.00
#> TCGA.WE.A8ZX.06 4 0.0000 0.9278 0.00 0.00 0.00 1.00
#> TCGA.GN.A4U5.01 1 0.0000 0.9823 1.00 0.00 0.00 0.00
#> TCGA.D3.A8GS.06 4 0.0000 0.9278 0.00 0.00 0.00 1.00
#> TCGA.WE.A8ZQ.06 2 0.0000 0.9392 0.00 1.00 0.00 0.00
#> TCGA.EE.A2MF.06 2 0.0000 0.9392 0.00 1.00 0.00 0.00
#> TCGA.D3.A5GU.06 3 0.3801 0.7600 0.00 0.00 0.78 0.22
#> TCGA.GN.A4U8.06 4 0.2011 0.8625 0.08 0.00 0.00 0.92
#> TCGA.EB.A42Y.01 2 0.2647 0.8505 0.00 0.88 0.12 0.00
#> TCGA.D3.A3ML.06 2 0.0000 0.9392 0.00 1.00 0.00 0.00
#> TCGA.EB.A551.01 4 0.4406 0.5715 0.30 0.00 0.00 0.70
#> TCGA.D3.A8GM.06 4 0.0000 0.9278 0.00 0.00 0.00 1.00
#> TCGA.D3.A8GL.06 2 0.0000 0.9392 0.00 1.00 0.00 0.00
#> TCGA.D3.A3MU.06 2 0.0000 0.9392 0.00 1.00 0.00 0.00
#> TCGA.FS.A4F0.06 2 0.0000 0.9392 0.00 1.00 0.00 0.00
#> TCGA.D3.A3MV.06 3 0.0000 0.8557 0.00 0.00 1.00 0.00
#> TCGA.GN.A4U7.06 3 0.0000 0.8557 0.00 0.00 1.00 0.00
#> TCGA.FR.A2OS.01 3 0.3801 0.7600 0.00 0.00 0.78 0.22
#> TCGA.D3.A2JE.06 2 0.3172 0.7730 0.00 0.84 0.16 0.00
#> TCGA.YD.A89C.06 3 0.4994 0.2365 0.00 0.00 0.52 0.48
#> TCGA.FR.A726.01 4 0.0000 0.9278 0.00 0.00 0.00 1.00
#> TCGA.BF.A5EP.01 3 0.4624 0.3627 0.00 0.34 0.66 0.00
#> TCGA.D3.A3MR.06 1 0.0000 0.9823 1.00 0.00 0.00 0.00
#> TCGA.D3.A8GR.06 3 0.4284 0.7441 0.00 0.20 0.78 0.02
#> TCGA.GN.A4U9.06 3 0.3975 0.7382 0.00 0.00 0.76 0.24
#> TCGA.EB.A6L9.06 1 0.0000 0.9823 1.00 0.00 0.00 0.00
#> TCGA.D3.A5GL.06 3 0.0000 0.8557 0.00 0.00 1.00 0.00
#> TCGA.EB.A430.01 1 0.0000 0.9823 1.00 0.00 0.00 0.00
#> TCGA.D3.A8GE.06 1 0.0000 0.9823 1.00 0.00 0.00 0.00
#> TCGA.D3.A8GD.06 1 0.0000 0.9823 1.00 0.00 0.00 0.00
#> TCGA.EB.A41A.01 2 0.0000 0.9392 0.00 1.00 0.00 0.00
#> TCGA.W3.A825.06 4 0.0000 0.9278 0.00 0.00 0.00 1.00
#> TCGA.EE.A183.06 1 0.0000 0.9823 1.00 0.00 0.00 0.00
#> TCGA.ER.A2NH.06 1 0.0000 0.9823 1.00 0.00 0.00 0.00
#> TCGA.D3.A5GR.06 4 0.3801 0.7034 0.22 0.00 0.00 0.78
#> TCGA.FR.A729.06 4 0.0000 0.9278 0.00 0.00 0.00 1.00
#> TCGA.D3.A1QA.06 2 0.0000 0.9392 0.00 1.00 0.00 0.00
#> TCGA.FS.A1YY.06 3 0.2647 0.8223 0.00 0.00 0.88 0.12
#> TCGA.EE.A2MK.06 3 0.0000 0.8557 0.00 0.00 1.00 0.00
#> TCGA.EE.A2M8.06 1 0.0000 0.9823 1.00 0.00 0.00 0.00
#> TCGA.EB.A5KH.06 2 0.0000 0.9392 0.00 1.00 0.00 0.00
#> TCGA.FS.A1ZR.06 3 0.3801 0.7600 0.00 0.00 0.78 0.22
#> TCGA.EE.A3AE.06 4 0.3400 0.7584 0.00 0.00 0.18 0.82
#> TCGA.EE.A29P.06 4 0.0000 0.9278 0.00 0.00 0.00 1.00
#> TCGA.EB.A553.01 4 0.0000 0.9278 0.00 0.00 0.00 1.00
#> TCGA.EE.A2MR.06 1 0.0000 0.9823 1.00 0.00 0.00 0.00
#> TCGA.GN.A26A.06 4 0.0000 0.9278 0.00 0.00 0.00 1.00
#> TCGA.FS.A1ZY.06 2 0.0000 0.9392 0.00 1.00 0.00 0.00
#> TCGA.EE.A20I.06 4 0.0000 0.9278 0.00 0.00 0.00 1.00
#> TCGA.DA.A1I5.06 1 0.0000 0.9823 1.00 0.00 0.00 0.00
#> TCGA.EE.A184.06 2 0.0000 0.9392 0.00 1.00 0.00 0.00
#> TCGA.EB.A85J.01 4 0.0000 0.9278 0.00 0.00 0.00 1.00
#> TCGA.RP.A6K9.06 4 0.0000 0.9278 0.00 0.00 0.00 1.00
#> TCGA.EE.A17Y.06 4 0.1211 0.8969 0.04 0.00 0.00 0.96
#> TCGA.D9.A149.06 4 0.0000 0.9278 0.00 0.00 0.00 1.00
#> TCGA.ER.A19D.06 1 0.1211 0.9434 0.96 0.00 0.00 0.04
#> TCGA.FS.A1ZZ.06 2 0.0000 0.9392 0.00 1.00 0.00 0.00
#> TCGA.EE.A2GP.06 3 0.3172 0.8054 0.00 0.00 0.84 0.16
#> TCGA.EE.A3AD.06 2 0.0000 0.9392 0.00 1.00 0.00 0.00
#> TCGA.D3.A1Q9.06 4 0.0000 0.9278 0.00 0.00 0.00 1.00
#> TCGA.GF.A2C7.01 2 0.0000 0.9392 0.00 1.00 0.00 0.00
#> TCGA.BF.A5ES.01 4 0.4994 -0.1053 0.00 0.00 0.48 0.52
#> TCGA.ER.A199.06 1 0.0000 0.9823 1.00 0.00 0.00 0.00
#> TCGA.EE.A3AH.06 2 0.0000 0.9392 0.00 1.00 0.00 0.00
#> TCGA.W3.A828.06 1 0.0000 0.9823 1.00 0.00 0.00 0.00
#> TCGA.EE.A2A5.06 3 0.3801 0.7289 0.00 0.22 0.78 0.00
#> TCGA.ER.A19L.06 4 0.0000 0.9278 0.00 0.00 0.00 1.00
#> TCGA.BF.A1PX.01 1 0.0000 0.9823 1.00 0.00 0.00 0.00
#> TCGA.ER.A19T.06 4 0.0000 0.9278 0.00 0.00 0.00 1.00
#> TCGA.EB.A51B.01 3 0.0000 0.8557 0.00 0.00 1.00 0.00
#> TCGA.FS.A1ZQ.06 3 0.0000 0.8557 0.00 0.00 1.00 0.00
#> TCGA.D3.A2JG.06 3 0.0000 0.8557 0.00 0.00 1.00 0.00
#> TCGA.EE.A2GH.06 1 0.0000 0.9823 1.00 0.00 0.00 0.00
#> TCGA.ER.A19F.06 3 0.0000 0.8557 0.00 0.00 1.00 0.00
#> TCGA.ER.A196.01 1 0.0000 0.9823 1.00 0.00 0.00 0.00
#> TCGA.D3.A2JC.06 4 0.0000 0.9278 0.00 0.00 0.00 1.00
#> TCGA.EE.A3AG.06 3 0.0000 0.8557 0.00 0.00 1.00 0.00
#> TCGA.ER.A19S.06 1 0.0000 0.9823 1.00 0.00 0.00 0.00
#> TCGA.EE.A2GC.06 3 0.3172 0.8054 0.00 0.00 0.84 0.16
#> TCGA.EE.A29N.06 1 0.0000 0.9823 1.00 0.00 0.00 0.00
#> TCGA.FR.A7U8.06 2 0.0000 0.9392 0.00 1.00 0.00 0.00
#> TCGA.BF.A5EO.01 4 0.2647 0.8233 0.12 0.00 0.00 0.88
#> TCGA.ER.A19B.06 3 0.0000 0.8557 0.00 0.00 1.00 0.00
#> TCGA.D3.A5GN.06 3 0.0000 0.8557 0.00 0.00 1.00 0.00
#> TCGA.D3.A2JB.06 1 0.0000 0.9823 1.00 0.00 0.00 0.00
#> TCGA.ER.A19J.06 2 0.0000 0.9392 0.00 1.00 0.00 0.00
#> TCGA.D3.A2JD.06 1 0.3801 0.7142 0.78 0.00 0.00 0.22
#> TCGA.FS.A1Z4.06 1 0.0000 0.9823 1.00 0.00 0.00 0.00
#> TCGA.FR.A7UA.06 1 0.0000 0.9823 1.00 0.00 0.00 0.00
#> TCGA.EE.A2M7.06 4 0.0000 0.9278 0.00 0.00 0.00 1.00
#> TCGA.D3.A1Q3.06 4 0.0000 0.9278 0.00 0.00 0.00 1.00
#> TCGA.EB.A85I.01 4 0.0000 0.9278 0.00 0.00 0.00 1.00
#> TCGA.EB.A82C.01 2 0.0000 0.9392 0.00 1.00 0.00 0.00
#> TCGA.ER.A19E.06 3 0.3400 0.7911 0.00 0.00 0.82 0.18
#> TCGA.FS.A1ZK.06 3 0.3172 0.7804 0.00 0.16 0.84 0.00
#> TCGA.FS.A1ZU.06 3 0.3975 0.7382 0.00 0.00 0.76 0.24
#> TCGA.EB.A5FP.01 2 0.0000 0.9392 0.00 1.00 0.00 0.00
#> TCGA.EB.A4XL.01 3 0.0000 0.8557 0.00 0.00 1.00 0.00
#> TCGA.DA.A1I2.06 3 0.4134 0.7141 0.00 0.00 0.74 0.26
#> TCGA.EE.A29L.06 2 0.0000 0.9392 0.00 1.00 0.00 0.00
#> TCGA.FS.A1ZN.01 2 0.0000 0.9392 0.00 1.00 0.00 0.00
#> TCGA.EB.A24D.01 3 0.4134 0.7133 0.00 0.00 0.74 0.26
#> TCGA.EE.A2GB.06 3 0.0000 0.8557 0.00 0.00 1.00 0.00
#> TCGA.DA.A1I7.06 4 0.0000 0.9278 0.00 0.00 0.00 1.00
#> TCGA.ER.A2NF.01 1 0.0000 0.9823 1.00 0.00 0.00 0.00
#> TCGA.GN.A263.01 1 0.0000 0.9823 1.00 0.00 0.00 0.00
#> TCGA.EE.A20C.06 2 0.0000 0.9392 0.00 1.00 0.00 0.00
#> TCGA.EE.A2MQ.06 3 0.3801 0.7277 0.00 0.22 0.78 0.00
#> TCGA.ER.A19N.06 1 0.0000 0.9823 1.00 0.00 0.00 0.00
#> TCGA.FS.A1Z3.06 3 0.4977 -0.0454 0.00 0.46 0.54 0.00
#> TCGA.DA.A1I8.06 3 0.0000 0.8557 0.00 0.00 1.00 0.00
#> TCGA.D3.A5GS.06 3 0.0000 0.8557 0.00 0.00 1.00 0.00
#> TCGA.EE.A181.06 4 0.0000 0.9278 0.00 0.00 0.00 1.00
#> TCGA.GN.A268.06 2 0.0000 0.9392 0.00 1.00 0.00 0.00
#> TCGA.W3.A824.06 3 0.3975 0.7382 0.00 0.00 0.76 0.24
#> TCGA.EE.A2GS.06 3 0.0000 0.8557 0.00 0.00 1.00 0.00
#> TCGA.FR.A7U9.06 1 0.0000 0.9823 1.00 0.00 0.00 0.00
#> TCGA.ER.A19Q.06 1 0.0000 0.9823 1.00 0.00 0.00 0.00
#> TCGA.FS.A1ZM.06 4 0.3400 0.7193 0.00 0.00 0.18 0.82
#> TCGA.EE.A2MG.06 1 0.0000 0.9823 1.00 0.00 0.00 0.00
#> TCGA.EE.A2MC.06 1 0.0000 0.9823 1.00 0.00 0.00 0.00
#> TCGA.EE.A17Z.06 3 0.3172 0.8054 0.00 0.00 0.84 0.16
#> TCGA.D3.A2JP.06 4 0.3975 0.6734 0.24 0.00 0.00 0.76
#> TCGA.ER.A19C.06 4 0.4907 0.1339 0.00 0.00 0.42 0.58
#> TCGA.EB.A82B.01 4 0.0000 0.9278 0.00 0.00 0.00 1.00
#> TCGA.EE.A2A0.06 1 0.0000 0.9823 1.00 0.00 0.00 0.00
#> TCGA.EE.A29G.06 1 0.0000 0.9823 1.00 0.00 0.00 0.00
#> TCGA.D3.A5GO.06 3 0.0000 0.8557 0.00 0.00 1.00 0.00
#> TCGA.GN.A269.01 1 0.0000 0.9823 1.00 0.00 0.00 0.00
#> TCGA.EE.A2A1.06 1 0.0000 0.9823 1.00 0.00 0.00 0.00
#> TCGA.ER.A1A1.06 1 0.0000 0.9823 1.00 0.00 0.00 0.00
#> TCGA.FS.A1ZG.06 2 0.0000 0.9392 0.00 1.00 0.00 0.00
#> TCGA.FS.A1ZE.06 2 0.0000 0.9392 0.00 1.00 0.00 0.00
#> TCGA.FS.A1ZH.06 4 0.2647 0.8233 0.12 0.00 0.00 0.88
#> TCGA.EE.A2MH.06 1 0.0000 0.9823 1.00 0.00 0.00 0.00
#> TCGA.D3.A2J6.06 4 0.0000 0.9278 0.00 0.00 0.00 1.00
#> TCGA.EE.A29Q.06 2 0.4134 0.7006 0.00 0.74 0.26 0.00
#> TCGA.BF.A1PZ.01 3 0.0000 0.8557 0.00 0.00 1.00 0.00
#> TCGA.D3.A3BZ.06 1 0.0000 0.9823 1.00 0.00 0.00 0.00
#> TCGA.D3.A2JO.06 4 0.4522 0.5327 0.32 0.00 0.00 0.68
#> TCGA.GN.A267.06 4 0.0000 0.9278 0.00 0.00 0.00 1.00
#> TCGA.EE.A2MN.06 3 0.3801 0.7289 0.00 0.22 0.78 0.00
#> TCGA.GN.A264.06 2 0.0000 0.9392 0.00 1.00 0.00 0.00
#> TCGA.ER.A197.06 1 0.0000 0.9823 1.00 0.00 0.00 0.00
#> TCGA.DA.A1IB.06 1 0.0000 0.9823 1.00 0.00 0.00 0.00
#> TCGA.D3.A3CC.06 4 0.0000 0.9278 0.00 0.00 0.00 1.00
#> TCGA.ER.A19T.01 3 0.3975 0.7382 0.00 0.00 0.76 0.24
#> TCGA.GN.A261.06 1 0.0000 0.9823 1.00 0.00 0.00 0.00
#> TCGA.FS.A1YW.06 2 0.0000 0.9392 0.00 1.00 0.00 0.00
#> TCGA.BF.A1PU.01 4 0.0000 0.9278 0.00 0.00 0.00 1.00
#> TCGA.D3.A1QB.06 1 0.0000 0.9823 1.00 0.00 0.00 0.00
#> TCGA.D3.A1Q6.06 4 0.0000 0.9278 0.00 0.00 0.00 1.00
#> TCGA.D3.A3C8.06 1 0.0000 0.9823 1.00 0.00 0.00 0.00
#> TCGA.ER.A19A.06 1 0.0000 0.9823 1.00 0.00 0.00 0.00
#> TCGA.EE.A2GN.06 3 0.3801 0.7289 0.00 0.22 0.78 0.00
#> TCGA.EE.A29M.06 1 0.0000 0.9823 1.00 0.00 0.00 0.00
#> TCGA.D3.A2J7.06 1 0.0000 0.9823 1.00 0.00 0.00 0.00
#> TCGA.EB.A24C.01 4 0.0000 0.9278 0.00 0.00 0.00 1.00
#> TCGA.GN.A262.06 2 0.0000 0.9392 0.00 1.00 0.00 0.00
#> TCGA.EE.A2GD.06 1 0.0000 0.9823 1.00 0.00 0.00 0.00
#> TCGA.D3.A2J9.06 1 0.0000 0.9823 1.00 0.00 0.00 0.00
#> TCGA.EE.A29B.06 3 0.3801 0.7289 0.00 0.22 0.78 0.00
#> TCGA.D9.A1JX.06 3 0.3975 0.5842 0.00 0.24 0.76 0.00
#> TCGA.EE.A29A.06 2 0.0000 0.9392 0.00 1.00 0.00 0.00
#> TCGA.D3.A2JL.06 4 0.0000 0.9278 0.00 0.00 0.00 1.00
#> TCGA.D3.A1Q4.06 1 0.0000 0.9823 1.00 0.00 0.00 0.00
#> TCGA.FS.A1ZS.06 4 0.3610 0.6871 0.00 0.00 0.20 0.80
#> TCGA.D3.A3C3.06 4 0.0000 0.9278 0.00 0.00 0.00 1.00
#> TCGA.D3.A2J8.06 1 0.0000 0.9823 1.00 0.00 0.00 0.00
#> TCGA.FS.A1ZF.06 2 0.3975 0.7263 0.00 0.76 0.24 0.00
#> TCGA.FS.A1ZC.06 2 0.3172 0.8130 0.00 0.84 0.16 0.00
#> TCGA.EE.A20H.06 3 0.0000 0.8557 0.00 0.00 1.00 0.00
#> TCGA.EE.A29W.06 3 0.0000 0.8557 0.00 0.00 1.00 0.00
#> TCGA.D3.A1QA.07 4 0.0000 0.9278 0.00 0.00 0.00 1.00
#> TCGA.BF.A1PV.01 3 0.3801 0.7289 0.00 0.22 0.78 0.00
#> TCGA.EE.A29S.06 3 0.3801 0.7600 0.00 0.00 0.78 0.22
#> TCGA.DA.A1HV.06 3 0.0000 0.8557 0.00 0.00 1.00 0.00
#> TCGA.FS.A1Z0.06 1 0.4406 0.5677 0.70 0.00 0.00 0.30
#> TCGA.EE.A2GO.06 2 0.1637 0.9003 0.00 0.94 0.06 0.00
#> TCGA.EB.A1NK.01 1 0.0000 0.9823 1.00 0.00 0.00 0.00
#> TCGA.GN.A26D.06 4 0.0000 0.9278 0.00 0.00 0.00 1.00
#> TCGA.EE.A2MJ.06 1 0.0000 0.9823 1.00 0.00 0.00 0.00
#> TCGA.ER.A198.06 3 0.3606 0.7925 0.00 0.14 0.84 0.02
#> TCGA.EE.A17X.06 2 0.4907 0.4075 0.00 0.58 0.42 0.00
#> TCGA.EE.A2M5.06 4 0.2011 0.8624 0.08 0.00 0.00 0.92
#> TCGA.GN.A266.06 4 0.4522 0.5322 0.32 0.00 0.00 0.68
#> TCGA.D3.A3C1.06 4 0.0000 0.9278 0.00 0.00 0.00 1.00
#> TCGA.D3.A2JH.06 1 0.0000 0.9823 1.00 0.00 0.00 0.00
#> TCGA.EE.A20F.06 4 0.0000 0.9278 0.00 0.00 0.00 1.00
#> TCGA.EE.A29E.06 1 0.0000 0.9823 1.00 0.00 0.00 0.00
#> TCGA.ER.A2NG.06 1 0.0000 0.9823 1.00 0.00 0.00 0.00
#> TCGA.ER.A193.06 4 0.0000 0.9278 0.00 0.00 0.00 1.00
#> TCGA.FS.A1ZW.06 4 0.0000 0.9278 0.00 0.00 0.00 1.00
#> TCGA.ER.A19O.06 4 0.4134 0.6418 0.26 0.00 0.00 0.74
#> TCGA.EE.A2ME.06 1 0.0000 0.9823 1.00 0.00 0.00 0.00
#> TCGA.EE.A20B.06 4 0.0000 0.9278 0.00 0.00 0.00 1.00
#> TCGA.EE.A3AF.06 3 0.0000 0.8557 0.00 0.00 1.00 0.00
#> TCGA.GN.A265.06 1 0.0000 0.9823 1.00 0.00 0.00 0.00
#> TCGA.FS.A1YX.06 3 0.4994 0.2332 0.00 0.00 0.52 0.48
#> TCGA.FS.A1ZJ.06 3 0.4907 0.4098 0.00 0.00 0.58 0.42
#> TCGA.ER.A19H.06 4 0.4134 0.6567 0.00 0.00 0.26 0.74
#> TCGA.EE.A3AC.06 3 0.3801 0.7600 0.00 0.00 0.78 0.22
#> TCGA.EE.A2MU.06 1 0.0000 0.9823 1.00 0.00 0.00 0.00
#> TCGA.ER.A194.01 4 0.0000 0.9278 0.00 0.00 0.00 1.00
#> TCGA.EE.A2MS.06 4 0.0000 0.9278 0.00 0.00 0.00 1.00
#> TCGA.EE.A29R.06 2 0.0000 0.9392 0.00 1.00 0.00 0.00
#> TCGA.D9.A1X3.06 2 0.0000 0.9392 0.00 1.00 0.00 0.00
#> TCGA.EE.A29X.06 3 0.3801 0.7600 0.00 0.00 0.78 0.22
#> TCGA.EE.A2GK.06 1 0.0000 0.9823 1.00 0.00 0.00 0.00
#> TCGA.EE.A3AA.06 1 0.0000 0.9823 1.00 0.00 0.00 0.00
#> TCGA.ER.A2NE.06 2 0.0000 0.9392 0.00 1.00 0.00 0.00
#> TCGA.EE.A2GR.06 3 0.0000 0.8557 0.00 0.00 1.00 0.00
#> TCGA.FS.A1ZD.06 3 0.4713 0.5472 0.00 0.00 0.64 0.36
#> TCGA.ER.A19P.06 1 0.0000 0.9823 1.00 0.00 0.00 0.00
#> TCGA.D3.A1Q8.06 1 0.3801 0.7142 0.78 0.00 0.00 0.22
#> TCGA.ER.A2NC.06 4 0.0000 0.9278 0.00 0.00 0.00 1.00
#> TCGA.BF.A1Q0.01 4 0.0000 0.9278 0.00 0.00 0.00 1.00
#> TCGA.FS.A1ZP.06 3 0.3172 0.7804 0.00 0.16 0.84 0.00
#> TCGA.EE.A182.06 4 0.0000 0.9278 0.00 0.00 0.00 1.00
#> TCGA.D9.A1JW.06 4 0.0000 0.9278 0.00 0.00 0.00 1.00
#> TCGA.D3.A1Q7.06 1 0.0000 0.9823 1.00 0.00 0.00 0.00
#> TCGA.EE.A185.06 2 0.0000 0.9392 0.00 1.00 0.00 0.00
#> TCGA.EE.A2GJ.06 4 0.0000 0.9278 0.00 0.00 0.00 1.00
#> TCGA.D3.A3CB.06 1 0.0000 0.9823 1.00 0.00 0.00 0.00
#> TCGA.EE.A2GU.06 4 0.0000 0.9278 0.00 0.00 0.00 1.00
#> TCGA.ER.A195.06 1 0.0000 0.9823 1.00 0.00 0.00 0.00
#> TCGA.FS.A1Z7.06 4 0.0000 0.9278 0.00 0.00 0.00 1.00
#> TCGA.EE.A2M6.06 2 0.0707 0.9262 0.00 0.98 0.02 0.00
#> TCGA.ER.A19K.01 4 0.0000 0.9278 0.00 0.00 0.00 1.00
#> TCGA.DA.A1HY.06 3 0.0000 0.8557 0.00 0.00 1.00 0.00
#> TCGA.D3.A3C7.06 3 0.0000 0.8557 0.00 0.00 1.00 0.00
#> TCGA.EE.A2MP.06 3 0.0000 0.8557 0.00 0.00 1.00 0.00
#> TCGA.EE.A29H.06 3 0.0000 0.8557 0.00 0.00 1.00 0.00
#> TCGA.FR.A3YO.06 4 0.0000 0.9278 0.00 0.00 0.00 1.00
#> TCGA.XV.AB01.01 3 0.4277 0.5056 0.00 0.28 0.72 0.00
#> TCGA.RP.A694.06 4 0.4406 0.4859 0.00 0.00 0.30 0.70
#> TCGA.EB.A5SF.01 1 0.0000 0.9823 1.00 0.00 0.00 0.00
#> TCGA.ER.A19G.06 3 0.0000 0.8557 0.00 0.00 1.00 0.00
#> TCGA.EE.A2GE.06 1 0.0000 0.9823 1.00 0.00 0.00 0.00
#> TCGA.GF.A3OT.06 1 0.0000 0.9823 1.00 0.00 0.00 0.00
#> TCGA.ER.A2NF.06 1 0.0000 0.9823 1.00 0.00 0.00 0.00
#> TCGA.RP.A695.06 3 0.3172 0.7804 0.00 0.16 0.84 0.00
#> TCGA.BF.AAP7.01 1 0.0000 0.9823 1.00 0.00 0.00 0.00
#> TCGA.EB.A3Y7.01 4 0.0000 0.9278 0.00 0.00 0.00 1.00
#> TCGA.EB.A3XC.01 3 0.0000 0.8557 0.00 0.00 1.00 0.00
#> TCGA.ER.A19W.06 1 0.0000 0.9823 1.00 0.00 0.00 0.00
#> TCGA.FR.A69P.06 3 0.3610 0.7755 0.00 0.00 0.80 0.20
#> TCGA.RP.A693.06 1 0.4277 0.6070 0.72 0.00 0.00 0.28
#> TCGA.FW.A3TV.06 1 0.0000 0.9823 1.00 0.00 0.00 0.00
#> TCGA.FW.A3R5.11 1 0.0000 0.9823 1.00 0.00 0.00 0.00
#> TCGA.FW.A3TU.06 4 0.4994 -0.1053 0.00 0.00 0.48 0.52
#> TCGA.BF.AAP8.01 4 0.0000 0.9278 0.00 0.00 0.00 1.00
#> TCGA.EE.A2MM.06 3 0.3801 0.7600 0.00 0.00 0.78 0.22
#> TCGA.DA.A1HW.06 4 0.0000 0.9278 0.00 0.00 0.00 1.00
#> TCGA.DA.A1IC.06 3 0.0000 0.8557 0.00 0.00 1.00 0.00
#> TCGA.XV.AAZV.01 1 0.0000 0.9823 1.00 0.00 0.00 0.00
#> TCGA.D3.A3C6.06 3 0.0000 0.8557 0.00 0.00 1.00 0.00
#> TCGA.EE.A29C.06 1 0.0000 0.9823 1.00 0.00 0.00 0.00
#> TCGA.BF.AAP2.01 2 0.3172 0.8130 0.00 0.84 0.16 0.00
#> TCGA.EE.A2A2.06 3 0.0000 0.8557 0.00 0.00 1.00 0.00
#> TCGA.GF.A6C8.06 4 0.0000 0.9278 0.00 0.00 0.00 1.00
#> TCGA.RP.A690.06 1 0.0000 0.9823 1.00 0.00 0.00 0.00
#> TCGA.FW.A5DY.06 1 0.0000 0.9823 1.00 0.00 0.00 0.00
#> TCGA.DA.A1I4.06 1 0.0000 0.9823 1.00 0.00 0.00 0.00
#> TCGA.EE.A29V.06 4 0.4522 0.5344 0.32 0.00 0.00 0.68
#> TCGA.GF.A6C9.06 1 0.0000 0.9823 1.00 0.00 0.00 0.00
#> TCGA.EE.A2GT.06 1 0.0000 0.9823 1.00 0.00 0.00 0.00
#> TCGA.GN.A9SD.06 1 0.0000 0.9823 1.00 0.00 0.00 0.00
#> TCGA.EE.A3AB.06 4 0.0000 0.9278 0.00 0.00 0.00 1.00
#> TCGA.BF.AAP6.01 3 0.0000 0.8557 0.00 0.00 1.00 0.00
#> TCGA.EB.A5SH.06 4 0.0000 0.9278 0.00 0.00 0.00 1.00
#> TCGA.D9.A6E9.06 4 0.0000 0.9278 0.00 0.00 0.00 1.00
#> TCGA.BF.AAP4.01 4 0.0000 0.9278 0.00 0.00 0.00 1.00
#> TCGA.EE.A2GM.06 2 0.0000 0.9392 0.00 1.00 0.00 0.00
#> TCGA.D3.A3CF.06 1 0.0000 0.9823 1.00 0.00 0.00 0.00
#> TCGA.D9.A6EC.06 2 0.0000 0.9392 0.00 1.00 0.00 0.00
#> TCGA.DA.A1I1.06 4 0.0000 0.9278 0.00 0.00 0.00 1.00
#> TCGA.HR.A2OH.06 1 0.0000 0.9823 1.00 0.00 0.00 0.00
#> TCGA.EE.A2MT.06 4 0.0000 0.9278 0.00 0.00 0.00 1.00
#> TCGA.ER.A19M.06 4 0.1637 0.8799 0.06 0.00 0.00 0.94
#> TCGA.GN.A26C.01 1 0.0000 0.9823 1.00 0.00 0.00 0.00
#> TCGA.FS.A1ZA.06 3 0.4713 0.5491 0.00 0.00 0.64 0.36
#> TCGA.EB.A5SE.01 2 0.0000 0.9392 0.00 1.00 0.00 0.00
#> TCGA.ER.A3PL.06 3 0.3610 0.7765 0.00 0.00 0.80 0.20
#> TCGA.FR.A3R1.01 3 0.0000 0.8557 0.00 0.00 1.00 0.00
#> TCGA.EE.A2MI.06 4 0.0000 0.9278 0.00 0.00 0.00 1.00
#> TCGA.D3.A3CE.06 3 0.3975 0.7382 0.00 0.00 0.76 0.24
#> TCGA.D3.A5GT.01 2 0.4994 -0.0736 0.00 0.52 0.48 0.00
#> TCGA.ER.A2NB.01 4 0.0000 0.9278 0.00 0.00 0.00 1.00
#> TCGA.D3.A1Q5.06 4 0.0000 0.9278 0.00 0.00 0.00 1.00
#> TCGA.EB.A5UN.06 1 0.0000 0.9823 1.00 0.00 0.00 0.00
#> TCGA.EB.A299.01 4 0.2647 0.8283 0.00 0.00 0.12 0.88
#> TCGA.DA.A1IA.06 3 0.3975 0.7071 0.00 0.24 0.76 0.00
#> TCGA.EB.A5SG.06 1 0.0000 0.9823 1.00 0.00 0.00 0.00
#> TCGA.D9.A6EA.06 2 0.0000 0.9392 0.00 1.00 0.00 0.00
#> TCGA.XV.AAZY.01 1 0.0000 0.9823 1.00 0.00 0.00 0.00
#> TCGA.EB.A57M.01 4 0.0000 0.9278 0.00 0.00 0.00 1.00
#> TCGA.EE.A2A6.06 4 0.0000 0.9278 0.00 0.00 0.00 1.00
#> TCGA.D3.A2JA.06 1 0.0000 0.9823 1.00 0.00 0.00 0.00
#> TCGA.D3.A1Q1.06 4 0.0000 0.9278 0.00 0.00 0.00 1.00
#> TCGA.EB.A3XF.01 3 0.0000 0.8557 0.00 0.00 1.00 0.00
#> TCGA.D3.A2JF.06 4 0.3610 0.7231 0.00 0.00 0.20 0.80
#> TCGA.XV.AAZW.01 3 0.4994 -0.1175 0.00 0.48 0.52 0.00
#> TCGA.EB.A3Y6.01 4 0.0000 0.9278 0.00 0.00 0.00 1.00
#> TCGA.EB.A3XE.01 4 0.0000 0.9278 0.00 0.00 0.00 1.00
#> TCGA.D9.A3Z4.01 3 0.3801 0.7600 0.00 0.00 0.78 0.22
#> TCGA.FW.A3R5.06 4 0.0000 0.9278 0.00 0.00 0.00 1.00
#> TCGA.EE.A2GI.06 4 0.0000 0.9278 0.00 0.00 0.00 1.00
#> TCGA.EE.A2GL.06 1 0.0000 0.9823 1.00 0.00 0.00 0.00
#> TCGA.EB.A3XB.01 4 0.0000 0.9278 0.00 0.00 0.00 1.00
#> TCGA.BF.AAOU.01 1 0.0000 0.9823 1.00 0.00 0.00 0.00
#> TCGA.EB.A3XD.01 1 0.0000 0.9823 1.00 0.00 0.00 0.00
#> TCGA.EE.A2MD.06 4 0.0000 0.9278 0.00 0.00 0.00 1.00
#> TCGA.YD.A9TB.06 3 0.2345 0.8303 0.00 0.00 0.90 0.10
#> TCGA.W3.AA1V.06 4 0.0000 0.9278 0.00 0.00 0.00 1.00
#> TCGA.ER.A2ND.06 4 0.4790 0.2681 0.00 0.00 0.38 0.62
#> TCGA.D3.A2JK.06 4 0.0000 0.9278 0.00 0.00 0.00 1.00
#> TCGA.FS.A1ZB.06 1 0.0000 0.9823 1.00 0.00 0.00 0.00
#> TCGA.EE.A29D.06 2 0.0000 0.9392 0.00 1.00 0.00 0.00
#> TCGA.EB.A5UM.01 4 0.0000 0.9278 0.00 0.00 0.00 1.00
#> TCGA.QB.A6FS.06 1 0.0000 0.9823 1.00 0.00 0.00 0.00
#> TCGA.D9.A3Z1.06 1 0.0000 0.9823 1.00 0.00 0.00 0.00
#> TCGA.D3.A2JN.06 1 0.0000 0.9823 1.00 0.00 0.00 0.00
#> TCGA.FR.A3YN.06 3 0.2921 0.7350 0.00 0.14 0.86 0.00
#> TCGA.FS.A1ZT.06 1 0.0000 0.9823 1.00 0.00 0.00 0.00
#> TCGA.D9.A148.06 4 0.0707 0.9128 0.02 0.00 0.00 0.98
#> TCGA.HR.A2OG.06 1 0.1637 0.9227 0.94 0.00 0.00 0.06
#> TCGA.EE.A2ML.06 4 0.1637 0.8738 0.00 0.00 0.06 0.94
#> TCGA.EB.A5UL.06 4 0.3610 0.7332 0.20 0.00 0.00 0.80
#> TCGA.EE.A29T.06 4 0.4713 0.4454 0.36 0.00 0.00 0.64
#> TCGA.D9.A3Z3.06 1 0.0000 0.9823 1.00 0.00 0.00 0.00
#> TCGA.D9.A4Z3.01 3 0.0000 0.8557 0.00 0.00 1.00 0.00
#> TCGA.ER.A3ES.06 4 0.0000 0.9278 0.00 0.00 0.00 1.00
#> TCGA.XV.A9VZ.01 1 0.0000 0.9823 1.00 0.00 0.00 0.00
#> TCGA.QB.AA9O.06 3 0.3801 0.7081 0.00 0.00 0.78 0.22
#> TCGA.EB.A44Q.06 4 0.0000 0.9278 0.00 0.00 0.00 1.00
#> TCGA.EB.A44R.06 4 0.0000 0.9278 0.00 0.00 0.00 1.00
#> TCGA.BF.A3DJ.01 3 0.0000 0.8557 0.00 0.00 1.00 0.00
#> TCGA.EE.A3JD.06 1 0.0000 0.9823 1.00 0.00 0.00 0.00
#> TCGA.D3.A51N.06 4 0.1211 0.8969 0.04 0.00 0.00 0.96
#> TCGA.EB.A44N.01 1 0.0000 0.9823 1.00 0.00 0.00 0.00
#> TCGA.EE.A3J3.06 3 0.0000 0.8557 0.00 0.00 1.00 0.00
#> TCGA.XV.A9W5.01 4 0.1211 0.9003 0.00 0.00 0.04 0.96
#> TCGA.D3.A51G.06 3 0.1637 0.8421 0.00 0.00 0.94 0.06
#> TCGA.EB.A4P0.01 2 0.3975 0.7263 0.00 0.76 0.24 0.00
#> TCGA.BF.AAP1.01 2 0.0000 0.9392 0.00 1.00 0.00 0.00
#> TCGA.EE.A3J4.06 2 0.3400 0.7354 0.00 0.82 0.18 0.00
#> TCGA.Z2.AA3V.06 1 0.0000 0.9823 1.00 0.00 0.00 0.00
#> TCGA.LH.A9QB.06 2 0.0000 0.9392 0.00 1.00 0.00 0.00
#> TCGA.D3.A51J.06 4 0.0000 0.9278 0.00 0.00 0.00 1.00
#> TCGA.3N.A9WC.06 4 0.0000 0.9278 0.00 0.00 0.00 1.00
#> TCGA.DA.A3F8.06 1 0.0000 0.9823 1.00 0.00 0.00 0.00
#> TCGA.D9.A4Z6.06 4 0.1637 0.8738 0.00 0.00 0.06 0.94
#> TCGA.D3.A51R.06 2 0.4948 0.3517 0.00 0.56 0.44 0.00
#> TCGA.EB.A4OZ.01 1 0.0000 0.9823 1.00 0.00 0.00 0.00
#> TCGA.FS.A4FB.06 3 0.0000 0.8557 0.00 0.00 1.00 0.00
#> TCGA.EE.A3JE.06 1 0.0000 0.9823 1.00 0.00 0.00 0.00
#> TCGA.W3.AA1W.06 1 0.0000 0.9823 1.00 0.00 0.00 0.00
#> TCGA.DA.A1I0.06 4 0.4855 0.3411 0.40 0.00 0.00 0.60
#> TCGA.D3.A51F.06 1 0.0000 0.9823 1.00 0.00 0.00 0.00
#> TCGA.IH.A3EA.01 3 0.2921 0.8147 0.00 0.00 0.86 0.14
#> TCGA.EB.A431.01 4 0.0000 0.9278 0.00 0.00 0.00 1.00
#> TCGA.EB.A97M.01 2 0.0000 0.9392 0.00 1.00 0.00 0.00
#> TCGA.BF.AAOX.01 4 0.0000 0.9278 0.00 0.00 0.00 1.00
#> TCGA.DA.A3F5.06 4 0.0000 0.9278 0.00 0.00 0.00 1.00
#> TCGA.YD.A9TA.06 4 0.2011 0.8624 0.08 0.00 0.00 0.92
#> TCGA.DA.A3F2.06 1 0.0000 0.9823 1.00 0.00 0.00 0.00
#> TCGA.EB.A44O.01 3 0.3801 0.7600 0.00 0.00 0.78 0.22
#> TCGA.EB.A4IQ.01 4 0.0000 0.9278 0.00 0.00 0.00 1.00
#> TCGA.EB.A4IS.01 1 0.0000 0.9823 1.00 0.00 0.00 0.00
#> TCGA.YG.AA3O.06 3 0.3172 0.7804 0.00 0.16 0.84 0.00
#> TCGA.ER.A3EV.06 4 0.0000 0.9278 0.00 0.00 0.00 1.00
#> TCGA.3N.A9WD.06 1 0.0000 0.9823 1.00 0.00 0.00 0.00
#> TCGA.BF.A3DM.01 3 0.0000 0.8557 0.00 0.00 1.00 0.00
#> TCGA.XV.A9W2.01 4 0.0000 0.9278 0.00 0.00 0.00 1.00
#> TCGA.W3.AA1Q.06 3 0.0000 0.8557 0.00 0.00 1.00 0.00
#> TCGA.WE.AAA0.06 4 0.2921 0.8028 0.14 0.00 0.00 0.86
#> TCGA.W3.AA1R.06 3 0.0000 0.8557 0.00 0.00 1.00 0.00
#> TCGA.EE.A3J5.06 4 0.0000 0.9278 0.00 0.00 0.00 1.00
#> TCGA.EB.A4OY.01 1 0.0000 0.9823 1.00 0.00 0.00 0.00
#> TCGA.FS.A4FD.06 4 0.0000 0.9278 0.00 0.00 0.00 1.00
#> TCGA.BF.AAP0.06 1 0.0000 0.9823 1.00 0.00 0.00 0.00
#> TCGA.YG.AA3P.06 3 0.4406 0.6550 0.00 0.00 0.70 0.30
#> TCGA.EE.A3JA.06 3 0.0000 0.8557 0.00 0.00 1.00 0.00
#> TCGA.W3.AA21.06 2 0.0000 0.9392 0.00 1.00 0.00 0.00
#> TCGA.WE.AAA3.06 4 0.0000 0.9278 0.00 0.00 0.00 1.00
#> TCGA.FS.A4F4.06 3 0.0000 0.8557 0.00 0.00 1.00 0.00
#> TCGA.BF.A3DN.01 3 0.0000 0.8557 0.00 0.00 1.00 0.00
#> TCGA.ER.A3ET.06 4 0.0000 0.9278 0.00 0.00 0.00 1.00
#> TCGA.W3.AA1O.06 3 0.4731 0.7664 0.00 0.16 0.78 0.06
#> TCGA.D3.A51E.06 4 0.4277 0.6231 0.00 0.00 0.28 0.72
#> TCGA.Z2.AA3S.06 2 0.0000 0.9392 0.00 1.00 0.00 0.00
#> TCGA.YG.AA3N.01 3 0.4790 0.5053 0.00 0.00 0.62 0.38
#> TCGA.WE.AA9Y.06 1 0.0000 0.9823 1.00 0.00 0.00 0.00
#> TCGA.FS.A4F5.06 2 0.0000 0.9392 0.00 1.00 0.00 0.00
#> TCGA.EE.A3J7.06 2 0.4948 0.0920 0.00 0.56 0.44 0.00
#> TCGA.FS.A4F8.06 1 0.0000 0.9823 1.00 0.00 0.00 0.00
#> TCGA.DA.A3F3.06 3 0.0000 0.8557 0.00 0.00 1.00 0.00
#> TCGA.D3.A51H.06 1 0.0000 0.9823 1.00 0.00 0.00 0.00
#> TCGA.BF.A3DL.01 1 0.4406 0.5677 0.70 0.00 0.00 0.30
#> TCGA.D3.A51T.06 3 0.4624 0.3622 0.00 0.34 0.66 0.00
#> TCGA.D3.A51K.06 3 0.0000 0.8557 0.00 0.00 1.00 0.00
#> TCGA.EB.A44P.01 3 0.0000 0.8557 0.00 0.00 1.00 0.00
#> TCGA.D9.A4Z5.01 2 0.0000 0.9392 0.00 1.00 0.00 0.00
#> TCGA.WE.AAA4.06 1 0.0000 0.9823 1.00 0.00 0.00 0.00
#> TCGA.3N.A9WB.06 2 0.0000 0.9392 0.00 1.00 0.00 0.00
#> TCGA.EE.A3J8.06 2 0.0000 0.9392 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.FR.A728.01 1 0.2280 0.8526 0.88 0.00 0.00 0.12 0.00
#> TCGA.GN.A4U8.11 1 0.0000 0.9885 1.00 0.00 0.00 0.00 0.00
#> TCGA.GN.A8LL.06 3 0.0000 0.9490 0.00 0.00 1.00 0.00 0.00
#> TCGA.FR.A8YC.06 2 0.4060 0.4379 0.00 0.64 0.00 0.00 0.36
#> TCGA.DA.A95X.06 2 0.1410 0.9264 0.00 0.94 0.06 0.00 0.00
#> TCGA.ER.A42K.06 3 0.0000 0.9490 0.00 0.00 1.00 0.00 0.00
#> TCGA.D3.A8GO.06 1 0.0000 0.9885 1.00 0.00 0.00 0.00 0.00
#> TCGA.D3.A8GK.06 5 0.0000 0.9796 0.00 0.00 0.00 0.00 1.00
#> TCGA.WE.A8JZ.06 2 0.0609 0.9641 0.00 0.98 0.02 0.00 0.00
#> TCGA.WE.A8ZO.06 5 0.0000 0.9796 0.00 0.00 0.00 0.00 1.00
#> TCGA.D3.A8GI.06 5 0.0000 0.9796 0.00 0.00 0.00 0.00 1.00
#> TCGA.FS.A4FC.06 4 0.0000 0.9852 0.00 0.00 0.00 1.00 0.00
#> TCGA.FS.A4F2.06 3 0.0000 0.9490 0.00 0.00 1.00 0.00 0.00
#> TCGA.WE.A8ZM.06 5 0.0000 0.9796 0.00 0.00 0.00 0.00 1.00
#> TCGA.WE.A8ZT.06 3 0.0000 0.9490 0.00 0.00 1.00 0.00 0.00
#> TCGA.D3.A8GQ.06 4 0.0000 0.9852 0.00 0.00 0.00 1.00 0.00
#> TCGA.D3.A8GB.06 1 0.0000 0.9885 1.00 0.00 0.00 0.00 0.00
#> TCGA.DA.A95Y.06 3 0.0000 0.9490 0.00 0.00 1.00 0.00 0.00
#> TCGA.EE.A3JI.06 2 0.0000 0.9806 0.00 1.00 0.00 0.00 0.00
#> TCGA.OD.A75X.06 2 0.0000 0.9806 0.00 1.00 0.00 0.00 0.00
#> TCGA.DA.A960.01 2 0.0000 0.9806 0.00 1.00 0.00 0.00 0.00
#> TCGA.D3.A8GV.06 2 0.0000 0.9806 0.00 1.00 0.00 0.00 0.00
#> TCGA.WE.A8ZN.06 1 0.0000 0.9885 1.00 0.00 0.00 0.00 0.00
#> TCGA.D3.A8GN.06 1 0.0000 0.9885 1.00 0.00 0.00 0.00 0.00
#> TCGA.EB.A550.01 1 0.0000 0.9885 1.00 0.00 0.00 0.00 0.00
#> TCGA.BF.A5EQ.01 4 0.0000 0.9852 0.00 0.00 0.00 1.00 0.00
#> TCGA.EB.A3HV.01 5 0.0000 0.9796 0.00 0.00 0.00 0.00 1.00
#> TCGA.HR.A5NC.01 5 0.0609 0.9575 0.00 0.00 0.00 0.02 0.98
#> TCGA.DA.A95Z.06 2 0.0000 0.9806 0.00 1.00 0.00 0.00 0.00
#> TCGA.EB.A6QZ.01 2 0.0000 0.9806 0.00 1.00 0.00 0.00 0.00
#> TCGA.FW.A3I3.06 2 0.0000 0.9806 0.00 1.00 0.00 0.00 0.00
#> TCGA.WE.A8K6.06 3 0.1410 0.9034 0.00 0.00 0.94 0.00 0.06
#> TCGA.D3.A8GP.06 2 0.0000 0.9806 0.00 1.00 0.00 0.00 0.00
#> TCGA.EB.A42Z.01 2 0.0000 0.9806 0.00 1.00 0.00 0.00 0.00
#> TCGA.GN.A4U4.06 2 0.6732 0.0795 0.00 0.40 0.34 0.00 0.26
#> TCGA.GF.A4EO.06 1 0.0000 0.9885 1.00 0.00 0.00 0.00 0.00
#> TCGA.GN.A8LK.06 5 0.0609 0.9615 0.00 0.02 0.00 0.00 0.98
#> TCGA.WE.A8K4.01 1 0.4302 0.0833 0.52 0.00 0.00 0.48 0.00
#> TCGA.DA.A95W.06 2 0.0000 0.9806 0.00 1.00 0.00 0.00 0.00
#> TCGA.FW.A5DX.01 2 0.0000 0.9806 0.00 1.00 0.00 0.00 0.00
#> TCGA.GN.A4U3.06 3 0.3424 0.6735 0.00 0.24 0.76 0.00 0.00
#> TCGA.EB.A6QY.01 1 0.0000 0.9885 1.00 0.00 0.00 0.00 0.00
#> TCGA.EB.A5VU.01 4 0.0000 0.9852 0.00 0.00 0.00 1.00 0.00
#> TCGA.Z2.A8RT.06 3 0.1410 0.9034 0.00 0.00 0.94 0.00 0.06
#> TCGA.WE.A8K1.06 1 0.0000 0.9885 1.00 0.00 0.00 0.00 0.00
#> TCGA.EB.A41B.01 3 0.0000 0.9490 0.00 0.00 1.00 0.00 0.00
#> TCGA.WE.A8ZY.06 2 0.0000 0.9806 0.00 1.00 0.00 0.00 0.00
#> TCGA.D9.A6EG.06 2 0.0000 0.9806 0.00 1.00 0.00 0.00 0.00
#> TCGA.BF.A5ER.01 5 0.0000 0.9796 0.00 0.00 0.00 0.00 1.00
#> TCGA.FR.A8YD.06 5 0.0000 0.9796 0.00 0.00 0.00 0.00 1.00
#> TCGA.FS.A4F9.06 5 0.0000 0.9796 0.00 0.00 0.00 0.00 1.00
#> TCGA.EB.A6R0.01 3 0.0000 0.9490 0.00 0.00 1.00 0.00 0.00
#> TCGA.ER.A42L.06 1 0.0000 0.9885 1.00 0.00 0.00 0.00 0.00
#> TCGA.D3.A8GJ.06 4 0.0000 0.9852 0.00 0.00 0.00 1.00 0.00
#> TCGA.FR.A8YE.06 1 0.0000 0.9885 1.00 0.00 0.00 0.00 0.00
#> TCGA.WE.A8ZR.06 4 0.3561 0.6501 0.00 0.00 0.00 0.74 0.26
#> TCGA.BF.A9VF.01 5 0.0000 0.9796 0.00 0.00 0.00 0.00 1.00
#> TCGA.EE.A3JH.06 1 0.0000 0.9885 1.00 0.00 0.00 0.00 0.00
#> TCGA.DA.A95V.06 4 0.0000 0.9852 0.00 0.00 0.00 1.00 0.00
#> TCGA.GF.A769.01 2 0.1648 0.9342 0.00 0.94 0.02 0.00 0.04
#> TCGA.D9.A4Z2.01 3 0.0000 0.9490 0.00 0.00 1.00 0.00 0.00
#> TCGA.FR.A44A.06 1 0.0000 0.9885 1.00 0.00 0.00 0.00 0.00
#> TCGA.EB.A5VV.06 1 0.0000 0.9885 1.00 0.00 0.00 0.00 0.00
#> TCGA.EE.A180.06 2 0.0000 0.9806 0.00 1.00 0.00 0.00 0.00
#> TCGA.D3.A8GC.06 5 0.2929 0.7693 0.00 0.18 0.00 0.00 0.82
#> TCGA.WE.A8K5.06 2 0.0000 0.9806 0.00 1.00 0.00 0.00 0.00
#> TCGA.GN.A8LN.01 2 0.2516 0.8325 0.00 0.86 0.14 0.00 0.00
#> TCGA.EE.A3JB.06 4 0.0000 0.9852 0.00 0.00 0.00 1.00 0.00
#> TCGA.D3.A3MO.06 5 0.3895 0.5188 0.00 0.00 0.32 0.00 0.68
#> TCGA.ER.A42H.01 5 0.0000 0.9796 0.00 0.00 0.00 0.00 1.00
#> TCGA.WE.A8ZX.06 4 0.0000 0.9852 0.00 0.00 0.00 1.00 0.00
#> TCGA.GN.A4U5.01 1 0.0000 0.9885 1.00 0.00 0.00 0.00 0.00
#> TCGA.D3.A8GS.06 4 0.0000 0.9852 0.00 0.00 0.00 1.00 0.00
#> TCGA.WE.A8ZQ.06 5 0.0000 0.9796 0.00 0.00 0.00 0.00 1.00
#> TCGA.EE.A2MF.06 2 0.0000 0.9806 0.00 1.00 0.00 0.00 0.00
#> TCGA.D3.A5GU.06 5 0.0000 0.9796 0.00 0.00 0.00 0.00 1.00
#> TCGA.GN.A4U8.06 4 0.0000 0.9852 0.00 0.00 0.00 1.00 0.00
#> TCGA.EB.A42Y.01 2 0.0000 0.9806 0.00 1.00 0.00 0.00 0.00
#> TCGA.D3.A3ML.06 5 0.0000 0.9796 0.00 0.00 0.00 0.00 1.00
#> TCGA.EB.A551.01 4 0.0000 0.9852 0.00 0.00 0.00 1.00 0.00
#> TCGA.D3.A8GM.06 4 0.0000 0.9852 0.00 0.00 0.00 1.00 0.00
#> TCGA.D3.A8GL.06 2 0.0000 0.9806 0.00 1.00 0.00 0.00 0.00
#> TCGA.D3.A3MU.06 2 0.0000 0.9806 0.00 1.00 0.00 0.00 0.00
#> TCGA.FS.A4F0.06 2 0.0000 0.9806 0.00 1.00 0.00 0.00 0.00
#> TCGA.D3.A3MV.06 3 0.0000 0.9490 0.00 0.00 1.00 0.00 0.00
#> TCGA.GN.A4U7.06 3 0.0000 0.9490 0.00 0.00 1.00 0.00 0.00
#> TCGA.FR.A2OS.01 5 0.0000 0.9796 0.00 0.00 0.00 0.00 1.00
#> TCGA.D3.A2JE.06 5 0.0000 0.9796 0.00 0.00 0.00 0.00 1.00
#> TCGA.YD.A89C.06 4 0.0609 0.9669 0.00 0.00 0.02 0.98 0.00
#> TCGA.FR.A726.01 4 0.0000 0.9852 0.00 0.00 0.00 1.00 0.00
#> TCGA.BF.A5EP.01 3 0.0000 0.9490 0.00 0.00 1.00 0.00 0.00
#> TCGA.D3.A3MR.06 1 0.0000 0.9885 1.00 0.00 0.00 0.00 0.00
#> TCGA.D3.A8GR.06 5 0.0000 0.9796 0.00 0.00 0.00 0.00 1.00
#> TCGA.GN.A4U9.06 5 0.0000 0.9796 0.00 0.00 0.00 0.00 1.00
#> TCGA.EB.A6L9.06 1 0.0000 0.9885 1.00 0.00 0.00 0.00 0.00
#> TCGA.D3.A5GL.06 3 0.0000 0.9490 0.00 0.00 1.00 0.00 0.00
#> TCGA.EB.A430.01 1 0.0000 0.9885 1.00 0.00 0.00 0.00 0.00
#> TCGA.D3.A8GE.06 1 0.0000 0.9885 1.00 0.00 0.00 0.00 0.00
#> TCGA.D3.A8GD.06 1 0.0000 0.9885 1.00 0.00 0.00 0.00 0.00
#> TCGA.EB.A41A.01 2 0.0000 0.9806 0.00 1.00 0.00 0.00 0.00
#> TCGA.W3.A825.06 4 0.0000 0.9852 0.00 0.00 0.00 1.00 0.00
#> TCGA.EE.A183.06 1 0.0000 0.9885 1.00 0.00 0.00 0.00 0.00
#> TCGA.ER.A2NH.06 1 0.0000 0.9885 1.00 0.00 0.00 0.00 0.00
#> TCGA.D3.A5GR.06 4 0.0000 0.9852 0.00 0.00 0.00 1.00 0.00
#> TCGA.FR.A729.06 4 0.0000 0.9852 0.00 0.00 0.00 1.00 0.00
#> TCGA.D3.A1QA.06 2 0.0000 0.9806 0.00 1.00 0.00 0.00 0.00
#> TCGA.FS.A1YY.06 3 0.0000 0.9490 0.00 0.00 1.00 0.00 0.00
#> TCGA.EE.A2MK.06 3 0.0000 0.9490 0.00 0.00 1.00 0.00 0.00
#> TCGA.EE.A2M8.06 1 0.0000 0.9885 1.00 0.00 0.00 0.00 0.00
#> TCGA.EB.A5KH.06 2 0.0000 0.9806 0.00 1.00 0.00 0.00 0.00
#> TCGA.FS.A1ZR.06 5 0.0000 0.9796 0.00 0.00 0.00 0.00 1.00
#> TCGA.EE.A3AE.06 3 0.3796 0.5901 0.00 0.00 0.70 0.30 0.00
#> TCGA.EE.A29P.06 4 0.0000 0.9852 0.00 0.00 0.00 1.00 0.00
#> TCGA.EB.A553.01 5 0.3274 0.7006 0.00 0.00 0.00 0.22 0.78
#> TCGA.EE.A2MR.06 1 0.0000 0.9885 1.00 0.00 0.00 0.00 0.00
#> TCGA.GN.A26A.06 4 0.0000 0.9852 0.00 0.00 0.00 1.00 0.00
#> TCGA.FS.A1ZY.06 2 0.0000 0.9806 0.00 1.00 0.00 0.00 0.00
#> TCGA.EE.A20I.06 4 0.0609 0.9670 0.00 0.00 0.02 0.98 0.00
#> TCGA.DA.A1I5.06 1 0.0000 0.9885 1.00 0.00 0.00 0.00 0.00
#> TCGA.EE.A184.06 2 0.0000 0.9806 0.00 1.00 0.00 0.00 0.00
#> TCGA.EB.A85J.01 4 0.0000 0.9852 0.00 0.00 0.00 1.00 0.00
#> TCGA.RP.A6K9.06 4 0.0000 0.9852 0.00 0.00 0.00 1.00 0.00
#> TCGA.EE.A17Y.06 4 0.0000 0.9852 0.00 0.00 0.00 1.00 0.00
#> TCGA.D9.A149.06 4 0.0000 0.9852 0.00 0.00 0.00 1.00 0.00
#> TCGA.ER.A19D.06 1 0.0000 0.9885 1.00 0.00 0.00 0.00 0.00
#> TCGA.FS.A1ZZ.06 2 0.0000 0.9806 0.00 1.00 0.00 0.00 0.00
#> TCGA.EE.A2GP.06 5 0.4227 0.2635 0.00 0.00 0.42 0.00 0.58
#> TCGA.EE.A3AD.06 2 0.0000 0.9806 0.00 1.00 0.00 0.00 0.00
#> TCGA.D3.A1Q9.06 4 0.0000 0.9852 0.00 0.00 0.00 1.00 0.00
#> TCGA.GF.A2C7.01 5 0.0000 0.9796 0.00 0.00 0.00 0.00 1.00
#> TCGA.BF.A5ES.01 5 0.0000 0.9796 0.00 0.00 0.00 0.00 1.00
#> TCGA.ER.A199.06 1 0.0000 0.9885 1.00 0.00 0.00 0.00 0.00
#> TCGA.EE.A3AH.06 2 0.0000 0.9806 0.00 1.00 0.00 0.00 0.00
#> TCGA.W3.A828.06 1 0.0000 0.9885 1.00 0.00 0.00 0.00 0.00
#> TCGA.EE.A2A5.06 5 0.0000 0.9796 0.00 0.00 0.00 0.00 1.00
#> TCGA.ER.A19L.06 4 0.0000 0.9852 0.00 0.00 0.00 1.00 0.00
#> TCGA.BF.A1PX.01 1 0.0000 0.9885 1.00 0.00 0.00 0.00 0.00
#> TCGA.ER.A19T.06 4 0.0000 0.9852 0.00 0.00 0.00 1.00 0.00
#> TCGA.EB.A51B.01 3 0.0609 0.9357 0.00 0.00 0.98 0.00 0.02
#> TCGA.FS.A1ZQ.06 3 0.0000 0.9490 0.00 0.00 1.00 0.00 0.00
#> TCGA.D3.A2JG.06 3 0.0000 0.9490 0.00 0.00 1.00 0.00 0.00
#> TCGA.EE.A2GH.06 1 0.0000 0.9885 1.00 0.00 0.00 0.00 0.00
#> TCGA.ER.A19F.06 3 0.0000 0.9490 0.00 0.00 1.00 0.00 0.00
#> TCGA.ER.A196.01 1 0.0000 0.9885 1.00 0.00 0.00 0.00 0.00
#> TCGA.D3.A2JC.06 4 0.0000 0.9852 0.00 0.00 0.00 1.00 0.00
#> TCGA.EE.A3AG.06 3 0.0000 0.9490 0.00 0.00 1.00 0.00 0.00
#> TCGA.ER.A19S.06 1 0.0000 0.9885 1.00 0.00 0.00 0.00 0.00
#> TCGA.EE.A2GC.06 5 0.0000 0.9796 0.00 0.00 0.00 0.00 1.00
#> TCGA.EE.A29N.06 1 0.0000 0.9885 1.00 0.00 0.00 0.00 0.00
#> TCGA.FR.A7U8.06 2 0.0609 0.9639 0.00 0.98 0.00 0.00 0.02
#> TCGA.BF.A5EO.01 4 0.0000 0.9852 0.00 0.00 0.00 1.00 0.00
#> TCGA.ER.A19B.06 3 0.0000 0.9490 0.00 0.00 1.00 0.00 0.00
#> TCGA.D3.A5GN.06 3 0.0000 0.9490 0.00 0.00 1.00 0.00 0.00
#> TCGA.D3.A2JB.06 1 0.0000 0.9885 1.00 0.00 0.00 0.00 0.00
#> TCGA.ER.A19J.06 2 0.0000 0.9806 0.00 1.00 0.00 0.00 0.00
#> TCGA.D3.A2JD.06 1 0.1410 0.9240 0.94 0.00 0.00 0.06 0.00
#> TCGA.FS.A1Z4.06 1 0.0000 0.9885 1.00 0.00 0.00 0.00 0.00
#> TCGA.FR.A7UA.06 1 0.0000 0.9885 1.00 0.00 0.00 0.00 0.00
#> TCGA.EE.A2M7.06 4 0.0000 0.9852 0.00 0.00 0.00 1.00 0.00
#> TCGA.D3.A1Q3.06 4 0.0000 0.9852 0.00 0.00 0.00 1.00 0.00
#> TCGA.EB.A85I.01 4 0.0000 0.9852 0.00 0.00 0.00 1.00 0.00
#> TCGA.EB.A82C.01 2 0.0000 0.9806 0.00 1.00 0.00 0.00 0.00
#> TCGA.ER.A19E.06 5 0.0000 0.9796 0.00 0.00 0.00 0.00 1.00
#> TCGA.FS.A1ZK.06 5 0.0000 0.9796 0.00 0.00 0.00 0.00 1.00
#> TCGA.FS.A1ZU.06 5 0.0000 0.9796 0.00 0.00 0.00 0.00 1.00
#> TCGA.EB.A5FP.01 2 0.0000 0.9806 0.00 1.00 0.00 0.00 0.00
#> TCGA.EB.A4XL.01 3 0.0000 0.9490 0.00 0.00 1.00 0.00 0.00
#> TCGA.DA.A1I2.06 4 0.4840 0.4774 0.00 0.00 0.04 0.64 0.32
#> TCGA.EE.A29L.06 2 0.0000 0.9806 0.00 1.00 0.00 0.00 0.00
#> TCGA.FS.A1ZN.01 2 0.0000 0.9806 0.00 1.00 0.00 0.00 0.00
#> TCGA.EB.A24D.01 5 0.0000 0.9796 0.00 0.00 0.00 0.00 1.00
#> TCGA.EE.A2GB.06 3 0.0000 0.9490 0.00 0.00 1.00 0.00 0.00
#> TCGA.DA.A1I7.06 4 0.0000 0.9852 0.00 0.00 0.00 1.00 0.00
#> TCGA.ER.A2NF.01 1 0.0000 0.9885 1.00 0.00 0.00 0.00 0.00
#> TCGA.GN.A263.01 1 0.0000 0.9885 1.00 0.00 0.00 0.00 0.00
#> TCGA.EE.A20C.06 2 0.0000 0.9806 0.00 1.00 0.00 0.00 0.00
#> TCGA.EE.A2MQ.06 5 0.0609 0.9611 0.00 0.00 0.02 0.00 0.98
#> TCGA.ER.A19N.06 1 0.0000 0.9885 1.00 0.00 0.00 0.00 0.00
#> TCGA.FS.A1Z3.06 3 0.2020 0.8659 0.00 0.10 0.90 0.00 0.00
#> TCGA.DA.A1I8.06 3 0.0000 0.9490 0.00 0.00 1.00 0.00 0.00
#> TCGA.D3.A5GS.06 3 0.0000 0.9490 0.00 0.00 1.00 0.00 0.00
#> TCGA.EE.A181.06 4 0.0000 0.9852 0.00 0.00 0.00 1.00 0.00
#> TCGA.GN.A268.06 2 0.0000 0.9806 0.00 1.00 0.00 0.00 0.00
#> TCGA.W3.A824.06 5 0.0000 0.9796 0.00 0.00 0.00 0.00 1.00
#> TCGA.EE.A2GS.06 3 0.0000 0.9490 0.00 0.00 1.00 0.00 0.00
#> TCGA.FR.A7U9.06 1 0.0000 0.9885 1.00 0.00 0.00 0.00 0.00
#> TCGA.ER.A19Q.06 1 0.0000 0.9885 1.00 0.00 0.00 0.00 0.00
#> TCGA.FS.A1ZM.06 4 0.0000 0.9852 0.00 0.00 0.00 1.00 0.00
#> TCGA.EE.A2MG.06 1 0.0000 0.9885 1.00 0.00 0.00 0.00 0.00
#> TCGA.EE.A2MC.06 1 0.0000 0.9885 1.00 0.00 0.00 0.00 0.00
#> TCGA.EE.A17Z.06 5 0.0000 0.9796 0.00 0.00 0.00 0.00 1.00
#> TCGA.D3.A2JP.06 4 0.0000 0.9852 0.00 0.00 0.00 1.00 0.00
#> TCGA.ER.A19C.06 4 0.0000 0.9852 0.00 0.00 0.00 1.00 0.00
#> TCGA.EB.A82B.01 4 0.0000 0.9852 0.00 0.00 0.00 1.00 0.00
#> TCGA.EE.A2A0.06 1 0.0000 0.9885 1.00 0.00 0.00 0.00 0.00
#> TCGA.EE.A29G.06 1 0.0000 0.9885 1.00 0.00 0.00 0.00 0.00
#> TCGA.D3.A5GO.06 3 0.0000 0.9490 0.00 0.00 1.00 0.00 0.00
#> TCGA.GN.A269.01 1 0.0000 0.9885 1.00 0.00 0.00 0.00 0.00
#> TCGA.EE.A2A1.06 1 0.0000 0.9885 1.00 0.00 0.00 0.00 0.00
#> TCGA.ER.A1A1.06 1 0.0000 0.9885 1.00 0.00 0.00 0.00 0.00
#> TCGA.FS.A1ZG.06 2 0.0000 0.9806 0.00 1.00 0.00 0.00 0.00
#> TCGA.FS.A1ZE.06 2 0.0000 0.9806 0.00 1.00 0.00 0.00 0.00
#> TCGA.FS.A1ZH.06 4 0.0000 0.9852 0.00 0.00 0.00 1.00 0.00
#> TCGA.EE.A2MH.06 1 0.0000 0.9885 1.00 0.00 0.00 0.00 0.00
#> TCGA.D3.A2J6.06 4 0.0000 0.9852 0.00 0.00 0.00 1.00 0.00
#> TCGA.EE.A29Q.06 3 0.1410 0.9036 0.00 0.06 0.94 0.00 0.00
#> TCGA.BF.A1PZ.01 3 0.3109 0.7413 0.00 0.00 0.80 0.00 0.20
#> TCGA.D3.A3BZ.06 1 0.0000 0.9885 1.00 0.00 0.00 0.00 0.00
#> TCGA.D3.A2JO.06 4 0.1043 0.9420 0.04 0.00 0.00 0.96 0.00
#> TCGA.GN.A267.06 4 0.0000 0.9852 0.00 0.00 0.00 1.00 0.00
#> TCGA.EE.A2MN.06 5 0.0000 0.9796 0.00 0.00 0.00 0.00 1.00
#> TCGA.GN.A264.06 2 0.0000 0.9806 0.00 1.00 0.00 0.00 0.00
#> TCGA.ER.A197.06 1 0.0000 0.9885 1.00 0.00 0.00 0.00 0.00
#> TCGA.DA.A1IB.06 1 0.0000 0.9885 1.00 0.00 0.00 0.00 0.00
#> TCGA.D3.A3CC.06 4 0.0000 0.9852 0.00 0.00 0.00 1.00 0.00
#> TCGA.ER.A19T.01 5 0.0000 0.9796 0.00 0.00 0.00 0.00 1.00
#> TCGA.GN.A261.06 1 0.0000 0.9885 1.00 0.00 0.00 0.00 0.00
#> TCGA.FS.A1YW.06 2 0.0000 0.9806 0.00 1.00 0.00 0.00 0.00
#> TCGA.BF.A1PU.01 4 0.0000 0.9852 0.00 0.00 0.00 1.00 0.00
#> TCGA.D3.A1QB.06 1 0.0000 0.9885 1.00 0.00 0.00 0.00 0.00
#> TCGA.D3.A1Q6.06 4 0.0000 0.9852 0.00 0.00 0.00 1.00 0.00
#> TCGA.D3.A3C8.06 1 0.0000 0.9885 1.00 0.00 0.00 0.00 0.00
#> TCGA.ER.A19A.06 1 0.0000 0.9885 1.00 0.00 0.00 0.00 0.00
#> TCGA.EE.A2GN.06 5 0.0000 0.9796 0.00 0.00 0.00 0.00 1.00
#> TCGA.EE.A29M.06 1 0.0000 0.9885 1.00 0.00 0.00 0.00 0.00
#> TCGA.D3.A2J7.06 1 0.0000 0.9885 1.00 0.00 0.00 0.00 0.00
#> TCGA.EB.A24C.01 4 0.0000 0.9852 0.00 0.00 0.00 1.00 0.00
#> TCGA.GN.A262.06 2 0.0000 0.9806 0.00 1.00 0.00 0.00 0.00
#> TCGA.EE.A2GD.06 1 0.0000 0.9885 1.00 0.00 0.00 0.00 0.00
#> TCGA.D3.A2J9.06 1 0.0000 0.9885 1.00 0.00 0.00 0.00 0.00
#> TCGA.EE.A29B.06 5 0.0000 0.9796 0.00 0.00 0.00 0.00 1.00
#> TCGA.D9.A1JX.06 3 0.0000 0.9490 0.00 0.00 1.00 0.00 0.00
#> TCGA.EE.A29A.06 2 0.0000 0.9806 0.00 1.00 0.00 0.00 0.00
#> TCGA.D3.A2JL.06 4 0.0000 0.9852 0.00 0.00 0.00 1.00 0.00
#> TCGA.D3.A1Q4.06 1 0.0000 0.9885 1.00 0.00 0.00 0.00 0.00
#> TCGA.FS.A1ZS.06 4 0.0000 0.9852 0.00 0.00 0.00 1.00 0.00
#> TCGA.D3.A3C3.06 4 0.0000 0.9852 0.00 0.00 0.00 1.00 0.00
#> TCGA.D3.A2J8.06 1 0.0000 0.9885 1.00 0.00 0.00 0.00 0.00
#> TCGA.FS.A1ZF.06 3 0.2280 0.8433 0.00 0.12 0.88 0.00 0.00
#> TCGA.FS.A1ZC.06 2 0.0609 0.9641 0.00 0.98 0.02 0.00 0.00
#> TCGA.EE.A20H.06 5 0.0000 0.9796 0.00 0.00 0.00 0.00 1.00
#> TCGA.EE.A29W.06 3 0.0000 0.9490 0.00 0.00 1.00 0.00 0.00
#> TCGA.D3.A1QA.07 4 0.0000 0.9852 0.00 0.00 0.00 1.00 0.00
#> TCGA.BF.A1PV.01 5 0.0000 0.9796 0.00 0.00 0.00 0.00 1.00
#> TCGA.EE.A29S.06 4 0.0609 0.9666 0.00 0.00 0.02 0.98 0.00
#> TCGA.DA.A1HV.06 3 0.0000 0.9490 0.00 0.00 1.00 0.00 0.00
#> TCGA.FS.A1Z0.06 1 0.3109 0.7471 0.80 0.00 0.00 0.20 0.00
#> TCGA.EE.A2GO.06 2 0.0000 0.9806 0.00 1.00 0.00 0.00 0.00
#> TCGA.EB.A1NK.01 1 0.0000 0.9885 1.00 0.00 0.00 0.00 0.00
#> TCGA.GN.A26D.06 4 0.0000 0.9852 0.00 0.00 0.00 1.00 0.00
#> TCGA.EE.A2MJ.06 1 0.0000 0.9885 1.00 0.00 0.00 0.00 0.00
#> TCGA.ER.A198.06 5 0.0000 0.9796 0.00 0.00 0.00 0.00 1.00
#> TCGA.EE.A17X.06 3 0.1043 0.9211 0.00 0.04 0.96 0.00 0.00
#> TCGA.EE.A2M5.06 4 0.0000 0.9852 0.00 0.00 0.00 1.00 0.00
#> TCGA.GN.A266.06 4 0.0000 0.9852 0.00 0.00 0.00 1.00 0.00
#> TCGA.D3.A3C1.06 4 0.0000 0.9852 0.00 0.00 0.00 1.00 0.00
#> TCGA.D3.A2JH.06 1 0.0000 0.9885 1.00 0.00 0.00 0.00 0.00
#> TCGA.EE.A20F.06 4 0.0000 0.9852 0.00 0.00 0.00 1.00 0.00
#> TCGA.EE.A29E.06 1 0.0000 0.9885 1.00 0.00 0.00 0.00 0.00
#> TCGA.ER.A2NG.06 1 0.0000 0.9885 1.00 0.00 0.00 0.00 0.00
#> TCGA.ER.A193.06 4 0.0000 0.9852 0.00 0.00 0.00 1.00 0.00
#> TCGA.FS.A1ZW.06 4 0.0000 0.9852 0.00 0.00 0.00 1.00 0.00
#> TCGA.ER.A19O.06 4 0.0609 0.9643 0.02 0.00 0.00 0.98 0.00
#> TCGA.EE.A2ME.06 1 0.0000 0.9885 1.00 0.00 0.00 0.00 0.00
#> TCGA.EE.A20B.06 4 0.0000 0.9852 0.00 0.00 0.00 1.00 0.00
#> TCGA.EE.A3AF.06 3 0.0000 0.9490 0.00 0.00 1.00 0.00 0.00
#> TCGA.GN.A265.06 1 0.0000 0.9885 1.00 0.00 0.00 0.00 0.00
#> TCGA.FS.A1YX.06 4 0.0000 0.9852 0.00 0.00 0.00 1.00 0.00
#> TCGA.FS.A1ZJ.06 5 0.0000 0.9796 0.00 0.00 0.00 0.00 1.00
#> TCGA.ER.A19H.06 3 0.1043 0.9166 0.00 0.00 0.96 0.04 0.00
#> TCGA.EE.A3AC.06 5 0.0000 0.9796 0.00 0.00 0.00 0.00 1.00
#> TCGA.EE.A2MU.06 1 0.0000 0.9885 1.00 0.00 0.00 0.00 0.00
#> TCGA.ER.A194.01 4 0.0000 0.9852 0.00 0.00 0.00 1.00 0.00
#> TCGA.EE.A2MS.06 4 0.0000 0.9852 0.00 0.00 0.00 1.00 0.00
#> TCGA.EE.A29R.06 2 0.0000 0.9806 0.00 1.00 0.00 0.00 0.00
#> TCGA.D9.A1X3.06 2 0.0000 0.9806 0.00 1.00 0.00 0.00 0.00
#> TCGA.EE.A29X.06 4 0.1732 0.9061 0.00 0.00 0.00 0.92 0.08
#> TCGA.EE.A2GK.06 1 0.0000 0.9885 1.00 0.00 0.00 0.00 0.00
#> TCGA.EE.A3AA.06 1 0.0000 0.9885 1.00 0.00 0.00 0.00 0.00
#> TCGA.ER.A2NE.06 2 0.0000 0.9806 0.00 1.00 0.00 0.00 0.00
#> TCGA.EE.A2GR.06 5 0.0000 0.9796 0.00 0.00 0.00 0.00 1.00
#> TCGA.FS.A1ZD.06 5 0.0000 0.9796 0.00 0.00 0.00 0.00 1.00
#> TCGA.ER.A19P.06 1 0.0000 0.9885 1.00 0.00 0.00 0.00 0.00
#> TCGA.D3.A1Q8.06 1 0.1732 0.9011 0.92 0.00 0.00 0.08 0.00
#> TCGA.ER.A2NC.06 4 0.0000 0.9852 0.00 0.00 0.00 1.00 0.00
#> TCGA.BF.A1Q0.01 4 0.0000 0.9852 0.00 0.00 0.00 1.00 0.00
#> TCGA.FS.A1ZP.06 5 0.0000 0.9796 0.00 0.00 0.00 0.00 1.00
#> TCGA.EE.A182.06 4 0.0000 0.9852 0.00 0.00 0.00 1.00 0.00
#> TCGA.D9.A1JW.06 4 0.0000 0.9852 0.00 0.00 0.00 1.00 0.00
#> TCGA.D3.A1Q7.06 1 0.0000 0.9885 1.00 0.00 0.00 0.00 0.00
#> TCGA.EE.A185.06 2 0.0000 0.9806 0.00 1.00 0.00 0.00 0.00
#> TCGA.EE.A2GJ.06 4 0.0000 0.9852 0.00 0.00 0.00 1.00 0.00
#> TCGA.D3.A3CB.06 1 0.0000 0.9885 1.00 0.00 0.00 0.00 0.00
#> TCGA.EE.A2GU.06 4 0.0000 0.9852 0.00 0.00 0.00 1.00 0.00
#> TCGA.ER.A195.06 1 0.0000 0.9885 1.00 0.00 0.00 0.00 0.00
#> TCGA.FS.A1Z7.06 4 0.0000 0.9852 0.00 0.00 0.00 1.00 0.00
#> TCGA.EE.A2M6.06 2 0.0000 0.9806 0.00 1.00 0.00 0.00 0.00
#> TCGA.ER.A19K.01 4 0.0000 0.9852 0.00 0.00 0.00 1.00 0.00
#> TCGA.DA.A1HY.06 3 0.0000 0.9490 0.00 0.00 1.00 0.00 0.00
#> TCGA.D3.A3C7.06 3 0.0609 0.9357 0.00 0.00 0.98 0.00 0.02
#> TCGA.EE.A2MP.06 3 0.0000 0.9490 0.00 0.00 1.00 0.00 0.00
#> TCGA.EE.A29H.06 3 0.0000 0.9490 0.00 0.00 1.00 0.00 0.00
#> TCGA.FR.A3YO.06 4 0.0000 0.9852 0.00 0.00 0.00 1.00 0.00
#> TCGA.XV.AB01.01 3 0.0000 0.9490 0.00 0.00 1.00 0.00 0.00
#> TCGA.RP.A694.06 4 0.0000 0.9852 0.00 0.00 0.00 1.00 0.00
#> TCGA.EB.A5SF.01 1 0.0000 0.9885 1.00 0.00 0.00 0.00 0.00
#> TCGA.ER.A19G.06 3 0.0000 0.9490 0.00 0.00 1.00 0.00 0.00
#> TCGA.EE.A2GE.06 1 0.0000 0.9885 1.00 0.00 0.00 0.00 0.00
#> TCGA.GF.A3OT.06 1 0.0000 0.9885 1.00 0.00 0.00 0.00 0.00
#> TCGA.ER.A2NF.06 1 0.0000 0.9885 1.00 0.00 0.00 0.00 0.00
#> TCGA.RP.A695.06 5 0.0000 0.9796 0.00 0.00 0.00 0.00 1.00
#> TCGA.BF.AAP7.01 1 0.0000 0.9885 1.00 0.00 0.00 0.00 0.00
#> TCGA.EB.A3Y7.01 4 0.0000 0.9852 0.00 0.00 0.00 1.00 0.00
#> TCGA.EB.A3XC.01 3 0.0000 0.9490 0.00 0.00 1.00 0.00 0.00
#> TCGA.ER.A19W.06 1 0.0000 0.9885 1.00 0.00 0.00 0.00 0.00
#> TCGA.FR.A69P.06 3 0.3796 0.5916 0.00 0.00 0.70 0.30 0.00
#> TCGA.RP.A693.06 1 0.2732 0.8014 0.84 0.00 0.00 0.16 0.00
#> TCGA.FW.A3TV.06 1 0.0000 0.9885 1.00 0.00 0.00 0.00 0.00
#> TCGA.FW.A3R5.11 1 0.0000 0.9885 1.00 0.00 0.00 0.00 0.00
#> TCGA.FW.A3TU.06 5 0.0000 0.9796 0.00 0.00 0.00 0.00 1.00
#> TCGA.BF.AAP8.01 4 0.0000 0.9852 0.00 0.00 0.00 1.00 0.00
#> TCGA.EE.A2MM.06 5 0.0000 0.9796 0.00 0.00 0.00 0.00 1.00
#> TCGA.DA.A1HW.06 4 0.0000 0.9852 0.00 0.00 0.00 1.00 0.00
#> TCGA.DA.A1IC.06 5 0.0000 0.9796 0.00 0.00 0.00 0.00 1.00
#> TCGA.XV.AAZV.01 1 0.0000 0.9885 1.00 0.00 0.00 0.00 0.00
#> TCGA.D3.A3C6.06 3 0.0000 0.9490 0.00 0.00 1.00 0.00 0.00
#> TCGA.EE.A29C.06 1 0.0000 0.9885 1.00 0.00 0.00 0.00 0.00
#> TCGA.BF.AAP2.01 2 0.1410 0.9264 0.00 0.94 0.06 0.00 0.00
#> TCGA.EE.A2A2.06 3 0.0000 0.9490 0.00 0.00 1.00 0.00 0.00
#> TCGA.GF.A6C8.06 4 0.0000 0.9852 0.00 0.00 0.00 1.00 0.00
#> TCGA.RP.A690.06 1 0.0000 0.9885 1.00 0.00 0.00 0.00 0.00
#> TCGA.FW.A5DY.06 1 0.0000 0.9885 1.00 0.00 0.00 0.00 0.00
#> TCGA.DA.A1I4.06 1 0.0000 0.9885 1.00 0.00 0.00 0.00 0.00
#> TCGA.EE.A29V.06 4 0.2280 0.8437 0.12 0.00 0.00 0.88 0.00
#> TCGA.GF.A6C9.06 1 0.0000 0.9885 1.00 0.00 0.00 0.00 0.00
#> TCGA.EE.A2GT.06 1 0.0000 0.9885 1.00 0.00 0.00 0.00 0.00
#> TCGA.GN.A9SD.06 1 0.0000 0.9885 1.00 0.00 0.00 0.00 0.00
#> TCGA.EE.A3AB.06 4 0.0000 0.9852 0.00 0.00 0.00 1.00 0.00
#> TCGA.BF.AAP6.01 3 0.0000 0.9490 0.00 0.00 1.00 0.00 0.00
#> TCGA.EB.A5SH.06 4 0.0000 0.9852 0.00 0.00 0.00 1.00 0.00
#> TCGA.D9.A6E9.06 4 0.0000 0.9852 0.00 0.00 0.00 1.00 0.00
#> TCGA.BF.AAP4.01 4 0.0000 0.9852 0.00 0.00 0.00 1.00 0.00
#> TCGA.EE.A2GM.06 2 0.0000 0.9806 0.00 1.00 0.00 0.00 0.00
#> TCGA.D3.A3CF.06 1 0.0000 0.9885 1.00 0.00 0.00 0.00 0.00
#> TCGA.D9.A6EC.06 2 0.0000 0.9806 0.00 1.00 0.00 0.00 0.00
#> TCGA.DA.A1I1.06 4 0.0000 0.9852 0.00 0.00 0.00 1.00 0.00
#> TCGA.HR.A2OH.06 1 0.0000 0.9885 1.00 0.00 0.00 0.00 0.00
#> TCGA.EE.A2MT.06 4 0.0000 0.9852 0.00 0.00 0.00 1.00 0.00
#> TCGA.ER.A19M.06 4 0.0000 0.9852 0.00 0.00 0.00 1.00 0.00
#> TCGA.GN.A26C.01 1 0.0000 0.9885 1.00 0.00 0.00 0.00 0.00
#> TCGA.FS.A1ZA.06 4 0.1043 0.9468 0.00 0.00 0.04 0.96 0.00
#> TCGA.EB.A5SE.01 2 0.0000 0.9806 0.00 1.00 0.00 0.00 0.00
#> TCGA.ER.A3PL.06 5 0.0000 0.9796 0.00 0.00 0.00 0.00 1.00
#> TCGA.FR.A3R1.01 3 0.0000 0.9490 0.00 0.00 1.00 0.00 0.00
#> TCGA.EE.A2MI.06 4 0.0000 0.9852 0.00 0.00 0.00 1.00 0.00
#> TCGA.D3.A3CE.06 4 0.2516 0.8283 0.00 0.00 0.14 0.86 0.00
#> TCGA.D3.A5GT.01 5 0.0000 0.9796 0.00 0.00 0.00 0.00 1.00
#> TCGA.ER.A2NB.01 4 0.0000 0.9852 0.00 0.00 0.00 1.00 0.00
#> TCGA.D3.A1Q5.06 4 0.0000 0.9852 0.00 0.00 0.00 1.00 0.00
#> TCGA.EB.A5UN.06 1 0.0000 0.9885 1.00 0.00 0.00 0.00 0.00
#> TCGA.EB.A299.01 3 0.3796 0.5901 0.00 0.00 0.70 0.30 0.00
#> TCGA.DA.A1IA.06 5 0.0000 0.9796 0.00 0.00 0.00 0.00 1.00
#> TCGA.EB.A5SG.06 1 0.0000 0.9885 1.00 0.00 0.00 0.00 0.00
#> TCGA.D9.A6EA.06 2 0.0000 0.9806 0.00 1.00 0.00 0.00 0.00
#> TCGA.XV.AAZY.01 1 0.0000 0.9885 1.00 0.00 0.00 0.00 0.00
#> TCGA.EB.A57M.01 4 0.0000 0.9852 0.00 0.00 0.00 1.00 0.00
#> TCGA.EE.A2A6.06 4 0.0000 0.9852 0.00 0.00 0.00 1.00 0.00
#> TCGA.D3.A2JA.06 1 0.0000 0.9885 1.00 0.00 0.00 0.00 0.00
#> TCGA.D3.A1Q1.06 4 0.0000 0.9852 0.00 0.00 0.00 1.00 0.00
#> TCGA.EB.A3XF.01 3 0.0000 0.9490 0.00 0.00 1.00 0.00 0.00
#> TCGA.D3.A2JF.06 3 0.4182 0.3597 0.00 0.00 0.60 0.40 0.00
#> TCGA.XV.AAZW.01 3 0.0609 0.9358 0.00 0.02 0.98 0.00 0.00
#> TCGA.EB.A3Y6.01 4 0.0000 0.9852 0.00 0.00 0.00 1.00 0.00
#> TCGA.EB.A3XE.01 4 0.0000 0.9852 0.00 0.00 0.00 1.00 0.00
#> TCGA.D9.A3Z4.01 5 0.0000 0.9796 0.00 0.00 0.00 0.00 1.00
#> TCGA.FW.A3R5.06 4 0.0000 0.9852 0.00 0.00 0.00 1.00 0.00
#> TCGA.EE.A2GI.06 4 0.0000 0.9852 0.00 0.00 0.00 1.00 0.00
#> TCGA.EE.A2GL.06 1 0.0000 0.9885 1.00 0.00 0.00 0.00 0.00
#> TCGA.EB.A3XB.01 4 0.0000 0.9852 0.00 0.00 0.00 1.00 0.00
#> TCGA.BF.AAOU.01 1 0.0000 0.9885 1.00 0.00 0.00 0.00 0.00
#> TCGA.EB.A3XD.01 1 0.0000 0.9885 1.00 0.00 0.00 0.00 0.00
#> TCGA.EE.A2MD.06 4 0.0000 0.9852 0.00 0.00 0.00 1.00 0.00
#> TCGA.YD.A9TB.06 5 0.0000 0.9796 0.00 0.00 0.00 0.00 1.00
#> TCGA.W3.AA1V.06 4 0.0000 0.9852 0.00 0.00 0.00 1.00 0.00
#> TCGA.ER.A2ND.06 5 0.1410 0.9114 0.00 0.00 0.00 0.06 0.94
#> TCGA.D3.A2JK.06 4 0.0000 0.9852 0.00 0.00 0.00 1.00 0.00
#> TCGA.FS.A1ZB.06 1 0.0000 0.9885 1.00 0.00 0.00 0.00 0.00
#> TCGA.EE.A29D.06 2 0.1410 0.9248 0.00 0.94 0.00 0.00 0.06
#> TCGA.EB.A5UM.01 4 0.0000 0.9852 0.00 0.00 0.00 1.00 0.00
#> TCGA.QB.A6FS.06 1 0.0000 0.9885 1.00 0.00 0.00 0.00 0.00
#> TCGA.D9.A3Z1.06 1 0.0000 0.9885 1.00 0.00 0.00 0.00 0.00
#> TCGA.D3.A2JN.06 1 0.0000 0.9885 1.00 0.00 0.00 0.00 0.00
#> TCGA.FR.A3YN.06 3 0.0000 0.9490 0.00 0.00 1.00 0.00 0.00
#> TCGA.FS.A1ZT.06 1 0.0000 0.9885 1.00 0.00 0.00 0.00 0.00
#> TCGA.D9.A148.06 4 0.0000 0.9852 0.00 0.00 0.00 1.00 0.00
#> TCGA.HR.A2OG.06 1 0.0609 0.9675 0.98 0.00 0.00 0.02 0.00
#> TCGA.EE.A2ML.06 4 0.0000 0.9852 0.00 0.00 0.00 1.00 0.00
#> TCGA.EB.A5UL.06 4 0.0000 0.9852 0.00 0.00 0.00 1.00 0.00
#> TCGA.EE.A29T.06 4 0.3983 0.4778 0.34 0.00 0.00 0.66 0.00
#> TCGA.D9.A3Z3.06 1 0.0000 0.9885 1.00 0.00 0.00 0.00 0.00
#> TCGA.D9.A4Z3.01 5 0.0000 0.9796 0.00 0.00 0.00 0.00 1.00
#> TCGA.ER.A3ES.06 4 0.0000 0.9852 0.00 0.00 0.00 1.00 0.00
#> TCGA.XV.A9VZ.01 1 0.0000 0.9885 1.00 0.00 0.00 0.00 0.00
#> TCGA.QB.AA9O.06 3 0.1043 0.9166 0.00 0.00 0.96 0.04 0.00
#> TCGA.EB.A44Q.06 4 0.0000 0.9852 0.00 0.00 0.00 1.00 0.00
#> TCGA.EB.A44R.06 4 0.0000 0.9852 0.00 0.00 0.00 1.00 0.00
#> TCGA.BF.A3DJ.01 3 0.0000 0.9490 0.00 0.00 1.00 0.00 0.00
#> TCGA.EE.A3JD.06 1 0.0000 0.9885 1.00 0.00 0.00 0.00 0.00
#> TCGA.D3.A51N.06 4 0.0000 0.9852 0.00 0.00 0.00 1.00 0.00
#> TCGA.EB.A44N.01 1 0.0000 0.9885 1.00 0.00 0.00 0.00 0.00
#> TCGA.EE.A3J3.06 3 0.4227 0.2773 0.00 0.00 0.58 0.00 0.42
#> TCGA.XV.A9W5.01 4 0.3424 0.6739 0.00 0.00 0.24 0.76 0.00
#> TCGA.D3.A51G.06 3 0.2516 0.8128 0.00 0.00 0.86 0.14 0.00
#> TCGA.EB.A4P0.01 3 0.2516 0.8188 0.00 0.14 0.86 0.00 0.00
#> TCGA.BF.AAP1.01 2 0.0000 0.9806 0.00 1.00 0.00 0.00 0.00
#> TCGA.EE.A3J4.06 5 0.0000 0.9796 0.00 0.00 0.00 0.00 1.00
#> TCGA.Z2.AA3V.06 1 0.0000 0.9885 1.00 0.00 0.00 0.00 0.00
#> TCGA.LH.A9QB.06 2 0.0000 0.9806 0.00 1.00 0.00 0.00 0.00
#> TCGA.D3.A51J.06 4 0.0000 0.9852 0.00 0.00 0.00 1.00 0.00
#> TCGA.3N.A9WC.06 4 0.0000 0.9852 0.00 0.00 0.00 1.00 0.00
#> TCGA.DA.A3F8.06 1 0.0000 0.9885 1.00 0.00 0.00 0.00 0.00
#> TCGA.D9.A4Z6.06 4 0.0000 0.9852 0.00 0.00 0.00 1.00 0.00
#> TCGA.D3.A51R.06 3 0.0000 0.9490 0.00 0.00 1.00 0.00 0.00
#> TCGA.EB.A4OZ.01 1 0.0000 0.9885 1.00 0.00 0.00 0.00 0.00
#> TCGA.FS.A4FB.06 3 0.0000 0.9490 0.00 0.00 1.00 0.00 0.00
#> TCGA.EE.A3JE.06 1 0.0000 0.9885 1.00 0.00 0.00 0.00 0.00
#> TCGA.W3.AA1W.06 1 0.0000 0.9885 1.00 0.00 0.00 0.00 0.00
#> TCGA.DA.A1I0.06 4 0.1732 0.8946 0.08 0.00 0.00 0.92 0.00
#> TCGA.D3.A51F.06 1 0.0000 0.9885 1.00 0.00 0.00 0.00 0.00
#> TCGA.IH.A3EA.01 5 0.0000 0.9796 0.00 0.00 0.00 0.00 1.00
#> TCGA.EB.A431.01 4 0.0000 0.9852 0.00 0.00 0.00 1.00 0.00
#> TCGA.EB.A97M.01 2 0.0000 0.9806 0.00 1.00 0.00 0.00 0.00
#> TCGA.BF.AAOX.01 4 0.0000 0.9852 0.00 0.00 0.00 1.00 0.00
#> TCGA.DA.A3F5.06 4 0.0000 0.9852 0.00 0.00 0.00 1.00 0.00
#> TCGA.YD.A9TA.06 4 0.0000 0.9852 0.00 0.00 0.00 1.00 0.00
#> TCGA.DA.A3F2.06 1 0.0000 0.9885 1.00 0.00 0.00 0.00 0.00
#> TCGA.EB.A44O.01 5 0.0000 0.9796 0.00 0.00 0.00 0.00 1.00
#> TCGA.EB.A4IQ.01 4 0.0000 0.9852 0.00 0.00 0.00 1.00 0.00
#> TCGA.EB.A4IS.01 1 0.0000 0.9885 1.00 0.00 0.00 0.00 0.00
#> TCGA.YG.AA3O.06 5 0.0000 0.9796 0.00 0.00 0.00 0.00 1.00
#> TCGA.ER.A3EV.06 4 0.0000 0.9852 0.00 0.00 0.00 1.00 0.00
#> TCGA.3N.A9WD.06 1 0.0000 0.9885 1.00 0.00 0.00 0.00 0.00
#> TCGA.BF.A3DM.01 3 0.0000 0.9490 0.00 0.00 1.00 0.00 0.00
#> TCGA.XV.A9W2.01 4 0.0000 0.9852 0.00 0.00 0.00 1.00 0.00
#> TCGA.W3.AA1Q.06 5 0.0000 0.9796 0.00 0.00 0.00 0.00 1.00
#> TCGA.WE.AAA0.06 4 0.0000 0.9852 0.00 0.00 0.00 1.00 0.00
#> TCGA.W3.AA1R.06 3 0.0000 0.9490 0.00 0.00 1.00 0.00 0.00
#> TCGA.EE.A3J5.06 4 0.0000 0.9852 0.00 0.00 0.00 1.00 0.00
#> TCGA.EB.A4OY.01 1 0.0000 0.9885 1.00 0.00 0.00 0.00 0.00
#> TCGA.FS.A4FD.06 4 0.0000 0.9852 0.00 0.00 0.00 1.00 0.00
#> TCGA.BF.AAP0.06 1 0.0000 0.9885 1.00 0.00 0.00 0.00 0.00
#> TCGA.YG.AA3P.06 5 0.0000 0.9796 0.00 0.00 0.00 0.00 1.00
#> TCGA.EE.A3JA.06 3 0.0000 0.9490 0.00 0.00 1.00 0.00 0.00
#> TCGA.W3.AA21.06 2 0.0000 0.9806 0.00 1.00 0.00 0.00 0.00
#> TCGA.WE.AAA3.06 4 0.0000 0.9852 0.00 0.00 0.00 1.00 0.00
#> TCGA.FS.A4F4.06 3 0.0000 0.9490 0.00 0.00 1.00 0.00 0.00
#> TCGA.BF.A3DN.01 3 0.2020 0.8642 0.00 0.00 0.90 0.00 0.10
#> TCGA.ER.A3ET.06 4 0.0000 0.9852 0.00 0.00 0.00 1.00 0.00
#> TCGA.W3.AA1O.06 5 0.0000 0.9796 0.00 0.00 0.00 0.00 1.00
#> TCGA.D3.A51E.06 3 0.2280 0.8350 0.00 0.00 0.88 0.12 0.00
#> TCGA.Z2.AA3S.06 2 0.0000 0.9806 0.00 1.00 0.00 0.00 0.00
#> TCGA.YG.AA3N.01 4 0.0000 0.9852 0.00 0.00 0.00 1.00 0.00
#> TCGA.WE.AA9Y.06 1 0.0000 0.9885 1.00 0.00 0.00 0.00 0.00
#> TCGA.FS.A4F5.06 2 0.0000 0.9806 0.00 1.00 0.00 0.00 0.00
#> TCGA.EE.A3J7.06 5 0.0000 0.9796 0.00 0.00 0.00 0.00 1.00
#> TCGA.FS.A4F8.06 1 0.0000 0.9885 1.00 0.00 0.00 0.00 0.00
#> TCGA.DA.A3F3.06 3 0.0000 0.9490 0.00 0.00 1.00 0.00 0.00
#> TCGA.D3.A51H.06 1 0.0000 0.9885 1.00 0.00 0.00 0.00 0.00
#> TCGA.BF.A3DL.01 1 0.3274 0.7187 0.78 0.00 0.00 0.22 0.00
#> TCGA.D3.A51T.06 3 0.0000 0.9490 0.00 0.00 1.00 0.00 0.00
#> TCGA.D3.A51K.06 5 0.0000 0.9796 0.00 0.00 0.00 0.00 1.00
#> TCGA.EB.A44P.01 5 0.0000 0.9796 0.00 0.00 0.00 0.00 1.00
#> TCGA.D9.A4Z5.01 2 0.0000 0.9806 0.00 1.00 0.00 0.00 0.00
#> TCGA.WE.AAA4.06 1 0.0000 0.9885 1.00 0.00 0.00 0.00 0.00
#> TCGA.3N.A9WB.06 2 0.0000 0.9806 0.00 1.00 0.00 0.00 0.00
#> TCGA.EE.A3J8.06 2 0.0000 0.9806 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.FR.A728.01 4 0.2260 0.8212 0.14 0.00 0.00 0.86 0.00 0.00
#> TCGA.GN.A4U8.11 1 0.0000 0.9880 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.GN.A8LL.06 3 0.0937 0.8722 0.00 0.04 0.96 0.00 0.00 0.00
#> TCGA.FR.A8YC.06 6 0.0937 0.8961 0.00 0.00 0.00 0.00 0.04 0.96
#> TCGA.DA.A95X.06 2 0.0000 0.8997 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.ER.A42K.06 3 0.0937 0.8722 0.00 0.04 0.96 0.00 0.00 0.00
#> TCGA.D3.A8GO.06 1 0.0000 0.9880 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D3.A8GK.06 5 0.0000 0.8513 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.WE.A8JZ.06 2 0.0937 0.9068 0.00 0.96 0.00 0.00 0.00 0.04
#> TCGA.WE.A8ZO.06 5 0.2260 0.7910 0.00 0.00 0.00 0.00 0.86 0.14
#> TCGA.D3.A8GI.06 6 0.3309 0.6274 0.00 0.00 0.00 0.00 0.28 0.72
#> TCGA.FS.A4FC.06 4 0.4067 0.6557 0.00 0.00 0.00 0.70 0.26 0.04
#> TCGA.FS.A4F2.06 3 0.0937 0.8722 0.00 0.04 0.96 0.00 0.00 0.00
#> TCGA.WE.A8ZM.06 5 0.1814 0.8179 0.00 0.00 0.00 0.00 0.90 0.10
#> TCGA.WE.A8ZT.06 3 0.1267 0.8659 0.00 0.06 0.94 0.00 0.00 0.00
#> TCGA.D3.A8GQ.06 4 0.0937 0.8958 0.00 0.00 0.04 0.96 0.00 0.00
#> TCGA.D3.A8GB.06 1 0.0000 0.9880 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DA.A95Y.06 2 0.0937 0.8844 0.00 0.96 0.04 0.00 0.00 0.00
#> TCGA.EE.A3JI.06 6 0.0937 0.9145 0.00 0.04 0.00 0.00 0.00 0.96
#> TCGA.OD.A75X.06 2 0.1267 0.9064 0.00 0.94 0.00 0.00 0.00 0.06
#> TCGA.DA.A960.01 2 0.1267 0.9064 0.00 0.94 0.00 0.00 0.00 0.06
#> TCGA.D3.A8GV.06 2 0.0937 0.9068 0.00 0.96 0.00 0.00 0.00 0.04
#> TCGA.WE.A8ZN.06 4 0.3076 0.6915 0.24 0.00 0.00 0.76 0.00 0.00
#> TCGA.D3.A8GN.06 1 0.0000 0.9880 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EB.A550.01 1 0.0547 0.9657 0.98 0.00 0.00 0.02 0.00 0.00
#> TCGA.BF.A5EQ.01 4 0.2190 0.8728 0.00 0.00 0.00 0.90 0.06 0.04
#> TCGA.EB.A3HV.01 5 0.0000 0.8513 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.HR.A5NC.01 5 0.1865 0.8213 0.00 0.00 0.00 0.04 0.92 0.04
#> TCGA.DA.A95Z.06 6 0.0937 0.9145 0.00 0.04 0.00 0.00 0.00 0.96
#> TCGA.EB.A6QZ.01 2 0.1267 0.9064 0.00 0.94 0.00 0.00 0.00 0.06
#> TCGA.FW.A3I3.06 2 0.1267 0.9064 0.00 0.94 0.00 0.00 0.00 0.06
#> TCGA.WE.A8K6.06 3 0.3821 0.6885 0.00 0.04 0.74 0.00 0.22 0.00
#> TCGA.D3.A8GP.06 6 0.1267 0.8992 0.00 0.06 0.00 0.00 0.00 0.94
#> TCGA.EB.A42Z.01 6 0.0937 0.9145 0.00 0.04 0.00 0.00 0.00 0.96
#> TCGA.GN.A4U4.06 2 0.4887 0.5961 0.00 0.70 0.02 0.00 0.16 0.12
#> TCGA.GF.A4EO.06 1 0.0000 0.9880 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.GN.A8LK.06 6 0.1556 0.8742 0.00 0.00 0.00 0.00 0.08 0.92
#> TCGA.WE.A8K4.01 4 0.1814 0.8527 0.10 0.00 0.00 0.90 0.00 0.00
#> TCGA.DA.A95W.06 6 0.0937 0.9145 0.00 0.04 0.00 0.00 0.00 0.96
#> TCGA.FW.A5DX.01 2 0.1267 0.9064 0.00 0.94 0.00 0.00 0.00 0.06
#> TCGA.GN.A4U3.06 2 0.0937 0.8844 0.00 0.96 0.04 0.00 0.00 0.00
#> TCGA.EB.A6QY.01 1 0.0000 0.9880 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EB.A5VU.01 4 0.4067 0.6405 0.00 0.00 0.26 0.70 0.04 0.00
#> TCGA.Z2.A8RT.06 3 0.4632 0.1935 0.00 0.04 0.52 0.00 0.44 0.00
#> TCGA.WE.A8K1.06 4 0.3499 0.5680 0.32 0.00 0.00 0.68 0.00 0.00
#> TCGA.EB.A41B.01 3 0.1267 0.8659 0.00 0.06 0.94 0.00 0.00 0.00
#> TCGA.WE.A8ZY.06 2 0.1267 0.9064 0.00 0.94 0.00 0.00 0.00 0.06
#> TCGA.D9.A6EG.06 6 0.0937 0.9145 0.00 0.04 0.00 0.00 0.00 0.96
#> TCGA.BF.A5ER.01 5 0.1814 0.8179 0.00 0.00 0.00 0.00 0.90 0.10
#> TCGA.FR.A8YD.06 6 0.1814 0.8593 0.00 0.00 0.00 0.00 0.10 0.90
#> TCGA.FS.A4F9.06 6 0.1814 0.8593 0.00 0.00 0.00 0.00 0.10 0.90
#> TCGA.EB.A6R0.01 3 0.0000 0.8665 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.ER.A42L.06 1 0.0000 0.9880 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D3.A8GJ.06 4 0.0937 0.8927 0.00 0.00 0.00 0.96 0.00 0.04
#> TCGA.FR.A8YE.06 1 0.0000 0.9880 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.WE.A8ZR.06 5 0.2956 0.7685 0.00 0.00 0.00 0.12 0.84 0.04
#> TCGA.BF.A9VF.01 5 0.2260 0.7910 0.00 0.00 0.00 0.00 0.86 0.14
#> TCGA.EE.A3JH.06 1 0.0000 0.9880 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DA.A95V.06 4 0.0937 0.8958 0.00 0.00 0.04 0.96 0.00 0.00
#> TCGA.GF.A769.01 2 0.1480 0.8726 0.00 0.94 0.00 0.00 0.02 0.04
#> TCGA.D9.A4Z2.01 3 0.2631 0.7581 0.00 0.18 0.82 0.00 0.00 0.00
#> TCGA.FR.A44A.06 1 0.0000 0.9880 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EB.A5VV.06 1 0.0000 0.9880 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EE.A180.06 6 0.0937 0.9145 0.00 0.04 0.00 0.00 0.00 0.96
#> TCGA.D3.A8GC.06 6 0.1556 0.8742 0.00 0.00 0.00 0.00 0.08 0.92
#> TCGA.WE.A8K5.06 6 0.0937 0.9145 0.00 0.04 0.00 0.00 0.00 0.96
#> TCGA.GN.A8LN.01 2 0.0547 0.8929 0.00 0.98 0.02 0.00 0.00 0.00
#> TCGA.EE.A3JB.06 4 0.0937 0.8958 0.00 0.00 0.04 0.96 0.00 0.00
#> TCGA.D3.A3MO.06 5 0.3821 0.6393 0.00 0.04 0.22 0.00 0.74 0.00
#> TCGA.ER.A42H.01 5 0.3828 0.1946 0.00 0.00 0.00 0.00 0.56 0.44
#> TCGA.WE.A8ZX.06 3 0.2941 0.7021 0.00 0.00 0.78 0.22 0.00 0.00
#> TCGA.GN.A4U5.01 1 0.0000 0.9880 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D3.A8GS.06 4 0.0937 0.8927 0.00 0.00 0.00 0.96 0.00 0.04
#> TCGA.WE.A8ZQ.06 6 0.1814 0.8593 0.00 0.00 0.00 0.00 0.10 0.90
#> TCGA.EE.A2MF.06 6 0.0937 0.9145 0.00 0.04 0.00 0.00 0.00 0.96
#> TCGA.D3.A5GU.06 5 0.0000 0.8513 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.GN.A4U8.06 4 0.0937 0.8958 0.00 0.00 0.04 0.96 0.00 0.00
#> TCGA.EB.A42Y.01 2 0.0937 0.9068 0.00 0.96 0.00 0.00 0.00 0.04
#> TCGA.D3.A3ML.06 6 0.1814 0.8593 0.00 0.00 0.00 0.00 0.10 0.90
#> TCGA.EB.A551.01 4 0.1556 0.8692 0.08 0.00 0.00 0.92 0.00 0.00
#> TCGA.D3.A8GM.06 4 0.0937 0.8958 0.00 0.00 0.04 0.96 0.00 0.00
#> TCGA.D3.A8GL.06 6 0.0937 0.9145 0.00 0.04 0.00 0.00 0.00 0.96
#> TCGA.D3.A3MU.06 6 0.0937 0.9145 0.00 0.04 0.00 0.00 0.00 0.96
#> TCGA.FS.A4F0.06 6 0.2454 0.7907 0.00 0.16 0.00 0.00 0.00 0.84
#> TCGA.D3.A3MV.06 3 0.1267 0.8659 0.00 0.06 0.94 0.00 0.00 0.00
#> TCGA.GN.A4U7.06 3 0.0937 0.8722 0.00 0.04 0.96 0.00 0.00 0.00
#> TCGA.FR.A2OS.01 5 0.0000 0.8513 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.D3.A2JE.06 6 0.3864 0.0888 0.00 0.00 0.00 0.00 0.48 0.52
#> TCGA.YD.A89C.06 3 0.3163 0.7658 0.00 0.00 0.82 0.14 0.04 0.00
#> TCGA.FR.A726.01 4 0.1267 0.8861 0.00 0.00 0.06 0.94 0.00 0.00
#> TCGA.BF.A5EP.01 2 0.1556 0.8562 0.00 0.92 0.08 0.00 0.00 0.00
#> TCGA.D3.A3MR.06 1 0.0000 0.9880 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D3.A8GR.06 5 0.2048 0.8055 0.00 0.00 0.00 0.00 0.88 0.12
#> TCGA.GN.A4U9.06 5 0.0000 0.8513 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.EB.A6L9.06 1 0.0000 0.9880 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D3.A5GL.06 3 0.2794 0.8275 0.00 0.06 0.86 0.00 0.08 0.00
#> TCGA.EB.A430.01 1 0.0000 0.9880 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D3.A8GE.06 1 0.0000 0.9880 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D3.A8GD.06 1 0.0000 0.9880 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EB.A41A.01 6 0.0937 0.9145 0.00 0.04 0.00 0.00 0.00 0.96
#> TCGA.W3.A825.06 4 0.1092 0.8977 0.00 0.00 0.02 0.96 0.00 0.02
#> TCGA.EE.A183.06 1 0.0000 0.9880 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.ER.A2NH.06 1 0.0000 0.9880 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D3.A5GR.06 4 0.1807 0.8816 0.06 0.00 0.00 0.92 0.00 0.02
#> TCGA.FR.A729.06 4 0.0937 0.8958 0.00 0.00 0.04 0.96 0.00 0.00
#> TCGA.D3.A1QA.06 2 0.1267 0.9064 0.00 0.94 0.00 0.00 0.00 0.06
#> TCGA.FS.A1YY.06 3 0.3076 0.6469 0.00 0.00 0.76 0.00 0.24 0.00
#> TCGA.EE.A2MK.06 3 0.0937 0.8722 0.00 0.04 0.96 0.00 0.00 0.00
#> TCGA.EE.A2M8.06 1 0.0000 0.9880 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EB.A5KH.06 2 0.1267 0.9064 0.00 0.94 0.00 0.00 0.00 0.06
#> TCGA.FS.A1ZR.06 5 0.0937 0.8445 0.00 0.00 0.00 0.00 0.96 0.04
#> TCGA.EE.A3AE.06 3 0.0937 0.8529 0.00 0.00 0.96 0.04 0.00 0.00
#> TCGA.EE.A29P.06 4 0.1480 0.8973 0.00 0.00 0.04 0.94 0.00 0.02
#> TCGA.EB.A553.01 5 0.2190 0.8111 0.00 0.00 0.00 0.06 0.90 0.04
#> TCGA.EE.A2MR.06 1 0.0000 0.9880 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.GN.A26A.06 4 0.0937 0.8958 0.00 0.00 0.04 0.96 0.00 0.00
#> TCGA.FS.A1ZY.06 2 0.0937 0.9068 0.00 0.96 0.00 0.00 0.00 0.04
#> TCGA.EE.A20I.06 3 0.3309 0.6212 0.00 0.00 0.72 0.28 0.00 0.00
#> TCGA.DA.A1I5.06 1 0.0000 0.9880 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EE.A184.06 6 0.3578 0.5069 0.00 0.34 0.00 0.00 0.00 0.66
#> TCGA.EB.A85J.01 4 0.2728 0.8504 0.00 0.00 0.00 0.86 0.10 0.04
#> TCGA.RP.A6K9.06 4 0.2728 0.8504 0.00 0.00 0.00 0.86 0.10 0.04
#> TCGA.EE.A17Y.06 4 0.0937 0.8958 0.00 0.00 0.04 0.96 0.00 0.00
#> TCGA.D9.A149.06 4 0.0937 0.8927 0.00 0.00 0.00 0.96 0.00 0.04
#> TCGA.ER.A19D.06 1 0.3198 0.6255 0.74 0.00 0.00 0.26 0.00 0.00
#> TCGA.FS.A1ZZ.06 2 0.1267 0.9064 0.00 0.94 0.00 0.00 0.00 0.06
#> TCGA.EE.A2GP.06 5 0.3198 0.6294 0.00 0.00 0.26 0.00 0.74 0.00
#> TCGA.EE.A3AD.06 2 0.1267 0.9064 0.00 0.94 0.00 0.00 0.00 0.06
#> TCGA.D3.A1Q9.06 3 0.3198 0.6540 0.00 0.00 0.74 0.26 0.00 0.00
#> TCGA.GF.A2C7.01 6 0.1814 0.8593 0.00 0.00 0.00 0.00 0.10 0.90
#> TCGA.BF.A5ES.01 5 0.0547 0.8463 0.00 0.00 0.00 0.00 0.98 0.02
#> TCGA.ER.A199.06 1 0.0000 0.9880 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EE.A3AH.06 2 0.1267 0.9064 0.00 0.94 0.00 0.00 0.00 0.06
#> TCGA.W3.A828.06 1 0.0000 0.9880 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EE.A2A5.06 5 0.2260 0.7910 0.00 0.00 0.00 0.00 0.86 0.14
#> TCGA.ER.A19L.06 4 0.2956 0.8355 0.00 0.00 0.00 0.84 0.12 0.04
#> TCGA.BF.A1PX.01 1 0.0000 0.9880 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.ER.A19T.06 5 0.4651 -0.0689 0.00 0.00 0.00 0.48 0.48 0.04
#> TCGA.EB.A51B.01 3 0.4482 0.4223 0.00 0.04 0.60 0.00 0.36 0.00
#> TCGA.FS.A1ZQ.06 3 0.0000 0.8665 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.D3.A2JG.06 2 0.3864 0.0364 0.00 0.52 0.48 0.00 0.00 0.00
#> TCGA.EE.A2GH.06 1 0.0000 0.9880 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.ER.A19F.06 3 0.0937 0.8722 0.00 0.04 0.96 0.00 0.00 0.00
#> TCGA.ER.A196.01 1 0.0000 0.9880 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D3.A2JC.06 4 0.0937 0.8927 0.00 0.00 0.00 0.96 0.00 0.04
#> TCGA.EE.A3AG.06 3 0.1267 0.8659 0.00 0.06 0.94 0.00 0.00 0.00
#> TCGA.ER.A19S.06 1 0.0000 0.9880 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EE.A2GC.06 5 0.1092 0.8471 0.00 0.00 0.02 0.00 0.96 0.02
#> TCGA.EE.A29N.06 1 0.0000 0.9880 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FR.A7U8.06 6 0.0937 0.9145 0.00 0.04 0.00 0.00 0.00 0.96
#> TCGA.BF.A5EO.01 4 0.0937 0.8958 0.00 0.00 0.04 0.96 0.00 0.00
#> TCGA.ER.A19B.06 3 0.0937 0.8722 0.00 0.04 0.96 0.00 0.00 0.00
#> TCGA.D3.A5GN.06 3 0.0000 0.8665 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.D3.A2JB.06 1 0.0000 0.9880 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.ER.A19J.06 2 0.1267 0.9064 0.00 0.94 0.00 0.00 0.00 0.06
#> TCGA.D3.A2JD.06 4 0.1814 0.8426 0.10 0.00 0.00 0.90 0.00 0.00
#> TCGA.FS.A1Z4.06 1 0.0000 0.9880 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FR.A7UA.06 1 0.0000 0.9880 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EE.A2M7.06 4 0.0937 0.8958 0.00 0.00 0.04 0.96 0.00 0.00
#> TCGA.D3.A1Q3.06 4 0.2728 0.8504 0.00 0.00 0.00 0.86 0.10 0.04
#> TCGA.EB.A85I.01 4 0.0937 0.8927 0.00 0.00 0.00 0.96 0.00 0.04
#> TCGA.EB.A82C.01 6 0.3756 0.3553 0.00 0.40 0.00 0.00 0.00 0.60
#> TCGA.ER.A19E.06 5 0.0000 0.8513 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.FS.A1ZK.06 5 0.2260 0.7910 0.00 0.00 0.00 0.00 0.86 0.14
#> TCGA.FS.A1ZU.06 5 0.0000 0.8513 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.EB.A5FP.01 2 0.1267 0.9064 0.00 0.94 0.00 0.00 0.00 0.06
#> TCGA.EB.A4XL.01 3 0.0937 0.8722 0.00 0.04 0.96 0.00 0.00 0.00
#> TCGA.DA.A1I2.06 5 0.2784 0.8129 0.00 0.00 0.04 0.04 0.88 0.04
#> TCGA.EE.A29L.06 2 0.1267 0.9064 0.00 0.94 0.00 0.00 0.00 0.06
#> TCGA.FS.A1ZN.01 2 0.1267 0.9064 0.00 0.94 0.00 0.00 0.00 0.06
#> TCGA.EB.A24D.01 5 0.0000 0.8513 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.EE.A2GB.06 3 0.1267 0.8659 0.00 0.06 0.94 0.00 0.00 0.00
#> TCGA.DA.A1I7.06 4 0.3103 0.8814 0.00 0.00 0.04 0.86 0.06 0.04
#> TCGA.ER.A2NF.01 1 0.0000 0.9880 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.GN.A263.01 1 0.0000 0.9880 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EE.A20C.06 2 0.1267 0.9064 0.00 0.94 0.00 0.00 0.00 0.06
#> TCGA.EE.A2MQ.06 5 0.3834 0.6985 0.00 0.02 0.02 0.00 0.76 0.20
#> TCGA.ER.A19N.06 1 0.0000 0.9880 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FS.A1Z3.06 2 0.0937 0.8844 0.00 0.96 0.04 0.00 0.00 0.00
#> TCGA.DA.A1I8.06 3 0.0937 0.8722 0.00 0.04 0.96 0.00 0.00 0.00
#> TCGA.D3.A5GS.06 3 0.0937 0.8722 0.00 0.04 0.96 0.00 0.00 0.00
#> TCGA.EE.A181.06 4 0.1267 0.8861 0.00 0.00 0.06 0.94 0.00 0.00
#> TCGA.GN.A268.06 6 0.1267 0.8992 0.00 0.06 0.00 0.00 0.00 0.94
#> TCGA.W3.A824.06 5 0.0000 0.8513 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.EE.A2GS.06 3 0.1267 0.8659 0.00 0.06 0.94 0.00 0.00 0.00
#> TCGA.FR.A7U9.06 1 0.0000 0.9880 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.ER.A19Q.06 1 0.0000 0.9880 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FS.A1ZM.06 5 0.4983 0.5894 0.00 0.00 0.06 0.22 0.68 0.04
#> TCGA.EE.A2MG.06 1 0.0000 0.9880 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EE.A2MC.06 1 0.0000 0.9880 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EE.A17Z.06 5 0.0000 0.8513 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.D3.A2JP.06 4 0.0937 0.8958 0.00 0.00 0.04 0.96 0.00 0.00
#> TCGA.ER.A19C.06 5 0.3697 0.7703 0.00 0.00 0.08 0.06 0.82 0.04
#> TCGA.EB.A82B.01 4 0.2474 0.8627 0.00 0.00 0.00 0.88 0.08 0.04
#> TCGA.EE.A2A0.06 4 0.3409 0.6292 0.30 0.00 0.00 0.70 0.00 0.00
#> TCGA.EE.A29G.06 1 0.0000 0.9880 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D3.A5GO.06 3 0.0937 0.8722 0.00 0.04 0.96 0.00 0.00 0.00
#> TCGA.GN.A269.01 1 0.0000 0.9880 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EE.A2A1.06 1 0.0000 0.9880 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.ER.A1A1.06 1 0.0000 0.9880 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FS.A1ZG.06 6 0.0937 0.9145 0.00 0.04 0.00 0.00 0.00 0.96
#> TCGA.FS.A1ZE.06 6 0.0937 0.9145 0.00 0.04 0.00 0.00 0.00 0.96
#> TCGA.FS.A1ZH.06 4 0.0937 0.8958 0.00 0.00 0.04 0.96 0.00 0.00
#> TCGA.EE.A2MH.06 1 0.3756 0.2670 0.60 0.00 0.00 0.40 0.00 0.00
#> TCGA.D3.A2J6.06 4 0.1480 0.8876 0.00 0.00 0.00 0.94 0.02 0.04
#> TCGA.EE.A29Q.06 2 0.0937 0.8844 0.00 0.96 0.04 0.00 0.00 0.00
#> TCGA.BF.A1PZ.01 3 0.4246 0.3238 0.00 0.02 0.58 0.00 0.40 0.00
#> TCGA.D3.A3BZ.06 1 0.0000 0.9880 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D3.A2JO.06 4 0.0937 0.8881 0.04 0.00 0.00 0.96 0.00 0.00
#> TCGA.GN.A267.06 4 0.3679 0.7486 0.00 0.00 0.00 0.76 0.20 0.04
#> TCGA.EE.A2MN.06 5 0.2260 0.7910 0.00 0.00 0.00 0.00 0.86 0.14
#> TCGA.GN.A264.06 6 0.2048 0.8514 0.00 0.12 0.00 0.00 0.00 0.88
#> TCGA.ER.A197.06 1 0.3647 0.3862 0.64 0.00 0.00 0.36 0.00 0.00
#> TCGA.DA.A1IB.06 1 0.0000 0.9880 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D3.A3CC.06 4 0.1865 0.8812 0.00 0.00 0.00 0.92 0.04 0.04
#> TCGA.ER.A19T.01 5 0.0000 0.8513 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.GN.A261.06 1 0.0000 0.9880 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FS.A1YW.06 2 0.3706 0.3826 0.00 0.62 0.00 0.00 0.00 0.38
#> TCGA.BF.A1PU.01 4 0.1865 0.8812 0.00 0.00 0.00 0.92 0.04 0.04
#> TCGA.D3.A1QB.06 1 0.0000 0.9880 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D3.A1Q6.06 4 0.0937 0.8958 0.00 0.00 0.04 0.96 0.00 0.00
#> TCGA.D3.A3C8.06 1 0.0000 0.9880 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.ER.A19A.06 1 0.0000 0.9880 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EE.A2GN.06 5 0.2260 0.7910 0.00 0.00 0.00 0.00 0.86 0.14
#> TCGA.EE.A29M.06 1 0.0000 0.9880 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D3.A2J7.06 1 0.0000 0.9880 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EB.A24C.01 5 0.2956 0.7685 0.00 0.00 0.00 0.12 0.84 0.04
#> TCGA.GN.A262.06 2 0.1267 0.9064 0.00 0.94 0.00 0.00 0.00 0.06
#> TCGA.EE.A2GD.06 4 0.3309 0.6569 0.28 0.00 0.00 0.72 0.00 0.00
#> TCGA.D3.A2J9.06 1 0.0000 0.9880 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EE.A29B.06 5 0.2048 0.8055 0.00 0.00 0.00 0.00 0.88 0.12
#> TCGA.D9.A1JX.06 2 0.2048 0.8210 0.00 0.88 0.12 0.00 0.00 0.00
#> TCGA.EE.A29A.06 6 0.0937 0.9145 0.00 0.04 0.00 0.00 0.00 0.96
#> TCGA.D3.A2JL.06 4 0.0937 0.8958 0.00 0.00 0.04 0.96 0.00 0.00
#> TCGA.D3.A1Q4.06 1 0.0000 0.9880 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FS.A1ZS.06 5 0.4541 0.6776 0.00 0.00 0.06 0.16 0.74 0.04
#> TCGA.D3.A3C3.06 4 0.0937 0.8958 0.00 0.00 0.04 0.96 0.00 0.00
#> TCGA.D3.A2J8.06 1 0.0000 0.9880 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FS.A1ZF.06 2 0.0937 0.8844 0.00 0.96 0.04 0.00 0.00 0.00
#> TCGA.FS.A1ZC.06 2 0.0547 0.9043 0.00 0.98 0.00 0.00 0.00 0.02
#> TCGA.EE.A20H.06 5 0.1480 0.8421 0.00 0.00 0.02 0.00 0.94 0.04
#> TCGA.EE.A29W.06 3 0.0937 0.8722 0.00 0.04 0.96 0.00 0.00 0.00
#> TCGA.D3.A1QA.07 3 0.3309 0.6292 0.00 0.00 0.72 0.28 0.00 0.00
#> TCGA.BF.A1PV.01 5 0.2260 0.7910 0.00 0.00 0.00 0.00 0.86 0.14
#> TCGA.EE.A29S.06 3 0.4646 0.0443 0.00 0.00 0.50 0.04 0.46 0.00
#> TCGA.DA.A1HV.06 3 0.0937 0.8722 0.00 0.04 0.96 0.00 0.00 0.00
#> TCGA.FS.A1Z0.06 4 0.2631 0.7797 0.18 0.00 0.00 0.82 0.00 0.00
#> TCGA.EE.A2GO.06 2 0.0000 0.8997 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.EB.A1NK.01 1 0.0000 0.9880 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.GN.A26D.06 4 0.2956 0.8355 0.00 0.00 0.00 0.84 0.12 0.04
#> TCGA.EE.A2MJ.06 1 0.0000 0.9880 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.ER.A198.06 5 0.1556 0.8284 0.00 0.00 0.00 0.00 0.92 0.08
#> TCGA.EE.A17X.06 2 0.0937 0.8844 0.00 0.96 0.04 0.00 0.00 0.00
#> TCGA.EE.A2M5.06 4 0.0937 0.8958 0.00 0.00 0.04 0.96 0.00 0.00
#> TCGA.GN.A266.06 4 0.1267 0.8802 0.06 0.00 0.00 0.94 0.00 0.00
#> TCGA.D3.A3C1.06 4 0.0937 0.8958 0.00 0.00 0.04 0.96 0.00 0.00
#> TCGA.D3.A2JH.06 1 0.0000 0.9880 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EE.A20F.06 4 0.1267 0.8861 0.00 0.00 0.06 0.94 0.00 0.00
#> TCGA.EE.A29E.06 1 0.0000 0.9880 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.ER.A2NG.06 1 0.0000 0.9880 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.ER.A193.06 4 0.2474 0.8627 0.00 0.00 0.00 0.88 0.08 0.04
#> TCGA.FS.A1ZW.06 4 0.0937 0.8958 0.00 0.00 0.04 0.96 0.00 0.00
#> TCGA.ER.A19O.06 4 0.0937 0.8881 0.04 0.00 0.00 0.96 0.00 0.00
#> TCGA.EE.A2ME.06 1 0.0000 0.9880 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EE.A20B.06 3 0.3499 0.5447 0.00 0.00 0.68 0.32 0.00 0.00
#> TCGA.EE.A3AF.06 3 0.3163 0.7789 0.00 0.04 0.82 0.00 0.14 0.00
#> TCGA.GN.A265.06 1 0.0000 0.9880 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FS.A1YX.06 5 0.3942 0.7549 0.00 0.00 0.10 0.06 0.80 0.04
#> TCGA.FS.A1ZJ.06 5 0.0000 0.8513 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.ER.A19H.06 3 0.0937 0.8529 0.00 0.00 0.96 0.04 0.00 0.00
#> TCGA.EE.A3AC.06 5 0.0937 0.8445 0.00 0.00 0.00 0.00 0.96 0.04
#> TCGA.EE.A2MU.06 1 0.0000 0.9880 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.ER.A194.01 4 0.0937 0.8958 0.00 0.00 0.04 0.96 0.00 0.00
#> TCGA.EE.A2MS.06 4 0.2728 0.8504 0.00 0.00 0.00 0.86 0.10 0.04
#> TCGA.EE.A29R.06 6 0.3499 0.5457 0.00 0.32 0.00 0.00 0.00 0.68
#> TCGA.D9.A1X3.06 6 0.0937 0.9145 0.00 0.04 0.00 0.00 0.00 0.96
#> TCGA.EE.A29X.06 5 0.2474 0.8109 0.00 0.00 0.08 0.00 0.88 0.04
#> TCGA.EE.A2GK.06 1 0.0000 0.9880 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EE.A3AA.06 1 0.0000 0.9880 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.ER.A2NE.06 2 0.1267 0.9064 0.00 0.94 0.00 0.00 0.00 0.06
#> TCGA.EE.A2GR.06 5 0.0937 0.8446 0.00 0.00 0.04 0.00 0.96 0.00
#> TCGA.FS.A1ZD.06 5 0.0547 0.8463 0.00 0.00 0.00 0.00 0.98 0.02
#> TCGA.ER.A19P.06 1 0.0000 0.9880 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D3.A1Q8.06 4 0.1556 0.8604 0.08 0.00 0.00 0.92 0.00 0.00
#> TCGA.ER.A2NC.06 5 0.4922 0.5260 0.00 0.00 0.04 0.26 0.66 0.04
#> TCGA.BF.A1Q0.01 5 0.4482 0.3748 0.00 0.00 0.00 0.36 0.60 0.04
#> TCGA.FS.A1ZP.06 5 0.2048 0.8055 0.00 0.00 0.00 0.00 0.88 0.12
#> TCGA.EE.A182.06 5 0.3523 0.7085 0.00 0.00 0.00 0.18 0.78 0.04
#> TCGA.D9.A1JW.06 4 0.0937 0.8927 0.00 0.00 0.00 0.96 0.00 0.04
#> TCGA.D3.A1Q7.06 1 0.0000 0.9880 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EE.A185.06 2 0.1267 0.9064 0.00 0.94 0.00 0.00 0.00 0.06
#> TCGA.EE.A2GJ.06 5 0.3821 0.6615 0.00 0.00 0.00 0.22 0.74 0.04
#> TCGA.D3.A3CB.06 1 0.0000 0.9880 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EE.A2GU.06 4 0.2728 0.8506 0.00 0.00 0.00 0.86 0.10 0.04
#> TCGA.ER.A195.06 1 0.0000 0.9880 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FS.A1Z7.06 4 0.3163 0.8180 0.00 0.00 0.00 0.82 0.14 0.04
#> TCGA.EE.A2M6.06 2 0.0937 0.9068 0.00 0.96 0.00 0.00 0.00 0.04
#> TCGA.ER.A19K.01 4 0.0937 0.8927 0.00 0.00 0.00 0.96 0.00 0.04
#> TCGA.DA.A1HY.06 3 0.0547 0.8704 0.00 0.02 0.98 0.00 0.00 0.00
#> TCGA.D3.A3C7.06 3 0.3309 0.5995 0.00 0.00 0.72 0.00 0.28 0.00
#> TCGA.EE.A2MP.06 3 0.0000 0.8665 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.EE.A29H.06 2 0.3499 0.5037 0.00 0.68 0.32 0.00 0.00 0.00
#> TCGA.FR.A3YO.06 4 0.0547 0.8954 0.00 0.00 0.00 0.98 0.00 0.02
#> TCGA.XV.AB01.01 2 0.0937 0.8844 0.00 0.96 0.04 0.00 0.00 0.00
#> TCGA.RP.A694.06 5 0.3420 0.7811 0.00 0.00 0.06 0.06 0.84 0.04
#> TCGA.EB.A5SF.01 1 0.0000 0.9880 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.ER.A19G.06 3 0.1267 0.8659 0.00 0.06 0.94 0.00 0.00 0.00
#> TCGA.EE.A2GE.06 1 0.0000 0.9880 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.GF.A3OT.06 1 0.0000 0.9880 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.ER.A2NF.06 1 0.0000 0.9880 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.RP.A695.06 5 0.2260 0.7910 0.00 0.00 0.00 0.00 0.86 0.14
#> TCGA.BF.AAP7.01 1 0.0000 0.9880 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EB.A3Y7.01 4 0.0937 0.8927 0.00 0.00 0.00 0.96 0.00 0.04
#> TCGA.EB.A3XC.01 3 0.0937 0.8722 0.00 0.04 0.96 0.00 0.00 0.00
#> TCGA.ER.A19W.06 1 0.0000 0.9880 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FR.A69P.06 3 0.0937 0.8529 0.00 0.00 0.96 0.04 0.00 0.00
#> TCGA.RP.A693.06 4 0.3163 0.8013 0.14 0.00 0.00 0.82 0.00 0.04
#> TCGA.FW.A3TV.06 1 0.0000 0.9880 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FW.A3R5.11 1 0.0000 0.9880 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FW.A3TU.06 5 0.0937 0.8389 0.00 0.00 0.00 0.00 0.96 0.04
#> TCGA.BF.AAP8.01 4 0.2474 0.8627 0.00 0.00 0.00 0.88 0.08 0.04
#> TCGA.EE.A2MM.06 5 0.0000 0.8513 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.DA.A1HW.06 4 0.0937 0.8958 0.00 0.00 0.04 0.96 0.00 0.00
#> TCGA.DA.A1IC.06 5 0.2094 0.8194 0.00 0.00 0.08 0.00 0.90 0.02
#> TCGA.XV.AAZV.01 1 0.0000 0.9880 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D3.A3C6.06 3 0.1267 0.8659 0.00 0.06 0.94 0.00 0.00 0.00
#> TCGA.EE.A29C.06 1 0.0547 0.9656 0.98 0.00 0.00 0.02 0.00 0.00
#> TCGA.BF.AAP2.01 2 0.0000 0.8997 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.EE.A2A2.06 3 0.1267 0.8659 0.00 0.06 0.94 0.00 0.00 0.00
#> TCGA.GF.A6C8.06 4 0.1092 0.8977 0.00 0.00 0.02 0.96 0.00 0.02
#> TCGA.RP.A690.06 1 0.0000 0.9880 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FW.A5DY.06 1 0.0000 0.9880 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DA.A1I4.06 1 0.0000 0.9880 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EE.A29V.06 4 0.0937 0.8958 0.00 0.00 0.04 0.96 0.00 0.00
#> TCGA.GF.A6C9.06 1 0.0000 0.9880 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EE.A2GT.06 1 0.0000 0.9880 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.GN.A9SD.06 1 0.0000 0.9880 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EE.A3AB.06 4 0.0937 0.8958 0.00 0.00 0.04 0.96 0.00 0.00
#> TCGA.BF.AAP6.01 3 0.0937 0.8722 0.00 0.04 0.96 0.00 0.00 0.00
#> TCGA.EB.A5SH.06 4 0.4067 0.6555 0.00 0.00 0.00 0.70 0.26 0.04
#> TCGA.D9.A6E9.06 4 0.0937 0.8927 0.00 0.00 0.00 0.96 0.00 0.04
#> TCGA.BF.AAP4.01 4 0.0000 0.8961 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.EE.A2GM.06 2 0.1267 0.9064 0.00 0.94 0.00 0.00 0.00 0.06
#> TCGA.D3.A3CF.06 1 0.0000 0.9880 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D9.A6EC.06 2 0.1267 0.9064 0.00 0.94 0.00 0.00 0.00 0.06
#> TCGA.DA.A1I1.06 4 0.2260 0.8223 0.00 0.00 0.14 0.86 0.00 0.00
#> TCGA.HR.A2OH.06 1 0.0000 0.9880 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EE.A2MT.06 4 0.2190 0.8728 0.00 0.00 0.00 0.90 0.06 0.04
#> TCGA.ER.A19M.06 4 0.0937 0.8958 0.00 0.00 0.04 0.96 0.00 0.00
#> TCGA.GN.A26C.01 1 0.0000 0.9880 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FS.A1ZA.06 3 0.4926 0.5483 0.00 0.00 0.64 0.12 0.24 0.00
#> TCGA.EB.A5SE.01 6 0.0937 0.9145 0.00 0.04 0.00 0.00 0.00 0.96
#> TCGA.ER.A3PL.06 5 0.0000 0.8513 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.FR.A3R1.01 3 0.3821 0.6803 0.00 0.04 0.74 0.00 0.22 0.00
#> TCGA.EE.A2MI.06 4 0.0937 0.8958 0.00 0.00 0.04 0.96 0.00 0.00
#> TCGA.D3.A3CE.06 3 0.0937 0.8529 0.00 0.00 0.96 0.04 0.00 0.00
#> TCGA.D3.A5GT.01 6 0.2631 0.7815 0.00 0.00 0.00 0.00 0.18 0.82
#> TCGA.ER.A2NB.01 4 0.0937 0.8927 0.00 0.00 0.00 0.96 0.00 0.04
#> TCGA.D3.A1Q5.06 4 0.3523 0.7756 0.00 0.00 0.00 0.78 0.18 0.04
#> TCGA.EB.A5UN.06 1 0.0000 0.9880 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EB.A299.01 3 0.1267 0.8417 0.00 0.00 0.94 0.06 0.00 0.00
#> TCGA.DA.A1IA.06 5 0.2941 0.7023 0.00 0.00 0.00 0.00 0.78 0.22
#> TCGA.EB.A5SG.06 1 0.0000 0.9880 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D9.A6EA.06 6 0.0937 0.9145 0.00 0.04 0.00 0.00 0.00 0.96
#> TCGA.XV.AAZY.01 1 0.0000 0.9880 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EB.A57M.01 4 0.3869 -0.0285 0.00 0.00 0.50 0.50 0.00 0.00
#> TCGA.EE.A2A6.06 4 0.0937 0.8927 0.00 0.00 0.00 0.96 0.00 0.04
#> TCGA.D3.A2JA.06 1 0.0000 0.9880 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D3.A1Q1.06 4 0.2956 0.8355 0.00 0.00 0.00 0.84 0.12 0.04
#> TCGA.EB.A3XF.01 3 0.0937 0.8722 0.00 0.04 0.96 0.00 0.00 0.00
#> TCGA.D3.A2JF.06 3 0.0937 0.8529 0.00 0.00 0.96 0.04 0.00 0.00
#> TCGA.XV.AAZW.01 2 0.1267 0.8716 0.00 0.94 0.06 0.00 0.00 0.00
#> TCGA.EB.A3Y6.01 4 0.1267 0.8861 0.00 0.00 0.06 0.94 0.00 0.00
#> TCGA.EB.A3XE.01 4 0.2956 0.8355 0.00 0.00 0.00 0.84 0.12 0.04
#> TCGA.D9.A3Z4.01 5 0.0000 0.8513 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.FW.A3R5.06 4 0.2728 0.8504 0.00 0.00 0.00 0.86 0.10 0.04
#> TCGA.EE.A2GI.06 4 0.1267 0.8861 0.00 0.00 0.06 0.94 0.00 0.00
#> TCGA.EE.A2GL.06 1 0.0000 0.9880 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EB.A3XB.01 4 0.0937 0.8958 0.00 0.00 0.04 0.96 0.00 0.00
#> TCGA.BF.AAOU.01 1 0.0000 0.9880 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EB.A3XD.01 1 0.0000 0.9880 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EE.A2MD.06 4 0.0937 0.8958 0.00 0.00 0.04 0.96 0.00 0.00
#> TCGA.YD.A9TB.06 5 0.0937 0.8445 0.00 0.00 0.00 0.00 0.96 0.04
#> TCGA.W3.AA1V.06 4 0.0937 0.8958 0.00 0.00 0.04 0.96 0.00 0.00
#> TCGA.ER.A2ND.06 5 0.1865 0.8213 0.00 0.00 0.00 0.04 0.92 0.04
#> TCGA.D3.A2JK.06 4 0.1556 0.8745 0.00 0.00 0.08 0.92 0.00 0.00
#> TCGA.FS.A1ZB.06 1 0.0547 0.9663 0.98 0.00 0.00 0.02 0.00 0.00
#> TCGA.EE.A29D.06 6 0.0937 0.9145 0.00 0.04 0.00 0.00 0.00 0.96
#> TCGA.EB.A5UM.01 4 0.4172 0.6191 0.00 0.00 0.00 0.68 0.28 0.04
#> TCGA.QB.A6FS.06 1 0.0000 0.9880 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D9.A3Z1.06 1 0.0000 0.9880 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D3.A2JN.06 1 0.2048 0.8413 0.88 0.00 0.00 0.12 0.00 0.00
#> TCGA.FR.A3YN.06 2 0.2454 0.7758 0.00 0.84 0.16 0.00 0.00 0.00
#> TCGA.FS.A1ZT.06 1 0.0000 0.9880 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D9.A148.06 4 0.0547 0.8970 0.00 0.00 0.02 0.98 0.00 0.00
#> TCGA.HR.A2OG.06 4 0.3198 0.6492 0.26 0.00 0.00 0.74 0.00 0.00
#> TCGA.EE.A2ML.06 3 0.2793 0.7250 0.00 0.00 0.80 0.20 0.00 0.00
#> TCGA.EB.A5UL.06 4 0.0937 0.8881 0.04 0.00 0.00 0.96 0.00 0.00
#> TCGA.EE.A29T.06 4 0.2728 0.8396 0.10 0.00 0.00 0.86 0.00 0.04
#> TCGA.D9.A3Z3.06 1 0.0000 0.9880 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D9.A4Z3.01 5 0.2260 0.7748 0.00 0.00 0.14 0.00 0.86 0.00
#> TCGA.ER.A3ES.06 5 0.3163 0.7509 0.00 0.00 0.00 0.14 0.82 0.04
#> TCGA.XV.A9VZ.01 1 0.0000 0.9880 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.QB.AA9O.06 3 0.0937 0.8529 0.00 0.00 0.96 0.04 0.00 0.00
#> TCGA.EB.A44Q.06 4 0.3163 0.8180 0.00 0.00 0.00 0.82 0.14 0.04
#> TCGA.EB.A44R.06 4 0.2728 0.8504 0.00 0.00 0.00 0.86 0.10 0.04
#> TCGA.BF.A3DJ.01 3 0.0937 0.8722 0.00 0.04 0.96 0.00 0.00 0.00
#> TCGA.EE.A3JD.06 1 0.0000 0.9880 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D3.A51N.06 4 0.0937 0.8958 0.00 0.00 0.04 0.96 0.00 0.00
#> TCGA.EB.A44N.01 1 0.0000 0.9880 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EE.A3J3.06 5 0.3711 0.5929 0.00 0.02 0.26 0.00 0.72 0.00
#> TCGA.XV.A9W5.01 3 0.1267 0.8417 0.00 0.00 0.94 0.06 0.00 0.00
#> TCGA.D3.A51G.06 3 0.0937 0.8529 0.00 0.00 0.96 0.04 0.00 0.00
#> TCGA.EB.A4P0.01 2 0.0937 0.8844 0.00 0.96 0.04 0.00 0.00 0.00
#> TCGA.BF.AAP1.01 6 0.0937 0.9145 0.00 0.04 0.00 0.00 0.00 0.96
#> TCGA.EE.A3J4.06 6 0.2260 0.8250 0.00 0.00 0.00 0.00 0.14 0.86
#> TCGA.Z2.AA3V.06 1 0.0000 0.9880 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.LH.A9QB.06 6 0.0937 0.9145 0.00 0.04 0.00 0.00 0.00 0.96
#> TCGA.D3.A51J.06 4 0.0937 0.8958 0.00 0.00 0.04 0.96 0.00 0.00
#> TCGA.3N.A9WC.06 4 0.0937 0.8927 0.00 0.00 0.00 0.96 0.00 0.04
#> TCGA.DA.A3F8.06 1 0.0000 0.9880 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D9.A4Z6.06 3 0.3829 0.6991 0.00 0.00 0.76 0.18 0.06 0.00
#> TCGA.D3.A51R.06 2 0.0937 0.8844 0.00 0.96 0.04 0.00 0.00 0.00
#> TCGA.EB.A4OZ.01 1 0.0000 0.9880 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FS.A4FB.06 3 0.1267 0.8659 0.00 0.06 0.94 0.00 0.00 0.00
#> TCGA.EE.A3JE.06 1 0.0000 0.9880 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.W3.AA1W.06 1 0.0000 0.9880 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DA.A1I0.06 4 0.0937 0.8881 0.04 0.00 0.00 0.96 0.00 0.00
#> TCGA.D3.A51F.06 1 0.0000 0.9880 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.IH.A3EA.01 5 0.0937 0.8447 0.00 0.00 0.04 0.00 0.96 0.00
#> TCGA.EB.A431.01 4 0.0937 0.8958 0.00 0.00 0.04 0.96 0.00 0.00
#> TCGA.EB.A97M.01 6 0.0937 0.9145 0.00 0.04 0.00 0.00 0.00 0.96
#> TCGA.BF.AAOX.01 4 0.2454 0.7967 0.00 0.00 0.16 0.84 0.00 0.00
#> TCGA.DA.A3F5.06 4 0.0937 0.8927 0.00 0.00 0.00 0.96 0.00 0.04
#> TCGA.YD.A9TA.06 4 0.0937 0.8958 0.00 0.00 0.04 0.96 0.00 0.00
#> TCGA.DA.A3F2.06 1 0.0000 0.9880 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EB.A44O.01 5 0.0000 0.8513 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.EB.A4IQ.01 4 0.2474 0.8627 0.00 0.00 0.00 0.88 0.08 0.04
#> TCGA.EB.A4IS.01 1 0.0000 0.9880 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.YG.AA3O.06 5 0.2260 0.7910 0.00 0.00 0.00 0.00 0.86 0.14
#> TCGA.ER.A3EV.06 4 0.2728 0.8504 0.00 0.00 0.00 0.86 0.10 0.04
#> TCGA.3N.A9WD.06 4 0.3647 0.5070 0.36 0.00 0.00 0.64 0.00 0.00
#> TCGA.BF.A3DM.01 3 0.1267 0.8659 0.00 0.06 0.94 0.00 0.00 0.00
#> TCGA.XV.A9W2.01 4 0.0937 0.8927 0.00 0.00 0.00 0.96 0.00 0.04
#> TCGA.W3.AA1Q.06 5 0.2190 0.8246 0.00 0.00 0.06 0.00 0.90 0.04
#> TCGA.WE.AAA0.06 4 0.0937 0.8958 0.00 0.00 0.04 0.96 0.00 0.00
#> TCGA.W3.AA1R.06 2 0.3797 0.2466 0.00 0.58 0.42 0.00 0.00 0.00
#> TCGA.EE.A3J5.06 4 0.0937 0.8958 0.00 0.00 0.04 0.96 0.00 0.00
#> TCGA.EB.A4OY.01 1 0.0000 0.9880 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FS.A4FD.06 4 0.2728 0.8504 0.00 0.00 0.00 0.86 0.10 0.04
#> TCGA.BF.AAP0.06 1 0.0000 0.9880 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.YG.AA3P.06 5 0.0000 0.8513 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.EE.A3JA.06 3 0.0937 0.8722 0.00 0.04 0.96 0.00 0.00 0.00
#> TCGA.W3.AA21.06 2 0.0937 0.9068 0.00 0.96 0.00 0.00 0.00 0.04
#> TCGA.WE.AAA3.06 4 0.3163 0.8180 0.00 0.00 0.00 0.82 0.14 0.04
#> TCGA.FS.A4F4.06 3 0.0000 0.8665 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.BF.A3DN.01 5 0.4632 0.0777 0.00 0.04 0.44 0.00 0.52 0.00
#> TCGA.ER.A3ET.06 5 0.3163 0.7505 0.00 0.00 0.00 0.14 0.82 0.04
#> TCGA.W3.AA1O.06 5 0.1814 0.8179 0.00 0.00 0.00 0.00 0.90 0.10
#> TCGA.D3.A51E.06 3 0.1267 0.8417 0.00 0.00 0.94 0.06 0.00 0.00
#> TCGA.Z2.AA3S.06 6 0.0937 0.9145 0.00 0.04 0.00 0.00 0.00 0.96
#> TCGA.YG.AA3N.01 5 0.3103 0.7954 0.00 0.00 0.06 0.04 0.86 0.04
#> TCGA.WE.AA9Y.06 1 0.0000 0.9880 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FS.A4F5.06 6 0.1814 0.8618 0.00 0.10 0.00 0.00 0.00 0.90
#> TCGA.EE.A3J7.06 6 0.2260 0.8257 0.00 0.00 0.00 0.00 0.14 0.86
#> TCGA.FS.A4F8.06 1 0.0000 0.9880 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DA.A3F3.06 3 0.2941 0.7051 0.00 0.22 0.78 0.00 0.00 0.00
#> TCGA.D3.A51H.06 1 0.0000 0.9880 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BF.A3DL.01 4 0.2631 0.7775 0.18 0.00 0.00 0.82 0.00 0.00
#> TCGA.D3.A51T.06 2 0.0937 0.8844 0.00 0.96 0.04 0.00 0.00 0.00
#> TCGA.D3.A51K.06 5 0.2794 0.8033 0.00 0.00 0.08 0.00 0.86 0.06
#> TCGA.EB.A44P.01 5 0.1865 0.8350 0.00 0.00 0.04 0.00 0.92 0.04
#> TCGA.D9.A4Z5.01 2 0.1814 0.8749 0.00 0.90 0.00 0.00 0.00 0.10
#> TCGA.WE.AAA4.06 1 0.0000 0.9880 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.3N.A9WB.06 6 0.0937 0.9145 0.00 0.04 0.00 0.00 0.00 0.96
#> TCGA.EE.A3J8.06 2 0.1267 0.9064 0.00 0.94 0.00 0.00 0.00 0.06
cbind(get_classes(res, k = 7), get_membership(res, k = 7))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7
#> TCGA.FR.A728.01 1 0.4146 0.58879 0.68 0.00 0.00 0.08 0.00 0.00 0.24
#> TCGA.GN.A4U8.11 1 0.0000 0.97664 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.GN.A8LL.06 3 0.0000 0.89312 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.FR.A8YC.06 6 0.0000 0.95160 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.DA.A95X.06 2 0.0000 0.94682 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.ER.A42K.06 3 0.0000 0.89312 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.D3.A8GO.06 1 0.0000 0.97664 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D3.A8GK.06 5 0.0504 0.87724 0.00 0.00 0.00 0.00 0.98 0.00 0.02
#> TCGA.WE.A8JZ.06 2 0.0000 0.94682 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.WE.A8ZO.06 5 0.0000 0.88536 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.D3.A8GI.06 5 0.3186 0.65139 0.00 0.00 0.00 0.00 0.76 0.22 0.02
#> TCGA.FS.A4FC.06 7 0.0504 0.90303 0.00 0.00 0.00 0.02 0.00 0.00 0.98
#> TCGA.FS.A4F2.06 3 0.0000 0.89312 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.WE.A8ZM.06 5 0.0000 0.88536 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.WE.A8ZT.06 3 0.0504 0.88734 0.00 0.02 0.98 0.00 0.00 0.00 0.00
#> TCGA.D3.A8GQ.06 4 0.0504 0.88943 0.00 0.00 0.00 0.98 0.00 0.00 0.02
#> TCGA.D3.A8GB.06 1 0.0000 0.97664 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DA.A95Y.06 2 0.0000 0.94682 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EE.A3JI.06 6 0.0000 0.95160 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.OD.A75X.06 2 0.0504 0.94846 0.00 0.98 0.00 0.00 0.00 0.02 0.00
#> TCGA.DA.A960.01 2 0.0504 0.94846 0.00 0.98 0.00 0.00 0.00 0.02 0.00
#> TCGA.D3.A8GV.06 2 0.0000 0.94682 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.WE.A8ZN.06 1 0.3525 0.21499 0.56 0.00 0.00 0.44 0.00 0.00 0.00
#> TCGA.D3.A8GN.06 1 0.1166 0.93289 0.94 0.00 0.00 0.06 0.00 0.00 0.00
#> TCGA.EB.A550.01 1 0.0504 0.96403 0.98 0.00 0.00 0.02 0.00 0.00 0.00
#> TCGA.BF.A5EQ.01 7 0.0504 0.90303 0.00 0.00 0.00 0.02 0.00 0.00 0.98
#> TCGA.EB.A3HV.01 5 0.0000 0.88536 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.HR.A5NC.01 7 0.3294 0.45728 0.00 0.00 0.00 0.00 0.34 0.00 0.66
#> TCGA.DA.A95Z.06 6 0.0000 0.95160 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.EB.A6QZ.01 2 0.0504 0.94846 0.00 0.98 0.00 0.00 0.00 0.02 0.00
#> TCGA.FW.A3I3.06 2 0.0504 0.94846 0.00 0.98 0.00 0.00 0.00 0.02 0.00
#> TCGA.WE.A8K6.06 3 0.2745 0.75300 0.00 0.02 0.82 0.00 0.16 0.00 0.00
#> TCGA.D3.A8GP.06 6 0.0000 0.95160 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.EB.A42Z.01 6 0.0000 0.95160 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.GN.A4U4.06 5 0.2906 0.73238 0.00 0.18 0.00 0.00 0.80 0.00 0.02
#> TCGA.GF.A4EO.06 1 0.0000 0.97664 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.GN.A8LK.06 6 0.0504 0.93783 0.00 0.00 0.00 0.00 0.02 0.98 0.00
#> TCGA.WE.A8K4.01 4 0.3519 0.64263 0.22 0.00 0.00 0.74 0.00 0.00 0.04
#> TCGA.DA.A95W.06 6 0.0000 0.95160 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.FW.A5DX.01 2 0.0504 0.94846 0.00 0.98 0.00 0.00 0.00 0.02 0.00
#> TCGA.GN.A4U3.06 2 0.0000 0.94682 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EB.A6QY.01 1 0.0863 0.94991 0.96 0.00 0.00 0.04 0.00 0.00 0.00
#> TCGA.EB.A5VU.01 4 0.3670 0.70513 0.00 0.00 0.10 0.76 0.00 0.00 0.14
#> TCGA.Z2.A8RT.06 5 0.4212 0.40850 0.00 0.02 0.34 0.00 0.62 0.00 0.02
#> TCGA.WE.A8K1.06 4 0.3546 0.13883 0.46 0.00 0.00 0.54 0.00 0.00 0.00
#> TCGA.EB.A41B.01 3 0.1363 0.86770 0.00 0.02 0.94 0.00 0.04 0.00 0.00
#> TCGA.WE.A8ZY.06 2 0.0504 0.94846 0.00 0.98 0.00 0.00 0.00 0.02 0.00
#> TCGA.D9.A6EG.06 6 0.0000 0.95160 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.BF.A5ER.01 5 0.0000 0.88536 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.FR.A8YD.06 6 0.0504 0.93783 0.00 0.00 0.00 0.00 0.02 0.98 0.00
#> TCGA.FS.A4F9.06 6 0.0504 0.93783 0.00 0.00 0.00 0.00 0.02 0.98 0.00
#> TCGA.EB.A6R0.01 3 0.0504 0.89159 0.00 0.00 0.98 0.02 0.00 0.00 0.00
#> TCGA.ER.A42L.06 1 0.0000 0.97664 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D3.A8GJ.06 7 0.2081 0.80691 0.00 0.00 0.00 0.14 0.00 0.00 0.86
#> TCGA.FR.A8YE.06 1 0.0000 0.97664 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.WE.A8ZR.06 7 0.0504 0.89291 0.00 0.00 0.00 0.00 0.02 0.00 0.98
#> TCGA.BF.A9VF.01 5 0.0504 0.87967 0.00 0.00 0.00 0.00 0.98 0.00 0.02
#> TCGA.EE.A3JH.06 1 0.0000 0.97664 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DA.A95V.06 4 0.1363 0.87457 0.00 0.00 0.02 0.94 0.00 0.00 0.04
#> TCGA.GF.A769.01 2 0.1664 0.88925 0.00 0.92 0.00 0.00 0.06 0.00 0.02
#> TCGA.D9.A4Z2.01 3 0.0863 0.87575 0.00 0.04 0.96 0.00 0.00 0.00 0.00
#> TCGA.FR.A44A.06 1 0.0000 0.97664 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EB.A5VV.06 1 0.0000 0.97664 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EE.A180.06 6 0.0000 0.95160 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.D3.A8GC.06 6 0.0000 0.95160 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.WE.A8K5.06 6 0.0000 0.95160 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.GN.A8LN.01 2 0.0000 0.94682 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EE.A3JB.06 4 0.0504 0.88943 0.00 0.00 0.00 0.98 0.00 0.00 0.02
#> TCGA.D3.A3MO.06 5 0.1006 0.87120 0.00 0.02 0.00 0.00 0.96 0.00 0.02
#> TCGA.ER.A42H.01 5 0.3294 0.42344 0.00 0.00 0.00 0.00 0.66 0.34 0.00
#> TCGA.WE.A8ZX.06 4 0.2081 0.77102 0.00 0.00 0.14 0.86 0.00 0.00 0.00
#> TCGA.GN.A4U5.01 1 0.0863 0.94991 0.96 0.00 0.00 0.04 0.00 0.00 0.00
#> TCGA.D3.A8GS.06 7 0.3294 0.47043 0.00 0.00 0.00 0.34 0.00 0.00 0.66
#> TCGA.WE.A8ZQ.06 6 0.0504 0.93783 0.00 0.00 0.00 0.00 0.02 0.98 0.00
#> TCGA.EE.A2MF.06 6 0.0000 0.95160 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.D3.A5GU.06 5 0.0000 0.88536 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.GN.A4U8.06 4 0.0504 0.88943 0.00 0.00 0.00 0.98 0.00 0.00 0.02
#> TCGA.EB.A42Y.01 2 0.0000 0.94682 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D3.A3ML.06 6 0.0504 0.93783 0.00 0.00 0.00 0.00 0.02 0.98 0.00
#> TCGA.EB.A551.01 4 0.4429 0.57220 0.12 0.00 0.00 0.66 0.00 0.00 0.22
#> TCGA.D3.A8GM.06 4 0.0504 0.88943 0.00 0.00 0.00 0.98 0.00 0.00 0.02
#> TCGA.D3.A8GL.06 6 0.0000 0.95160 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.D3.A3MU.06 6 0.0000 0.95160 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.FS.A4F0.06 6 0.0000 0.95160 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.D3.A3MV.06 3 0.1006 0.89017 0.00 0.02 0.96 0.02 0.00 0.00 0.00
#> TCGA.GN.A4U7.06 3 0.0000 0.89312 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.FR.A2OS.01 5 0.0000 0.88536 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.D3.A2JE.06 5 0.1006 0.87217 0.00 0.00 0.00 0.00 0.96 0.02 0.02
#> TCGA.YD.A89C.06 4 0.5966 0.13260 0.00 0.00 0.32 0.48 0.14 0.00 0.06
#> TCGA.FR.A726.01 4 0.1006 0.86593 0.00 0.00 0.02 0.96 0.00 0.00 0.02
#> TCGA.BF.A5EP.01 2 0.2376 0.82894 0.00 0.86 0.12 0.00 0.00 0.00 0.02
#> TCGA.D3.A3MR.06 1 0.0000 0.97664 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D3.A8GR.06 5 0.0504 0.87657 0.00 0.00 0.00 0.00 0.98 0.02 0.00
#> TCGA.GN.A4U9.06 5 0.0000 0.88536 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.EB.A6L9.06 1 0.0000 0.97664 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D3.A5GL.06 3 0.4249 0.61515 0.00 0.02 0.70 0.02 0.24 0.00 0.02
#> TCGA.EB.A430.01 1 0.0000 0.97664 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D3.A8GE.06 1 0.0000 0.97664 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D3.A8GD.06 1 0.0000 0.97664 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EB.A41A.01 6 0.0000 0.95160 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.W3.A825.06 4 0.3413 0.39507 0.00 0.00 0.00 0.62 0.00 0.00 0.38
#> TCGA.EE.A183.06 1 0.0000 0.97664 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.ER.A2NH.06 1 0.1166 0.93289 0.94 0.00 0.00 0.06 0.00 0.00 0.00
#> TCGA.D3.A5GR.06 4 0.3519 0.67459 0.04 0.00 0.00 0.74 0.00 0.00 0.22
#> TCGA.FR.A729.06 4 0.0504 0.88943 0.00 0.00 0.00 0.98 0.00 0.00 0.02
#> TCGA.D3.A1QA.06 2 0.0504 0.94846 0.00 0.98 0.00 0.00 0.00 0.02 0.00
#> TCGA.FS.A1YY.06 5 0.4317 0.31590 0.00 0.00 0.38 0.02 0.58 0.00 0.02
#> TCGA.EE.A2MK.06 3 0.0000 0.89312 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.EE.A2M8.06 1 0.0000 0.97664 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EB.A5KH.06 2 0.0504 0.94846 0.00 0.98 0.00 0.00 0.00 0.02 0.00
#> TCGA.FS.A1ZR.06 5 0.0000 0.88536 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.EE.A3AE.06 3 0.2708 0.72261 0.00 0.00 0.78 0.22 0.00 0.00 0.00
#> TCGA.EE.A29P.06 4 0.1671 0.84411 0.00 0.00 0.00 0.90 0.00 0.00 0.10
#> TCGA.EB.A553.01 7 0.0863 0.87593 0.00 0.00 0.00 0.00 0.04 0.00 0.96
#> TCGA.EE.A2MR.06 1 0.0000 0.97664 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.GN.A26A.06 4 0.0504 0.88943 0.00 0.00 0.00 0.98 0.00 0.00 0.02
#> TCGA.FS.A1ZY.06 2 0.0000 0.94682 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EE.A20I.06 4 0.1433 0.83172 0.00 0.00 0.08 0.92 0.00 0.00 0.00
#> TCGA.DA.A1I5.06 1 0.0863 0.94991 0.96 0.00 0.00 0.04 0.00 0.00 0.00
#> TCGA.EE.A184.06 6 0.4718 0.42299 0.00 0.32 0.00 0.00 0.06 0.60 0.02
#> TCGA.EB.A85J.01 7 0.0504 0.90303 0.00 0.00 0.00 0.02 0.00 0.00 0.98
#> TCGA.RP.A6K9.06 7 0.0504 0.90303 0.00 0.00 0.00 0.02 0.00 0.00 0.98
#> TCGA.EE.A17Y.06 4 0.0504 0.88943 0.00 0.00 0.00 0.98 0.00 0.00 0.02
#> TCGA.D9.A149.06 7 0.1166 0.88308 0.00 0.00 0.00 0.06 0.00 0.00 0.94
#> TCGA.ER.A19D.06 1 0.1363 0.93613 0.94 0.00 0.00 0.04 0.00 0.00 0.02
#> TCGA.FS.A1ZZ.06 2 0.0863 0.93527 0.00 0.96 0.00 0.00 0.00 0.04 0.00
#> TCGA.EE.A2GP.06 5 0.2421 0.80986 0.00 0.00 0.08 0.02 0.88 0.00 0.02
#> TCGA.EE.A3AD.06 2 0.0504 0.94846 0.00 0.98 0.00 0.00 0.00 0.02 0.00
#> TCGA.D3.A1Q9.06 4 0.1671 0.81303 0.00 0.00 0.10 0.90 0.00 0.00 0.00
#> TCGA.GF.A2C7.01 6 0.0504 0.93783 0.00 0.00 0.00 0.00 0.02 0.98 0.00
#> TCGA.BF.A5ES.01 5 0.3546 0.12223 0.00 0.00 0.00 0.00 0.54 0.00 0.46
#> TCGA.ER.A199.06 1 0.0000 0.97664 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EE.A3AH.06 2 0.0504 0.94846 0.00 0.98 0.00 0.00 0.00 0.02 0.00
#> TCGA.W3.A828.06 1 0.0000 0.97664 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EE.A2A5.06 5 0.0000 0.88536 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.ER.A19L.06 7 0.0504 0.90303 0.00 0.00 0.00 0.02 0.00 0.00 0.98
#> TCGA.BF.A1PX.01 1 0.0000 0.97664 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.ER.A19T.06 7 0.0504 0.89291 0.00 0.00 0.00 0.00 0.02 0.00 0.98
#> TCGA.EB.A51B.01 3 0.3994 0.03061 0.00 0.00 0.50 0.00 0.48 0.00 0.02
#> TCGA.FS.A1ZQ.06 3 0.0504 0.89159 0.00 0.00 0.98 0.02 0.00 0.00 0.00
#> TCGA.D3.A2JG.06 3 0.5622 0.42289 0.00 0.24 0.52 0.00 0.22 0.00 0.02
#> TCGA.EE.A2GH.06 1 0.0000 0.97664 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.ER.A19F.06 3 0.0000 0.89312 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.ER.A196.01 1 0.0000 0.97664 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D3.A2JC.06 4 0.3294 0.49838 0.00 0.00 0.00 0.66 0.00 0.00 0.34
#> TCGA.EE.A3AG.06 3 0.0504 0.88734 0.00 0.02 0.98 0.00 0.00 0.00 0.00
#> TCGA.ER.A19S.06 1 0.0000 0.97664 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EE.A2GC.06 5 0.0000 0.88536 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.EE.A29N.06 1 0.0863 0.94991 0.96 0.00 0.00 0.04 0.00 0.00 0.00
#> TCGA.FR.A7U8.06 6 0.0000 0.95160 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.BF.A5EO.01 4 0.0504 0.88943 0.00 0.00 0.00 0.98 0.00 0.00 0.02
#> TCGA.ER.A19B.06 3 0.0000 0.89312 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.D3.A5GN.06 3 0.0863 0.88358 0.00 0.00 0.96 0.04 0.00 0.00 0.00
#> TCGA.D3.A2JB.06 1 0.0000 0.97664 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.ER.A19J.06 2 0.0504 0.94846 0.00 0.98 0.00 0.00 0.00 0.02 0.00
#> TCGA.D3.A2JD.06 4 0.2163 0.80950 0.10 0.00 0.00 0.88 0.00 0.00 0.02
#> TCGA.FS.A1Z4.06 1 0.0000 0.97664 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FR.A7UA.06 1 0.0000 0.97664 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EE.A2M7.06 4 0.0504 0.88943 0.00 0.00 0.00 0.98 0.00 0.00 0.02
#> TCGA.D3.A1Q3.06 7 0.0504 0.90303 0.00 0.00 0.00 0.02 0.00 0.00 0.98
#> TCGA.EB.A85I.01 7 0.0863 0.89466 0.00 0.00 0.00 0.04 0.00 0.00 0.96
#> TCGA.EB.A82C.01 6 0.4426 0.30185 0.00 0.38 0.00 0.00 0.06 0.56 0.00
#> TCGA.ER.A19E.06 5 0.0000 0.88536 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.FS.A1ZK.06 5 0.0504 0.87824 0.00 0.00 0.00 0.00 0.98 0.02 0.00
#> TCGA.FS.A1ZU.06 5 0.0504 0.87724 0.00 0.00 0.00 0.00 0.98 0.00 0.02
#> TCGA.EB.A5FP.01 2 0.0504 0.94846 0.00 0.98 0.00 0.00 0.00 0.02 0.00
#> TCGA.EB.A4XL.01 3 0.0000 0.89312 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DA.A1I2.06 5 0.4869 0.27785 0.00 0.00 0.06 0.02 0.54 0.00 0.38
#> TCGA.EE.A29L.06 2 0.0504 0.94846 0.00 0.98 0.00 0.00 0.00 0.02 0.00
#> TCGA.FS.A1ZN.01 2 0.0504 0.94846 0.00 0.98 0.00 0.00 0.00 0.02 0.00
#> TCGA.EB.A24D.01 5 0.1433 0.83395 0.00 0.00 0.00 0.00 0.92 0.00 0.08
#> TCGA.EE.A2GB.06 3 0.0504 0.88734 0.00 0.02 0.98 0.00 0.00 0.00 0.00
#> TCGA.DA.A1I7.06 7 0.3546 0.15614 0.00 0.00 0.00 0.46 0.00 0.00 0.54
#> TCGA.ER.A2NF.01 1 0.0000 0.97664 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.GN.A263.01 1 0.0000 0.97664 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EE.A20C.06 2 0.0504 0.94846 0.00 0.98 0.00 0.00 0.00 0.02 0.00
#> TCGA.EE.A2MQ.06 5 0.1006 0.87120 0.00 0.02 0.00 0.00 0.96 0.00 0.02
#> TCGA.ER.A19N.06 1 0.0000 0.97664 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FS.A1Z3.06 2 0.0504 0.93906 0.00 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.DA.A1I8.06 3 0.0504 0.89159 0.00 0.00 0.98 0.02 0.00 0.00 0.00
#> TCGA.D3.A5GS.06 3 0.0000 0.89312 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.EE.A181.06 4 0.0863 0.86044 0.00 0.00 0.04 0.96 0.00 0.00 0.00
#> TCGA.GN.A268.06 6 0.0000 0.95160 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.W3.A824.06 5 0.0504 0.87724 0.00 0.00 0.00 0.00 0.98 0.00 0.02
#> TCGA.EE.A2GS.06 3 0.0504 0.88734 0.00 0.02 0.98 0.00 0.00 0.00 0.00
#> TCGA.FR.A7U9.06 1 0.0000 0.97664 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.ER.A19Q.06 1 0.0000 0.97664 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FS.A1ZM.06 7 0.5875 0.30674 0.00 0.00 0.02 0.30 0.24 0.00 0.44
#> TCGA.EE.A2MG.06 1 0.0000 0.97664 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EE.A2MC.06 1 0.0000 0.97664 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EE.A17Z.06 5 0.0000 0.88536 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.D3.A2JP.06 4 0.0504 0.88943 0.00 0.00 0.00 0.98 0.00 0.00 0.02
#> TCGA.ER.A19C.06 7 0.5077 0.22776 0.00 0.00 0.02 0.08 0.38 0.00 0.52
#> TCGA.EB.A82B.01 7 0.0504 0.90303 0.00 0.00 0.00 0.02 0.00 0.00 0.98
#> TCGA.EE.A2A0.06 1 0.4033 0.62466 0.70 0.00 0.00 0.08 0.00 0.00 0.22
#> TCGA.EE.A29G.06 1 0.0000 0.97664 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D3.A5GO.06 3 0.0000 0.89312 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.GN.A269.01 1 0.0000 0.97664 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EE.A2A1.06 1 0.0000 0.97664 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.ER.A1A1.06 1 0.0000 0.97664 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FS.A1ZG.06 6 0.0000 0.95160 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.FS.A1ZE.06 6 0.0000 0.95160 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.FS.A1ZH.06 4 0.0504 0.88943 0.00 0.00 0.00 0.98 0.00 0.00 0.02
#> TCGA.EE.A2MH.06 1 0.1664 0.91737 0.92 0.00 0.00 0.06 0.00 0.00 0.02
#> TCGA.D3.A2J6.06 7 0.1166 0.88308 0.00 0.00 0.00 0.06 0.00 0.00 0.94
#> TCGA.EE.A29Q.06 2 0.0000 0.94682 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BF.A1PZ.01 3 0.2945 0.62543 0.00 0.00 0.74 0.00 0.26 0.00 0.00
#> TCGA.D3.A3BZ.06 1 0.0000 0.97664 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D3.A2JO.06 4 0.1363 0.87328 0.02 0.00 0.00 0.94 0.00 0.00 0.04
#> TCGA.GN.A267.06 7 0.0504 0.89291 0.00 0.00 0.00 0.00 0.02 0.00 0.98
#> TCGA.EE.A2MN.06 5 0.0000 0.88536 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.GN.A264.06 6 0.0000 0.95160 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.ER.A197.06 1 0.2016 0.90023 0.90 0.00 0.00 0.06 0.00 0.00 0.04
#> TCGA.DA.A1IB.06 1 0.0000 0.97664 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D3.A3CC.06 7 0.0504 0.90303 0.00 0.00 0.00 0.02 0.00 0.00 0.98
#> TCGA.ER.A19T.01 5 0.0504 0.87724 0.00 0.00 0.00 0.00 0.98 0.00 0.02
#> TCGA.GN.A261.06 1 0.0000 0.97664 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FS.A1YW.06 2 0.3815 0.42126 0.00 0.62 0.00 0.00 0.00 0.36 0.02
#> TCGA.BF.A1PU.01 7 0.0863 0.89420 0.00 0.00 0.00 0.04 0.00 0.00 0.96
#> TCGA.D3.A1QB.06 1 0.0000 0.97664 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D3.A1Q6.06 4 0.0504 0.88943 0.00 0.00 0.00 0.98 0.00 0.00 0.02
#> TCGA.D3.A3C8.06 1 0.0000 0.97664 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.ER.A19A.06 1 0.0000 0.97664 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EE.A2GN.06 5 0.0000 0.88536 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.EE.A29M.06 1 0.0000 0.97664 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D3.A2J7.06 1 0.0863 0.94991 0.96 0.00 0.00 0.04 0.00 0.00 0.00
#> TCGA.EB.A24C.01 7 0.0863 0.87593 0.00 0.00 0.00 0.00 0.04 0.00 0.96
#> TCGA.GN.A262.06 2 0.0504 0.94846 0.00 0.98 0.00 0.00 0.00 0.02 0.00
#> TCGA.EE.A2GD.06 1 0.4146 0.58879 0.68 0.00 0.00 0.08 0.00 0.00 0.24
#> TCGA.D3.A2J9.06 1 0.0000 0.97664 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EE.A29B.06 5 0.0000 0.88536 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.D9.A1JX.06 2 0.1664 0.89462 0.00 0.92 0.06 0.00 0.00 0.00 0.02
#> TCGA.EE.A29A.06 6 0.0000 0.95160 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.D3.A2JL.06 4 0.0504 0.88943 0.00 0.00 0.00 0.98 0.00 0.00 0.02
#> TCGA.D3.A1Q4.06 1 0.0000 0.97664 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FS.A1ZS.06 7 0.5293 0.52973 0.00 0.00 0.02 0.24 0.16 0.00 0.58
#> TCGA.D3.A3C3.06 4 0.0504 0.88943 0.00 0.00 0.00 0.98 0.00 0.00 0.02
#> TCGA.D3.A2J8.06 1 0.0000 0.97664 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FS.A1ZF.06 2 0.0000 0.94682 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FS.A1ZC.06 2 0.0000 0.94682 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EE.A20H.06 5 0.0000 0.88536 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.EE.A29W.06 3 0.0504 0.89159 0.00 0.00 0.98 0.02 0.00 0.00 0.00
#> TCGA.D3.A1QA.07 4 0.1433 0.83172 0.00 0.00 0.08 0.92 0.00 0.00 0.00
#> TCGA.BF.A1PV.01 5 0.0504 0.87967 0.00 0.00 0.00 0.00 0.98 0.00 0.02
#> TCGA.EE.A29S.06 5 0.5567 0.28359 0.00 0.00 0.28 0.18 0.52 0.00 0.02
#> TCGA.DA.A1HV.06 3 0.0504 0.89159 0.00 0.00 0.98 0.02 0.00 0.00 0.00
#> TCGA.FS.A1Z0.06 1 0.2722 0.82581 0.84 0.00 0.00 0.12 0.00 0.00 0.04
#> TCGA.EE.A2GO.06 2 0.0504 0.93906 0.00 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.EB.A1NK.01 1 0.0504 0.96403 0.98 0.00 0.00 0.02 0.00 0.00 0.00
#> TCGA.GN.A26D.06 7 0.0504 0.90303 0.00 0.00 0.00 0.02 0.00 0.00 0.98
#> TCGA.EE.A2MJ.06 1 0.0000 0.97664 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.ER.A198.06 5 0.0000 0.88536 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.EE.A17X.06 2 0.0504 0.93906 0.00 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.EE.A2M5.06 4 0.0504 0.88943 0.00 0.00 0.00 0.98 0.00 0.00 0.02
#> TCGA.GN.A266.06 4 0.2572 0.81531 0.06 0.00 0.00 0.86 0.00 0.00 0.08
#> TCGA.D3.A3C1.06 4 0.1166 0.87409 0.00 0.00 0.00 0.94 0.00 0.00 0.06
#> TCGA.D3.A2JH.06 1 0.0000 0.97664 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EE.A20F.06 4 0.0504 0.88943 0.00 0.00 0.00 0.98 0.00 0.00 0.02
#> TCGA.EE.A29E.06 1 0.0000 0.97664 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.ER.A2NG.06 1 0.0504 0.96403 0.98 0.00 0.00 0.02 0.00 0.00 0.00
#> TCGA.ER.A193.06 7 0.0504 0.90303 0.00 0.00 0.00 0.02 0.00 0.00 0.98
#> TCGA.FS.A1ZW.06 4 0.0504 0.88943 0.00 0.00 0.00 0.98 0.00 0.00 0.02
#> TCGA.ER.A19O.06 4 0.1166 0.87042 0.00 0.00 0.00 0.94 0.00 0.00 0.06
#> TCGA.EE.A2ME.06 1 0.0000 0.97664 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EE.A20B.06 4 0.1433 0.82924 0.00 0.00 0.08 0.92 0.00 0.00 0.00
#> TCGA.EE.A3AF.06 3 0.4212 0.42516 0.00 0.00 0.62 0.02 0.34 0.00 0.02
#> TCGA.GN.A265.06 1 0.0000 0.97664 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FS.A1YX.06 7 0.5829 0.06141 0.00 0.00 0.02 0.20 0.38 0.00 0.40
#> TCGA.FS.A1ZJ.06 5 0.3413 0.36029 0.00 0.00 0.00 0.00 0.62 0.00 0.38
#> TCGA.ER.A19H.06 3 0.2832 0.69242 0.00 0.00 0.76 0.24 0.00 0.00 0.00
#> TCGA.EE.A3AC.06 5 0.0000 0.88536 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.EE.A2MU.06 1 0.0000 0.97664 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.ER.A194.01 4 0.0504 0.88943 0.00 0.00 0.00 0.98 0.00 0.00 0.02
#> TCGA.EE.A2MS.06 7 0.0504 0.90303 0.00 0.00 0.00 0.02 0.00 0.00 0.98
#> TCGA.EE.A29R.06 6 0.2832 0.66514 0.00 0.24 0.00 0.00 0.00 0.76 0.00
#> TCGA.D9.A1X3.06 6 0.0000 0.95160 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.EE.A29X.06 5 0.3902 0.72354 0.00 0.00 0.04 0.04 0.76 0.00 0.16
#> TCGA.EE.A2GK.06 1 0.0000 0.97664 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EE.A3AA.06 1 0.0000 0.97664 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.ER.A2NE.06 2 0.0863 0.93527 0.00 0.96 0.00 0.00 0.00 0.04 0.00
#> TCGA.EE.A2GR.06 5 0.0000 0.88536 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.FS.A1ZD.06 5 0.3294 0.45601 0.00 0.00 0.00 0.00 0.66 0.00 0.34
#> TCGA.ER.A19P.06 1 0.0000 0.97664 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D3.A1Q8.06 4 0.1928 0.83066 0.08 0.00 0.00 0.90 0.00 0.00 0.02
#> TCGA.ER.A2NC.06 7 0.4714 0.49923 0.00 0.00 0.00 0.28 0.12 0.00 0.60
#> TCGA.BF.A1Q0.01 7 0.0504 0.89291 0.00 0.00 0.00 0.00 0.02 0.00 0.98
#> TCGA.FS.A1ZP.06 5 0.0000 0.88536 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.EE.A182.06 7 0.0504 0.89291 0.00 0.00 0.00 0.00 0.02 0.00 0.98
#> TCGA.D9.A1JW.06 7 0.0863 0.89466 0.00 0.00 0.00 0.04 0.00 0.00 0.96
#> TCGA.D3.A1Q7.06 1 0.0000 0.97664 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EE.A185.06 2 0.0504 0.94846 0.00 0.98 0.00 0.00 0.00 0.02 0.00
#> TCGA.EE.A2GJ.06 7 0.0504 0.89291 0.00 0.00 0.00 0.00 0.02 0.00 0.98
#> TCGA.D3.A3CB.06 1 0.0000 0.97664 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EE.A2GU.06 7 0.0504 0.90303 0.00 0.00 0.00 0.02 0.00 0.00 0.98
#> TCGA.ER.A195.06 1 0.0504 0.96403 0.98 0.00 0.00 0.02 0.00 0.00 0.00
#> TCGA.FS.A1Z7.06 7 0.0504 0.90303 0.00 0.00 0.00 0.02 0.00 0.00 0.98
#> TCGA.EE.A2M6.06 2 0.0504 0.94846 0.00 0.98 0.00 0.00 0.00 0.02 0.00
#> TCGA.ER.A19K.01 7 0.1166 0.88298 0.00 0.00 0.00 0.06 0.00 0.00 0.94
#> TCGA.DA.A1HY.06 3 0.0504 0.89159 0.00 0.00 0.98 0.02 0.00 0.00 0.00
#> TCGA.D3.A3C7.06 5 0.4421 0.07643 0.00 0.00 0.46 0.02 0.50 0.00 0.02
#> TCGA.EE.A2MP.06 3 0.0504 0.89159 0.00 0.00 0.98 0.02 0.00 0.00 0.00
#> TCGA.EE.A29H.06 2 0.3909 0.30095 0.00 0.58 0.40 0.00 0.00 0.00 0.02
#> TCGA.FR.A3YO.06 4 0.2572 0.73556 0.00 0.00 0.00 0.80 0.00 0.00 0.20
#> TCGA.XV.AB01.01 2 0.0504 0.93906 0.00 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.RP.A694.06 5 0.5517 0.16941 0.00 0.00 0.02 0.14 0.48 0.00 0.36
#> TCGA.EB.A5SF.01 1 0.0000 0.97664 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.ER.A19G.06 3 0.1505 0.88350 0.00 0.02 0.94 0.02 0.00 0.00 0.02
#> TCGA.EE.A2GE.06 1 0.0000 0.97664 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.GF.A3OT.06 1 0.0863 0.94991 0.96 0.00 0.00 0.04 0.00 0.00 0.00
#> TCGA.ER.A2NF.06 1 0.0000 0.97664 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.RP.A695.06 5 0.0504 0.87967 0.00 0.00 0.00 0.00 0.98 0.00 0.02
#> TCGA.BF.AAP7.01 1 0.0000 0.97664 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EB.A3Y7.01 7 0.1166 0.88308 0.00 0.00 0.00 0.06 0.00 0.00 0.94
#> TCGA.EB.A3XC.01 3 0.0504 0.89159 0.00 0.00 0.98 0.02 0.00 0.00 0.00
#> TCGA.ER.A19W.06 1 0.0504 0.96403 0.98 0.00 0.00 0.02 0.00 0.00 0.00
#> TCGA.FR.A69P.06 3 0.2259 0.79350 0.00 0.00 0.84 0.16 0.00 0.00 0.00
#> TCGA.RP.A693.06 7 0.1166 0.88308 0.00 0.00 0.00 0.06 0.00 0.00 0.94
#> TCGA.FW.A3TV.06 1 0.0000 0.97664 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FW.A3R5.11 1 0.0000 0.97664 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FW.A3TU.06 7 0.3562 -0.00705 0.00 0.00 0.00 0.00 0.50 0.00 0.50
#> TCGA.BF.AAP8.01 7 0.0504 0.90303 0.00 0.00 0.00 0.02 0.00 0.00 0.98
#> TCGA.EE.A2MM.06 5 0.0000 0.88536 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.DA.A1HW.06 4 0.0863 0.88108 0.00 0.00 0.00 0.96 0.00 0.00 0.04
#> TCGA.DA.A1IC.06 5 0.0504 0.87967 0.00 0.00 0.00 0.00 0.98 0.00 0.02
#> TCGA.XV.AAZV.01 1 0.0000 0.97664 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D3.A3C6.06 3 0.0504 0.88734 0.00 0.02 0.98 0.00 0.00 0.00 0.00
#> TCGA.EE.A29C.06 1 0.0863 0.94991 0.96 0.00 0.00 0.04 0.00 0.00 0.00
#> TCGA.BF.AAP2.01 2 0.0000 0.94682 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EE.A2A2.06 3 0.1006 0.89017 0.00 0.02 0.96 0.02 0.00 0.00 0.00
#> TCGA.GF.A6C8.06 4 0.2259 0.79076 0.00 0.00 0.00 0.84 0.00 0.00 0.16
#> TCGA.RP.A690.06 1 0.0000 0.97664 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FW.A5DY.06 1 0.0000 0.97664 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DA.A1I4.06 1 0.0000 0.97664 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EE.A29V.06 4 0.1363 0.86585 0.04 0.00 0.00 0.94 0.00 0.00 0.02
#> TCGA.GF.A6C9.06 1 0.0000 0.97664 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EE.A2GT.06 1 0.0000 0.97664 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.GN.A9SD.06 1 0.0000 0.97664 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EE.A3AB.06 4 0.0504 0.88943 0.00 0.00 0.00 0.98 0.00 0.00 0.02
#> TCGA.BF.AAP6.01 3 0.0000 0.89312 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.EB.A5SH.06 7 0.0504 0.89291 0.00 0.00 0.00 0.00 0.02 0.00 0.98
#> TCGA.D9.A6E9.06 7 0.2422 0.75445 0.00 0.00 0.00 0.18 0.00 0.00 0.82
#> TCGA.BF.AAP4.01 4 0.1886 0.82528 0.00 0.00 0.00 0.88 0.00 0.00 0.12
#> TCGA.EE.A2GM.06 2 0.0504 0.94846 0.00 0.98 0.00 0.00 0.00 0.02 0.00
#> TCGA.D3.A3CF.06 1 0.0000 0.97664 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D9.A6EC.06 2 0.0504 0.94846 0.00 0.98 0.00 0.00 0.00 0.02 0.00
#> TCGA.DA.A1I1.06 4 0.1166 0.84592 0.00 0.00 0.06 0.94 0.00 0.00 0.00
#> TCGA.HR.A2OH.06 1 0.0000 0.97664 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EE.A2MT.06 7 0.0504 0.90303 0.00 0.00 0.00 0.02 0.00 0.00 0.98
#> TCGA.ER.A19M.06 4 0.0504 0.88943 0.00 0.00 0.00 0.98 0.00 0.00 0.02
#> TCGA.GN.A26C.01 1 0.0000 0.97664 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FS.A1ZA.06 4 0.5973 -0.04589 0.00 0.00 0.30 0.40 0.28 0.00 0.02
#> TCGA.EB.A5SE.01 6 0.0000 0.95160 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.ER.A3PL.06 5 0.0000 0.88536 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.FR.A3R1.01 5 0.4421 0.06212 0.00 0.00 0.46 0.02 0.50 0.00 0.02
#> TCGA.EE.A2MI.06 4 0.0504 0.88943 0.00 0.00 0.00 0.98 0.00 0.00 0.02
#> TCGA.D3.A3CE.06 3 0.4338 0.57034 0.00 0.00 0.64 0.28 0.08 0.00 0.00
#> TCGA.D3.A5GT.01 6 0.3413 0.40158 0.00 0.00 0.00 0.00 0.38 0.62 0.00
#> TCGA.ER.A2NB.01 7 0.1166 0.88308 0.00 0.00 0.00 0.06 0.00 0.00 0.94
#> TCGA.D3.A1Q5.06 7 0.3052 0.71698 0.00 0.00 0.00 0.20 0.02 0.00 0.78
#> TCGA.EB.A5UN.06 1 0.0000 0.97664 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EB.A299.01 3 0.3459 0.37657 0.00 0.00 0.60 0.40 0.00 0.00 0.00
#> TCGA.DA.A1IA.06 5 0.1886 0.78805 0.00 0.00 0.00 0.00 0.88 0.12 0.00
#> TCGA.EB.A5SG.06 1 0.0000 0.97664 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D9.A6EA.06 6 0.0000 0.95160 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.XV.AAZY.01 1 0.0504 0.96403 0.98 0.00 0.00 0.02 0.00 0.00 0.00
#> TCGA.EB.A57M.01 4 0.1433 0.82924 0.00 0.00 0.08 0.92 0.00 0.00 0.00
#> TCGA.EE.A2A6.06 4 0.3139 0.58130 0.00 0.00 0.00 0.70 0.00 0.00 0.30
#> TCGA.D3.A2JA.06 1 0.1166 0.93289 0.94 0.00 0.00 0.06 0.00 0.00 0.00
#> TCGA.D3.A1Q1.06 7 0.0504 0.90303 0.00 0.00 0.00 0.02 0.00 0.00 0.98
#> TCGA.EB.A3XF.01 3 0.0504 0.89159 0.00 0.00 0.98 0.02 0.00 0.00 0.00
#> TCGA.D3.A2JF.06 3 0.3546 0.20664 0.00 0.00 0.54 0.46 0.00 0.00 0.00
#> TCGA.XV.AAZW.01 2 0.0504 0.93906 0.00 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.EB.A3Y6.01 4 0.0863 0.86044 0.00 0.00 0.04 0.96 0.00 0.00 0.00
#> TCGA.EB.A3XE.01 7 0.0504 0.90303 0.00 0.00 0.00 0.02 0.00 0.00 0.98
#> TCGA.D9.A3Z4.01 5 0.0000 0.88536 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.FW.A3R5.06 7 0.0504 0.90303 0.00 0.00 0.00 0.02 0.00 0.00 0.98
#> TCGA.EE.A2GI.06 4 0.0000 0.87923 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.EE.A2GL.06 1 0.0000 0.97664 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EB.A3XB.01 4 0.0504 0.88943 0.00 0.00 0.00 0.98 0.00 0.00 0.02
#> TCGA.BF.AAOU.01 1 0.1166 0.92502 0.94 0.00 0.00 0.00 0.00 0.00 0.06
#> TCGA.EB.A3XD.01 1 0.0000 0.97664 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EE.A2MD.06 4 0.0504 0.88943 0.00 0.00 0.00 0.98 0.00 0.00 0.02
#> TCGA.YD.A9TB.06 5 0.0000 0.88536 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.W3.AA1V.06 4 0.0504 0.88943 0.00 0.00 0.00 0.98 0.00 0.00 0.02
#> TCGA.ER.A2ND.06 7 0.3139 0.53897 0.00 0.00 0.00 0.00 0.30 0.00 0.70
#> TCGA.D3.A2JK.06 4 0.0863 0.86044 0.00 0.00 0.04 0.96 0.00 0.00 0.00
#> TCGA.FS.A1ZB.06 1 0.1166 0.93289 0.94 0.00 0.00 0.06 0.00 0.00 0.00
#> TCGA.EE.A29D.06 6 0.0000 0.95160 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.EB.A5UM.01 7 0.0504 0.89291 0.00 0.00 0.00 0.00 0.02 0.00 0.98
#> TCGA.QB.A6FS.06 1 0.0000 0.97664 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D9.A3Z1.06 1 0.0000 0.97664 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D3.A2JN.06 1 0.1166 0.93289 0.94 0.00 0.00 0.06 0.00 0.00 0.00
#> TCGA.FR.A3YN.06 2 0.3417 0.62172 0.00 0.72 0.26 0.00 0.00 0.00 0.02
#> TCGA.FS.A1ZT.06 1 0.0000 0.97664 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D9.A148.06 4 0.1433 0.85796 0.00 0.00 0.00 0.92 0.00 0.00 0.08
#> TCGA.HR.A2OG.06 4 0.2081 0.76549 0.14 0.00 0.00 0.86 0.00 0.00 0.00
#> TCGA.EE.A2ML.06 4 0.1671 0.81458 0.00 0.00 0.10 0.90 0.00 0.00 0.00
#> TCGA.EB.A5UL.06 4 0.1433 0.85724 0.00 0.00 0.00 0.92 0.00 0.00 0.08
#> TCGA.EE.A29T.06 7 0.1166 0.88308 0.00 0.00 0.00 0.06 0.00 0.00 0.94
#> TCGA.D9.A3Z3.06 1 0.0504 0.96403 0.98 0.00 0.00 0.02 0.00 0.00 0.00
#> TCGA.D9.A4Z3.01 5 0.1006 0.87120 0.00 0.02 0.00 0.00 0.96 0.00 0.02
#> TCGA.ER.A3ES.06 7 0.1433 0.84321 0.00 0.00 0.00 0.00 0.08 0.00 0.92
#> TCGA.XV.A9VZ.01 1 0.0000 0.97664 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.QB.AA9O.06 3 0.2945 0.66251 0.00 0.00 0.74 0.26 0.00 0.00 0.00
#> TCGA.EB.A44Q.06 7 0.0504 0.90303 0.00 0.00 0.00 0.02 0.00 0.00 0.98
#> TCGA.EB.A44R.06 7 0.0504 0.90303 0.00 0.00 0.00 0.02 0.00 0.00 0.98
#> TCGA.BF.A3DJ.01 3 0.1505 0.88350 0.00 0.02 0.94 0.02 0.00 0.00 0.02
#> TCGA.EE.A3JD.06 1 0.0000 0.97664 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D3.A51N.06 4 0.0504 0.88943 0.00 0.00 0.00 0.98 0.00 0.00 0.02
#> TCGA.EB.A44N.01 1 0.0000 0.97664 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EE.A3J3.06 5 0.1006 0.87143 0.00 0.00 0.02 0.00 0.96 0.00 0.02
#> TCGA.XV.A9W5.01 4 0.3459 0.26855 0.00 0.00 0.40 0.60 0.00 0.00 0.00
#> TCGA.D3.A51G.06 3 0.2081 0.81228 0.00 0.00 0.86 0.14 0.00 0.00 0.00
#> TCGA.EB.A4P0.01 2 0.0000 0.94682 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BF.AAP1.01 6 0.0000 0.95160 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.EE.A3J4.06 6 0.2081 0.81931 0.00 0.00 0.00 0.00 0.14 0.86 0.00
#> TCGA.Z2.AA3V.06 1 0.0000 0.97664 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.LH.A9QB.06 6 0.0000 0.95160 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.D3.A51J.06 4 0.1886 0.82528 0.00 0.00 0.00 0.88 0.00 0.00 0.12
#> TCGA.3N.A9WC.06 7 0.0863 0.89466 0.00 0.00 0.00 0.04 0.00 0.00 0.96
#> TCGA.DA.A3F8.06 1 0.0000 0.97664 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D9.A4Z6.06 4 0.4615 0.40269 0.00 0.00 0.30 0.60 0.00 0.00 0.10
#> TCGA.D3.A51R.06 2 0.0000 0.94682 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EB.A4OZ.01 1 0.0000 0.97664 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FS.A4FB.06 3 0.0504 0.88734 0.00 0.02 0.98 0.00 0.00 0.00 0.00
#> TCGA.EE.A3JE.06 1 0.0000 0.97664 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.W3.AA1W.06 1 0.0000 0.97664 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DA.A1I0.06 4 0.0504 0.88943 0.00 0.00 0.00 0.98 0.00 0.00 0.02
#> TCGA.D3.A51F.06 1 0.0000 0.97664 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.IH.A3EA.01 5 0.0504 0.87967 0.00 0.00 0.00 0.00 0.98 0.00 0.02
#> TCGA.EB.A431.01 4 0.0504 0.88943 0.00 0.00 0.00 0.98 0.00 0.00 0.02
#> TCGA.EB.A97M.01 6 0.0000 0.95160 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.BF.AAOX.01 4 0.0863 0.86044 0.00 0.00 0.04 0.96 0.00 0.00 0.00
#> TCGA.DA.A3F5.06 7 0.0863 0.89466 0.00 0.00 0.00 0.04 0.00 0.00 0.96
#> TCGA.YD.A9TA.06 4 0.0504 0.88943 0.00 0.00 0.00 0.98 0.00 0.00 0.02
#> TCGA.DA.A3F2.06 1 0.0000 0.97664 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EB.A44O.01 5 0.0000 0.88536 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.EB.A4IQ.01 7 0.0504 0.90303 0.00 0.00 0.00 0.02 0.00 0.00 0.98
#> TCGA.EB.A4IS.01 1 0.0000 0.97664 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.YG.AA3O.06 5 0.0504 0.87967 0.00 0.00 0.00 0.00 0.98 0.00 0.02
#> TCGA.ER.A3EV.06 7 0.0504 0.90303 0.00 0.00 0.00 0.02 0.00 0.00 0.98
#> TCGA.3N.A9WD.06 1 0.2313 0.87728 0.88 0.00 0.00 0.06 0.00 0.00 0.06
#> TCGA.BF.A3DM.01 3 0.0504 0.88734 0.00 0.02 0.98 0.00 0.00 0.00 0.00
#> TCGA.XV.A9W2.01 7 0.1166 0.88308 0.00 0.00 0.00 0.06 0.00 0.00 0.94
#> TCGA.W3.AA1Q.06 5 0.0504 0.87967 0.00 0.00 0.00 0.00 0.98 0.00 0.02
#> TCGA.WE.AAA0.06 4 0.0504 0.88943 0.00 0.00 0.00 0.98 0.00 0.00 0.02
#> TCGA.W3.AA1R.06 2 0.3985 0.11380 0.00 0.52 0.46 0.00 0.00 0.00 0.02
#> TCGA.EE.A3J5.06 4 0.0504 0.88943 0.00 0.00 0.00 0.98 0.00 0.00 0.02
#> TCGA.EB.A4OY.01 1 0.0000 0.97664 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FS.A4FD.06 7 0.0504 0.90303 0.00 0.00 0.00 0.02 0.00 0.00 0.98
#> TCGA.BF.AAP0.06 1 0.0000 0.97664 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.YG.AA3P.06 5 0.2832 0.64023 0.00 0.00 0.00 0.00 0.76 0.00 0.24
#> TCGA.EE.A3JA.06 3 0.0000 0.89312 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.W3.AA21.06 2 0.0504 0.94846 0.00 0.98 0.00 0.00 0.00 0.02 0.00
#> TCGA.WE.AAA3.06 7 0.0504 0.90303 0.00 0.00 0.00 0.02 0.00 0.00 0.98
#> TCGA.FS.A4F4.06 3 0.0504 0.89159 0.00 0.00 0.98 0.02 0.00 0.00 0.00
#> TCGA.BF.A3DN.01 5 0.3661 0.63731 0.00 0.02 0.22 0.00 0.74 0.00 0.02
#> TCGA.ER.A3ET.06 7 0.0863 0.88028 0.00 0.00 0.00 0.00 0.04 0.00 0.96
#> TCGA.W3.AA1O.06 5 0.0000 0.88536 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.D3.A51E.06 3 0.2081 0.81401 0.00 0.00 0.86 0.14 0.00 0.00 0.00
#> TCGA.Z2.AA3S.06 6 0.0000 0.95160 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.YG.AA3N.01 5 0.4318 0.64047 0.00 0.00 0.04 0.04 0.70 0.00 0.22
#> TCGA.WE.AA9Y.06 1 0.0000 0.97664 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FS.A4F5.06 6 0.0000 0.95160 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.EE.A3J7.06 6 0.2832 0.68182 0.00 0.00 0.00 0.00 0.24 0.76 0.00
#> TCGA.FS.A4F8.06 1 0.0000 0.97664 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DA.A3F3.06 3 0.2803 0.79381 0.00 0.06 0.84 0.00 0.10 0.00 0.00
#> TCGA.D3.A51H.06 1 0.0000 0.97664 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BF.A3DL.01 1 0.3617 0.72580 0.76 0.00 0.00 0.16 0.00 0.00 0.08
#> TCGA.D3.A51T.06 2 0.0504 0.93906 0.00 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.D3.A51K.06 5 0.0000 0.88536 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.EB.A44P.01 5 0.0504 0.87967 0.00 0.00 0.00 0.00 0.98 0.00 0.02
#> TCGA.D9.A4Z5.01 2 0.1433 0.89859 0.00 0.92 0.00 0.00 0.00 0.08 0.00
#> TCGA.WE.AAA4.06 1 0.0000 0.97664 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.3N.A9WB.06 6 0.0000 0.95160 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.EE.A3J8.06 2 0.0504 0.94846 0.00 0.98 0.00 0.00 0.00 0.02 0.00
cbind(get_classes(res, k = 8), get_membership(res, k = 8))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7 p8
#> TCGA.FR.A728.01 1 0.6162 0.15586 0.36 0.00 0.00 0.26 0.00 0.00 0.08 0.30
#> TCGA.GN.A4U8.11 1 0.0000 0.84866 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.GN.A8LL.06 3 0.2114 0.51515 0.00 0.00 0.84 0.00 0.00 0.00 0.00 0.16
#> TCGA.FR.A8YC.06 6 0.0000 0.94582 0.00 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.DA.A95X.06 2 0.0000 0.91799 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.ER.A42K.06 3 0.3318 -0.30081 0.00 0.00 0.54 0.00 0.00 0.00 0.00 0.46
#> TCGA.D3.A8GO.06 1 0.2852 0.73146 0.72 0.00 0.00 0.00 0.00 0.00 0.00 0.28
#> TCGA.D3.A8GK.06 5 0.0808 0.77785 0.00 0.00 0.00 0.00 0.96 0.00 0.04 0.00
#> TCGA.WE.A8JZ.06 2 0.0000 0.91799 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.WE.A8ZO.06 5 0.1557 0.76793 0.00 0.00 0.00 0.00 0.92 0.02 0.00 0.06
#> TCGA.D3.A8GI.06 5 0.2025 0.73068 0.00 0.00 0.00 0.00 0.88 0.10 0.00 0.02
#> TCGA.FS.A4FC.06 7 0.0000 0.82698 0.00 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.FS.A4F2.06 3 0.2569 0.50987 0.00 0.02 0.82 0.00 0.00 0.00 0.00 0.16
#> TCGA.WE.A8ZM.06 5 0.0471 0.78511 0.00 0.00 0.00 0.00 0.98 0.00 0.02 0.00
#> TCGA.WE.A8ZT.06 3 0.2856 0.46890 0.00 0.02 0.78 0.00 0.00 0.00 0.00 0.20
#> TCGA.D3.A8GQ.06 4 0.0471 0.74368 0.00 0.00 0.00 0.98 0.00 0.00 0.00 0.02
#> TCGA.D3.A8GB.06 1 0.0000 0.84866 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DA.A95Y.06 2 0.0808 0.90345 0.00 0.96 0.00 0.00 0.00 0.00 0.00 0.04
#> TCGA.EE.A3JI.06 6 0.0000 0.94582 0.00 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.OD.A75X.06 2 0.0471 0.92255 0.00 0.98 0.00 0.00 0.00 0.02 0.00 0.00
#> TCGA.DA.A960.01 2 0.0471 0.92255 0.00 0.98 0.00 0.00 0.00 0.02 0.00 0.00
#> TCGA.D3.A8GV.06 2 0.0000 0.91799 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.WE.A8ZN.06 4 0.4952 0.41902 0.20 0.00 0.00 0.50 0.00 0.00 0.00 0.30
#> TCGA.D3.A8GN.06 1 0.5033 0.41735 0.48 0.00 0.00 0.22 0.00 0.00 0.00 0.30
#> TCGA.EB.A550.01 1 0.3922 0.66145 0.64 0.00 0.00 0.06 0.00 0.00 0.00 0.30
#> TCGA.BF.A5EQ.01 7 0.0471 0.82729 0.00 0.00 0.00 0.00 0.00 0.00 0.98 0.02
#> TCGA.EB.A3HV.01 5 0.0471 0.78511 0.00 0.00 0.00 0.00 0.98 0.00 0.02 0.00
#> TCGA.HR.A5NC.01 7 0.2756 0.54483 0.00 0.00 0.00 0.00 0.26 0.00 0.74 0.00
#> TCGA.DA.A95Z.06 6 0.0000 0.94582 0.00 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.EB.A6QZ.01 2 0.0471 0.92255 0.00 0.98 0.00 0.00 0.00 0.02 0.00 0.00
#> TCGA.FW.A3I3.06 2 0.0471 0.92255 0.00 0.98 0.00 0.00 0.00 0.02 0.00 0.00
#> TCGA.WE.A8K6.06 8 0.4471 0.60099 0.00 0.02 0.34 0.00 0.06 0.00 0.00 0.58
#> TCGA.D3.A8GP.06 6 0.0000 0.94582 0.00 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.EB.A42Z.01 6 0.0000 0.94582 0.00 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.GN.A4U4.06 5 0.3895 0.57026 0.00 0.12 0.02 0.00 0.74 0.00 0.00 0.12
#> TCGA.GF.A4EO.06 1 0.2534 0.76566 0.78 0.00 0.00 0.00 0.00 0.00 0.00 0.22
#> TCGA.GN.A8LK.06 6 0.0471 0.93011 0.00 0.00 0.00 0.00 0.02 0.98 0.00 0.00
#> TCGA.WE.A8K4.01 4 0.3374 0.65856 0.02 0.00 0.00 0.68 0.00 0.00 0.00 0.30
#> TCGA.DA.A95W.06 6 0.0000 0.94582 0.00 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.FW.A5DX.01 2 0.0471 0.92255 0.00 0.98 0.00 0.00 0.00 0.02 0.00 0.00
#> TCGA.GN.A4U3.06 2 0.0808 0.90345 0.00 0.96 0.00 0.00 0.00 0.00 0.00 0.04
#> TCGA.EB.A6QY.01 1 0.3594 0.70118 0.68 0.00 0.00 0.04 0.00 0.00 0.00 0.28
#> TCGA.EB.A5VU.01 4 0.4255 0.21407 0.00 0.00 0.34 0.58 0.00 0.00 0.08 0.00
#> TCGA.Z2.A8RT.06 5 0.4730 0.22068 0.00 0.00 0.26 0.00 0.56 0.00 0.00 0.18
#> TCGA.WE.A8K1.06 4 0.4134 0.59296 0.08 0.00 0.00 0.62 0.00 0.00 0.00 0.30
#> TCGA.EB.A41B.01 8 0.3015 0.63269 0.00 0.00 0.32 0.00 0.00 0.00 0.00 0.68
#> TCGA.WE.A8ZY.06 2 0.0471 0.92255 0.00 0.98 0.00 0.00 0.00 0.02 0.00 0.00
#> TCGA.D9.A6EG.06 6 0.0000 0.94582 0.00 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.BF.A5ER.01 5 0.0471 0.78164 0.00 0.00 0.00 0.00 0.98 0.00 0.00 0.02
#> TCGA.FR.A8YD.06 6 0.0471 0.93011 0.00 0.00 0.00 0.00 0.02 0.98 0.00 0.00
#> TCGA.FS.A4F9.06 6 0.0471 0.93011 0.00 0.00 0.00 0.00 0.02 0.98 0.00 0.00
#> TCGA.EB.A6R0.01 3 0.1341 0.55727 0.00 0.00 0.92 0.00 0.00 0.00 0.00 0.08
#> TCGA.ER.A42L.06 1 0.0000 0.84866 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D3.A8GJ.06 7 0.5116 0.16666 0.00 0.00 0.00 0.26 0.00 0.00 0.46 0.28
#> TCGA.FR.A8YE.06 1 0.0000 0.84866 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.WE.A8ZR.06 7 0.0000 0.82698 0.00 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.BF.A9VF.01 5 0.0808 0.77579 0.00 0.00 0.00 0.00 0.96 0.00 0.00 0.04
#> TCGA.EE.A3JH.06 1 0.0000 0.84866 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DA.A95V.06 4 0.2114 0.60923 0.00 0.00 0.16 0.84 0.00 0.00 0.00 0.00
#> TCGA.GF.A769.01 2 0.3054 0.75475 0.00 0.80 0.00 0.00 0.12 0.00 0.00 0.08
#> TCGA.D9.A4Z2.01 3 0.3657 0.36925 0.00 0.08 0.72 0.00 0.00 0.00 0.00 0.20
#> TCGA.FR.A44A.06 1 0.1947 0.80574 0.86 0.00 0.00 0.00 0.00 0.00 0.00 0.14
#> TCGA.EB.A5VV.06 1 0.0000 0.84866 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EE.A180.06 6 0.0000 0.94582 0.00 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.D3.A8GC.06 6 0.0000 0.94582 0.00 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.WE.A8K5.06 6 0.0000 0.94582 0.00 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.GN.A8LN.01 2 0.0000 0.91799 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EE.A3JB.06 4 0.1563 0.75214 0.00 0.00 0.00 0.90 0.00 0.00 0.00 0.10
#> TCGA.D3.A3MO.06 8 0.3992 -0.07126 0.00 0.00 0.04 0.00 0.44 0.00 0.00 0.52
#> TCGA.ER.A42H.01 5 0.1563 0.72883 0.00 0.00 0.00 0.00 0.90 0.10 0.00 0.00
#> TCGA.WE.A8ZX.06 4 0.3015 0.37160 0.00 0.00 0.32 0.68 0.00 0.00 0.00 0.00
#> TCGA.GN.A4U5.01 1 0.4897 0.48180 0.52 0.00 0.00 0.20 0.00 0.00 0.00 0.28
#> TCGA.D3.A8GS.06 4 0.5203 0.28303 0.00 0.00 0.00 0.42 0.00 0.00 0.30 0.28
#> TCGA.WE.A8ZQ.06 6 0.0471 0.93011 0.00 0.00 0.00 0.00 0.02 0.98 0.00 0.00
#> TCGA.EE.A2MF.06 6 0.0000 0.94582 0.00 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.D3.A5GU.06 5 0.0471 0.78511 0.00 0.00 0.00 0.00 0.98 0.00 0.02 0.00
#> TCGA.GN.A4U8.06 4 0.2114 0.74376 0.00 0.00 0.00 0.84 0.00 0.00 0.00 0.16
#> TCGA.EB.A42Y.01 2 0.0000 0.91799 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D3.A3ML.06 6 0.0471 0.93011 0.00 0.00 0.00 0.00 0.02 0.98 0.00 0.00
#> TCGA.EB.A551.01 4 0.3922 0.63579 0.00 0.00 0.00 0.64 0.00 0.00 0.06 0.30
#> TCGA.D3.A8GM.06 4 0.1341 0.75264 0.00 0.00 0.00 0.92 0.00 0.00 0.00 0.08
#> TCGA.D3.A8GL.06 6 0.0000 0.94582 0.00 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.D3.A3MU.06 6 0.0000 0.94582 0.00 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.FS.A4F0.06 6 0.0808 0.90969 0.00 0.04 0.00 0.00 0.00 0.96 0.00 0.00
#> TCGA.D3.A3MV.06 3 0.2404 0.53260 0.00 0.02 0.84 0.00 0.00 0.00 0.00 0.14
#> TCGA.GN.A4U7.06 3 0.2267 0.50510 0.00 0.00 0.82 0.00 0.00 0.00 0.00 0.18
#> TCGA.FR.A2OS.01 5 0.0471 0.78511 0.00 0.00 0.00 0.00 0.98 0.00 0.02 0.00
#> TCGA.D3.A2JE.06 5 0.2132 0.75771 0.00 0.00 0.00 0.00 0.88 0.04 0.00 0.08
#> TCGA.YD.A89C.06 3 0.3971 0.31374 0.00 0.00 0.54 0.42 0.00 0.00 0.00 0.04
#> TCGA.FR.A726.01 4 0.2406 0.56475 0.00 0.00 0.20 0.80 0.00 0.00 0.00 0.00
#> TCGA.BF.A5EP.01 2 0.2623 0.80052 0.00 0.84 0.06 0.00 0.00 0.00 0.00 0.10
#> TCGA.D3.A3MR.06 1 0.0000 0.84866 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D3.A8GR.06 5 0.0471 0.78204 0.00 0.00 0.00 0.00 0.98 0.02 0.00 0.00
#> TCGA.GN.A4U9.06 8 0.5070 -0.11079 0.00 0.00 0.04 0.02 0.44 0.00 0.04 0.46
#> TCGA.EB.A6L9.06 1 0.0000 0.84866 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D3.A5GL.06 3 0.5273 -0.02618 0.00 0.02 0.46 0.00 0.36 0.00 0.00 0.16
#> TCGA.EB.A430.01 1 0.1091 0.83397 0.94 0.00 0.00 0.00 0.00 0.00 0.00 0.06
#> TCGA.D3.A8GE.06 1 0.0000 0.84866 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D3.A8GD.06 1 0.2852 0.73181 0.72 0.00 0.00 0.00 0.00 0.00 0.00 0.28
#> TCGA.EB.A41A.01 6 0.0000 0.94582 0.00 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.W3.A825.06 4 0.2852 0.48017 0.00 0.00 0.00 0.72 0.00 0.00 0.28 0.00
#> TCGA.EE.A183.06 1 0.2852 0.73181 0.72 0.00 0.00 0.00 0.00 0.00 0.00 0.28
#> TCGA.ER.A2NH.06 1 0.5033 0.41735 0.48 0.00 0.00 0.22 0.00 0.00 0.00 0.30
#> TCGA.D3.A5GR.06 4 0.3922 0.63579 0.00 0.00 0.00 0.64 0.00 0.00 0.06 0.30
#> TCGA.FR.A729.06 4 0.2114 0.74376 0.00 0.00 0.00 0.84 0.00 0.00 0.00 0.16
#> TCGA.D3.A1QA.06 2 0.0471 0.92255 0.00 0.98 0.00 0.00 0.00 0.02 0.00 0.00
#> TCGA.FS.A1YY.06 3 0.5256 0.22036 0.00 0.00 0.54 0.10 0.30 0.00 0.00 0.06
#> TCGA.EE.A2MK.06 3 0.2267 0.50510 0.00 0.00 0.82 0.00 0.00 0.00 0.00 0.18
#> TCGA.EE.A2M8.06 1 0.0000 0.84866 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EB.A5KH.06 2 0.0471 0.92255 0.00 0.98 0.00 0.00 0.00 0.02 0.00 0.00
#> TCGA.FS.A1ZR.06 5 0.0471 0.78511 0.00 0.00 0.00 0.00 0.98 0.00 0.02 0.00
#> TCGA.EE.A3AE.06 3 0.2650 0.48454 0.00 0.00 0.76 0.24 0.00 0.00 0.00 0.00
#> TCGA.EE.A29P.06 4 0.0808 0.73418 0.00 0.00 0.00 0.96 0.00 0.00 0.04 0.00
#> TCGA.EB.A553.01 7 0.0000 0.82698 0.00 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.EE.A2MR.06 1 0.0000 0.84866 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.GN.A26A.06 4 0.0471 0.74368 0.00 0.00 0.00 0.98 0.00 0.00 0.00 0.02
#> TCGA.FS.A1ZY.06 2 0.0471 0.92255 0.00 0.98 0.00 0.00 0.00 0.02 0.00 0.00
#> TCGA.EE.A20I.06 4 0.2852 0.44774 0.00 0.00 0.28 0.72 0.00 0.00 0.00 0.00
#> TCGA.DA.A1I5.06 1 0.4897 0.48180 0.52 0.00 0.00 0.20 0.00 0.00 0.00 0.28
#> TCGA.EE.A184.06 6 0.4673 0.33125 0.00 0.34 0.00 0.00 0.08 0.56 0.00 0.02
#> TCGA.EB.A85J.01 7 0.0471 0.82729 0.00 0.00 0.00 0.00 0.00 0.00 0.98 0.02
#> TCGA.RP.A6K9.06 7 0.0471 0.82729 0.00 0.00 0.00 0.00 0.00 0.00 0.98 0.02
#> TCGA.EE.A17Y.06 4 0.1947 0.74871 0.00 0.00 0.00 0.86 0.00 0.00 0.00 0.14
#> TCGA.D9.A149.06 7 0.3660 0.61954 0.00 0.00 0.00 0.06 0.00 0.00 0.70 0.24
#> TCGA.ER.A19D.06 1 0.4480 0.58676 0.58 0.00 0.00 0.12 0.00 0.00 0.00 0.30
#> TCGA.FS.A1ZZ.06 2 0.0471 0.92255 0.00 0.98 0.00 0.00 0.00 0.02 0.00 0.00
#> TCGA.EE.A2GP.06 5 0.4350 0.35703 0.00 0.00 0.30 0.02 0.62 0.00 0.00 0.06
#> TCGA.EE.A3AD.06 2 0.0471 0.92255 0.00 0.98 0.00 0.00 0.00 0.02 0.00 0.00
#> TCGA.D3.A1Q9.06 4 0.2852 0.44763 0.00 0.00 0.28 0.72 0.00 0.00 0.00 0.00
#> TCGA.GF.A2C7.01 6 0.0471 0.93011 0.00 0.00 0.00 0.00 0.02 0.98 0.00 0.00
#> TCGA.BF.A5ES.01 7 0.3318 0.03494 0.00 0.00 0.00 0.00 0.46 0.00 0.54 0.00
#> TCGA.ER.A199.06 1 0.0000 0.84866 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EE.A3AH.06 2 0.0471 0.92255 0.00 0.98 0.00 0.00 0.00 0.02 0.00 0.00
#> TCGA.W3.A828.06 1 0.0000 0.84866 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EE.A2A5.06 5 0.0471 0.78204 0.00 0.00 0.00 0.00 0.98 0.02 0.00 0.00
#> TCGA.ER.A19L.06 7 0.0471 0.82729 0.00 0.00 0.00 0.00 0.00 0.00 0.98 0.02
#> TCGA.BF.A1PX.01 1 0.0000 0.84866 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.ER.A19T.06 7 0.0000 0.82698 0.00 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.EB.A51B.01 5 0.5101 0.10969 0.00 0.02 0.28 0.00 0.54 0.00 0.00 0.16
#> TCGA.FS.A1ZQ.06 3 0.0808 0.56749 0.00 0.00 0.96 0.04 0.00 0.00 0.00 0.00
#> TCGA.D3.A2JG.06 3 0.6335 -0.06815 0.00 0.24 0.40 0.00 0.22 0.00 0.00 0.14
#> TCGA.EE.A2GH.06 1 0.0000 0.84866 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.ER.A19F.06 3 0.2267 0.50510 0.00 0.00 0.82 0.00 0.00 0.00 0.00 0.18
#> TCGA.ER.A196.01 1 0.0000 0.84866 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D3.A2JC.06 4 0.4480 0.58580 0.00 0.00 0.00 0.58 0.00 0.00 0.12 0.30
#> TCGA.EE.A3AG.06 3 0.2856 0.46890 0.00 0.02 0.78 0.00 0.00 0.00 0.00 0.20
#> TCGA.ER.A19S.06 1 0.2938 0.71837 0.70 0.00 0.00 0.00 0.00 0.00 0.00 0.30
#> TCGA.EE.A2GC.06 5 0.1091 0.77439 0.00 0.00 0.00 0.00 0.94 0.00 0.00 0.06
#> TCGA.EE.A29N.06 1 0.4318 0.61346 0.60 0.00 0.00 0.10 0.00 0.00 0.00 0.30
#> TCGA.FR.A7U8.06 6 0.0000 0.94582 0.00 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.BF.A5EO.01 4 0.2267 0.73693 0.00 0.00 0.00 0.82 0.00 0.00 0.00 0.18
#> TCGA.ER.A19B.06 3 0.2856 0.46890 0.00 0.02 0.78 0.00 0.00 0.00 0.00 0.20
#> TCGA.D3.A5GN.06 3 0.2719 0.51281 0.00 0.00 0.80 0.18 0.00 0.00 0.00 0.02
#> TCGA.D3.A2JB.06 1 0.0000 0.84866 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.ER.A19J.06 2 0.0471 0.92255 0.00 0.98 0.00 0.00 0.00 0.02 0.00 0.00
#> TCGA.D3.A2JD.06 4 0.3374 0.65856 0.02 0.00 0.00 0.68 0.00 0.00 0.00 0.30
#> TCGA.FS.A1Z4.06 1 0.0000 0.84866 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FR.A7UA.06 1 0.0000 0.84866 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EE.A2M7.06 4 0.0000 0.73566 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.D3.A1Q3.06 7 0.0471 0.82729 0.00 0.00 0.00 0.00 0.00 0.00 0.98 0.02
#> TCGA.EB.A85I.01 7 0.3170 0.67851 0.00 0.00 0.00 0.04 0.00 0.00 0.76 0.20
#> TCGA.EB.A82C.01 6 0.4740 0.41326 0.00 0.30 0.00 0.00 0.10 0.58 0.00 0.02
#> TCGA.ER.A19E.06 5 0.2025 0.74548 0.00 0.00 0.00 0.00 0.88 0.00 0.02 0.10
#> TCGA.FS.A1ZK.06 5 0.3714 0.17964 0.00 0.00 0.00 0.00 0.54 0.02 0.00 0.44
#> TCGA.FS.A1ZU.06 5 0.4213 0.50899 0.00 0.00 0.00 0.00 0.66 0.00 0.16 0.18
#> TCGA.EB.A5FP.01 2 0.0471 0.92255 0.00 0.98 0.00 0.00 0.00 0.02 0.00 0.00
#> TCGA.EB.A4XL.01 3 0.2569 0.50987 0.00 0.02 0.82 0.00 0.00 0.00 0.00 0.16
#> TCGA.DA.A1I2.06 5 0.4677 0.31137 0.00 0.00 0.14 0.00 0.54 0.00 0.32 0.00
#> TCGA.EE.A29L.06 2 0.0471 0.92255 0.00 0.98 0.00 0.00 0.00 0.02 0.00 0.00
#> TCGA.FS.A1ZN.01 2 0.0471 0.92255 0.00 0.98 0.00 0.00 0.00 0.02 0.00 0.00
#> TCGA.EB.A24D.01 5 0.5116 0.19129 0.00 0.00 0.00 0.00 0.46 0.00 0.28 0.26
#> TCGA.EE.A2GB.06 3 0.2856 0.46890 0.00 0.02 0.78 0.00 0.00 0.00 0.00 0.20
#> TCGA.DA.A1I7.06 4 0.4910 -0.03312 0.00 0.00 0.16 0.44 0.00 0.00 0.40 0.00
#> TCGA.ER.A2NF.01 1 0.0000 0.84866 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.GN.A263.01 1 0.0000 0.84866 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EE.A20C.06 2 0.0471 0.92255 0.00 0.98 0.00 0.00 0.00 0.02 0.00 0.00
#> TCGA.EE.A2MQ.06 5 0.1557 0.75559 0.00 0.00 0.02 0.00 0.92 0.00 0.00 0.06
#> TCGA.ER.A19N.06 1 0.1091 0.83408 0.94 0.00 0.00 0.00 0.00 0.00 0.00 0.06
#> TCGA.FS.A1Z3.06 2 0.1804 0.86620 0.00 0.90 0.00 0.00 0.02 0.00 0.00 0.08
#> TCGA.DA.A1I8.06 3 0.2404 0.52515 0.00 0.02 0.84 0.00 0.00 0.00 0.00 0.14
#> TCGA.D3.A5GS.06 3 0.2856 0.46890 0.00 0.02 0.78 0.00 0.00 0.00 0.00 0.20
#> TCGA.EE.A181.06 4 0.2406 0.56475 0.00 0.00 0.20 0.80 0.00 0.00 0.00 0.00
#> TCGA.GN.A268.06 6 0.0000 0.94582 0.00 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.W3.A824.06 5 0.1563 0.73407 0.00 0.00 0.00 0.00 0.90 0.00 0.10 0.00
#> TCGA.EE.A2GS.06 8 0.3658 0.52292 0.00 0.02 0.40 0.00 0.00 0.00 0.00 0.58
#> TCGA.FR.A7U9.06 1 0.0000 0.84866 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.ER.A19Q.06 1 0.0000 0.84866 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FS.A1ZM.06 7 0.6086 0.16142 0.00 0.00 0.22 0.30 0.04 0.00 0.42 0.02
#> TCGA.EE.A2MG.06 1 0.0000 0.84866 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EE.A2MC.06 1 0.0000 0.84866 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EE.A17Z.06 5 0.1557 0.76941 0.00 0.00 0.00 0.00 0.92 0.00 0.02 0.06
#> TCGA.D3.A2JP.06 4 0.2650 0.71007 0.00 0.00 0.00 0.76 0.00 0.00 0.00 0.24
#> TCGA.ER.A19C.06 7 0.5711 0.39387 0.00 0.00 0.18 0.12 0.10 0.00 0.58 0.02
#> TCGA.EB.A82B.01 7 0.0471 0.82729 0.00 0.00 0.00 0.00 0.00 0.00 0.98 0.02
#> TCGA.EE.A2A0.06 1 0.6073 0.27237 0.40 0.00 0.00 0.22 0.00 0.00 0.08 0.30
#> TCGA.EE.A29G.06 1 0.2852 0.73181 0.72 0.00 0.00 0.00 0.00 0.00 0.00 0.28
#> TCGA.D3.A5GO.06 3 0.1947 0.53716 0.00 0.00 0.86 0.00 0.00 0.00 0.00 0.14
#> TCGA.GN.A269.01 1 0.1341 0.82755 0.92 0.00 0.00 0.00 0.00 0.00 0.00 0.08
#> TCGA.EE.A2A1.06 1 0.0000 0.84866 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.ER.A1A1.06 1 0.0000 0.84866 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FS.A1ZG.06 6 0.0000 0.94582 0.00 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.FS.A1ZE.06 6 0.0000 0.94582 0.00 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.FS.A1ZH.06 4 0.1563 0.75214 0.00 0.00 0.00 0.90 0.00 0.00 0.00 0.10
#> TCGA.EE.A2MH.06 1 0.5033 0.41735 0.48 0.00 0.00 0.22 0.00 0.00 0.00 0.30
#> TCGA.D3.A2J6.06 7 0.3095 0.65473 0.00 0.00 0.00 0.02 0.00 0.00 0.74 0.24
#> TCGA.EE.A29Q.06 2 0.0808 0.90345 0.00 0.96 0.00 0.00 0.00 0.00 0.00 0.04
#> TCGA.BF.A1PZ.01 8 0.4199 0.62058 0.00 0.00 0.32 0.00 0.08 0.00 0.00 0.60
#> TCGA.D3.A3BZ.06 1 0.0000 0.84866 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D3.A2JO.06 4 0.2938 0.67463 0.00 0.00 0.00 0.70 0.00 0.00 0.00 0.30
#> TCGA.GN.A267.06 7 0.0000 0.82698 0.00 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.EE.A2MN.06 5 0.0941 0.78216 0.00 0.00 0.00 0.00 0.96 0.02 0.00 0.02
#> TCGA.GN.A264.06 6 0.1341 0.86366 0.00 0.08 0.00 0.00 0.00 0.92 0.00 0.00
#> TCGA.ER.A197.06 1 0.4622 0.55789 0.56 0.00 0.00 0.14 0.00 0.00 0.00 0.30
#> TCGA.DA.A1IB.06 1 0.0000 0.84866 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D3.A3CC.06 7 0.1091 0.81118 0.00 0.00 0.00 0.00 0.00 0.00 0.94 0.06
#> TCGA.ER.A19T.01 5 0.2888 0.64641 0.00 0.00 0.00 0.00 0.80 0.00 0.16 0.04
#> TCGA.GN.A261.06 1 0.0000 0.84866 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FS.A1YW.06 2 0.3690 0.27804 0.00 0.56 0.00 0.00 0.00 0.42 0.00 0.02
#> TCGA.BF.A1PU.01 7 0.2406 0.70899 0.00 0.00 0.00 0.00 0.00 0.00 0.80 0.20
#> TCGA.D3.A1QB.06 1 0.0000 0.84866 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D3.A1Q6.06 4 0.1947 0.74871 0.00 0.00 0.00 0.86 0.00 0.00 0.00 0.14
#> TCGA.D3.A3C8.06 1 0.0000 0.84866 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.ER.A19A.06 1 0.0000 0.84866 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EE.A2GN.06 5 0.1557 0.76532 0.00 0.00 0.00 0.00 0.92 0.02 0.00 0.06
#> TCGA.EE.A29M.06 1 0.0000 0.84866 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D3.A2J7.06 1 0.4480 0.58669 0.58 0.00 0.00 0.12 0.00 0.00 0.00 0.30
#> TCGA.EB.A24C.01 7 0.0000 0.82698 0.00 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.GN.A262.06 2 0.0471 0.92255 0.00 0.98 0.00 0.00 0.00 0.02 0.00 0.00
#> TCGA.EE.A2GD.06 1 0.6073 0.27237 0.40 0.00 0.00 0.22 0.00 0.00 0.08 0.30
#> TCGA.D3.A2J9.06 1 0.0000 0.84866 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EE.A29B.06 5 0.0471 0.78204 0.00 0.00 0.00 0.00 0.98 0.02 0.00 0.00
#> TCGA.D9.A1JX.06 2 0.3078 0.78130 0.00 0.82 0.06 0.00 0.02 0.00 0.00 0.10
#> TCGA.EE.A29A.06 6 0.0000 0.94582 0.00 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.D3.A2JL.06 4 0.0471 0.74368 0.00 0.00 0.00 0.98 0.00 0.00 0.00 0.02
#> TCGA.D3.A1Q4.06 1 0.1765 0.81288 0.88 0.00 0.00 0.00 0.00 0.00 0.00 0.12
#> TCGA.FS.A1ZS.06 7 0.5986 0.30442 0.00 0.00 0.18 0.24 0.02 0.00 0.50 0.06
#> TCGA.D3.A3C3.06 4 0.0000 0.73566 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.D3.A2J8.06 1 0.0000 0.84866 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FS.A1ZF.06 2 0.0808 0.90345 0.00 0.96 0.00 0.00 0.00 0.00 0.00 0.04
#> TCGA.FS.A1ZC.06 2 0.0000 0.91799 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EE.A20H.06 5 0.3714 0.18871 0.00 0.00 0.00 0.00 0.54 0.00 0.02 0.44
#> TCGA.EE.A29W.06 3 0.1341 0.56000 0.00 0.00 0.92 0.00 0.00 0.00 0.00 0.08
#> TCGA.D3.A1QA.07 4 0.3449 0.33858 0.00 0.00 0.32 0.66 0.00 0.00 0.00 0.02
#> TCGA.BF.A1PV.01 5 0.0471 0.78164 0.00 0.00 0.00 0.00 0.98 0.00 0.00 0.02
#> TCGA.EE.A29S.06 3 0.5792 0.26225 0.00 0.00 0.46 0.28 0.20 0.00 0.00 0.06
#> TCGA.DA.A1HV.06 3 0.1275 0.55725 0.00 0.00 0.94 0.00 0.02 0.00 0.00 0.04
#> TCGA.FS.A1Z0.06 1 0.5158 0.32380 0.44 0.00 0.00 0.26 0.00 0.00 0.00 0.30
#> TCGA.EE.A2GO.06 2 0.1341 0.87955 0.00 0.92 0.00 0.00 0.00 0.00 0.00 0.08
#> TCGA.EB.A1NK.01 1 0.2756 0.74300 0.74 0.00 0.00 0.00 0.00 0.00 0.00 0.26
#> TCGA.GN.A26D.06 7 0.0000 0.82698 0.00 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.EE.A2MJ.06 1 0.0000 0.84866 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.ER.A198.06 5 0.0471 0.78164 0.00 0.00 0.00 0.00 0.98 0.00 0.00 0.02
#> TCGA.EE.A17X.06 2 0.1091 0.89360 0.00 0.94 0.00 0.00 0.00 0.00 0.00 0.06
#> TCGA.EE.A2M5.06 4 0.2114 0.74376 0.00 0.00 0.00 0.84 0.00 0.00 0.00 0.16
#> TCGA.GN.A266.06 4 0.3374 0.65856 0.02 0.00 0.00 0.68 0.00 0.00 0.00 0.30
#> TCGA.D3.A3C1.06 4 0.0941 0.72594 0.00 0.00 0.02 0.96 0.00 0.00 0.02 0.00
#> TCGA.D3.A2JH.06 1 0.0000 0.84866 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EE.A20F.06 4 0.0000 0.73566 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.EE.A29E.06 1 0.2267 0.78619 0.82 0.00 0.00 0.00 0.00 0.00 0.00 0.18
#> TCGA.ER.A2NG.06 1 0.3374 0.70258 0.68 0.00 0.00 0.02 0.00 0.00 0.00 0.30
#> TCGA.ER.A193.06 7 0.0471 0.82729 0.00 0.00 0.00 0.00 0.00 0.00 0.98 0.02
#> TCGA.FS.A1ZW.06 4 0.0471 0.74368 0.00 0.00 0.00 0.98 0.00 0.00 0.00 0.02
#> TCGA.ER.A19O.06 4 0.2938 0.67463 0.00 0.00 0.00 0.70 0.00 0.00 0.00 0.30
#> TCGA.EE.A2ME.06 1 0.0000 0.84866 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EE.A20B.06 4 0.2534 0.53600 0.00 0.00 0.22 0.78 0.00 0.00 0.00 0.00
#> TCGA.EE.A3AF.06 3 0.4677 0.12332 0.00 0.00 0.54 0.00 0.32 0.00 0.00 0.14
#> TCGA.GN.A265.06 1 0.0000 0.84866 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FS.A1YX.06 3 0.6965 0.10319 0.00 0.00 0.32 0.26 0.12 0.00 0.26 0.04
#> TCGA.FS.A1ZJ.06 5 0.3333 0.08576 0.00 0.00 0.00 0.00 0.50 0.00 0.50 0.00
#> TCGA.ER.A19H.06 3 0.2534 0.49383 0.00 0.00 0.78 0.22 0.00 0.00 0.00 0.00
#> TCGA.EE.A3AC.06 5 0.0471 0.78511 0.00 0.00 0.00 0.00 0.98 0.00 0.02 0.00
#> TCGA.EE.A2MU.06 1 0.2852 0.73146 0.72 0.00 0.00 0.00 0.00 0.00 0.00 0.28
#> TCGA.ER.A194.01 4 0.0000 0.73566 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.EE.A2MS.06 7 0.0471 0.82729 0.00 0.00 0.00 0.00 0.00 0.00 0.98 0.02
#> TCGA.EE.A29R.06 6 0.2994 0.74099 0.00 0.14 0.00 0.00 0.00 0.80 0.00 0.06
#> TCGA.D9.A1X3.06 6 0.0000 0.94582 0.00 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.EE.A29X.06 5 0.5371 0.36234 0.00 0.00 0.22 0.10 0.60 0.00 0.02 0.06
#> TCGA.EE.A2GK.06 1 0.0000 0.84866 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EE.A3AA.06 1 0.0000 0.84866 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.ER.A2NE.06 2 0.0471 0.92255 0.00 0.98 0.00 0.00 0.00 0.02 0.00 0.00
#> TCGA.EE.A2GR.06 5 0.1275 0.78249 0.00 0.00 0.00 0.00 0.94 0.00 0.02 0.04
#> TCGA.FS.A1ZD.06 5 0.3237 0.35935 0.00 0.00 0.00 0.00 0.60 0.00 0.40 0.00
#> TCGA.ER.A19P.06 1 0.0000 0.84866 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D3.A1Q8.06 4 0.3374 0.65856 0.02 0.00 0.00 0.68 0.00 0.00 0.00 0.30
#> TCGA.ER.A2NC.06 7 0.4575 0.49449 0.00 0.00 0.12 0.22 0.00 0.00 0.64 0.02
#> TCGA.BF.A1Q0.01 7 0.0000 0.82698 0.00 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.FS.A1ZP.06 5 0.1563 0.76227 0.00 0.00 0.00 0.00 0.90 0.00 0.00 0.10
#> TCGA.EE.A182.06 7 0.0000 0.82698 0.00 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.D9.A1JW.06 7 0.1887 0.79046 0.00 0.00 0.00 0.04 0.00 0.00 0.90 0.06
#> TCGA.D3.A1Q7.06 1 0.1947 0.80508 0.86 0.00 0.00 0.00 0.00 0.00 0.00 0.14
#> TCGA.EE.A185.06 2 0.0471 0.92255 0.00 0.98 0.00 0.00 0.00 0.02 0.00 0.00
#> TCGA.EE.A2GJ.06 7 0.0000 0.82698 0.00 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.D3.A3CB.06 1 0.0000 0.84866 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EE.A2GU.06 7 0.0808 0.81067 0.00 0.00 0.00 0.04 0.00 0.00 0.96 0.00
#> TCGA.ER.A195.06 1 0.2938 0.71837 0.70 0.00 0.00 0.00 0.00 0.00 0.00 0.30
#> TCGA.FS.A1Z7.06 7 0.0000 0.82698 0.00 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.EE.A2M6.06 2 0.0471 0.92255 0.00 0.98 0.00 0.00 0.00 0.02 0.00 0.00
#> TCGA.ER.A19K.01 7 0.2025 0.77939 0.00 0.00 0.00 0.10 0.00 0.00 0.88 0.02
#> TCGA.DA.A1HY.06 3 0.0000 0.56966 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D3.A3C7.06 3 0.4100 0.14754 0.00 0.00 0.58 0.00 0.36 0.00 0.00 0.06
#> TCGA.EE.A2MP.06 3 0.0808 0.56749 0.00 0.00 0.96 0.04 0.00 0.00 0.00 0.00
#> TCGA.EE.A29H.06 2 0.5163 0.09855 0.00 0.48 0.36 0.00 0.02 0.00 0.00 0.14
#> TCGA.FR.A3YO.06 4 0.3729 0.69162 0.00 0.00 0.00 0.72 0.00 0.00 0.10 0.18
#> TCGA.XV.AB01.01 2 0.1804 0.86620 0.00 0.90 0.00 0.00 0.02 0.00 0.00 0.08
#> TCGA.RP.A694.06 7 0.6592 0.16087 0.00 0.00 0.22 0.24 0.08 0.00 0.42 0.04
#> TCGA.EB.A5SF.01 1 0.0000 0.84866 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.ER.A19G.06 3 0.2680 0.52454 0.00 0.02 0.84 0.00 0.02 0.00 0.00 0.12
#> TCGA.EE.A2GE.06 1 0.0000 0.84866 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.GF.A3OT.06 1 0.4686 0.54918 0.56 0.00 0.00 0.16 0.00 0.00 0.00 0.28
#> TCGA.ER.A2NF.06 1 0.1765 0.81288 0.88 0.00 0.00 0.00 0.00 0.00 0.00 0.12
#> TCGA.RP.A695.06 5 0.1804 0.75112 0.00 0.00 0.02 0.00 0.90 0.00 0.00 0.08
#> TCGA.BF.AAP7.01 1 0.0471 0.84452 0.98 0.00 0.00 0.00 0.00 0.00 0.00 0.02
#> TCGA.EB.A3Y7.01 7 0.3404 0.63990 0.00 0.00 0.00 0.04 0.00 0.00 0.72 0.24
#> TCGA.EB.A3XC.01 3 0.0471 0.56860 0.00 0.00 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.ER.A19W.06 1 0.3374 0.70258 0.68 0.00 0.00 0.02 0.00 0.00 0.00 0.30
#> TCGA.FR.A69P.06 3 0.1947 0.53133 0.00 0.00 0.86 0.14 0.00 0.00 0.00 0.00
#> TCGA.RP.A693.06 7 0.3198 0.63430 0.00 0.00 0.00 0.02 0.00 0.00 0.72 0.26
#> TCGA.FW.A3TV.06 1 0.0000 0.84866 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FW.A3R5.11 1 0.0000 0.84866 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FW.A3TU.06 7 0.3015 0.43116 0.00 0.00 0.00 0.00 0.32 0.00 0.68 0.00
#> TCGA.BF.AAP8.01 7 0.1091 0.81118 0.00 0.00 0.00 0.00 0.00 0.00 0.94 0.06
#> TCGA.EE.A2MM.06 5 0.0471 0.78511 0.00 0.00 0.00 0.00 0.98 0.00 0.02 0.00
#> TCGA.DA.A1HW.06 4 0.2856 0.72378 0.00 0.00 0.00 0.78 0.00 0.00 0.02 0.20
#> TCGA.DA.A1IC.06 5 0.1804 0.75112 0.00 0.00 0.02 0.00 0.90 0.00 0.00 0.08
#> TCGA.XV.AAZV.01 1 0.0000 0.84866 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D3.A3C6.06 3 0.2856 0.46890 0.00 0.02 0.78 0.00 0.00 0.00 0.00 0.20
#> TCGA.EE.A29C.06 1 0.3675 0.68306 0.66 0.00 0.00 0.04 0.00 0.00 0.00 0.30
#> TCGA.BF.AAP2.01 2 0.0000 0.91799 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EE.A2A2.06 3 0.2680 0.53405 0.00 0.02 0.84 0.00 0.02 0.00 0.00 0.12
#> TCGA.GF.A6C8.06 4 0.1563 0.69396 0.00 0.00 0.00 0.90 0.00 0.00 0.10 0.00
#> TCGA.RP.A690.06 1 0.1765 0.81288 0.88 0.00 0.00 0.00 0.00 0.00 0.00 0.12
#> TCGA.FW.A5DY.06 1 0.0000 0.84866 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DA.A1I4.06 1 0.0471 0.84452 0.98 0.00 0.00 0.00 0.00 0.00 0.00 0.02
#> TCGA.EE.A29V.06 4 0.3291 0.67177 0.02 0.00 0.00 0.70 0.00 0.00 0.00 0.28
#> TCGA.GF.A6C9.06 1 0.0000 0.84866 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EE.A2GT.06 1 0.0000 0.84866 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.GN.A9SD.06 1 0.0471 0.84452 0.98 0.00 0.00 0.00 0.00 0.00 0.00 0.02
#> TCGA.EE.A3AB.06 4 0.0471 0.72396 0.00 0.00 0.02 0.98 0.00 0.00 0.00 0.00
#> TCGA.BF.AAP6.01 3 0.2856 0.46890 0.00 0.02 0.78 0.00 0.00 0.00 0.00 0.20
#> TCGA.EB.A5SH.06 7 0.0000 0.82698 0.00 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.D9.A6E9.06 7 0.5165 0.11198 0.00 0.00 0.00 0.28 0.00 0.00 0.44 0.28
#> TCGA.BF.AAP4.01 4 0.2719 0.73192 0.00 0.00 0.00 0.80 0.00 0.00 0.02 0.18
#> TCGA.EE.A2GM.06 2 0.0471 0.92255 0.00 0.98 0.00 0.00 0.00 0.02 0.00 0.00
#> TCGA.D3.A3CF.06 1 0.0000 0.84866 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D9.A6EC.06 2 0.0471 0.92255 0.00 0.98 0.00 0.00 0.00 0.02 0.00 0.00
#> TCGA.DA.A1I1.06 4 0.3095 0.48959 0.00 0.00 0.24 0.74 0.00 0.00 0.00 0.02
#> TCGA.HR.A2OH.06 1 0.2938 0.71837 0.70 0.00 0.00 0.00 0.00 0.00 0.00 0.30
#> TCGA.EE.A2MT.06 7 0.1091 0.81118 0.00 0.00 0.00 0.00 0.00 0.00 0.94 0.06
#> TCGA.ER.A19M.06 4 0.1947 0.74887 0.00 0.00 0.00 0.86 0.00 0.00 0.00 0.14
#> TCGA.GN.A26C.01 1 0.0808 0.83959 0.96 0.00 0.00 0.00 0.00 0.00 0.00 0.04
#> TCGA.FS.A1ZA.06 3 0.4968 0.32848 0.00 0.00 0.52 0.38 0.02 0.00 0.02 0.06
#> TCGA.EB.A5SE.01 6 0.0000 0.94582 0.00 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.ER.A3PL.06 5 0.0471 0.78511 0.00 0.00 0.00 0.00 0.98 0.00 0.02 0.00
#> TCGA.FR.A3R1.01 3 0.4100 0.14571 0.00 0.00 0.58 0.00 0.36 0.00 0.00 0.06
#> TCGA.EE.A2MI.06 4 0.0000 0.73566 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.D3.A3CE.06 3 0.3746 0.41776 0.00 0.00 0.64 0.32 0.00 0.00 0.00 0.04
#> TCGA.D3.A5GT.01 5 0.3142 0.37462 0.00 0.00 0.00 0.00 0.64 0.36 0.00 0.00
#> TCGA.ER.A2NB.01 7 0.3404 0.63990 0.00 0.00 0.00 0.04 0.00 0.00 0.72 0.24
#> TCGA.D3.A1Q5.06 7 0.4918 0.18659 0.00 0.00 0.02 0.10 0.00 0.00 0.50 0.38
#> TCGA.EB.A5UN.06 1 0.2938 0.71837 0.70 0.00 0.00 0.00 0.00 0.00 0.00 0.30
#> TCGA.EB.A299.01 3 0.2852 0.45793 0.00 0.00 0.72 0.28 0.00 0.00 0.00 0.00
#> TCGA.DA.A1IA.06 5 0.0808 0.77459 0.00 0.00 0.00 0.00 0.96 0.04 0.00 0.00
#> TCGA.EB.A5SG.06 1 0.0000 0.84866 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D9.A6EA.06 6 0.0000 0.94582 0.00 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.XV.AAZY.01 1 0.2852 0.73146 0.72 0.00 0.00 0.00 0.00 0.00 0.00 0.28
#> TCGA.EB.A57M.01 4 0.2756 0.47806 0.00 0.00 0.26 0.74 0.00 0.00 0.00 0.00
#> TCGA.EE.A2A6.06 4 0.4144 0.65008 0.00 0.00 0.00 0.66 0.00 0.00 0.12 0.22
#> TCGA.D3.A2JA.06 1 0.4799 0.51701 0.54 0.00 0.00 0.18 0.00 0.00 0.00 0.28
#> TCGA.D3.A1Q1.06 7 0.0000 0.82698 0.00 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.EB.A3XF.01 3 0.1563 0.55477 0.00 0.00 0.90 0.00 0.00 0.00 0.00 0.10
#> TCGA.D3.A2JF.06 3 0.3570 0.39587 0.00 0.00 0.62 0.36 0.00 0.00 0.00 0.02
#> TCGA.XV.AAZW.01 2 0.1804 0.86620 0.00 0.90 0.00 0.00 0.02 0.00 0.00 0.08
#> TCGA.EB.A3Y6.01 4 0.2406 0.56475 0.00 0.00 0.20 0.80 0.00 0.00 0.00 0.00
#> TCGA.EB.A3XE.01 7 0.0000 0.82698 0.00 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.D9.A3Z4.01 5 0.0471 0.78511 0.00 0.00 0.00 0.00 0.98 0.00 0.02 0.00
#> TCGA.FW.A3R5.06 7 0.0471 0.82729 0.00 0.00 0.00 0.00 0.00 0.00 0.98 0.02
#> TCGA.EE.A2GI.06 4 0.1563 0.66647 0.00 0.00 0.10 0.90 0.00 0.00 0.00 0.00
#> TCGA.EE.A2GL.06 1 0.0000 0.84866 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EB.A3XB.01 4 0.0471 0.74368 0.00 0.00 0.00 0.98 0.00 0.00 0.00 0.02
#> TCGA.BF.AAOU.01 1 0.2938 0.71837 0.70 0.00 0.00 0.00 0.00 0.00 0.00 0.30
#> TCGA.EB.A3XD.01 1 0.0000 0.84866 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EE.A2MD.06 4 0.1341 0.75188 0.00 0.00 0.00 0.92 0.00 0.00 0.00 0.08
#> TCGA.YD.A9TB.06 5 0.0000 0.78377 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.W3.AA1V.06 4 0.0808 0.71194 0.00 0.00 0.04 0.96 0.00 0.00 0.00 0.00
#> TCGA.ER.A2ND.06 7 0.1341 0.76723 0.00 0.00 0.00 0.00 0.08 0.00 0.92 0.00
#> TCGA.D3.A2JK.06 4 0.2406 0.56475 0.00 0.00 0.20 0.80 0.00 0.00 0.00 0.00
#> TCGA.FS.A1ZB.06 1 0.5033 0.41735 0.48 0.00 0.00 0.22 0.00 0.00 0.00 0.30
#> TCGA.EE.A29D.06 6 0.0000 0.94582 0.00 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.EB.A5UM.01 7 0.0000 0.82698 0.00 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.QB.A6FS.06 1 0.1341 0.82755 0.92 0.00 0.00 0.00 0.00 0.00 0.00 0.08
#> TCGA.D9.A3Z1.06 1 0.2852 0.73146 0.72 0.00 0.00 0.00 0.00 0.00 0.00 0.28
#> TCGA.D3.A2JN.06 1 0.5033 0.41735 0.48 0.00 0.00 0.22 0.00 0.00 0.00 0.30
#> TCGA.FR.A3YN.06 2 0.4211 0.59732 0.00 0.70 0.16 0.00 0.02 0.00 0.00 0.12
#> TCGA.FS.A1ZT.06 1 0.0000 0.84866 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D9.A148.06 4 0.3095 0.70309 0.00 0.00 0.00 0.74 0.00 0.00 0.02 0.24
#> TCGA.HR.A2OG.06 4 0.3291 0.67177 0.02 0.00 0.00 0.70 0.00 0.00 0.00 0.28
#> TCGA.EE.A2ML.06 4 0.3971 0.00999 0.00 0.00 0.42 0.54 0.00 0.00 0.00 0.04
#> TCGA.EB.A5UL.06 4 0.3374 0.66270 0.00 0.00 0.00 0.68 0.00 0.00 0.02 0.30
#> TCGA.EE.A29T.06 7 0.3198 0.63430 0.00 0.00 0.00 0.02 0.00 0.00 0.72 0.26
#> TCGA.D9.A3Z3.06 1 0.4686 0.54959 0.56 0.00 0.00 0.16 0.00 0.00 0.00 0.28
#> TCGA.D9.A4Z3.01 5 0.3237 0.35504 0.00 0.00 0.00 0.00 0.60 0.00 0.00 0.40
#> TCGA.ER.A3ES.06 7 0.0000 0.82698 0.00 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.XV.A9VZ.01 1 0.0000 0.84866 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.QB.AA9O.06 3 0.3291 0.45437 0.00 0.00 0.70 0.28 0.00 0.00 0.00 0.02
#> TCGA.EB.A44Q.06 7 0.0000 0.82698 0.00 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.EB.A44R.06 7 0.0471 0.82729 0.00 0.00 0.00 0.00 0.00 0.00 0.98 0.02
#> TCGA.BF.A3DJ.01 3 0.3178 0.50036 0.00 0.02 0.80 0.00 0.04 0.00 0.00 0.14
#> TCGA.EE.A3JD.06 1 0.0000 0.84866 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D3.A51N.06 4 0.0471 0.74368 0.00 0.00 0.00 0.98 0.00 0.00 0.00 0.02
#> TCGA.EB.A44N.01 1 0.2756 0.74300 0.74 0.00 0.00 0.00 0.00 0.00 0.00 0.26
#> TCGA.EE.A3J3.06 5 0.2623 0.70728 0.00 0.00 0.06 0.00 0.84 0.00 0.00 0.10
#> TCGA.XV.A9W5.01 3 0.3658 0.36826 0.00 0.00 0.58 0.40 0.00 0.00 0.00 0.02
#> TCGA.D3.A51G.06 3 0.1341 0.55604 0.00 0.00 0.92 0.08 0.00 0.00 0.00 0.00
#> TCGA.EB.A4P0.01 2 0.0808 0.90345 0.00 0.96 0.00 0.00 0.00 0.00 0.00 0.04
#> TCGA.BF.AAP1.01 6 0.0000 0.94582 0.00 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.EE.A3J4.06 6 0.3193 0.37729 0.00 0.00 0.00 0.00 0.38 0.62 0.00 0.00
#> TCGA.Z2.AA3V.06 1 0.0471 0.84452 0.98 0.00 0.00 0.00 0.00 0.00 0.00 0.02
#> TCGA.LH.A9QB.06 6 0.0000 0.94582 0.00 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.D3.A51J.06 4 0.3293 0.70713 0.00 0.00 0.00 0.74 0.00 0.00 0.04 0.22
#> TCGA.3N.A9WC.06 7 0.1607 0.80269 0.00 0.00 0.00 0.04 0.00 0.00 0.92 0.04
#> TCGA.DA.A3F8.06 1 0.1341 0.82755 0.92 0.00 0.00 0.00 0.00 0.00 0.00 0.08
#> TCGA.D9.A4Z6.06 3 0.3237 0.36068 0.00 0.00 0.60 0.40 0.00 0.00 0.00 0.00
#> TCGA.D3.A51R.06 2 0.0808 0.90345 0.00 0.96 0.00 0.00 0.00 0.00 0.00 0.04
#> TCGA.EB.A4OZ.01 1 0.0000 0.84866 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FS.A4FB.06 3 0.2856 0.46890 0.00 0.02 0.78 0.00 0.00 0.00 0.00 0.20
#> TCGA.EE.A3JE.06 1 0.0000 0.84866 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.W3.AA1W.06 1 0.2852 0.73181 0.72 0.00 0.00 0.00 0.00 0.00 0.00 0.28
#> TCGA.DA.A1I0.06 4 0.2938 0.67463 0.00 0.00 0.00 0.70 0.00 0.00 0.00 0.30
#> TCGA.D3.A51F.06 1 0.0000 0.84866 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.IH.A3EA.01 5 0.1557 0.75559 0.00 0.00 0.02 0.00 0.92 0.00 0.00 0.06
#> TCGA.EB.A431.01 4 0.0471 0.74368 0.00 0.00 0.00 0.98 0.00 0.00 0.00 0.02
#> TCGA.EB.A97M.01 6 0.0000 0.94582 0.00 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.BF.AAOX.01 4 0.2406 0.56475 0.00 0.00 0.20 0.80 0.00 0.00 0.00 0.00
#> TCGA.DA.A3F5.06 7 0.2407 0.76281 0.00 0.00 0.00 0.08 0.00 0.00 0.86 0.06
#> TCGA.YD.A9TA.06 4 0.1341 0.75188 0.00 0.00 0.00 0.92 0.00 0.00 0.00 0.08
#> TCGA.DA.A3F2.06 1 0.0000 0.84866 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EB.A44O.01 5 0.0471 0.78511 0.00 0.00 0.00 0.00 0.98 0.00 0.02 0.00
#> TCGA.EB.A4IQ.01 7 0.1091 0.81118 0.00 0.00 0.00 0.00 0.00 0.00 0.94 0.06
#> TCGA.EB.A4IS.01 1 0.1563 0.82156 0.90 0.00 0.00 0.00 0.00 0.00 0.00 0.10
#> TCGA.YG.AA3O.06 5 0.0808 0.77579 0.00 0.00 0.00 0.00 0.96 0.00 0.00 0.04
#> TCGA.ER.A3EV.06 7 0.0471 0.82729 0.00 0.00 0.00 0.00 0.00 0.00 0.98 0.02
#> TCGA.3N.A9WD.06 1 0.5033 0.41735 0.48 0.00 0.00 0.22 0.00 0.00 0.00 0.30
#> TCGA.BF.A3DM.01 8 0.3570 0.59060 0.00 0.02 0.36 0.00 0.00 0.00 0.00 0.62
#> TCGA.XV.A9W2.01 7 0.3657 0.64343 0.00 0.00 0.00 0.08 0.00 0.00 0.72 0.20
#> TCGA.W3.AA1Q.06 5 0.1804 0.75112 0.00 0.00 0.02 0.00 0.90 0.00 0.00 0.08
#> TCGA.WE.AAA0.06 4 0.2114 0.74376 0.00 0.00 0.00 0.84 0.00 0.00 0.00 0.16
#> TCGA.W3.AA1R.06 2 0.5163 0.09457 0.00 0.48 0.36 0.00 0.02 0.00 0.00 0.14
#> TCGA.EE.A3J5.06 4 0.1947 0.74884 0.00 0.00 0.00 0.86 0.00 0.00 0.00 0.14
#> TCGA.EB.A4OY.01 1 0.1947 0.80508 0.86 0.00 0.00 0.00 0.00 0.00 0.00 0.14
#> TCGA.FS.A4FD.06 7 0.0000 0.82698 0.00 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.BF.AAP0.06 1 0.0000 0.84866 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.YG.AA3P.06 5 0.4628 0.27163 0.00 0.00 0.00 0.00 0.52 0.00 0.36 0.12
#> TCGA.EE.A3JA.06 3 0.1947 0.53325 0.00 0.00 0.86 0.00 0.00 0.00 0.00 0.14
#> TCGA.W3.AA21.06 2 0.0471 0.92255 0.00 0.98 0.00 0.00 0.00 0.02 0.00 0.00
#> TCGA.WE.AAA3.06 7 0.0000 0.82698 0.00 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.FS.A4F4.06 3 0.0000 0.56966 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BF.A3DN.01 5 0.4211 0.47351 0.00 0.02 0.12 0.00 0.70 0.00 0.00 0.16
#> TCGA.ER.A3ET.06 7 0.0000 0.82698 0.00 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.W3.AA1O.06 5 0.0471 0.78511 0.00 0.00 0.00 0.00 0.98 0.00 0.02 0.00
#> TCGA.D3.A51E.06 3 0.2404 0.53404 0.00 0.00 0.84 0.14 0.00 0.00 0.00 0.02
#> TCGA.Z2.AA3S.06 6 0.0000 0.94582 0.00 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.YG.AA3N.01 5 0.6649 0.17730 0.00 0.00 0.22 0.16 0.46 0.00 0.10 0.06
#> TCGA.WE.AA9Y.06 1 0.0000 0.84866 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FS.A4F5.06 6 0.0000 0.94582 0.00 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.EE.A3J7.06 6 0.2888 0.71710 0.00 0.00 0.00 0.00 0.16 0.80 0.00 0.04
#> TCGA.FS.A4F8.06 1 0.0000 0.84866 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DA.A3F3.06 8 0.3015 0.63269 0.00 0.00 0.32 0.00 0.00 0.00 0.00 0.68
#> TCGA.D3.A51H.06 1 0.0000 0.84866 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BF.A3DL.01 1 0.5237 0.21068 0.40 0.00 0.00 0.30 0.00 0.00 0.00 0.30
#> TCGA.D3.A51T.06 2 0.1804 0.86620 0.00 0.90 0.00 0.00 0.02 0.00 0.00 0.08
#> TCGA.D3.A51K.06 5 0.3329 0.10136 0.00 0.00 0.00 0.00 0.52 0.00 0.00 0.48
#> TCGA.EB.A44P.01 5 0.0808 0.77579 0.00 0.00 0.00 0.00 0.96 0.00 0.00 0.04
#> TCGA.D9.A4Z5.01 2 0.1563 0.85334 0.00 0.90 0.00 0.00 0.00 0.10 0.00 0.00
#> TCGA.WE.AAA4.06 1 0.0471 0.84452 0.98 0.00 0.00 0.00 0.00 0.00 0.00 0.02
#> TCGA.3N.A9WB.06 6 0.0000 0.94582 0.00 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.EE.A3J8.06 2 0.0471 0.92255 0.00 0.98 0.00 0.00 0.00 0.02 0.00 0.00
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
consensus_heatmap(res, k = 7)
consensus_heatmap(res, k = 8)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
membership_heatmap(res, k = 7)
membership_heatmap(res, k = 8)
As soon as the classes for columns are determined, the signatures that are significantly different between subgroups can be looked for. Following are the heatmaps for signatures.
get_signatures(res, k = 2)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
get_signatures(res, k = 7)
get_signatures(res, k = 8)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. To get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows (which is done by automatically selecting number of clusters).If there are too many signatures, top_signatures = ... can be set to only show the
signatures with the highest FDRs:
# code only for demonstration
# e.g. to show the top 500 most significant rows
tb = get_signature(res, k = ..., top_signatures = 500)
If the signatures are defined as these which are uniquely high in current group, diff_method argument
can be set to "uniquely_high_in_one_group":
# code only for demonstration
tb = get_signature(res, k = ..., diff_method = "uniquely_high_in_one_group")
UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
dimension_reduction(res, k = 7, method = "UMAP")
dimension_reduction(res, k = 8, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
If matrix rows can be associated to genes, consider to use functional_enrichment(res,
...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.
Parent node: Node0. Child nodes: Node011 , Node012 , Node013 , Node014-leaf , Node021 , Node022 , Node023-leaf , Node031 , Node032 , Node041 , Node042 , Node043 , Node044 , Node051 , Node052 .
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 134 columns.
#> Top rows (1000) are extracted by 'SD' method.
#> Subgroups are detected by 'skmeans' method.
#> Performed in total 350 partitions by row resampling.
#> Best k for subgroups seems to be 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 0.4971 0.503 0.503
#> 3 3 1.000 0.991 0.989 0.3062 0.847 0.696
#> 4 4 1.000 0.976 0.981 0.1495 0.903 0.722
#> 5 5 0.868 0.877 0.917 0.0490 0.942 0.778
#> 6 6 0.811 0.807 0.862 0.0276 0.964 0.836
#> 7 7 0.811 0.766 0.803 0.0216 0.968 0.852
#> 8 8 0.786 0.586 0.803 0.0235 0.968 0.852
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.FR.A728.01 2 0 1 0 1
#> TCGA.GN.A4U8.11 1 0 1 1 0
#> TCGA.D3.A8GO.06 2 0 1 0 1
#> TCGA.D3.A8GB.06 1 0 1 1 0
#> TCGA.WE.A8ZN.06 1 0 1 1 0
#> TCGA.D3.A8GN.06 2 0 1 0 1
#> TCGA.EB.A550.01 2 0 1 0 1
#> TCGA.GF.A4EO.06 2 0 1 0 1
#> TCGA.WE.A8K4.01 1 0 1 1 0
#> TCGA.EB.A6QY.01 1 0 1 1 0
#> TCGA.WE.A8K1.06 1 0 1 1 0
#> TCGA.ER.A42L.06 1 0 1 1 0
#> TCGA.FR.A8YE.06 1 0 1 1 0
#> TCGA.EE.A3JH.06 1 0 1 1 0
#> TCGA.FR.A44A.06 2 0 1 0 1
#> TCGA.EB.A5VV.06 2 0 1 0 1
#> TCGA.GN.A4U5.01 2 0 1 0 1
#> TCGA.D3.A3MR.06 1 0 1 1 0
#> TCGA.EB.A6L9.06 1 0 1 1 0
#> TCGA.EB.A430.01 1 0 1 1 0
#> TCGA.D3.A8GE.06 1 0 1 1 0
#> TCGA.D3.A8GD.06 2 0 1 0 1
#> TCGA.EE.A183.06 1 0 1 1 0
#> TCGA.ER.A2NH.06 1 0 1 1 0
#> TCGA.EE.A2M8.06 2 0 1 0 1
#> TCGA.EE.A2MR.06 1 0 1 1 0
#> TCGA.DA.A1I5.06 2 0 1 0 1
#> TCGA.ER.A19D.06 2 0 1 0 1
#> TCGA.ER.A199.06 2 0 1 0 1
#> TCGA.W3.A828.06 1 0 1 1 0
#> TCGA.BF.A1PX.01 1 0 1 1 0
#> TCGA.EE.A2GH.06 1 0 1 1 0
#> TCGA.ER.A196.01 2 0 1 0 1
#> TCGA.ER.A19S.06 2 0 1 0 1
#> TCGA.EE.A29N.06 1 0 1 1 0
#> TCGA.D3.A2JB.06 2 0 1 0 1
#> TCGA.D3.A2JD.06 1 0 1 1 0
#> TCGA.FS.A1Z4.06 1 0 1 1 0
#> TCGA.FR.A7UA.06 2 0 1 0 1
#> TCGA.ER.A2NF.01 1 0 1 1 0
#> TCGA.GN.A263.01 1 0 1 1 0
#> TCGA.ER.A19N.06 1 0 1 1 0
#> TCGA.FR.A7U9.06 2 0 1 0 1
#> TCGA.ER.A19Q.06 2 0 1 0 1
#> TCGA.EE.A2MG.06 1 0 1 1 0
#> TCGA.EE.A2MC.06 1 0 1 1 0
#> TCGA.EE.A2A0.06 2 0 1 0 1
#> TCGA.EE.A29G.06 1 0 1 1 0
#> TCGA.GN.A269.01 1 0 1 1 0
#> TCGA.EE.A2A1.06 1 0 1 1 0
#> TCGA.ER.A1A1.06 1 0 1 1 0
#> TCGA.EE.A2MH.06 1 0 1 1 0
#> TCGA.D3.A3BZ.06 1 0 1 1 0
#> TCGA.ER.A197.06 2 0 1 0 1
#> TCGA.DA.A1IB.06 2 0 1 0 1
#> TCGA.GN.A261.06 2 0 1 0 1
#> TCGA.D3.A1QB.06 2 0 1 0 1
#> TCGA.D3.A3C8.06 2 0 1 0 1
#> TCGA.ER.A19A.06 1 0 1 1 0
#> TCGA.EE.A29M.06 2 0 1 0 1
#> TCGA.D3.A2J7.06 1 0 1 1 0
#> TCGA.EE.A2GD.06 2 0 1 0 1
#> TCGA.D3.A2J9.06 1 0 1 1 0
#> TCGA.D3.A1Q4.06 2 0 1 0 1
#> TCGA.D3.A2J8.06 1 0 1 1 0
#> TCGA.FS.A1Z0.06 2 0 1 0 1
#> TCGA.EB.A1NK.01 1 0 1 1 0
#> TCGA.EE.A2MJ.06 1 0 1 1 0
#> TCGA.D3.A2JH.06 1 0 1 1 0
#> TCGA.EE.A29E.06 1 0 1 1 0
#> TCGA.ER.A2NG.06 2 0 1 0 1
#> TCGA.EE.A2ME.06 1 0 1 1 0
#> TCGA.GN.A265.06 1 0 1 1 0
#> TCGA.EE.A2MU.06 1 0 1 1 0
#> TCGA.EE.A2GK.06 2 0 1 0 1
#> TCGA.EE.A3AA.06 1 0 1 1 0
#> TCGA.ER.A19P.06 2 0 1 0 1
#> TCGA.D3.A1Q8.06 1 0 1 1 0
#> TCGA.D3.A1Q7.06 2 0 1 0 1
#> TCGA.D3.A3CB.06 1 0 1 1 0
#> TCGA.ER.A195.06 1 0 1 1 0
#> TCGA.EB.A5SF.01 2 0 1 0 1
#> TCGA.EE.A2GE.06 1 0 1 1 0
#> TCGA.GF.A3OT.06 2 0 1 0 1
#> TCGA.ER.A2NF.06 1 0 1 1 0
#> TCGA.BF.AAP7.01 2 0 1 0 1
#> TCGA.ER.A19W.06 2 0 1 0 1
#> TCGA.RP.A693.06 1 0 1 1 0
#> TCGA.FW.A3TV.06 2 0 1 0 1
#> TCGA.FW.A3R5.11 1 0 1 1 0
#> TCGA.XV.AAZV.01 2 0 1 0 1
#> TCGA.EE.A29C.06 1 0 1 1 0
#> TCGA.RP.A690.06 2 0 1 0 1
#> TCGA.FW.A5DY.06 2 0 1 0 1
#> TCGA.DA.A1I4.06 1 0 1 1 0
#> TCGA.GF.A6C9.06 1 0 1 1 0
#> TCGA.EE.A2GT.06 1 0 1 1 0
#> TCGA.GN.A9SD.06 2 0 1 0 1
#> TCGA.D3.A3CF.06 2 0 1 0 1
#> TCGA.HR.A2OH.06 2 0 1 0 1
#> TCGA.GN.A26C.01 1 0 1 1 0
#> TCGA.EB.A5UN.06 1 0 1 1 0
#> TCGA.EB.A5SG.06 2 0 1 0 1
#> TCGA.XV.AAZY.01 2 0 1 0 1
#> TCGA.D3.A2JA.06 1 0 1 1 0
#> TCGA.EE.A2GL.06 2 0 1 0 1
#> TCGA.BF.AAOU.01 2 0 1 0 1
#> TCGA.EB.A3XD.01 2 0 1 0 1
#> TCGA.FS.A1ZB.06 1 0 1 1 0
#> TCGA.QB.A6FS.06 1 0 1 1 0
#> TCGA.D9.A3Z1.06 1 0 1 1 0
#> TCGA.D3.A2JN.06 2 0 1 0 1
#> TCGA.FS.A1ZT.06 1 0 1 1 0
#> TCGA.HR.A2OG.06 2 0 1 0 1
#> TCGA.D9.A3Z3.06 2 0 1 0 1
#> TCGA.XV.A9VZ.01 2 0 1 0 1
#> TCGA.EE.A3JD.06 1 0 1 1 0
#> TCGA.EB.A44N.01 1 0 1 1 0
#> TCGA.Z2.AA3V.06 2 0 1 0 1
#> TCGA.DA.A3F8.06 1 0 1 1 0
#> TCGA.EB.A4OZ.01 2 0 1 0 1
#> TCGA.EE.A3JE.06 1 0 1 1 0
#> TCGA.W3.AA1W.06 1 0 1 1 0
#> TCGA.D3.A51F.06 1 0 1 1 0
#> TCGA.DA.A3F2.06 1 0 1 1 0
#> TCGA.EB.A4IS.01 1 0 1 1 0
#> TCGA.3N.A9WD.06 1 0 1 1 0
#> TCGA.EB.A4OY.01 2 0 1 0 1
#> TCGA.BF.AAP0.06 2 0 1 0 1
#> TCGA.WE.AA9Y.06 1 0 1 1 0
#> TCGA.FS.A4F8.06 1 0 1 1 0
#> TCGA.D3.A51H.06 1 0 1 1 0
#> TCGA.BF.A3DL.01 2 0 1 0 1
#> TCGA.WE.AAA4.06 2 0 1 0 1
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.FR.A728.01 2 0.0892 0.991 0.00 0.98 0.02
#> TCGA.GN.A4U8.11 1 0.0000 0.992 1.00 0.00 0.00
#> TCGA.D3.A8GO.06 2 0.0000 0.992 0.00 1.00 0.00
#> TCGA.D3.A8GB.06 3 0.0892 0.999 0.02 0.00 0.98
#> TCGA.WE.A8ZN.06 1 0.0000 0.992 1.00 0.00 0.00
#> TCGA.D3.A8GN.06 2 0.0892 0.991 0.00 0.98 0.02
#> TCGA.EB.A550.01 2 0.0000 0.992 0.00 1.00 0.00
#> TCGA.GF.A4EO.06 2 0.0892 0.991 0.00 0.98 0.02
#> TCGA.WE.A8K4.01 1 0.0000 0.992 1.00 0.00 0.00
#> TCGA.EB.A6QY.01 3 0.0892 0.999 0.02 0.00 0.98
#> TCGA.WE.A8K1.06 1 0.0000 0.992 1.00 0.00 0.00
#> TCGA.ER.A42L.06 1 0.0000 0.992 1.00 0.00 0.00
#> TCGA.FR.A8YE.06 1 0.0000 0.992 1.00 0.00 0.00
#> TCGA.EE.A3JH.06 1 0.0000 0.992 1.00 0.00 0.00
#> TCGA.FR.A44A.06 2 0.0892 0.991 0.00 0.98 0.02
#> TCGA.EB.A5VV.06 2 0.0000 0.992 0.00 1.00 0.00
#> TCGA.GN.A4U5.01 2 0.0892 0.991 0.00 0.98 0.02
#> TCGA.D3.A3MR.06 1 0.0000 0.992 1.00 0.00 0.00
#> TCGA.EB.A6L9.06 3 0.0892 0.999 0.02 0.00 0.98
#> TCGA.EB.A430.01 3 0.0892 0.999 0.02 0.00 0.98
#> TCGA.D3.A8GE.06 3 0.0892 0.999 0.02 0.00 0.98
#> TCGA.D3.A8GD.06 2 0.0892 0.991 0.00 0.98 0.02
#> TCGA.EE.A183.06 1 0.0000 0.992 1.00 0.00 0.00
#> TCGA.ER.A2NH.06 1 0.0000 0.992 1.00 0.00 0.00
#> TCGA.EE.A2M8.06 2 0.0000 0.992 0.00 1.00 0.00
#> TCGA.EE.A2MR.06 1 0.0000 0.992 1.00 0.00 0.00
#> TCGA.DA.A1I5.06 2 0.0000 0.992 0.00 1.00 0.00
#> TCGA.ER.A19D.06 2 0.0000 0.992 0.00 1.00 0.00
#> TCGA.ER.A199.06 2 0.0892 0.991 0.00 0.98 0.02
#> TCGA.W3.A828.06 3 0.0892 0.999 0.02 0.00 0.98
#> TCGA.BF.A1PX.01 1 0.0000 0.992 1.00 0.00 0.00
#> TCGA.EE.A2GH.06 1 0.0000 0.992 1.00 0.00 0.00
#> TCGA.ER.A196.01 2 0.0000 0.992 0.00 1.00 0.00
#> TCGA.ER.A19S.06 2 0.0892 0.991 0.00 0.98 0.02
#> TCGA.EE.A29N.06 1 0.0000 0.992 1.00 0.00 0.00
#> TCGA.D3.A2JB.06 2 0.0000 0.992 0.00 1.00 0.00
#> TCGA.D3.A2JD.06 1 0.0000 0.992 1.00 0.00 0.00
#> TCGA.FS.A1Z4.06 3 0.0892 0.999 0.02 0.00 0.98
#> TCGA.FR.A7UA.06 2 0.0892 0.991 0.00 0.98 0.02
#> TCGA.ER.A2NF.01 3 0.0892 0.999 0.02 0.00 0.98
#> TCGA.GN.A263.01 3 0.0892 0.999 0.02 0.00 0.98
#> TCGA.ER.A19N.06 1 0.0000 0.992 1.00 0.00 0.00
#> TCGA.FR.A7U9.06 2 0.0000 0.992 0.00 1.00 0.00
#> TCGA.ER.A19Q.06 2 0.0000 0.992 0.00 1.00 0.00
#> TCGA.EE.A2MG.06 3 0.0892 0.999 0.02 0.00 0.98
#> TCGA.EE.A2MC.06 3 0.0892 0.999 0.02 0.00 0.98
#> TCGA.EE.A2A0.06 2 0.0892 0.991 0.00 0.98 0.02
#> TCGA.EE.A29G.06 1 0.0000 0.992 1.00 0.00 0.00
#> TCGA.GN.A269.01 1 0.0000 0.992 1.00 0.00 0.00
#> TCGA.EE.A2A1.06 3 0.0892 0.999 0.02 0.00 0.98
#> TCGA.ER.A1A1.06 3 0.0892 0.999 0.02 0.00 0.98
#> TCGA.EE.A2MH.06 1 0.0000 0.992 1.00 0.00 0.00
#> TCGA.D3.A3BZ.06 3 0.0892 0.999 0.02 0.00 0.98
#> TCGA.ER.A197.06 2 0.0892 0.991 0.00 0.98 0.02
#> TCGA.DA.A1IB.06 2 0.0892 0.991 0.00 0.98 0.02
#> TCGA.GN.A261.06 2 0.0000 0.992 0.00 1.00 0.00
#> TCGA.D3.A1QB.06 2 0.0000 0.992 0.00 1.00 0.00
#> TCGA.D3.A3C8.06 2 0.0892 0.991 0.00 0.98 0.02
#> TCGA.ER.A19A.06 3 0.0892 0.999 0.02 0.00 0.98
#> TCGA.EE.A29M.06 2 0.0000 0.992 0.00 1.00 0.00
#> TCGA.D3.A2J7.06 1 0.0000 0.992 1.00 0.00 0.00
#> TCGA.EE.A2GD.06 2 0.0892 0.991 0.00 0.98 0.02
#> TCGA.D3.A2J9.06 1 0.0000 0.992 1.00 0.00 0.00
#> TCGA.D3.A1Q4.06 2 0.0000 0.992 0.00 1.00 0.00
#> TCGA.D3.A2J8.06 3 0.0892 0.999 0.02 0.00 0.98
#> TCGA.FS.A1Z0.06 2 0.0000 0.992 0.00 1.00 0.00
#> TCGA.EB.A1NK.01 3 0.0892 0.999 0.02 0.00 0.98
#> TCGA.EE.A2MJ.06 1 0.0000 0.992 1.00 0.00 0.00
#> TCGA.D3.A2JH.06 1 0.0000 0.992 1.00 0.00 0.00
#> TCGA.EE.A29E.06 3 0.0892 0.999 0.02 0.00 0.98
#> TCGA.ER.A2NG.06 2 0.0892 0.991 0.00 0.98 0.02
#> TCGA.EE.A2ME.06 1 0.0000 0.992 1.00 0.00 0.00
#> TCGA.GN.A265.06 1 0.0000 0.992 1.00 0.00 0.00
#> TCGA.EE.A2MU.06 1 0.0000 0.992 1.00 0.00 0.00
#> TCGA.EE.A2GK.06 2 0.0000 0.992 0.00 1.00 0.00
#> TCGA.EE.A3AA.06 1 0.0000 0.992 1.00 0.00 0.00
#> TCGA.ER.A19P.06 2 0.0892 0.991 0.00 0.98 0.02
#> TCGA.D3.A1Q8.06 1 0.0000 0.992 1.00 0.00 0.00
#> TCGA.D3.A1Q7.06 2 0.0892 0.991 0.00 0.98 0.02
#> TCGA.D3.A3CB.06 1 0.0000 0.992 1.00 0.00 0.00
#> TCGA.ER.A195.06 3 0.0892 0.999 0.02 0.00 0.98
#> TCGA.EB.A5SF.01 2 0.0000 0.992 0.00 1.00 0.00
#> TCGA.EE.A2GE.06 1 0.0000 0.992 1.00 0.00 0.00
#> TCGA.GF.A3OT.06 2 0.0892 0.991 0.00 0.98 0.02
#> TCGA.ER.A2NF.06 3 0.0892 0.999 0.02 0.00 0.98
#> TCGA.BF.AAP7.01 2 0.0000 0.992 0.00 1.00 0.00
#> TCGA.ER.A19W.06 2 0.0892 0.991 0.00 0.98 0.02
#> TCGA.RP.A693.06 1 0.0000 0.992 1.00 0.00 0.00
#> TCGA.FW.A3TV.06 2 0.0000 0.992 0.00 1.00 0.00
#> TCGA.FW.A3R5.11 3 0.0892 0.999 0.02 0.00 0.98
#> TCGA.XV.AAZV.01 2 0.0000 0.992 0.00 1.00 0.00
#> TCGA.EE.A29C.06 3 0.1529 0.979 0.04 0.00 0.96
#> TCGA.RP.A690.06 2 0.0000 0.992 0.00 1.00 0.00
#> TCGA.FW.A5DY.06 2 0.0892 0.991 0.00 0.98 0.02
#> TCGA.DA.A1I4.06 3 0.0892 0.999 0.02 0.00 0.98
#> TCGA.GF.A6C9.06 1 0.0000 0.992 1.00 0.00 0.00
#> TCGA.EE.A2GT.06 3 0.0892 0.999 0.02 0.00 0.98
#> TCGA.GN.A9SD.06 2 0.0892 0.991 0.00 0.98 0.02
#> TCGA.D3.A3CF.06 2 0.0000 0.992 0.00 1.00 0.00
#> TCGA.HR.A2OH.06 2 0.0892 0.991 0.00 0.98 0.02
#> TCGA.GN.A26C.01 1 0.3686 0.838 0.86 0.00 0.14
#> TCGA.EB.A5UN.06 1 0.0000 0.992 1.00 0.00 0.00
#> TCGA.EB.A5SG.06 2 0.0892 0.991 0.00 0.98 0.02
#> TCGA.XV.AAZY.01 2 0.0892 0.991 0.00 0.98 0.02
#> TCGA.D3.A2JA.06 3 0.0892 0.999 0.02 0.00 0.98
#> TCGA.EE.A2GL.06 2 0.0892 0.991 0.00 0.98 0.02
#> TCGA.BF.AAOU.01 2 0.0892 0.991 0.00 0.98 0.02
#> TCGA.EB.A3XD.01 2 0.0000 0.992 0.00 1.00 0.00
#> TCGA.FS.A1ZB.06 1 0.3686 0.837 0.86 0.00 0.14
#> TCGA.QB.A6FS.06 3 0.0892 0.999 0.02 0.00 0.98
#> TCGA.D9.A3Z1.06 1 0.0000 0.992 1.00 0.00 0.00
#> TCGA.D3.A2JN.06 2 0.0892 0.991 0.00 0.98 0.02
#> TCGA.FS.A1ZT.06 3 0.0892 0.999 0.02 0.00 0.98
#> TCGA.HR.A2OG.06 2 0.0000 0.992 0.00 1.00 0.00
#> TCGA.D9.A3Z3.06 2 0.0000 0.992 0.00 1.00 0.00
#> TCGA.XV.A9VZ.01 2 0.0000 0.992 0.00 1.00 0.00
#> TCGA.EE.A3JD.06 3 0.0892 0.999 0.02 0.00 0.98
#> TCGA.EB.A44N.01 1 0.0000 0.992 1.00 0.00 0.00
#> TCGA.Z2.AA3V.06 2 0.0000 0.992 0.00 1.00 0.00
#> TCGA.DA.A3F8.06 1 0.0000 0.992 1.00 0.00 0.00
#> TCGA.EB.A4OZ.01 2 0.0000 0.992 0.00 1.00 0.00
#> TCGA.EE.A3JE.06 1 0.0000 0.992 1.00 0.00 0.00
#> TCGA.W3.AA1W.06 1 0.0000 0.992 1.00 0.00 0.00
#> TCGA.D3.A51F.06 3 0.0892 0.999 0.02 0.00 0.98
#> TCGA.DA.A3F2.06 3 0.0892 0.999 0.02 0.00 0.98
#> TCGA.EB.A4IS.01 1 0.0000 0.992 1.00 0.00 0.00
#> TCGA.3N.A9WD.06 1 0.0000 0.992 1.00 0.00 0.00
#> TCGA.EB.A4OY.01 2 0.0000 0.992 0.00 1.00 0.00
#> TCGA.BF.AAP0.06 2 0.0000 0.992 0.00 1.00 0.00
#> TCGA.WE.AA9Y.06 1 0.1529 0.954 0.96 0.00 0.04
#> TCGA.FS.A4F8.06 1 0.0000 0.992 1.00 0.00 0.00
#> TCGA.D3.A51H.06 3 0.0892 0.999 0.02 0.00 0.98
#> TCGA.BF.A3DL.01 2 0.0000 0.992 0.00 1.00 0.00
#> TCGA.WE.AAA4.06 2 0.0892 0.991 0.00 0.98 0.02
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> TCGA.FR.A728.01 4 0.0707 0.995 0.00 0.02 0.00 0.98
#> TCGA.GN.A4U8.11 1 0.0000 0.987 1.00 0.00 0.00 0.00
#> TCGA.D3.A8GO.06 2 0.0000 0.969 0.00 1.00 0.00 0.00
#> TCGA.D3.A8GB.06 3 0.0000 0.991 0.00 0.00 1.00 0.00
#> TCGA.WE.A8ZN.06 1 0.0000 0.987 1.00 0.00 0.00 0.00
#> TCGA.D3.A8GN.06 4 0.0707 0.995 0.00 0.02 0.00 0.98
#> TCGA.EB.A550.01 2 0.0000 0.969 0.00 1.00 0.00 0.00
#> TCGA.GF.A4EO.06 4 0.0707 0.995 0.00 0.02 0.00 0.98
#> TCGA.WE.A8K4.01 1 0.0000 0.987 1.00 0.00 0.00 0.00
#> TCGA.EB.A6QY.01 3 0.0707 0.990 0.00 0.00 0.98 0.02
#> TCGA.WE.A8K1.06 1 0.0000 0.987 1.00 0.00 0.00 0.00
#> TCGA.ER.A42L.06 1 0.0000 0.987 1.00 0.00 0.00 0.00
#> TCGA.FR.A8YE.06 1 0.0707 0.974 0.98 0.00 0.02 0.00
#> TCGA.EE.A3JH.06 1 0.0000 0.987 1.00 0.00 0.00 0.00
#> TCGA.FR.A44A.06 4 0.0707 0.995 0.00 0.02 0.00 0.98
#> TCGA.EB.A5VV.06 2 0.1637 0.944 0.00 0.94 0.00 0.06
#> TCGA.GN.A4U5.01 4 0.0707 0.995 0.00 0.02 0.00 0.98
#> TCGA.D3.A3MR.06 1 0.0000 0.987 1.00 0.00 0.00 0.00
#> TCGA.EB.A6L9.06 3 0.0000 0.991 0.00 0.00 1.00 0.00
#> TCGA.EB.A430.01 3 0.0707 0.990 0.00 0.00 0.98 0.02
#> TCGA.D3.A8GE.06 3 0.0000 0.991 0.00 0.00 1.00 0.00
#> TCGA.D3.A8GD.06 4 0.0707 0.995 0.00 0.02 0.00 0.98
#> TCGA.EE.A183.06 1 0.0000 0.987 1.00 0.00 0.00 0.00
#> TCGA.ER.A2NH.06 1 0.0000 0.987 1.00 0.00 0.00 0.00
#> TCGA.EE.A2M8.06 2 0.1637 0.944 0.00 0.94 0.00 0.06
#> TCGA.EE.A2MR.06 1 0.0707 0.974 0.98 0.00 0.02 0.00
#> TCGA.DA.A1I5.06 2 0.2647 0.892 0.00 0.88 0.00 0.12
#> TCGA.ER.A19D.06 2 0.0000 0.969 0.00 1.00 0.00 0.00
#> TCGA.ER.A199.06 4 0.0707 0.995 0.00 0.02 0.00 0.98
#> TCGA.W3.A828.06 3 0.0707 0.990 0.00 0.00 0.98 0.02
#> TCGA.BF.A1PX.01 1 0.0000 0.987 1.00 0.00 0.00 0.00
#> TCGA.EE.A2GH.06 1 0.0000 0.987 1.00 0.00 0.00 0.00
#> TCGA.ER.A196.01 2 0.0000 0.969 0.00 1.00 0.00 0.00
#> TCGA.ER.A19S.06 4 0.0707 0.995 0.00 0.02 0.00 0.98
#> TCGA.EE.A29N.06 1 0.0000 0.987 1.00 0.00 0.00 0.00
#> TCGA.D3.A2JB.06 2 0.0000 0.969 0.00 1.00 0.00 0.00
#> TCGA.D3.A2JD.06 1 0.0000 0.987 1.00 0.00 0.00 0.00
#> TCGA.FS.A1Z4.06 3 0.0000 0.991 0.00 0.00 1.00 0.00
#> TCGA.FR.A7UA.06 4 0.0707 0.995 0.00 0.02 0.00 0.98
#> TCGA.ER.A2NF.01 3 0.0707 0.990 0.00 0.00 0.98 0.02
#> TCGA.GN.A263.01 3 0.0707 0.990 0.00 0.00 0.98 0.02
#> TCGA.ER.A19N.06 1 0.0000 0.987 1.00 0.00 0.00 0.00
#> TCGA.FR.A7U9.06 2 0.0000 0.969 0.00 1.00 0.00 0.00
#> TCGA.ER.A19Q.06 2 0.1637 0.944 0.00 0.94 0.00 0.06
#> TCGA.EE.A2MG.06 3 0.0000 0.991 0.00 0.00 1.00 0.00
#> TCGA.EE.A2MC.06 3 0.0000 0.991 0.00 0.00 1.00 0.00
#> TCGA.EE.A2A0.06 4 0.0707 0.995 0.00 0.02 0.00 0.98
#> TCGA.EE.A29G.06 1 0.0000 0.987 1.00 0.00 0.00 0.00
#> TCGA.GN.A269.01 1 0.0000 0.987 1.00 0.00 0.00 0.00
#> TCGA.EE.A2A1.06 3 0.0000 0.991 0.00 0.00 1.00 0.00
#> TCGA.ER.A1A1.06 3 0.0000 0.991 0.00 0.00 1.00 0.00
#> TCGA.EE.A2MH.06 1 0.0000 0.987 1.00 0.00 0.00 0.00
#> TCGA.D3.A3BZ.06 3 0.0000 0.991 0.00 0.00 1.00 0.00
#> TCGA.ER.A197.06 4 0.0707 0.995 0.00 0.02 0.00 0.98
#> TCGA.DA.A1IB.06 4 0.0707 0.995 0.00 0.02 0.00 0.98
#> TCGA.GN.A261.06 2 0.0000 0.969 0.00 1.00 0.00 0.00
#> TCGA.D3.A1QB.06 2 0.0000 0.969 0.00 1.00 0.00 0.00
#> TCGA.D3.A3C8.06 4 0.0707 0.995 0.00 0.02 0.00 0.98
#> TCGA.ER.A19A.06 3 0.0000 0.991 0.00 0.00 1.00 0.00
#> TCGA.EE.A29M.06 2 0.0000 0.969 0.00 1.00 0.00 0.00
#> TCGA.D3.A2J7.06 1 0.0000 0.987 1.00 0.00 0.00 0.00
#> TCGA.EE.A2GD.06 4 0.0707 0.995 0.00 0.02 0.00 0.98
#> TCGA.D3.A2J9.06 1 0.1211 0.959 0.96 0.00 0.04 0.00
#> TCGA.D3.A1Q4.06 2 0.0000 0.969 0.00 1.00 0.00 0.00
#> TCGA.D3.A2J8.06 3 0.0000 0.991 0.00 0.00 1.00 0.00
#> TCGA.FS.A1Z0.06 2 0.0000 0.969 0.00 1.00 0.00 0.00
#> TCGA.EB.A1NK.01 3 0.0707 0.990 0.00 0.00 0.98 0.02
#> TCGA.EE.A2MJ.06 1 0.0000 0.987 1.00 0.00 0.00 0.00
#> TCGA.D3.A2JH.06 1 0.0000 0.987 1.00 0.00 0.00 0.00
#> TCGA.EE.A29E.06 3 0.0707 0.990 0.00 0.00 0.98 0.02
#> TCGA.ER.A2NG.06 4 0.0707 0.995 0.00 0.02 0.00 0.98
#> TCGA.EE.A2ME.06 1 0.0707 0.974 0.98 0.00 0.02 0.00
#> TCGA.GN.A265.06 1 0.0000 0.987 1.00 0.00 0.00 0.00
#> TCGA.EE.A2MU.06 1 0.0000 0.987 1.00 0.00 0.00 0.00
#> TCGA.EE.A2GK.06 2 0.1637 0.944 0.00 0.94 0.00 0.06
#> TCGA.EE.A3AA.06 1 0.0000 0.987 1.00 0.00 0.00 0.00
#> TCGA.ER.A19P.06 4 0.0707 0.995 0.00 0.02 0.00 0.98
#> TCGA.D3.A1Q8.06 1 0.0000 0.987 1.00 0.00 0.00 0.00
#> TCGA.D3.A1Q7.06 4 0.0707 0.995 0.00 0.02 0.00 0.98
#> TCGA.D3.A3CB.06 1 0.0000 0.987 1.00 0.00 0.00 0.00
#> TCGA.ER.A195.06 3 0.0707 0.990 0.00 0.00 0.98 0.02
#> TCGA.EB.A5SF.01 2 0.0000 0.969 0.00 1.00 0.00 0.00
#> TCGA.EE.A2GE.06 1 0.0000 0.987 1.00 0.00 0.00 0.00
#> TCGA.GF.A3OT.06 4 0.0707 0.995 0.00 0.02 0.00 0.98
#> TCGA.ER.A2NF.06 3 0.0707 0.990 0.00 0.00 0.98 0.02
#> TCGA.BF.AAP7.01 2 0.2921 0.871 0.00 0.86 0.00 0.14
#> TCGA.ER.A19W.06 4 0.0707 0.995 0.00 0.02 0.00 0.98
#> TCGA.RP.A693.06 1 0.0000 0.987 1.00 0.00 0.00 0.00
#> TCGA.FW.A3TV.06 2 0.0000 0.969 0.00 1.00 0.00 0.00
#> TCGA.FW.A3R5.11 3 0.0707 0.990 0.00 0.00 0.98 0.02
#> TCGA.XV.AAZV.01 2 0.0000 0.969 0.00 1.00 0.00 0.00
#> TCGA.EE.A29C.06 3 0.1913 0.952 0.04 0.00 0.94 0.02
#> TCGA.RP.A690.06 2 0.0000 0.969 0.00 1.00 0.00 0.00
#> TCGA.FW.A5DY.06 4 0.0707 0.995 0.00 0.02 0.00 0.98
#> TCGA.DA.A1I4.06 3 0.0707 0.990 0.00 0.00 0.98 0.02
#> TCGA.GF.A6C9.06 1 0.2011 0.921 0.92 0.00 0.08 0.00
#> TCGA.EE.A2GT.06 3 0.0000 0.991 0.00 0.00 1.00 0.00
#> TCGA.GN.A9SD.06 4 0.0707 0.995 0.00 0.02 0.00 0.98
#> TCGA.D3.A3CF.06 2 0.1637 0.944 0.00 0.94 0.00 0.06
#> TCGA.HR.A2OH.06 4 0.0707 0.995 0.00 0.02 0.00 0.98
#> TCGA.GN.A26C.01 1 0.2921 0.845 0.86 0.00 0.14 0.00
#> TCGA.EB.A5UN.06 1 0.0000 0.987 1.00 0.00 0.00 0.00
#> TCGA.EB.A5SG.06 4 0.0707 0.995 0.00 0.02 0.00 0.98
#> TCGA.XV.AAZY.01 4 0.0707 0.995 0.00 0.02 0.00 0.98
#> TCGA.D3.A2JA.06 3 0.0707 0.990 0.00 0.00 0.98 0.02
#> TCGA.EE.A2GL.06 4 0.0707 0.995 0.00 0.02 0.00 0.98
#> TCGA.BF.AAOU.01 4 0.3172 0.842 0.00 0.16 0.00 0.84
#> TCGA.EB.A3XD.01 2 0.0000 0.969 0.00 1.00 0.00 0.00
#> TCGA.FS.A1ZB.06 1 0.4079 0.768 0.80 0.00 0.18 0.02
#> TCGA.QB.A6FS.06 3 0.0707 0.990 0.00 0.00 0.98 0.02
#> TCGA.D9.A3Z1.06 1 0.0000 0.987 1.00 0.00 0.00 0.00
#> TCGA.D3.A2JN.06 4 0.0707 0.995 0.00 0.02 0.00 0.98
#> TCGA.FS.A1ZT.06 3 0.0707 0.990 0.00 0.00 0.98 0.02
#> TCGA.HR.A2OG.06 2 0.2647 0.892 0.00 0.88 0.00 0.12
#> TCGA.D9.A3Z3.06 2 0.1637 0.944 0.00 0.94 0.00 0.06
#> TCGA.XV.A9VZ.01 2 0.0000 0.969 0.00 1.00 0.00 0.00
#> TCGA.EE.A3JD.06 3 0.0000 0.991 0.00 0.00 1.00 0.00
#> TCGA.EB.A44N.01 1 0.0000 0.987 1.00 0.00 0.00 0.00
#> TCGA.Z2.AA3V.06 2 0.0000 0.969 0.00 1.00 0.00 0.00
#> TCGA.DA.A3F8.06 1 0.0000 0.987 1.00 0.00 0.00 0.00
#> TCGA.EB.A4OZ.01 2 0.0707 0.962 0.00 0.98 0.00 0.02
#> TCGA.EE.A3JE.06 1 0.0000 0.987 1.00 0.00 0.00 0.00
#> TCGA.W3.AA1W.06 1 0.0000 0.987 1.00 0.00 0.00 0.00
#> TCGA.D3.A51F.06 3 0.0000 0.991 0.00 0.00 1.00 0.00
#> TCGA.DA.A3F2.06 3 0.0000 0.991 0.00 0.00 1.00 0.00
#> TCGA.EB.A4IS.01 1 0.0000 0.987 1.00 0.00 0.00 0.00
#> TCGA.3N.A9WD.06 1 0.0000 0.987 1.00 0.00 0.00 0.00
#> TCGA.EB.A4OY.01 2 0.0000 0.969 0.00 1.00 0.00 0.00
#> TCGA.BF.AAP0.06 2 0.3172 0.846 0.00 0.84 0.00 0.16
#> TCGA.WE.AA9Y.06 1 0.1637 0.936 0.94 0.00 0.06 0.00
#> TCGA.FS.A4F8.06 1 0.0000 0.987 1.00 0.00 0.00 0.00
#> TCGA.D3.A51H.06 3 0.0000 0.991 0.00 0.00 1.00 0.00
#> TCGA.BF.A3DL.01 2 0.0000 0.969 0.00 1.00 0.00 0.00
#> TCGA.WE.AAA4.06 4 0.0707 0.995 0.00 0.02 0.00 0.98
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> TCGA.FR.A728.01 4 0.0000 0.991 0.00 0.00 0.00 1.00 0.00
#> TCGA.GN.A4U8.11 1 0.0000 0.981 1.00 0.00 0.00 0.00 0.00
#> TCGA.D3.A8GO.06 2 0.3641 0.838 0.00 0.82 0.00 0.06 0.12
#> TCGA.D3.A8GB.06 3 0.0000 0.823 0.00 0.00 1.00 0.00 0.00
#> TCGA.WE.A8ZN.06 1 0.2873 0.856 0.86 0.00 0.02 0.00 0.12
#> TCGA.D3.A8GN.06 4 0.0000 0.991 0.00 0.00 0.00 1.00 0.00
#> TCGA.EB.A550.01 2 0.1410 0.858 0.00 0.94 0.00 0.00 0.06
#> TCGA.GF.A4EO.06 4 0.0000 0.991 0.00 0.00 0.00 1.00 0.00
#> TCGA.WE.A8K4.01 1 0.0000 0.981 1.00 0.00 0.00 0.00 0.00
#> TCGA.EB.A6QY.01 5 0.3109 0.901 0.00 0.00 0.20 0.00 0.80
#> TCGA.WE.A8K1.06 1 0.0000 0.981 1.00 0.00 0.00 0.00 0.00
#> TCGA.ER.A42L.06 1 0.0000 0.981 1.00 0.00 0.00 0.00 0.00
#> TCGA.FR.A8YE.06 3 0.3424 0.584 0.24 0.00 0.76 0.00 0.00
#> TCGA.EE.A3JH.06 1 0.0000 0.981 1.00 0.00 0.00 0.00 0.00
#> TCGA.FR.A44A.06 4 0.0000 0.991 0.00 0.00 0.00 1.00 0.00
#> TCGA.EB.A5VV.06 2 0.4437 0.816 0.00 0.76 0.00 0.14 0.10
#> TCGA.GN.A4U5.01 4 0.0609 0.974 0.00 0.00 0.00 0.98 0.02
#> TCGA.D3.A3MR.06 1 0.0000 0.981 1.00 0.00 0.00 0.00 0.00
#> TCGA.EB.A6L9.06 3 0.0000 0.823 0.00 0.00 1.00 0.00 0.00
#> TCGA.EB.A430.01 5 0.4060 0.787 0.00 0.00 0.36 0.00 0.64
#> TCGA.D3.A8GE.06 3 0.2020 0.709 0.00 0.00 0.90 0.00 0.10
#> TCGA.D3.A8GD.06 4 0.0000 0.991 0.00 0.00 0.00 1.00 0.00
#> TCGA.EE.A183.06 1 0.0000 0.981 1.00 0.00 0.00 0.00 0.00
#> TCGA.ER.A2NH.06 1 0.0000 0.981 1.00 0.00 0.00 0.00 0.00
#> TCGA.EE.A2M8.06 2 0.5050 0.780 0.00 0.70 0.00 0.18 0.12
#> TCGA.EE.A2MR.06 1 0.2020 0.882 0.90 0.00 0.10 0.00 0.00
#> TCGA.DA.A1I5.06 2 0.5484 0.711 0.00 0.64 0.00 0.24 0.12
#> TCGA.ER.A19D.06 2 0.1410 0.858 0.00 0.94 0.00 0.00 0.06
#> TCGA.ER.A199.06 4 0.0000 0.991 0.00 0.00 0.00 1.00 0.00
#> TCGA.W3.A828.06 5 0.3274 0.903 0.00 0.00 0.22 0.00 0.78
#> TCGA.BF.A1PX.01 1 0.0000 0.981 1.00 0.00 0.00 0.00 0.00
#> TCGA.EE.A2GH.06 1 0.0000 0.981 1.00 0.00 0.00 0.00 0.00
#> TCGA.ER.A196.01 2 0.0000 0.862 0.00 1.00 0.00 0.00 0.00
#> TCGA.ER.A19S.06 4 0.0000 0.991 0.00 0.00 0.00 1.00 0.00
#> TCGA.EE.A29N.06 1 0.0000 0.981 1.00 0.00 0.00 0.00 0.00
#> TCGA.D3.A2JB.06 2 0.3697 0.838 0.00 0.82 0.00 0.08 0.10
#> TCGA.D3.A2JD.06 1 0.0000 0.981 1.00 0.00 0.00 0.00 0.00
#> TCGA.FS.A1Z4.06 3 0.0000 0.823 0.00 0.00 1.00 0.00 0.00
#> TCGA.FR.A7UA.06 4 0.0000 0.991 0.00 0.00 0.00 1.00 0.00
#> TCGA.ER.A2NF.01 5 0.3274 0.907 0.00 0.00 0.22 0.00 0.78
#> TCGA.GN.A263.01 5 0.3796 0.843 0.00 0.00 0.30 0.00 0.70
#> TCGA.ER.A19N.06 1 0.0000 0.981 1.00 0.00 0.00 0.00 0.00
#> TCGA.FR.A7U9.06 2 0.0609 0.861 0.00 0.98 0.00 0.00 0.02
#> TCGA.ER.A19Q.06 2 0.4872 0.794 0.00 0.72 0.00 0.16 0.12
#> TCGA.EE.A2MG.06 3 0.0000 0.823 0.00 0.00 1.00 0.00 0.00
#> TCGA.EE.A2MC.06 3 0.0000 0.823 0.00 0.00 1.00 0.00 0.00
#> TCGA.EE.A2A0.06 4 0.0000 0.991 0.00 0.00 0.00 1.00 0.00
#> TCGA.EE.A29G.06 1 0.0000 0.981 1.00 0.00 0.00 0.00 0.00
#> TCGA.GN.A269.01 1 0.1043 0.955 0.96 0.00 0.00 0.00 0.04
#> TCGA.EE.A2A1.06 3 0.1043 0.787 0.00 0.00 0.96 0.00 0.04
#> TCGA.ER.A1A1.06 3 0.0000 0.823 0.00 0.00 1.00 0.00 0.00
#> TCGA.EE.A2MH.06 1 0.0000 0.981 1.00 0.00 0.00 0.00 0.00
#> TCGA.D3.A3BZ.06 3 0.0000 0.823 0.00 0.00 1.00 0.00 0.00
#> TCGA.ER.A197.06 4 0.0000 0.991 0.00 0.00 0.00 1.00 0.00
#> TCGA.DA.A1IB.06 4 0.0000 0.991 0.00 0.00 0.00 1.00 0.00
#> TCGA.GN.A261.06 2 0.1410 0.858 0.00 0.94 0.00 0.00 0.06
#> TCGA.D3.A1QB.06 2 0.1410 0.858 0.00 0.94 0.00 0.00 0.06
#> TCGA.D3.A3C8.06 4 0.0000 0.991 0.00 0.00 0.00 1.00 0.00
#> TCGA.ER.A19A.06 3 0.0000 0.823 0.00 0.00 1.00 0.00 0.00
#> TCGA.EE.A29M.06 2 0.0000 0.862 0.00 1.00 0.00 0.00 0.00
#> TCGA.D3.A2J7.06 1 0.0000 0.981 1.00 0.00 0.00 0.00 0.00
#> TCGA.EE.A2GD.06 4 0.0000 0.991 0.00 0.00 0.00 1.00 0.00
#> TCGA.D3.A2J9.06 3 0.3424 0.584 0.24 0.00 0.76 0.00 0.00
#> TCGA.D3.A1Q4.06 2 0.1410 0.858 0.00 0.94 0.00 0.00 0.06
#> TCGA.D3.A2J8.06 3 0.0000 0.823 0.00 0.00 1.00 0.00 0.00
#> TCGA.FS.A1Z0.06 2 0.1410 0.858 0.00 0.94 0.00 0.00 0.06
#> TCGA.EB.A1NK.01 5 0.2929 0.897 0.00 0.00 0.18 0.00 0.82
#> TCGA.EE.A2MJ.06 1 0.0000 0.981 1.00 0.00 0.00 0.00 0.00
#> TCGA.D3.A2JH.06 1 0.0000 0.981 1.00 0.00 0.00 0.00 0.00
#> TCGA.EE.A29E.06 5 0.3109 0.905 0.00 0.00 0.20 0.00 0.80
#> TCGA.ER.A2NG.06 4 0.0000 0.991 0.00 0.00 0.00 1.00 0.00
#> TCGA.EE.A2ME.06 3 0.3424 0.584 0.24 0.00 0.76 0.00 0.00
#> TCGA.GN.A265.06 1 0.0000 0.981 1.00 0.00 0.00 0.00 0.00
#> TCGA.EE.A2MU.06 1 0.0000 0.981 1.00 0.00 0.00 0.00 0.00
#> TCGA.EE.A2GK.06 2 0.4437 0.816 0.00 0.76 0.00 0.14 0.10
#> TCGA.EE.A3AA.06 1 0.0000 0.981 1.00 0.00 0.00 0.00 0.00
#> TCGA.ER.A19P.06 4 0.0000 0.991 0.00 0.00 0.00 1.00 0.00
#> TCGA.D3.A1Q8.06 1 0.0609 0.968 0.98 0.00 0.00 0.00 0.02
#> TCGA.D3.A1Q7.06 4 0.0000 0.991 0.00 0.00 0.00 1.00 0.00
#> TCGA.D3.A3CB.06 1 0.0000 0.981 1.00 0.00 0.00 0.00 0.00
#> TCGA.ER.A195.06 5 0.3424 0.897 0.00 0.00 0.24 0.00 0.76
#> TCGA.EB.A5SF.01 2 0.1410 0.858 0.00 0.94 0.00 0.00 0.06
#> TCGA.EE.A2GE.06 1 0.0000 0.981 1.00 0.00 0.00 0.00 0.00
#> TCGA.GF.A3OT.06 4 0.0609 0.974 0.00 0.00 0.00 0.98 0.02
#> TCGA.ER.A2NF.06 5 0.3274 0.907 0.00 0.00 0.22 0.00 0.78
#> TCGA.BF.AAP7.01 2 0.5355 0.736 0.00 0.66 0.00 0.22 0.12
#> TCGA.ER.A19W.06 4 0.0000 0.991 0.00 0.00 0.00 1.00 0.00
#> TCGA.RP.A693.06 1 0.0000 0.981 1.00 0.00 0.00 0.00 0.00
#> TCGA.FW.A3TV.06 2 0.0000 0.862 0.00 1.00 0.00 0.00 0.00
#> TCGA.FW.A3R5.11 5 0.4060 0.780 0.00 0.00 0.36 0.00 0.64
#> TCGA.XV.AAZV.01 2 0.0000 0.862 0.00 1.00 0.00 0.00 0.00
#> TCGA.EE.A29C.06 5 0.2929 0.897 0.00 0.00 0.18 0.00 0.82
#> TCGA.RP.A690.06 2 0.1410 0.858 0.00 0.94 0.00 0.00 0.06
#> TCGA.FW.A5DY.06 4 0.0000 0.991 0.00 0.00 0.00 1.00 0.00
#> TCGA.DA.A1I4.06 5 0.3109 0.905 0.00 0.00 0.20 0.00 0.80
#> TCGA.GF.A6C9.06 3 0.4302 0.104 0.48 0.00 0.52 0.00 0.00
#> TCGA.EE.A2GT.06 3 0.3684 0.305 0.00 0.00 0.72 0.00 0.28
#> TCGA.GN.A9SD.06 4 0.0000 0.991 0.00 0.00 0.00 1.00 0.00
#> TCGA.D3.A3CF.06 2 0.4216 0.826 0.00 0.78 0.00 0.10 0.12
#> TCGA.HR.A2OH.06 4 0.0000 0.991 0.00 0.00 0.00 1.00 0.00
#> TCGA.GN.A26C.01 1 0.3109 0.738 0.80 0.00 0.20 0.00 0.00
#> TCGA.EB.A5UN.06 1 0.0000 0.981 1.00 0.00 0.00 0.00 0.00
#> TCGA.EB.A5SG.06 4 0.0000 0.991 0.00 0.00 0.00 1.00 0.00
#> TCGA.XV.AAZY.01 4 0.0000 0.991 0.00 0.00 0.00 1.00 0.00
#> TCGA.D3.A2JA.06 3 0.4829 -0.434 0.02 0.00 0.50 0.00 0.48
#> TCGA.EE.A2GL.06 4 0.0000 0.991 0.00 0.00 0.00 1.00 0.00
#> TCGA.BF.AAOU.01 4 0.3109 0.743 0.00 0.20 0.00 0.80 0.00
#> TCGA.EB.A3XD.01 2 0.1648 0.862 0.00 0.94 0.00 0.04 0.02
#> TCGA.FS.A1ZB.06 5 0.3731 0.648 0.16 0.00 0.04 0.00 0.80
#> TCGA.QB.A6FS.06 5 0.3684 0.881 0.00 0.00 0.28 0.00 0.72
#> TCGA.D9.A3Z1.06 1 0.0000 0.981 1.00 0.00 0.00 0.00 0.00
#> TCGA.D3.A2JN.06 4 0.0000 0.991 0.00 0.00 0.00 1.00 0.00
#> TCGA.FS.A1ZT.06 5 0.3561 0.892 0.00 0.00 0.26 0.00 0.74
#> TCGA.HR.A2OG.06 2 0.5210 0.759 0.00 0.68 0.00 0.20 0.12
#> TCGA.D9.A3Z3.06 2 0.5050 0.779 0.00 0.70 0.00 0.18 0.12
#> TCGA.XV.A9VZ.01 2 0.1410 0.858 0.00 0.94 0.00 0.00 0.06
#> TCGA.EE.A3JD.06 3 0.0000 0.823 0.00 0.00 1.00 0.00 0.00
#> TCGA.EB.A44N.01 1 0.0609 0.968 0.98 0.00 0.00 0.00 0.02
#> TCGA.Z2.AA3V.06 2 0.1732 0.856 0.00 0.92 0.00 0.08 0.00
#> TCGA.DA.A3F8.06 1 0.0000 0.981 1.00 0.00 0.00 0.00 0.00
#> TCGA.EB.A4OZ.01 2 0.3946 0.833 0.00 0.80 0.00 0.08 0.12
#> TCGA.EE.A3JE.06 1 0.0000 0.981 1.00 0.00 0.00 0.00 0.00
#> TCGA.W3.AA1W.06 1 0.0000 0.981 1.00 0.00 0.00 0.00 0.00
#> TCGA.D3.A51F.06 3 0.0000 0.823 0.00 0.00 1.00 0.00 0.00
#> TCGA.DA.A3F2.06 3 0.0000 0.823 0.00 0.00 1.00 0.00 0.00
#> TCGA.EB.A4IS.01 1 0.1648 0.938 0.94 0.00 0.02 0.00 0.04
#> TCGA.3N.A9WD.06 1 0.0609 0.968 0.98 0.00 0.00 0.00 0.02
#> TCGA.EB.A4OY.01 2 0.1410 0.858 0.00 0.94 0.00 0.00 0.06
#> TCGA.BF.AAP0.06 2 0.5700 0.649 0.00 0.60 0.00 0.28 0.12
#> TCGA.WE.AA9Y.06 1 0.2331 0.895 0.90 0.00 0.08 0.00 0.02
#> TCGA.FS.A4F8.06 1 0.0000 0.981 1.00 0.00 0.00 0.00 0.00
#> TCGA.D3.A51H.06 3 0.0000 0.823 0.00 0.00 1.00 0.00 0.00
#> TCGA.BF.A3DL.01 2 0.1410 0.858 0.00 0.94 0.00 0.00 0.06
#> TCGA.WE.AAA4.06 4 0.0000 0.991 0.00 0.00 0.00 1.00 0.00
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> TCGA.FR.A728.01 4 0.0000 0.9693 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.GN.A4U8.11 1 0.0547 0.9168 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.D3.A8GO.06 2 0.5424 -0.5374 0.00 0.46 0.00 0.04 0.04 0.46
#> TCGA.D3.A8GB.06 3 0.0000 0.8841 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.WE.A8ZN.06 1 0.4711 0.5559 0.64 0.00 0.00 0.00 0.28 0.08
#> TCGA.D3.A8GN.06 4 0.0000 0.9693 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.EB.A550.01 2 0.0000 0.7120 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.GF.A4EO.06 4 0.0547 0.9652 0.00 0.00 0.00 0.98 0.00 0.02
#> TCGA.WE.A8K4.01 1 0.0937 0.9133 0.96 0.00 0.00 0.00 0.00 0.04
#> TCGA.EB.A6QY.01 5 0.2474 0.8375 0.00 0.00 0.04 0.00 0.88 0.08
#> TCGA.WE.A8K1.06 1 0.1556 0.8983 0.92 0.00 0.00 0.00 0.00 0.08
#> TCGA.ER.A42L.06 1 0.0000 0.9184 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FR.A8YE.06 3 0.2631 0.6989 0.18 0.00 0.82 0.00 0.00 0.00
#> TCGA.EE.A3JH.06 1 0.1556 0.8983 0.92 0.00 0.00 0.00 0.00 0.08
#> TCGA.FR.A44A.06 4 0.0937 0.9535 0.00 0.00 0.00 0.96 0.00 0.04
#> TCGA.EB.A5VV.06 6 0.5406 0.8192 0.00 0.38 0.00 0.12 0.00 0.50
#> TCGA.GN.A4U5.01 4 0.1865 0.9212 0.00 0.00 0.00 0.92 0.04 0.04
#> TCGA.D3.A3MR.06 1 0.1267 0.9065 0.94 0.00 0.00 0.00 0.00 0.06
#> TCGA.EB.A6L9.06 3 0.0000 0.8841 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.EB.A430.01 5 0.4247 0.7510 0.00 0.00 0.24 0.00 0.70 0.06
#> TCGA.D3.A8GE.06 3 0.4380 0.4910 0.00 0.00 0.70 0.00 0.22 0.08
#> TCGA.D3.A8GD.06 4 0.0000 0.9693 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.EE.A183.06 1 0.0937 0.9164 0.96 0.00 0.00 0.00 0.00 0.04
#> TCGA.ER.A2NH.06 1 0.0937 0.9125 0.96 0.00 0.00 0.00 0.00 0.04
#> TCGA.EE.A2M8.06 6 0.5618 0.8332 0.00 0.34 0.00 0.16 0.00 0.50
#> TCGA.EE.A2MR.06 1 0.4121 0.6855 0.72 0.00 0.22 0.00 0.00 0.06
#> TCGA.DA.A1I5.06 6 0.6365 0.8142 0.00 0.28 0.00 0.18 0.04 0.50
#> TCGA.ER.A19D.06 2 0.0000 0.7120 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.ER.A199.06 4 0.0000 0.9693 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.W3.A828.06 5 0.4680 0.7926 0.00 0.00 0.12 0.00 0.68 0.20
#> TCGA.BF.A1PX.01 1 0.1267 0.9112 0.94 0.00 0.00 0.00 0.00 0.06
#> TCGA.EE.A2GH.06 1 0.1480 0.9078 0.94 0.00 0.02 0.00 0.00 0.04
#> TCGA.ER.A196.01 2 0.3499 0.4280 0.00 0.68 0.00 0.00 0.00 0.32
#> TCGA.ER.A19S.06 4 0.0000 0.9693 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.EE.A29N.06 1 0.1267 0.9062 0.94 0.00 0.00 0.00 0.00 0.06
#> TCGA.D3.A2JB.06 6 0.5265 0.7752 0.00 0.40 0.00 0.10 0.00 0.50
#> TCGA.D3.A2JD.06 1 0.1556 0.8983 0.92 0.00 0.00 0.00 0.00 0.08
#> TCGA.FS.A1Z4.06 3 0.0000 0.8841 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.FR.A7UA.06 4 0.1267 0.9376 0.00 0.00 0.00 0.94 0.00 0.06
#> TCGA.ER.A2NF.01 5 0.3928 0.8334 0.00 0.00 0.08 0.00 0.76 0.16
#> TCGA.GN.A263.01 5 0.3045 0.8375 0.00 0.00 0.10 0.00 0.84 0.06
#> TCGA.ER.A19N.06 1 0.0547 0.9168 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.FR.A7U9.06 2 0.3499 0.4280 0.00 0.68 0.00 0.00 0.00 0.32
#> TCGA.ER.A19Q.06 6 0.6120 0.8162 0.00 0.34 0.00 0.12 0.04 0.50
#> TCGA.EE.A2MG.06 3 0.0000 0.8841 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.EE.A2MC.06 3 0.0547 0.8715 0.00 0.00 0.98 0.00 0.00 0.02
#> TCGA.EE.A2A0.06 4 0.0000 0.9693 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.EE.A29G.06 1 0.1814 0.9072 0.90 0.00 0.00 0.00 0.00 0.10
#> TCGA.GN.A269.01 1 0.2474 0.8839 0.88 0.00 0.00 0.00 0.04 0.08
#> TCGA.EE.A2A1.06 3 0.3746 0.6529 0.00 0.00 0.78 0.00 0.14 0.08
#> TCGA.ER.A1A1.06 3 0.0000 0.8841 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.EE.A2MH.06 1 0.1267 0.9112 0.94 0.00 0.00 0.00 0.00 0.06
#> TCGA.D3.A3BZ.06 3 0.0000 0.8841 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.ER.A197.06 4 0.0000 0.9693 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.DA.A1IB.06 4 0.0547 0.9652 0.00 0.00 0.00 0.98 0.00 0.02
#> TCGA.GN.A261.06 2 0.0547 0.7093 0.00 0.98 0.00 0.00 0.00 0.02
#> TCGA.D3.A1QB.06 2 0.1092 0.7034 0.00 0.96 0.00 0.02 0.00 0.02
#> TCGA.D3.A3C8.06 4 0.0000 0.9693 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.ER.A19A.06 3 0.0000 0.8841 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.EE.A29M.06 2 0.3198 0.5257 0.00 0.74 0.00 0.00 0.00 0.26
#> TCGA.D3.A2J7.06 1 0.0000 0.9184 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EE.A2GD.06 4 0.0000 0.9693 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.D3.A2J9.06 3 0.2793 0.6774 0.20 0.00 0.80 0.00 0.00 0.00
#> TCGA.D3.A1Q4.06 2 0.0547 0.7011 0.00 0.98 0.00 0.02 0.00 0.00
#> TCGA.D3.A2J8.06 3 0.0000 0.8841 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.FS.A1Z0.06 2 0.0000 0.7120 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.EB.A1NK.01 5 0.2512 0.8465 0.00 0.00 0.06 0.00 0.88 0.06
#> TCGA.EE.A2MJ.06 1 0.0547 0.9186 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.D3.A2JH.06 1 0.0547 0.9168 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.EE.A29E.06 5 0.2512 0.8487 0.00 0.00 0.06 0.00 0.88 0.06
#> TCGA.ER.A2NG.06 4 0.0000 0.9693 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.EE.A2ME.06 3 0.2631 0.7014 0.18 0.00 0.82 0.00 0.00 0.00
#> TCGA.GN.A265.06 1 0.0547 0.9168 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.EE.A2MU.06 1 0.1267 0.9065 0.94 0.00 0.00 0.00 0.00 0.06
#> TCGA.EE.A2GK.06 6 0.5406 0.8192 0.00 0.38 0.00 0.12 0.00 0.50
#> TCGA.EE.A3AA.06 1 0.0937 0.9164 0.96 0.00 0.00 0.00 0.00 0.04
#> TCGA.ER.A19P.06 4 0.1267 0.9379 0.00 0.00 0.00 0.94 0.00 0.06
#> TCGA.D3.A1Q8.06 1 0.1556 0.9060 0.92 0.00 0.00 0.00 0.00 0.08
#> TCGA.D3.A1Q7.06 4 0.0000 0.9693 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.D3.A3CB.06 1 0.0937 0.9164 0.96 0.00 0.00 0.00 0.00 0.04
#> TCGA.ER.A195.06 5 0.4265 0.8012 0.02 0.00 0.14 0.00 0.76 0.08
#> TCGA.EB.A5SF.01 2 0.0000 0.7120 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.EE.A2GE.06 1 0.0937 0.9125 0.96 0.00 0.00 0.00 0.00 0.04
#> TCGA.GF.A3OT.06 4 0.0937 0.9535 0.00 0.00 0.00 0.96 0.00 0.04
#> TCGA.ER.A2NF.06 5 0.3928 0.8334 0.00 0.00 0.08 0.00 0.76 0.16
#> TCGA.BF.AAP7.01 6 0.6365 0.8142 0.00 0.28 0.00 0.18 0.04 0.50
#> TCGA.ER.A19W.06 4 0.0000 0.9693 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.RP.A693.06 1 0.1556 0.9052 0.92 0.00 0.00 0.00 0.00 0.08
#> TCGA.FW.A3TV.06 2 0.3499 0.4280 0.00 0.68 0.00 0.00 0.00 0.32
#> TCGA.FW.A3R5.11 5 0.5406 0.4656 0.00 0.00 0.38 0.00 0.50 0.12
#> TCGA.XV.AAZV.01 2 0.3499 0.4280 0.00 0.68 0.00 0.00 0.00 0.32
#> TCGA.EE.A29C.06 5 0.3258 0.8266 0.02 0.00 0.04 0.00 0.84 0.10
#> TCGA.RP.A690.06 2 0.0000 0.7120 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.FW.A5DY.06 4 0.0547 0.9652 0.00 0.00 0.00 0.98 0.00 0.02
#> TCGA.DA.A1I4.06 5 0.2512 0.8510 0.00 0.00 0.06 0.00 0.88 0.06
#> TCGA.GF.A6C9.06 1 0.4892 0.1229 0.50 0.00 0.44 0.00 0.00 0.06
#> TCGA.EE.A2GT.06 3 0.5288 0.0337 0.02 0.00 0.54 0.00 0.38 0.06
#> TCGA.GN.A9SD.06 4 0.0937 0.9541 0.00 0.00 0.00 0.96 0.00 0.04
#> TCGA.D3.A3CF.06 6 0.5406 0.8192 0.00 0.38 0.00 0.12 0.00 0.50
#> TCGA.HR.A2OH.06 4 0.0000 0.9693 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.GN.A26C.01 1 0.4803 0.7210 0.72 0.00 0.16 0.00 0.04 0.08
#> TCGA.EB.A5UN.06 1 0.2190 0.8944 0.90 0.00 0.00 0.00 0.04 0.06
#> TCGA.EB.A5SG.06 4 0.0547 0.9652 0.00 0.00 0.00 0.98 0.00 0.02
#> TCGA.XV.AAZY.01 4 0.0547 0.9652 0.00 0.00 0.00 0.98 0.00 0.02
#> TCGA.D3.A2JA.06 5 0.4810 0.7288 0.00 0.00 0.22 0.00 0.66 0.12
#> TCGA.EE.A2GL.06 4 0.0000 0.9693 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.BF.AAOU.01 4 0.3309 0.5762 0.00 0.28 0.00 0.72 0.00 0.00
#> TCGA.EB.A3XD.01 2 0.4608 0.2424 0.00 0.68 0.00 0.22 0.00 0.10
#> TCGA.FS.A1ZB.06 5 0.3846 0.7717 0.08 0.00 0.02 0.00 0.80 0.10
#> TCGA.QB.A6FS.06 5 0.2728 0.8485 0.00 0.00 0.10 0.00 0.86 0.04
#> TCGA.D9.A3Z1.06 1 0.0000 0.9184 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D3.A2JN.06 4 0.0547 0.9565 0.00 0.02 0.00 0.98 0.00 0.00
#> TCGA.FS.A1ZT.06 5 0.4566 0.7895 0.00 0.00 0.16 0.00 0.70 0.14
#> TCGA.HR.A2OG.06 6 0.6305 0.8340 0.00 0.30 0.00 0.16 0.04 0.50
#> TCGA.D9.A3Z3.06 6 0.6305 0.8340 0.00 0.30 0.00 0.16 0.04 0.50
#> TCGA.XV.A9VZ.01 2 0.0547 0.7093 0.00 0.98 0.00 0.00 0.00 0.02
#> TCGA.EE.A3JD.06 3 0.0000 0.8841 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.EB.A44N.01 1 0.1556 0.9052 0.92 0.00 0.00 0.00 0.00 0.08
#> TCGA.Z2.AA3V.06 2 0.4631 0.1661 0.00 0.62 0.00 0.06 0.00 0.32
#> TCGA.DA.A3F8.06 1 0.1267 0.9112 0.94 0.00 0.00 0.00 0.00 0.06
#> TCGA.EB.A4OZ.01 6 0.5265 0.7752 0.00 0.40 0.00 0.10 0.00 0.50
#> TCGA.EE.A3JE.06 1 0.0000 0.9184 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.W3.AA1W.06 1 0.0937 0.9164 0.96 0.00 0.00 0.00 0.00 0.04
#> TCGA.D3.A51F.06 3 0.0000 0.8841 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.DA.A3F2.06 3 0.0000 0.8841 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.EB.A4IS.01 1 0.2190 0.8902 0.90 0.00 0.00 0.00 0.04 0.06
#> TCGA.3N.A9WD.06 1 0.2474 0.8839 0.88 0.00 0.00 0.00 0.04 0.08
#> TCGA.EB.A4OY.01 2 0.0547 0.7011 0.00 0.98 0.00 0.02 0.00 0.00
#> TCGA.BF.AAP0.06 6 0.5801 0.7451 0.00 0.26 0.00 0.24 0.00 0.50
#> TCGA.WE.AA9Y.06 1 0.3324 0.8486 0.84 0.00 0.06 0.00 0.02 0.08
#> TCGA.FS.A4F8.06 1 0.1267 0.9112 0.94 0.00 0.00 0.00 0.00 0.06
#> TCGA.D3.A51H.06 3 0.0000 0.8841 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.BF.A3DL.01 2 0.3198 0.5218 0.00 0.74 0.00 0.00 0.00 0.26
#> TCGA.WE.AAA4.06 4 0.0547 0.9652 0.00 0.00 0.00 0.98 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.FR.A728.01 4 0.0000 0.948 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.GN.A4U8.11 1 0.2016 0.871 0.90 0.00 0.04 0.00 0.00 0.00 0.06
#> TCGA.D3.A8GO.06 2 0.4121 0.602 0.00 0.70 0.10 0.00 0.00 0.00 0.20
#> TCGA.D3.A8GB.06 6 0.0000 0.876 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.WE.A8ZN.06 1 0.5065 0.447 0.58 0.00 0.10 0.00 0.30 0.00 0.02
#> TCGA.D3.A8GN.06 4 0.0000 0.948 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.EB.A550.01 2 0.3546 0.555 0.00 0.54 0.00 0.00 0.00 0.00 0.46
#> TCGA.GF.A4EO.06 4 0.0863 0.935 0.00 0.00 0.00 0.96 0.00 0.00 0.04
#> TCGA.WE.A8K4.01 1 0.1664 0.881 0.92 0.00 0.02 0.00 0.00 0.00 0.06
#> TCGA.EB.A6QY.01 5 0.3370 0.735 0.00 0.00 0.16 0.00 0.78 0.00 0.06
#> TCGA.WE.A8K1.06 1 0.2572 0.862 0.86 0.00 0.06 0.00 0.00 0.00 0.08
#> TCGA.ER.A42L.06 1 0.0504 0.880 0.98 0.00 0.02 0.00 0.00 0.00 0.00
#> TCGA.FR.A8YE.06 6 0.1886 0.770 0.12 0.00 0.00 0.00 0.00 0.88 0.00
#> TCGA.EE.A3JH.06 1 0.2572 0.862 0.86 0.00 0.06 0.00 0.00 0.00 0.08
#> TCGA.FR.A44A.06 4 0.1664 0.918 0.00 0.00 0.02 0.92 0.00 0.00 0.06
#> TCGA.EB.A5VV.06 2 0.4833 0.602 0.00 0.70 0.10 0.10 0.00 0.00 0.10
#> TCGA.GN.A4U5.01 4 0.3670 0.770 0.00 0.00 0.10 0.76 0.00 0.00 0.14
#> TCGA.D3.A3MR.06 1 0.2313 0.867 0.88 0.00 0.06 0.00 0.00 0.00 0.06
#> TCGA.EB.A6L9.06 6 0.0000 0.876 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.EB.A430.01 5 0.6054 0.667 0.00 0.00 0.16 0.00 0.54 0.20 0.10
#> TCGA.D3.A8GE.06 6 0.5196 0.298 0.00 0.00 0.16 0.00 0.22 0.60 0.02
#> TCGA.D3.A8GD.06 4 0.0000 0.948 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.EE.A183.06 1 0.1166 0.873 0.94 0.00 0.06 0.00 0.00 0.00 0.00
#> TCGA.ER.A2NH.06 1 0.2016 0.876 0.90 0.00 0.06 0.00 0.00 0.00 0.04
#> TCGA.EE.A2M8.06 2 0.5373 0.563 0.00 0.64 0.10 0.14 0.00 0.00 0.12
#> TCGA.EE.A2MR.06 1 0.3911 0.627 0.70 0.00 0.06 0.00 0.00 0.24 0.00
#> TCGA.DA.A1I5.06 2 0.6465 0.472 0.00 0.46 0.14 0.14 0.00 0.00 0.26
#> TCGA.ER.A19D.06 2 0.3546 0.555 0.00 0.54 0.00 0.00 0.00 0.00 0.46
#> TCGA.ER.A199.06 4 0.0000 0.948 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.W3.A828.06 5 0.4990 0.692 0.00 0.00 0.44 0.00 0.48 0.04 0.04
#> TCGA.BF.A1PX.01 1 0.1166 0.873 0.94 0.00 0.06 0.00 0.00 0.00 0.00
#> TCGA.EE.A2GH.06 1 0.2572 0.860 0.86 0.00 0.08 0.00 0.00 0.00 0.06
#> TCGA.ER.A196.01 2 0.0504 0.659 0.00 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.ER.A19S.06 4 0.0000 0.948 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.EE.A29N.06 1 0.2016 0.876 0.90 0.00 0.04 0.00 0.00 0.00 0.06
#> TCGA.D3.A2JB.06 2 0.4100 0.623 0.00 0.76 0.10 0.04 0.00 0.00 0.10
#> TCGA.D3.A2JD.06 1 0.2572 0.862 0.86 0.00 0.06 0.00 0.00 0.00 0.08
#> TCGA.FS.A1Z4.06 6 0.0504 0.866 0.00 0.00 0.00 0.00 0.02 0.98 0.00
#> TCGA.FR.A7UA.06 4 0.3630 0.805 0.00 0.04 0.10 0.80 0.00 0.00 0.06
#> TCGA.ER.A2NF.01 5 0.4127 0.738 0.00 0.00 0.36 0.00 0.60 0.04 0.00
#> TCGA.GN.A263.01 5 0.4937 0.676 0.00 0.00 0.12 0.00 0.68 0.14 0.06
#> TCGA.ER.A19N.06 1 0.1718 0.877 0.92 0.00 0.04 0.00 0.00 0.00 0.04
#> TCGA.FR.A7U9.06 2 0.0863 0.657 0.00 0.96 0.04 0.00 0.00 0.00 0.00
#> TCGA.ER.A19Q.06 2 0.5545 0.552 0.00 0.56 0.14 0.04 0.00 0.00 0.26
#> TCGA.EE.A2MG.06 6 0.0000 0.876 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.EE.A2MC.06 6 0.1718 0.831 0.00 0.00 0.04 0.00 0.04 0.92 0.00
#> TCGA.EE.A2A0.06 4 0.0000 0.948 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.EE.A29G.06 1 0.3114 0.849 0.84 0.00 0.08 0.00 0.04 0.00 0.04
#> TCGA.GN.A269.01 1 0.2313 0.849 0.88 0.00 0.06 0.00 0.06 0.00 0.00
#> TCGA.EE.A2A1.06 6 0.3835 0.589 0.00 0.00 0.10 0.00 0.16 0.74 0.00
#> TCGA.ER.A1A1.06 6 0.0000 0.876 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.EE.A2MH.06 1 0.1433 0.874 0.92 0.00 0.08 0.00 0.00 0.00 0.00
#> TCGA.D3.A3BZ.06 6 0.0000 0.876 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.ER.A197.06 4 0.0000 0.948 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.DA.A1IB.06 4 0.1928 0.893 0.00 0.02 0.08 0.90 0.00 0.00 0.00
#> TCGA.GN.A261.06 2 0.3867 0.574 0.00 0.60 0.02 0.00 0.00 0.00 0.38
#> TCGA.D3.A1QB.06 2 0.3546 0.555 0.00 0.54 0.00 0.00 0.00 0.00 0.46
#> TCGA.D3.A3C8.06 4 0.1433 0.909 0.00 0.00 0.08 0.92 0.00 0.00 0.00
#> TCGA.ER.A19A.06 6 0.0000 0.876 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.EE.A29M.06 2 0.0504 0.659 0.00 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.D3.A2J7.06 1 0.1363 0.882 0.94 0.00 0.02 0.00 0.00 0.00 0.04
#> TCGA.EE.A2GD.06 4 0.0000 0.948 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.D3.A2J9.06 6 0.1928 0.804 0.08 0.00 0.02 0.00 0.00 0.90 0.00
#> TCGA.D3.A1Q4.06 2 0.3546 0.555 0.00 0.54 0.00 0.00 0.00 0.00 0.46
#> TCGA.D3.A2J8.06 6 0.0000 0.876 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.FS.A1Z0.06 2 0.3546 0.555 0.00 0.54 0.00 0.00 0.00 0.00 0.46
#> TCGA.EB.A1NK.01 5 0.2509 0.773 0.00 0.00 0.06 0.00 0.88 0.04 0.02
#> TCGA.EE.A2MJ.06 1 0.0863 0.882 0.96 0.00 0.04 0.00 0.00 0.00 0.00
#> TCGA.D3.A2JH.06 1 0.2016 0.871 0.90 0.00 0.04 0.00 0.00 0.00 0.06
#> TCGA.EE.A29E.06 5 0.3000 0.784 0.00 0.00 0.10 0.00 0.84 0.04 0.02
#> TCGA.ER.A2NG.06 4 0.0000 0.948 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.EE.A2ME.06 6 0.1433 0.810 0.08 0.00 0.00 0.00 0.00 0.92 0.00
#> TCGA.GN.A265.06 1 0.1718 0.877 0.92 0.00 0.04 0.00 0.00 0.00 0.04
#> TCGA.EE.A2MU.06 1 0.2572 0.862 0.86 0.00 0.06 0.00 0.00 0.00 0.08
#> TCGA.EE.A2GK.06 2 0.4833 0.602 0.00 0.70 0.10 0.10 0.00 0.00 0.10
#> TCGA.EE.A3AA.06 1 0.1166 0.873 0.94 0.00 0.06 0.00 0.00 0.00 0.00
#> TCGA.ER.A19P.06 4 0.1363 0.926 0.00 0.00 0.02 0.94 0.00 0.00 0.04
#> TCGA.D3.A1Q8.06 1 0.3058 0.848 0.82 0.00 0.08 0.00 0.00 0.00 0.10
#> TCGA.D3.A1Q7.06 4 0.0000 0.948 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.D3.A3CB.06 1 0.1166 0.873 0.94 0.00 0.06 0.00 0.00 0.00 0.00
#> TCGA.ER.A195.06 5 0.5046 0.647 0.06 0.00 0.10 0.00 0.66 0.18 0.00
#> TCGA.EB.A5SF.01 2 0.3867 0.571 0.00 0.60 0.02 0.00 0.00 0.00 0.38
#> TCGA.EE.A2GE.06 1 0.2829 0.852 0.84 0.00 0.08 0.00 0.00 0.00 0.08
#> TCGA.GF.A3OT.06 4 0.1860 0.915 0.00 0.02 0.02 0.92 0.00 0.00 0.04
#> TCGA.ER.A2NF.06 5 0.4127 0.738 0.00 0.00 0.36 0.00 0.60 0.04 0.00
#> TCGA.BF.AAP7.01 2 0.6196 0.501 0.00 0.50 0.12 0.12 0.00 0.00 0.26
#> TCGA.ER.A19W.06 4 0.0000 0.948 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.RP.A693.06 1 0.2159 0.867 0.90 0.00 0.06 0.00 0.02 0.00 0.02
#> TCGA.FW.A3TV.06 2 0.0504 0.659 0.00 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.FW.A3R5.11 5 0.5526 0.646 0.00 0.00 0.24 0.00 0.54 0.20 0.02
#> TCGA.XV.AAZV.01 2 0.0504 0.659 0.00 0.98 0.02 0.00 0.00 0.00 0.00
#> TCGA.EE.A29C.06 5 0.2654 0.750 0.02 0.00 0.10 0.00 0.86 0.00 0.02
#> TCGA.RP.A690.06 2 0.3943 0.557 0.00 0.56 0.02 0.00 0.00 0.00 0.42
#> TCGA.FW.A5DY.06 4 0.0504 0.941 0.00 0.00 0.02 0.98 0.00 0.00 0.00
#> TCGA.DA.A1I4.06 5 0.2016 0.779 0.00 0.00 0.06 0.00 0.90 0.04 0.00
#> TCGA.GF.A6C9.06 6 0.4960 0.371 0.30 0.00 0.06 0.00 0.04 0.60 0.00
#> TCGA.EE.A2GT.06 6 0.5220 0.333 0.04 0.00 0.10 0.00 0.26 0.60 0.00
#> TCGA.GN.A9SD.06 4 0.2313 0.888 0.00 0.00 0.06 0.88 0.00 0.00 0.06
#> TCGA.D3.A3CF.06 2 0.4812 0.604 0.00 0.70 0.10 0.08 0.00 0.00 0.12
#> TCGA.HR.A2OH.06 4 0.0000 0.948 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.GN.A26C.01 1 0.5142 0.474 0.60 0.00 0.06 0.00 0.06 0.28 0.00
#> TCGA.EB.A5UN.06 1 0.2016 0.859 0.90 0.00 0.06 0.00 0.04 0.00 0.00
#> TCGA.EB.A5SG.06 4 0.0000 0.948 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.XV.AAZY.01 4 0.0504 0.943 0.00 0.00 0.00 0.98 0.00 0.00 0.02
#> TCGA.D3.A2JA.06 5 0.5723 0.420 0.02 0.00 0.20 0.00 0.48 0.30 0.00
#> TCGA.EE.A2GL.06 4 0.0000 0.948 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.BF.AAOU.01 4 0.4177 0.574 0.00 0.18 0.00 0.70 0.00 0.00 0.12
#> TCGA.EB.A3XD.01 2 0.3770 0.617 0.00 0.74 0.00 0.08 0.00 0.00 0.18
#> TCGA.FS.A1ZB.06 5 0.3315 0.717 0.08 0.00 0.08 0.00 0.82 0.00 0.02
#> TCGA.QB.A6FS.06 5 0.2572 0.777 0.00 0.00 0.06 0.00 0.86 0.08 0.00
#> TCGA.D9.A3Z1.06 1 0.1166 0.883 0.94 0.00 0.00 0.00 0.00 0.00 0.06
#> TCGA.D3.A2JN.06 4 0.1928 0.904 0.00 0.02 0.00 0.90 0.00 0.00 0.08
#> TCGA.FS.A1ZT.06 5 0.4033 0.759 0.00 0.00 0.22 0.00 0.70 0.08 0.00
#> TCGA.HR.A2OG.06 2 0.6179 0.510 0.00 0.50 0.14 0.10 0.00 0.00 0.26
#> TCGA.D9.A3Z3.06 2 0.5856 0.535 0.00 0.54 0.12 0.08 0.00 0.00 0.26
#> TCGA.XV.A9VZ.01 2 0.3867 0.574 0.00 0.60 0.02 0.00 0.00 0.00 0.38
#> TCGA.EE.A3JD.06 6 0.0000 0.876 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.EB.A44N.01 1 0.2857 0.852 0.86 0.00 0.06 0.00 0.04 0.00 0.04
#> TCGA.Z2.AA3V.06 2 0.1664 0.653 0.00 0.92 0.06 0.02 0.00 0.00 0.00
#> TCGA.DA.A3F8.06 1 0.1664 0.866 0.92 0.00 0.06 0.00 0.02 0.00 0.00
#> TCGA.EB.A4OZ.01 2 0.4574 0.613 0.00 0.72 0.10 0.06 0.00 0.00 0.12
#> TCGA.EE.A3JE.06 1 0.1363 0.880 0.94 0.00 0.04 0.00 0.00 0.00 0.02
#> TCGA.W3.AA1W.06 1 0.1166 0.873 0.94 0.00 0.06 0.00 0.00 0.00 0.00
#> TCGA.D3.A51F.06 6 0.0000 0.876 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.DA.A3F2.06 6 0.0000 0.876 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.EB.A4IS.01 1 0.5046 0.666 0.66 0.00 0.18 0.00 0.10 0.00 0.06
#> TCGA.3N.A9WD.06 1 0.3061 0.825 0.84 0.00 0.06 0.00 0.08 0.00 0.02
#> TCGA.EB.A4OY.01 2 0.3546 0.555 0.00 0.54 0.00 0.00 0.00 0.00 0.46
#> TCGA.BF.AAP0.06 2 0.5769 0.506 0.00 0.58 0.10 0.20 0.00 0.00 0.12
#> TCGA.WE.AA9Y.06 1 0.3833 0.758 0.78 0.00 0.06 0.00 0.04 0.12 0.00
#> TCGA.FS.A4F8.06 1 0.1166 0.873 0.94 0.00 0.06 0.00 0.00 0.00 0.00
#> TCGA.D3.A51H.06 6 0.0000 0.876 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.BF.A3DL.01 2 0.2422 0.637 0.00 0.82 0.00 0.00 0.00 0.00 0.18
#> TCGA.WE.AAA4.06 4 0.0000 0.948 0.00 0.00 0.00 1.00 0.00 0.00 0.00
cbind(get_classes(res, k = 8), get_membership(res, k = 8))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7 p8
#> TCGA.FR.A728.01 4 0.0000 0.9267 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.GN.A4U8.11 1 0.3142 0.4720 0.64 0.00 0.00 0.00 0.00 0.00 0.36 0.00
#> TCGA.D3.A8GO.06 2 0.3729 0.5608 0.00 0.72 0.10 0.00 0.00 0.00 0.00 0.18
#> TCGA.D3.A8GB.06 6 0.0808 0.7865 0.00 0.00 0.04 0.00 0.00 0.96 0.00 0.00
#> TCGA.WE.A8ZN.06 1 0.4673 -0.2262 0.56 0.00 0.02 0.00 0.34 0.00 0.08 0.00
#> TCGA.D3.A8GN.06 4 0.0471 0.9241 0.00 0.02 0.00 0.98 0.00 0.00 0.00 0.00
#> TCGA.EB.A550.01 8 0.2532 0.8108 0.00 0.04 0.02 0.04 0.00 0.00 0.02 0.88
#> TCGA.GF.A4EO.06 4 0.0941 0.9210 0.00 0.02 0.02 0.96 0.00 0.00 0.00 0.00
#> TCGA.WE.A8K4.01 1 0.2852 0.5517 0.72 0.00 0.00 0.00 0.00 0.00 0.28 0.00
#> TCGA.EB.A6QY.01 5 0.4031 0.4621 0.00 0.00 0.10 0.00 0.72 0.00 0.16 0.02
#> TCGA.WE.A8K1.06 1 0.3193 0.4303 0.62 0.00 0.00 0.00 0.00 0.00 0.38 0.00
#> TCGA.ER.A42L.06 1 0.1091 0.6162 0.94 0.00 0.00 0.00 0.00 0.00 0.06 0.00
#> TCGA.FR.A8YE.06 6 0.2547 0.6611 0.12 0.00 0.00 0.00 0.00 0.84 0.04 0.00
#> TCGA.EE.A3JH.06 1 0.3272 0.4003 0.58 0.00 0.00 0.00 0.00 0.00 0.42 0.00
#> TCGA.FR.A44A.06 4 0.2132 0.8802 0.00 0.08 0.04 0.88 0.00 0.00 0.00 0.00
#> TCGA.EB.A5VV.06 2 0.3494 0.6474 0.00 0.78 0.04 0.04 0.00 0.00 0.00 0.14
#> TCGA.GN.A4U5.01 4 0.4144 0.6318 0.00 0.22 0.12 0.66 0.00 0.00 0.00 0.00
#> TCGA.D3.A3MR.06 1 0.3299 0.3376 0.56 0.00 0.00 0.00 0.00 0.00 0.44 0.00
#> TCGA.EB.A6L9.06 6 0.0000 0.8134 0.00 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.EB.A430.01 5 0.6085 -0.1474 0.00 0.00 0.28 0.00 0.44 0.16 0.12 0.00
#> TCGA.D3.A8GE.06 6 0.4885 -0.0084 0.00 0.00 0.26 0.00 0.10 0.60 0.04 0.00
#> TCGA.D3.A8GD.06 4 0.0000 0.9267 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.EE.A183.06 1 0.0471 0.6112 0.98 0.00 0.00 0.00 0.00 0.00 0.02 0.00
#> TCGA.ER.A2NH.06 1 0.3083 0.4982 0.66 0.00 0.00 0.00 0.00 0.00 0.34 0.00
#> TCGA.EE.A2M8.06 2 0.2591 0.6540 0.00 0.86 0.02 0.04 0.00 0.00 0.00 0.08
#> TCGA.EE.A2MR.06 1 0.3293 0.1965 0.74 0.00 0.00 0.00 0.00 0.22 0.04 0.00
#> TCGA.DA.A1I5.06 2 0.3169 0.5892 0.00 0.78 0.18 0.00 0.00 0.00 0.02 0.02
#> TCGA.ER.A19D.06 8 0.2532 0.8098 0.00 0.04 0.04 0.02 0.00 0.00 0.02 0.88
#> TCGA.ER.A199.06 4 0.0471 0.9236 0.00 0.02 0.00 0.98 0.00 0.00 0.00 0.00
#> TCGA.W3.A828.06 5 0.5622 0.2084 0.04 0.00 0.30 0.00 0.46 0.00 0.20 0.00
#> TCGA.BF.A1PX.01 1 0.0471 0.6002 0.98 0.00 0.00 0.00 0.00 0.00 0.02 0.00
#> TCGA.EE.A2GH.06 1 0.3971 0.2650 0.54 0.00 0.00 0.00 0.00 0.04 0.42 0.00
#> TCGA.ER.A196.01 2 0.3329 0.2775 0.00 0.52 0.00 0.00 0.00 0.00 0.00 0.48
#> TCGA.ER.A19S.06 4 0.0000 0.9267 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.EE.A29N.06 1 0.2852 0.5517 0.72 0.00 0.00 0.00 0.00 0.00 0.28 0.00
#> TCGA.D3.A2JB.06 2 0.3483 0.6505 0.00 0.76 0.04 0.02 0.00 0.00 0.00 0.18
#> TCGA.D3.A2JD.06 1 0.3237 0.4000 0.60 0.00 0.00 0.00 0.00 0.00 0.40 0.00
#> TCGA.FS.A1Z4.06 6 0.0000 0.8134 0.00 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.FR.A7UA.06 4 0.3291 0.6851 0.00 0.28 0.02 0.70 0.00 0.00 0.00 0.00
#> TCGA.ER.A2NF.01 5 0.4622 0.1456 0.00 0.00 0.30 0.00 0.56 0.00 0.14 0.00
#> TCGA.GN.A263.01 5 0.5210 0.3595 0.02 0.00 0.02 0.00 0.64 0.12 0.18 0.02
#> TCGA.ER.A19N.06 1 0.3083 0.5122 0.66 0.00 0.00 0.00 0.00 0.00 0.34 0.00
#> TCGA.FR.A7U9.06 2 0.3237 0.4497 0.00 0.60 0.00 0.00 0.00 0.00 0.00 0.40
#> TCGA.ER.A19Q.06 2 0.3169 0.5892 0.00 0.78 0.18 0.00 0.00 0.00 0.02 0.02
#> TCGA.EE.A2MG.06 6 0.0000 0.8134 0.00 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.EE.A2MC.06 6 0.2547 0.6627 0.00 0.00 0.12 0.00 0.04 0.84 0.00 0.00
#> TCGA.EE.A2A0.06 4 0.0000 0.9267 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.EE.A29G.06 1 0.1804 0.5727 0.90 0.00 0.02 0.00 0.00 0.00 0.08 0.00
#> TCGA.GN.A269.01 1 0.2484 0.4407 0.86 0.00 0.02 0.00 0.10 0.00 0.02 0.00
#> TCGA.EE.A2A1.06 6 0.3856 0.3294 0.00 0.00 0.20 0.00 0.10 0.70 0.00 0.00
#> TCGA.ER.A1A1.06 6 0.0000 0.8134 0.00 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.EE.A2MH.06 1 0.0941 0.5884 0.96 0.00 0.02 0.00 0.00 0.00 0.02 0.00
#> TCGA.D3.A3BZ.06 6 0.0941 0.7893 0.00 0.00 0.02 0.00 0.02 0.96 0.00 0.00
#> TCGA.ER.A197.06 4 0.0000 0.9267 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DA.A1IB.06 4 0.2224 0.8582 0.00 0.12 0.02 0.86 0.00 0.00 0.00 0.00
#> TCGA.GN.A261.06 8 0.1765 0.7718 0.00 0.12 0.00 0.00 0.00 0.00 0.00 0.88
#> TCGA.D3.A1QB.06 8 0.2404 0.7781 0.00 0.14 0.00 0.02 0.00 0.00 0.00 0.84
#> TCGA.D3.A3C8.06 4 0.2224 0.8582 0.00 0.12 0.02 0.86 0.00 0.00 0.00 0.00
#> TCGA.ER.A19A.06 6 0.0000 0.8134 0.00 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.EE.A29M.06 2 0.3737 0.2454 0.00 0.50 0.02 0.00 0.00 0.00 0.00 0.48
#> TCGA.D3.A2J7.06 1 0.2650 0.5768 0.76 0.00 0.00 0.00 0.00 0.00 0.24 0.00
#> TCGA.EE.A2GD.06 4 0.0000 0.9267 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.D3.A2J9.06 6 0.2350 0.6894 0.10 0.00 0.00 0.00 0.00 0.86 0.04 0.00
#> TCGA.D3.A1Q4.06 8 0.2532 0.8098 0.00 0.04 0.04 0.02 0.00 0.00 0.02 0.88
#> TCGA.D3.A2J8.06 6 0.0000 0.8134 0.00 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.FS.A1Z0.06 8 0.2532 0.8098 0.00 0.04 0.04 0.02 0.00 0.00 0.02 0.88
#> TCGA.EB.A1NK.01 5 0.2020 0.4854 0.00 0.00 0.02 0.00 0.90 0.00 0.06 0.02
#> TCGA.EE.A2MJ.06 1 0.2267 0.5748 0.82 0.00 0.00 0.00 0.00 0.00 0.18 0.00
#> TCGA.D3.A2JH.06 1 0.3237 0.4087 0.60 0.00 0.00 0.00 0.00 0.00 0.40 0.00
#> TCGA.EE.A29E.06 5 0.2547 0.4325 0.00 0.00 0.12 0.00 0.84 0.00 0.04 0.00
#> TCGA.ER.A2NG.06 4 0.0000 0.9267 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.EE.A2ME.06 6 0.1804 0.7325 0.08 0.00 0.00 0.00 0.00 0.90 0.02 0.00
#> TCGA.GN.A265.06 1 0.2756 0.5681 0.74 0.00 0.00 0.00 0.00 0.00 0.26 0.00
#> TCGA.EE.A2MU.06 1 0.2938 0.5364 0.70 0.00 0.00 0.00 0.00 0.00 0.30 0.00
#> TCGA.EE.A2GK.06 2 0.3494 0.6474 0.00 0.78 0.04 0.04 0.00 0.00 0.00 0.14
#> TCGA.EE.A3AA.06 1 0.0808 0.6085 0.96 0.00 0.00 0.00 0.00 0.00 0.04 0.00
#> TCGA.ER.A19P.06 4 0.1804 0.8942 0.00 0.08 0.02 0.90 0.00 0.00 0.00 0.00
#> TCGA.D3.A1Q8.06 1 0.3193 0.4314 0.62 0.00 0.00 0.00 0.00 0.00 0.38 0.00
#> TCGA.D3.A1Q7.06 4 0.0471 0.9236 0.00 0.02 0.00 0.98 0.00 0.00 0.00 0.00
#> TCGA.D3.A3CB.06 1 0.0000 0.6022 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.ER.A195.06 5 0.5130 0.3228 0.22 0.00 0.02 0.00 0.62 0.10 0.04 0.00
#> TCGA.EB.A5SF.01 8 0.1765 0.7802 0.00 0.12 0.00 0.00 0.00 0.00 0.00 0.88
#> TCGA.EE.A2GE.06 1 0.3272 0.3801 0.58 0.00 0.00 0.00 0.00 0.00 0.42 0.00
#> TCGA.GF.A3OT.06 4 0.1275 0.9068 0.00 0.04 0.02 0.94 0.00 0.00 0.00 0.00
#> TCGA.ER.A2NF.06 5 0.4622 0.1456 0.00 0.00 0.30 0.00 0.56 0.00 0.14 0.00
#> TCGA.BF.AAP7.01 2 0.3178 0.6096 0.00 0.80 0.14 0.04 0.00 0.00 0.00 0.02
#> TCGA.ER.A19W.06 4 0.0000 0.9267 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.RP.A693.06 1 0.0941 0.5891 0.96 0.00 0.02 0.00 0.00 0.00 0.02 0.00
#> TCGA.FW.A3TV.06 2 0.3333 0.2657 0.00 0.50 0.00 0.00 0.00 0.00 0.00 0.50
#> TCGA.FW.A3R5.11 3 0.5836 0.0000 0.00 0.00 0.36 0.00 0.34 0.26 0.04 0.00
#> TCGA.XV.AAZV.01 2 0.3272 0.4091 0.00 0.58 0.00 0.00 0.00 0.00 0.00 0.42
#> TCGA.EE.A29C.06 5 0.3913 0.4587 0.16 0.00 0.04 0.00 0.74 0.00 0.06 0.00
#> TCGA.RP.A690.06 8 0.1275 0.8115 0.00 0.04 0.00 0.00 0.00 0.00 0.02 0.94
#> TCGA.FW.A5DY.06 4 0.0941 0.9210 0.00 0.02 0.02 0.96 0.00 0.00 0.00 0.00
#> TCGA.DA.A1I4.06 5 0.1607 0.5004 0.04 0.00 0.00 0.00 0.92 0.00 0.04 0.00
#> TCGA.GF.A6C9.06 6 0.4284 0.2579 0.36 0.00 0.00 0.00 0.02 0.58 0.04 0.00
#> TCGA.EE.A2GT.06 6 0.5089 -0.2045 0.12 0.00 0.02 0.00 0.42 0.44 0.00 0.00
#> TCGA.GN.A9SD.06 4 0.2350 0.8648 0.00 0.10 0.04 0.86 0.00 0.00 0.00 0.00
#> TCGA.D3.A3CF.06 2 0.2569 0.6650 0.00 0.82 0.00 0.02 0.00 0.00 0.00 0.16
#> TCGA.HR.A2OH.06 4 0.0471 0.9236 0.00 0.02 0.00 0.98 0.00 0.00 0.00 0.00
#> TCGA.GN.A26C.01 1 0.4880 0.0862 0.68 0.00 0.02 0.00 0.10 0.14 0.06 0.00
#> TCGA.EB.A5UN.06 1 0.1275 0.5657 0.94 0.00 0.00 0.00 0.04 0.00 0.02 0.00
#> TCGA.EB.A5SG.06 4 0.0941 0.9210 0.00 0.02 0.02 0.96 0.00 0.00 0.00 0.00
#> TCGA.XV.AAZY.01 4 0.1275 0.9102 0.00 0.04 0.02 0.94 0.00 0.00 0.00 0.00
#> TCGA.D3.A2JA.06 5 0.6540 -0.0231 0.04 0.00 0.20 0.00 0.46 0.20 0.10 0.00
#> TCGA.EE.A2GL.06 4 0.0000 0.9267 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.BF.AAOU.01 4 0.3504 0.5996 0.00 0.04 0.00 0.70 0.00 0.00 0.00 0.26
#> TCGA.EB.A3XD.01 8 0.4412 0.3831 0.00 0.28 0.00 0.12 0.00 0.00 0.00 0.60
#> TCGA.FS.A1ZB.06 5 0.4276 0.4312 0.18 0.00 0.04 0.00 0.70 0.00 0.08 0.00
#> TCGA.QB.A6FS.06 5 0.2648 0.3406 0.00 0.00 0.08 0.00 0.84 0.08 0.00 0.00
#> TCGA.D9.A3Z1.06 1 0.2756 0.5660 0.74 0.00 0.00 0.00 0.00 0.00 0.26 0.00
#> TCGA.D3.A2JN.06 4 0.1741 0.8877 0.00 0.02 0.02 0.92 0.00 0.00 0.00 0.04
#> TCGA.FS.A1ZT.06 5 0.4471 -0.0802 0.00 0.00 0.34 0.00 0.58 0.06 0.02 0.00
#> TCGA.HR.A2OG.06 2 0.3483 0.5870 0.00 0.76 0.18 0.00 0.00 0.00 0.02 0.04
#> TCGA.D9.A3Z3.06 2 0.3928 0.5957 0.00 0.74 0.18 0.02 0.00 0.00 0.02 0.04
#> TCGA.XV.A9VZ.01 8 0.1947 0.7596 0.00 0.14 0.00 0.00 0.00 0.00 0.00 0.86
#> TCGA.EE.A3JD.06 6 0.0000 0.8134 0.00 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.EB.A44N.01 1 0.2807 0.5057 0.84 0.00 0.04 0.00 0.02 0.00 0.10 0.00
#> TCGA.Z2.AA3V.06 2 0.3618 0.4756 0.00 0.60 0.00 0.02 0.00 0.00 0.00 0.38
#> TCGA.DA.A3F8.06 1 0.0808 0.6085 0.96 0.00 0.00 0.00 0.00 0.00 0.04 0.00
#> TCGA.EB.A4OZ.01 2 0.2719 0.6572 0.00 0.80 0.00 0.02 0.00 0.00 0.00 0.18
#> TCGA.EE.A3JE.06 1 0.2938 0.5314 0.70 0.00 0.00 0.00 0.00 0.00 0.30 0.00
#> TCGA.W3.AA1W.06 1 0.0471 0.6112 0.98 0.00 0.00 0.00 0.00 0.00 0.02 0.00
#> TCGA.D3.A51F.06 6 0.0000 0.8134 0.00 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.DA.A3F2.06 6 0.0000 0.8134 0.00 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.EB.A4IS.01 7 0.5603 0.0000 0.28 0.00 0.06 0.00 0.16 0.00 0.50 0.00
#> TCGA.3N.A9WD.06 1 0.2807 0.4079 0.84 0.00 0.04 0.00 0.10 0.00 0.02 0.00
#> TCGA.EB.A4OY.01 8 0.2071 0.8139 0.00 0.04 0.02 0.04 0.00 0.00 0.00 0.90
#> TCGA.BF.AAP0.06 2 0.2591 0.6288 0.00 0.86 0.02 0.08 0.00 0.00 0.00 0.04
#> TCGA.WE.AA9Y.06 1 0.3262 0.3958 0.82 0.00 0.02 0.00 0.02 0.10 0.04 0.00
#> TCGA.FS.A4F8.06 1 0.0471 0.6002 0.98 0.00 0.00 0.00 0.00 0.00 0.02 0.00
#> TCGA.D3.A51H.06 6 0.0000 0.8134 0.00 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.BF.A3DL.01 8 0.2938 0.4539 0.00 0.30 0.00 0.00 0.00 0.00 0.00 0.70
#> TCGA.WE.AAA4.06 4 0.0471 0.9241 0.00 0.02 0.00 0.98 0.00 0.00 0.00 0.00
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
consensus_heatmap(res, k = 7)
consensus_heatmap(res, k = 8)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
membership_heatmap(res, k = 7)
membership_heatmap(res, k = 8)
As soon as the classes for columns are determined, the signatures that are significantly different between subgroups can be looked for. Following are the heatmaps for signatures.
get_signatures(res, k = 2)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
get_signatures(res, k = 7)
get_signatures(res, k = 8)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. To get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows (which is done by automatically selecting number of clusters).If there are too many signatures, top_signatures = ... can be set to only show the
signatures with the highest FDRs:
# code only for demonstration
# e.g. to show the top 500 most significant rows
tb = get_signature(res, k = ..., top_signatures = 500)
If the signatures are defined as these which are uniquely high in current group, diff_method argument
can be set to "uniquely_high_in_one_group":
# code only for demonstration
tb = get_signature(res, k = ..., diff_method = "uniquely_high_in_one_group")
UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
dimension_reduction(res, k = 7, method = "UMAP")
dimension_reduction(res, k = 8, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
If matrix rows can be associated to genes, consider to use functional_enrichment(res,
...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.
Parent node: Node01. Child nodes: Node0111 , Node0112-leaf , Node0113 , Node0121-leaf , Node0122-leaf , Node0123-leaf , Node0124-leaf , Node0125-leaf , Node0131 , Node0132-leaf , Node0133-leaf , Node0211-leaf , Node0212 , Node0221-leaf , Node0222-leaf , Node0311 , Node0312-leaf , Node0321-leaf , Node0322 , Node0323 , Node0411 , Node0412 , Node0413-leaf , Node0421-leaf , Node0422-leaf , Node0423-leaf , Node0431-leaf , Node0432-leaf , Node0433-leaf , Node0441-leaf , Node0442 , Node0443-leaf , Node0511 , Node0512-leaf , Node0513-leaf , Node0521-leaf , Node0522-leaf , Node0523-leaf , Node0524-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 44 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 0.990 0.995 0.5104 0.489 0.489
#> 3 3 1.000 0.953 0.978 0.3251 0.697 0.454
#> 4 4 0.707 0.738 0.850 0.1068 0.853 0.588
#> 5 5 0.788 0.670 0.804 0.0625 0.960 0.846
#> 6 6 0.726 0.628 0.782 0.0380 0.863 0.474
#> 7 7 0.755 0.657 0.787 0.0247 0.907 0.514
#> 8 8 0.762 0.650 0.725 0.0174 0.953 0.705
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.GN.A4U8.11 2 0.000 1.00 0.0 1.0
#> TCGA.WE.A8ZN.06 2 0.000 1.00 0.0 1.0
#> TCGA.WE.A8K4.01 2 0.000 1.00 0.0 1.0
#> TCGA.WE.A8K1.06 2 0.000 1.00 0.0 1.0
#> TCGA.ER.A42L.06 1 0.000 0.99 1.0 0.0
#> TCGA.FR.A8YE.06 1 0.000 0.99 1.0 0.0
#> TCGA.EE.A3JH.06 2 0.000 1.00 0.0 1.0
#> TCGA.D3.A3MR.06 2 0.000 1.00 0.0 1.0
#> TCGA.EE.A183.06 1 0.000 0.99 1.0 0.0
#> TCGA.ER.A2NH.06 2 0.000 1.00 0.0 1.0
#> TCGA.EE.A2MR.06 1 0.000 0.99 1.0 0.0
#> TCGA.BF.A1PX.01 1 0.000 0.99 1.0 0.0
#> TCGA.EE.A2GH.06 2 0.000 1.00 0.0 1.0
#> TCGA.EE.A29N.06 2 0.000 1.00 0.0 1.0
#> TCGA.D3.A2JD.06 2 0.000 1.00 0.0 1.0
#> TCGA.ER.A19N.06 2 0.000 1.00 0.0 1.0
#> TCGA.EE.A29G.06 1 0.000 0.99 1.0 0.0
#> TCGA.GN.A269.01 1 0.000 0.99 1.0 0.0
#> TCGA.EE.A2MH.06 1 0.000 0.99 1.0 0.0
#> TCGA.D3.A2J7.06 2 0.000 1.00 0.0 1.0
#> TCGA.D3.A2J9.06 2 0.000 1.00 0.0 1.0
#> TCGA.EE.A2MJ.06 2 0.000 1.00 0.0 1.0
#> TCGA.D3.A2JH.06 2 0.000 1.00 0.0 1.0
#> TCGA.EE.A2ME.06 1 0.000 0.99 1.0 0.0
#> TCGA.GN.A265.06 2 0.000 1.00 0.0 1.0
#> TCGA.EE.A2MU.06 2 0.000 1.00 0.0 1.0
#> TCGA.EE.A3AA.06 1 0.000 0.99 1.0 0.0
#> TCGA.D3.A1Q8.06 2 0.000 1.00 0.0 1.0
#> TCGA.D3.A3CB.06 1 0.000 0.99 1.0 0.0
#> TCGA.EE.A2GE.06 2 0.000 1.00 0.0 1.0
#> TCGA.RP.A693.06 1 0.000 0.99 1.0 0.0
#> TCGA.GF.A6C9.06 1 0.000 0.99 1.0 0.0
#> TCGA.GN.A26C.01 1 0.000 0.99 1.0 0.0
#> TCGA.EB.A5UN.06 1 0.000 0.99 1.0 0.0
#> TCGA.FS.A1ZB.06 2 0.000 1.00 0.0 1.0
#> TCGA.D9.A3Z1.06 2 0.000 1.00 0.0 1.0
#> TCGA.EB.A44N.01 2 0.000 1.00 0.0 1.0
#> TCGA.DA.A3F8.06 1 0.722 0.75 0.8 0.2
#> TCGA.EE.A3JE.06 1 0.000 0.99 1.0 0.0
#> TCGA.W3.AA1W.06 1 0.000 0.99 1.0 0.0
#> TCGA.EB.A4IS.01 2 0.000 1.00 0.0 1.0
#> TCGA.3N.A9WD.06 1 0.000 0.99 1.0 0.0
#> TCGA.WE.AA9Y.06 1 0.000 0.99 1.0 0.0
#> TCGA.FS.A4F8.06 1 0.000 0.99 1.0 0.0
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.GN.A4U8.11 3 0.000 0.989 0.00 0.00 1.00
#> TCGA.WE.A8ZN.06 2 0.207 0.930 0.00 0.94 0.06
#> TCGA.WE.A8K4.01 2 0.207 0.930 0.00 0.94 0.06
#> TCGA.WE.A8K1.06 2 0.000 0.934 0.00 1.00 0.00
#> TCGA.ER.A42L.06 3 0.000 0.989 0.00 0.00 1.00
#> TCGA.FR.A8YE.06 3 0.000 0.989 0.00 0.00 1.00
#> TCGA.EE.A3JH.06 2 0.207 0.930 0.00 0.94 0.06
#> TCGA.D3.A3MR.06 2 0.000 0.934 0.00 1.00 0.00
#> TCGA.EE.A183.06 1 0.000 1.000 1.00 0.00 0.00
#> TCGA.ER.A2NH.06 2 0.207 0.930 0.00 0.94 0.06
#> TCGA.EE.A2MR.06 1 0.000 1.000 1.00 0.00 0.00
#> TCGA.BF.A1PX.01 1 0.000 1.000 1.00 0.00 0.00
#> TCGA.EE.A2GH.06 2 0.000 0.934 0.00 1.00 0.00
#> TCGA.EE.A29N.06 3 0.000 0.989 0.00 0.00 1.00
#> TCGA.D3.A2JD.06 2 0.000 0.934 0.00 1.00 0.00
#> TCGA.ER.A19N.06 2 0.630 0.138 0.00 0.52 0.48
#> TCGA.EE.A29G.06 3 0.000 0.989 0.00 0.00 1.00
#> TCGA.GN.A269.01 1 0.000 1.000 1.00 0.00 0.00
#> TCGA.EE.A2MH.06 1 0.000 1.000 1.00 0.00 0.00
#> TCGA.D3.A2J7.06 3 0.000 0.989 0.00 0.00 1.00
#> TCGA.D3.A2J9.06 3 0.000 0.989 0.00 0.00 1.00
#> TCGA.EE.A2MJ.06 3 0.000 0.989 0.00 0.00 1.00
#> TCGA.D3.A2JH.06 2 0.207 0.930 0.00 0.94 0.06
#> TCGA.EE.A2ME.06 1 0.000 1.000 1.00 0.00 0.00
#> TCGA.GN.A265.06 3 0.000 0.989 0.00 0.00 1.00
#> TCGA.EE.A2MU.06 3 0.254 0.903 0.00 0.08 0.92
#> TCGA.EE.A3AA.06 1 0.000 1.000 1.00 0.00 0.00
#> TCGA.D3.A1Q8.06 2 0.000 0.934 0.00 1.00 0.00
#> TCGA.D3.A3CB.06 1 0.000 1.000 1.00 0.00 0.00
#> TCGA.EE.A2GE.06 2 0.000 0.934 0.00 1.00 0.00
#> TCGA.RP.A693.06 1 0.000 1.000 1.00 0.00 0.00
#> TCGA.GF.A6C9.06 3 0.000 0.989 0.00 0.00 1.00
#> TCGA.GN.A26C.01 1 0.000 1.000 1.00 0.00 0.00
#> TCGA.EB.A5UN.06 1 0.000 1.000 1.00 0.00 0.00
#> TCGA.FS.A1ZB.06 2 0.207 0.930 0.00 0.94 0.06
#> TCGA.D9.A3Z1.06 3 0.000 0.989 0.00 0.00 1.00
#> TCGA.EB.A44N.01 3 0.000 0.989 0.00 0.00 1.00
#> TCGA.DA.A3F8.06 3 0.000 0.989 0.00 0.00 1.00
#> TCGA.EE.A3JE.06 3 0.000 0.989 0.00 0.00 1.00
#> TCGA.W3.AA1W.06 1 0.000 1.000 1.00 0.00 0.00
#> TCGA.EB.A4IS.01 2 0.000 0.934 0.00 1.00 0.00
#> TCGA.3N.A9WD.06 3 0.207 0.923 0.06 0.00 0.94
#> TCGA.WE.AA9Y.06 1 0.000 1.000 1.00 0.00 0.00
#> TCGA.FS.A4F8.06 1 0.000 1.000 1.00 0.00 0.00
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> TCGA.GN.A4U8.11 4 0.3400 0.6378 0.00 0.00 0.18 0.82
#> TCGA.WE.A8ZN.06 4 0.3975 0.6916 0.00 0.24 0.00 0.76
#> TCGA.WE.A8K4.01 4 0.3975 0.6916 0.00 0.24 0.00 0.76
#> TCGA.WE.A8K1.06 2 0.0000 1.0000 0.00 1.00 0.00 0.00
#> TCGA.ER.A42L.06 3 0.0000 0.7981 0.00 0.00 1.00 0.00
#> TCGA.FR.A8YE.06 3 0.0000 0.7981 0.00 0.00 1.00 0.00
#> TCGA.EE.A3JH.06 4 0.3975 0.6916 0.00 0.24 0.00 0.76
#> TCGA.D3.A3MR.06 2 0.0000 1.0000 0.00 1.00 0.00 0.00
#> TCGA.EE.A183.06 1 0.0000 0.8760 1.00 0.00 0.00 0.00
#> TCGA.ER.A2NH.06 4 0.3975 0.6916 0.00 0.24 0.00 0.76
#> TCGA.EE.A2MR.06 1 0.2345 0.8727 0.90 0.00 0.00 0.10
#> TCGA.BF.A1PX.01 1 0.1637 0.8717 0.94 0.00 0.00 0.06
#> TCGA.EE.A2GH.06 2 0.0000 1.0000 0.00 1.00 0.00 0.00
#> TCGA.EE.A29N.06 3 0.4134 0.6108 0.00 0.00 0.74 0.26
#> TCGA.D3.A2JD.06 2 0.0000 1.0000 0.00 1.00 0.00 0.00
#> TCGA.ER.A19N.06 4 0.3853 0.6526 0.00 0.02 0.16 0.82
#> TCGA.EE.A29G.06 3 0.0707 0.7892 0.00 0.00 0.98 0.02
#> TCGA.GN.A269.01 1 0.6089 0.6161 0.64 0.00 0.28 0.08
#> TCGA.EE.A2MH.06 1 0.4292 0.8066 0.82 0.00 0.10 0.08
#> TCGA.D3.A2J7.06 3 0.4134 0.6108 0.00 0.00 0.74 0.26
#> TCGA.D3.A2J9.06 4 0.5000 0.0112 0.00 0.00 0.50 0.50
#> TCGA.EE.A2MJ.06 3 0.4277 0.5769 0.00 0.00 0.72 0.28
#> TCGA.D3.A2JH.06 4 0.3975 0.6916 0.00 0.24 0.00 0.76
#> TCGA.EE.A2ME.06 1 0.1637 0.8717 0.94 0.00 0.00 0.06
#> TCGA.GN.A265.06 4 0.5000 0.0112 0.00 0.00 0.50 0.50
#> TCGA.EE.A2MU.06 4 0.3400 0.6378 0.00 0.00 0.18 0.82
#> TCGA.EE.A3AA.06 1 0.2011 0.8653 0.92 0.00 0.00 0.08
#> TCGA.D3.A1Q8.06 2 0.0000 1.0000 0.00 1.00 0.00 0.00
#> TCGA.D3.A3CB.06 1 0.2345 0.8727 0.90 0.00 0.00 0.10
#> TCGA.EE.A2GE.06 2 0.0000 1.0000 0.00 1.00 0.00 0.00
#> TCGA.RP.A693.06 1 0.2345 0.8727 0.90 0.00 0.00 0.10
#> TCGA.GF.A6C9.06 3 0.2706 0.7312 0.02 0.00 0.90 0.08
#> TCGA.GN.A26C.01 1 0.2345 0.8727 0.90 0.00 0.00 0.10
#> TCGA.EB.A5UN.06 1 0.1637 0.8717 0.94 0.00 0.00 0.06
#> TCGA.FS.A1ZB.06 4 0.3975 0.6916 0.00 0.24 0.00 0.76
#> TCGA.D9.A3Z1.06 3 0.4522 0.4932 0.00 0.00 0.68 0.32
#> TCGA.EB.A44N.01 4 0.4994 0.0777 0.00 0.00 0.48 0.52
#> TCGA.DA.A3F8.06 3 0.0000 0.7981 0.00 0.00 1.00 0.00
#> TCGA.EE.A3JE.06 3 0.0000 0.7981 0.00 0.00 1.00 0.00
#> TCGA.W3.AA1W.06 1 0.2345 0.8727 0.90 0.00 0.00 0.10
#> TCGA.EB.A4IS.01 2 0.0000 1.0000 0.00 1.00 0.00 0.00
#> TCGA.3N.A9WD.06 3 0.4292 0.6496 0.10 0.00 0.82 0.08
#> TCGA.WE.AA9Y.06 1 0.2345 0.8727 0.90 0.00 0.00 0.10
#> TCGA.FS.A4F8.06 1 0.6089 0.6161 0.64 0.00 0.28 0.08
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> TCGA.GN.A4U8.11 4 0.2020 0.7313 0.00 0.00 0.10 0.90 0.00
#> TCGA.WE.A8ZN.06 4 0.3684 0.6990 0.00 0.00 0.00 0.72 0.28
#> TCGA.WE.A8K4.01 4 0.2929 0.7422 0.00 0.00 0.00 0.82 0.18
#> TCGA.WE.A8K1.06 2 0.4287 0.7564 0.00 0.54 0.00 0.00 0.46
#> TCGA.ER.A42L.06 3 0.0000 0.8037 0.00 0.00 1.00 0.00 0.00
#> TCGA.FR.A8YE.06 3 0.0609 0.8007 0.00 0.02 0.98 0.00 0.00
#> TCGA.EE.A3JH.06 4 0.0000 0.7792 0.00 0.00 0.00 1.00 0.00
#> TCGA.D3.A3MR.06 2 0.4818 0.7520 0.00 0.52 0.00 0.02 0.46
#> TCGA.EE.A183.06 1 0.3684 0.7954 0.72 0.28 0.00 0.00 0.00
#> TCGA.ER.A2NH.06 4 0.2516 0.7493 0.00 0.00 0.00 0.86 0.14
#> TCGA.EE.A2MR.06 1 0.0000 0.8136 1.00 0.00 0.00 0.00 0.00
#> TCGA.BF.A1PX.01 1 0.3796 0.7910 0.70 0.30 0.00 0.00 0.00
#> TCGA.EE.A2GH.06 2 0.4818 0.7520 0.00 0.52 0.00 0.02 0.46
#> TCGA.EE.A29N.06 3 0.4876 0.7350 0.00 0.00 0.70 0.08 0.22
#> TCGA.D3.A2JD.06 2 0.4287 0.7564 0.00 0.54 0.00 0.00 0.46
#> TCGA.ER.A19N.06 4 0.0000 0.7792 0.00 0.00 0.00 1.00 0.00
#> TCGA.EE.A29G.06 3 0.5555 0.7293 0.00 0.14 0.64 0.00 0.22
#> TCGA.GN.A269.01 2 0.6592 -0.4189 0.30 0.46 0.24 0.00 0.00
#> TCGA.EE.A2MH.06 1 0.5689 0.5878 0.48 0.44 0.08 0.00 0.00
#> TCGA.D3.A2J7.06 3 0.4876 0.7350 0.00 0.00 0.70 0.08 0.22
#> TCGA.D3.A2J9.06 4 0.4182 0.3520 0.00 0.00 0.40 0.60 0.00
#> TCGA.EE.A2MJ.06 3 0.4818 0.7207 0.00 0.00 0.72 0.10 0.18
#> TCGA.D3.A2JH.06 4 0.0000 0.7792 0.00 0.00 0.00 1.00 0.00
#> TCGA.EE.A2ME.06 1 0.3796 0.7910 0.70 0.30 0.00 0.00 0.00
#> TCGA.GN.A265.06 4 0.4182 0.3520 0.00 0.00 0.40 0.60 0.00
#> TCGA.EE.A2MU.06 4 0.0000 0.7792 0.00 0.00 0.00 1.00 0.00
#> TCGA.EE.A3AA.06 1 0.4126 0.7370 0.62 0.38 0.00 0.00 0.00
#> TCGA.D3.A1Q8.06 2 0.4287 0.7564 0.00 0.54 0.00 0.00 0.46
#> TCGA.D3.A3CB.06 1 0.0000 0.8136 1.00 0.00 0.00 0.00 0.00
#> TCGA.EE.A2GE.06 2 0.4818 0.7520 0.00 0.52 0.00 0.02 0.46
#> TCGA.RP.A693.06 1 0.0000 0.8136 1.00 0.00 0.00 0.00 0.00
#> TCGA.GF.A6C9.06 3 0.2732 0.7343 0.00 0.16 0.84 0.00 0.00
#> TCGA.GN.A26C.01 1 0.0000 0.8136 1.00 0.00 0.00 0.00 0.00
#> TCGA.EB.A5UN.06 1 0.3796 0.7910 0.70 0.30 0.00 0.00 0.00
#> TCGA.FS.A1ZB.06 4 0.3684 0.6990 0.00 0.00 0.00 0.72 0.28
#> TCGA.D9.A3Z1.06 3 0.5733 0.5604 0.00 0.00 0.62 0.22 0.16
#> TCGA.EB.A44N.01 4 0.6047 0.0919 0.00 0.00 0.40 0.48 0.12
#> TCGA.DA.A3F8.06 3 0.0609 0.8007 0.00 0.02 0.98 0.00 0.00
#> TCGA.EE.A3JE.06 3 0.0000 0.8037 0.00 0.00 1.00 0.00 0.00
#> TCGA.W3.AA1W.06 1 0.0000 0.8136 1.00 0.00 0.00 0.00 0.00
#> TCGA.EB.A4IS.01 2 0.4287 0.7564 0.00 0.54 0.00 0.00 0.46
#> TCGA.3N.A9WD.06 3 0.4075 0.7202 0.00 0.16 0.78 0.00 0.06
#> TCGA.WE.AA9Y.06 1 0.0000 0.8136 1.00 0.00 0.00 0.00 0.00
#> TCGA.FS.A4F8.06 2 0.6592 -0.4189 0.30 0.46 0.24 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.GN.A4U8.11 6 0.3706 0.0673 0.00 0.00 0.00 0.38 0.00 0.62
#> TCGA.WE.A8ZN.06 4 0.3162 0.6852 0.00 0.02 0.08 0.86 0.02 0.02
#> TCGA.WE.A8K4.01 4 0.3111 0.6963 0.00 0.02 0.02 0.84 0.12 0.00
#> TCGA.WE.A8K1.06 2 0.0000 0.9206 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.ER.A42L.06 3 0.5636 0.7681 0.00 0.00 0.52 0.00 0.18 0.30
#> TCGA.FR.A8YE.06 3 0.5747 0.7739 0.00 0.00 0.50 0.00 0.20 0.30
#> TCGA.EE.A3JH.06 4 0.4334 0.7084 0.00 0.02 0.00 0.72 0.04 0.22
#> TCGA.D3.A3MR.06 2 0.2956 0.8858 0.00 0.84 0.00 0.12 0.04 0.00
#> TCGA.EE.A183.06 1 0.4282 -0.3485 0.56 0.00 0.00 0.02 0.42 0.00
#> TCGA.ER.A2NH.06 4 0.3007 0.7344 0.00 0.02 0.00 0.86 0.04 0.08
#> TCGA.EE.A2MR.06 1 0.0000 0.7695 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BF.A1PX.01 5 0.3864 0.4300 0.48 0.00 0.00 0.00 0.52 0.00
#> TCGA.EE.A2GH.06 2 0.2956 0.8858 0.00 0.84 0.00 0.12 0.04 0.00
#> TCGA.EE.A29N.06 6 0.3711 0.5181 0.00 0.00 0.26 0.00 0.02 0.72
#> TCGA.D3.A2JD.06 2 0.0000 0.9206 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.ER.A19N.06 4 0.3409 0.6480 0.00 0.00 0.00 0.70 0.00 0.30
#> TCGA.EE.A29G.06 3 0.3073 0.5970 0.00 0.00 0.84 0.00 0.08 0.08
#> TCGA.GN.A269.01 5 0.3567 0.5554 0.10 0.00 0.10 0.00 0.80 0.00
#> TCGA.EE.A2MH.06 5 0.6011 0.5571 0.26 0.00 0.12 0.02 0.58 0.02
#> TCGA.D3.A2J7.06 6 0.3711 0.5181 0.00 0.00 0.26 0.00 0.02 0.72
#> TCGA.D3.A2J9.06 6 0.2790 0.6734 0.00 0.00 0.02 0.14 0.00 0.84
#> TCGA.EE.A2MJ.06 6 0.2631 0.6048 0.00 0.00 0.18 0.00 0.00 0.82
#> TCGA.D3.A2JH.06 4 0.4334 0.7084 0.00 0.02 0.00 0.72 0.04 0.22
#> TCGA.EE.A2ME.06 5 0.3864 0.4300 0.48 0.00 0.00 0.00 0.52 0.00
#> TCGA.GN.A265.06 6 0.2790 0.6734 0.00 0.00 0.02 0.14 0.00 0.84
#> TCGA.EE.A2MU.06 4 0.3869 0.1914 0.00 0.00 0.00 0.50 0.00 0.50
#> TCGA.EE.A3AA.06 5 0.3828 0.4916 0.44 0.00 0.00 0.00 0.56 0.00
#> TCGA.D3.A1Q8.06 2 0.0000 0.9206 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.D3.A3CB.06 1 0.0000 0.7695 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EE.A2GE.06 2 0.2956 0.8858 0.00 0.84 0.00 0.12 0.04 0.00
#> TCGA.RP.A693.06 1 0.0000 0.7695 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.GF.A6C9.06 3 0.5490 0.7703 0.00 0.00 0.56 0.00 0.26 0.18
#> TCGA.GN.A26C.01 1 0.0547 0.7620 0.98 0.00 0.00 0.00 0.02 0.00
#> TCGA.EB.A5UN.06 1 0.4806 -0.5528 0.48 0.00 0.00 0.02 0.48 0.02
#> TCGA.FS.A1ZB.06 4 0.3162 0.6852 0.00 0.02 0.08 0.86 0.02 0.02
#> TCGA.D9.A3Z1.06 6 0.1092 0.6950 0.00 0.00 0.02 0.02 0.00 0.96
#> TCGA.EB.A44N.01 6 0.2581 0.6842 0.00 0.00 0.02 0.12 0.00 0.86
#> TCGA.DA.A3F8.06 3 0.5490 0.7822 0.00 0.00 0.56 0.00 0.18 0.26
#> TCGA.EE.A3JE.06 3 0.5569 0.7509 0.00 0.00 0.52 0.00 0.16 0.32
#> TCGA.W3.AA1W.06 1 0.0000 0.7695 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EB.A4IS.01 2 0.0000 0.9206 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.3N.A9WD.06 3 0.3523 0.6373 0.00 0.00 0.78 0.00 0.18 0.04
#> TCGA.WE.AA9Y.06 1 0.0547 0.7620 0.98 0.00 0.00 0.00 0.02 0.00
#> TCGA.FS.A4F8.06 5 0.3567 0.5554 0.10 0.00 0.10 0.00 0.80 0.00
cbind(get_classes(res, k = 7), get_membership(res, k = 7))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7
#> TCGA.GN.A4U8.11 4 0.0504 0.5906 0.00 0.00 0.02 0.98 0.00 0.00 0.00
#> TCGA.WE.A8ZN.06 7 0.2081 0.7470 0.00 0.00 0.00 0.14 0.00 0.00 0.86
#> TCGA.WE.A8K4.01 7 0.6848 0.3805 0.00 0.00 0.00 0.28 0.22 0.14 0.36
#> TCGA.WE.A8K1.06 2 0.1166 0.8434 0.00 0.94 0.00 0.00 0.06 0.00 0.00
#> TCGA.ER.A42L.06 3 0.0504 0.9232 0.00 0.00 0.98 0.02 0.00 0.00 0.00
#> TCGA.FR.A8YE.06 3 0.0504 0.9232 0.00 0.00 0.98 0.02 0.00 0.00 0.00
#> TCGA.EE.A3JH.06 4 0.5166 0.2425 0.00 0.02 0.00 0.66 0.04 0.08 0.20
#> TCGA.D3.A3MR.06 2 0.4136 0.7911 0.00 0.78 0.00 0.02 0.04 0.08 0.08
#> TCGA.EE.A183.06 5 0.4701 0.6227 0.44 0.00 0.00 0.00 0.50 0.04 0.02
#> TCGA.ER.A2NH.06 4 0.5776 -0.3256 0.00 0.00 0.00 0.46 0.06 0.10 0.38
#> TCGA.EE.A2MR.06 1 0.0000 0.9628 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BF.A1PX.01 5 0.3413 0.7418 0.38 0.00 0.00 0.00 0.62 0.00 0.00
#> TCGA.EE.A2GH.06 2 0.4136 0.7911 0.00 0.78 0.00 0.02 0.04 0.08 0.08
#> TCGA.EE.A29N.06 6 0.4177 0.6721 0.00 0.00 0.12 0.18 0.00 0.70 0.00
#> TCGA.D3.A2JD.06 2 0.1166 0.8434 0.00 0.94 0.00 0.00 0.06 0.00 0.00
#> TCGA.ER.A19N.06 4 0.2569 0.4713 0.00 0.00 0.00 0.84 0.00 0.02 0.14
#> TCGA.EE.A29G.06 6 0.4901 0.0612 0.00 0.00 0.40 0.00 0.06 0.52 0.02
#> TCGA.GN.A269.01 5 0.4191 0.5800 0.06 0.00 0.30 0.00 0.64 0.00 0.00
#> TCGA.EE.A2MH.06 5 0.5399 0.7010 0.20 0.00 0.10 0.00 0.62 0.08 0.00
#> TCGA.D3.A2J7.06 6 0.4177 0.6721 0.00 0.00 0.12 0.18 0.00 0.70 0.00
#> TCGA.D3.A2J9.06 4 0.2722 0.5282 0.00 0.00 0.12 0.84 0.00 0.04 0.00
#> TCGA.EE.A2MJ.06 6 0.5561 0.3001 0.00 0.00 0.14 0.42 0.02 0.42 0.00
#> TCGA.D3.A2JH.06 4 0.5166 0.2425 0.00 0.02 0.00 0.66 0.04 0.08 0.20
#> TCGA.EE.A2ME.06 5 0.3413 0.7418 0.38 0.00 0.00 0.00 0.62 0.00 0.00
#> TCGA.GN.A265.06 4 0.2722 0.5282 0.00 0.00 0.12 0.84 0.00 0.04 0.00
#> TCGA.EE.A2MU.06 4 0.0504 0.5746 0.00 0.00 0.00 0.98 0.00 0.00 0.02
#> TCGA.EE.A3AA.06 5 0.3358 0.7471 0.36 0.00 0.00 0.00 0.64 0.00 0.00
#> TCGA.D3.A1Q8.06 2 0.0000 0.8426 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D3.A3CB.06 1 0.0863 0.9659 0.96 0.00 0.00 0.00 0.00 0.00 0.04
#> TCGA.EE.A2GE.06 2 0.4136 0.7911 0.00 0.78 0.00 0.02 0.04 0.08 0.08
#> TCGA.RP.A693.06 1 0.0863 0.9659 0.96 0.00 0.00 0.00 0.00 0.00 0.04
#> TCGA.GF.A6C9.06 3 0.0000 0.9167 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.GN.A26C.01 1 0.0504 0.9553 0.98 0.00 0.00 0.00 0.02 0.00 0.00
#> TCGA.EB.A5UN.06 5 0.4577 0.7331 0.36 0.00 0.00 0.00 0.58 0.04 0.02
#> TCGA.FS.A1ZB.06 7 0.2081 0.7470 0.00 0.00 0.00 0.14 0.00 0.00 0.86
#> TCGA.D9.A3Z1.06 4 0.4870 -0.0618 0.00 0.00 0.14 0.58 0.00 0.28 0.00
#> TCGA.EB.A44N.01 4 0.4455 0.3137 0.00 0.00 0.10 0.70 0.00 0.18 0.02
#> TCGA.DA.A3F8.06 3 0.0504 0.9097 0.00 0.00 0.98 0.00 0.00 0.00 0.02
#> TCGA.EE.A3JE.06 3 0.0504 0.9232 0.00 0.00 0.98 0.02 0.00 0.00 0.00
#> TCGA.W3.AA1W.06 1 0.0863 0.9659 0.96 0.00 0.00 0.00 0.00 0.00 0.04
#> TCGA.EB.A4IS.01 2 0.1166 0.8434 0.00 0.94 0.00 0.00 0.06 0.00 0.00
#> TCGA.3N.A9WD.06 3 0.3848 0.6536 0.00 0.00 0.76 0.00 0.06 0.16 0.02
#> TCGA.WE.AA9Y.06 1 0.0504 0.9553 0.98 0.00 0.00 0.00 0.02 0.00 0.00
#> TCGA.FS.A4F8.06 5 0.4191 0.5800 0.06 0.00 0.30 0.00 0.64 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.GN.A4U8.11 4 0.0471 0.7124 0.00 0.00 0.00 0.98 0.00 0.00 0.02 0.00
#> TCGA.WE.A8ZN.06 7 0.0808 0.5542 0.00 0.00 0.00 0.04 0.00 0.00 0.96 0.00
#> TCGA.WE.A8K4.01 7 0.6513 0.1861 0.00 0.00 0.00 0.12 0.06 0.08 0.42 0.32
#> TCGA.WE.A8K1.06 2 0.0000 0.7361 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.ER.A42L.06 3 0.1275 0.7899 0.00 0.00 0.94 0.04 0.00 0.02 0.00 0.00
#> TCGA.FR.A8YE.06 3 0.0808 0.7887 0.00 0.00 0.96 0.04 0.00 0.00 0.00 0.00
#> TCGA.EE.A3JH.06 8 0.5178 1.0000 0.00 0.00 0.00 0.36 0.00 0.00 0.24 0.40
#> TCGA.D3.A3MR.06 2 0.4105 0.6085 0.00 0.54 0.00 0.00 0.02 0.00 0.02 0.42
#> TCGA.EE.A183.06 5 0.5458 0.4723 0.40 0.00 0.00 0.00 0.42 0.14 0.00 0.04
#> TCGA.ER.A2NH.06 7 0.5033 -0.3291 0.00 0.00 0.00 0.22 0.00 0.00 0.48 0.30
#> TCGA.EE.A2MR.06 1 0.1091 0.9087 0.94 0.00 0.00 0.00 0.00 0.06 0.00 0.00
#> TCGA.BF.A1PX.01 5 0.2938 0.6661 0.30 0.00 0.00 0.00 0.70 0.00 0.00 0.00
#> TCGA.EE.A2GH.06 2 0.4105 0.6085 0.00 0.54 0.00 0.00 0.02 0.00 0.02 0.42
#> TCGA.EE.A29N.06 6 0.4621 0.9450 0.00 0.00 0.08 0.32 0.02 0.58 0.00 0.00
#> TCGA.D3.A2JD.06 2 0.0000 0.7361 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.ER.A19N.06 4 0.3291 0.0904 0.00 0.00 0.00 0.70 0.00 0.00 0.28 0.02
#> TCGA.EE.A29G.06 3 0.5973 0.3152 0.00 0.00 0.40 0.00 0.06 0.26 0.00 0.28
#> TCGA.GN.A269.01 5 0.3198 0.5634 0.00 0.00 0.26 0.00 0.72 0.02 0.00 0.00
#> TCGA.EE.A2MH.06 5 0.6877 0.6153 0.12 0.00 0.12 0.00 0.48 0.20 0.02 0.06
#> TCGA.D3.A2J7.06 6 0.4255 0.9436 0.00 0.00 0.08 0.34 0.00 0.58 0.00 0.00
#> TCGA.D3.A2J9.06 4 0.1091 0.7289 0.00 0.00 0.06 0.94 0.00 0.00 0.00 0.00
#> TCGA.EE.A2MJ.06 4 0.4917 -0.2683 0.00 0.00 0.06 0.62 0.04 0.26 0.00 0.02
#> TCGA.D3.A2JH.06 8 0.5178 1.0000 0.00 0.00 0.00 0.36 0.00 0.00 0.24 0.40
#> TCGA.EE.A2ME.06 5 0.3198 0.6966 0.26 0.00 0.02 0.00 0.72 0.00 0.00 0.00
#> TCGA.GN.A265.06 4 0.1091 0.7289 0.00 0.00 0.06 0.94 0.00 0.00 0.00 0.00
#> TCGA.EE.A2MU.06 4 0.1804 0.6475 0.00 0.00 0.00 0.90 0.00 0.00 0.08 0.02
#> TCGA.EE.A3AA.06 5 0.3198 0.6966 0.26 0.00 0.02 0.00 0.72 0.00 0.00 0.00
#> TCGA.D3.A1Q8.06 2 0.2407 0.7252 0.00 0.86 0.00 0.00 0.08 0.00 0.00 0.06
#> TCGA.D3.A3CB.06 1 0.0000 0.9180 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EE.A2GE.06 2 0.4105 0.6085 0.00 0.54 0.00 0.00 0.02 0.00 0.02 0.42
#> TCGA.RP.A693.06 1 0.0000 0.9180 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.GF.A6C9.06 3 0.0941 0.7846 0.00 0.00 0.96 0.02 0.02 0.00 0.00 0.00
#> TCGA.GN.A26C.01 1 0.2623 0.8566 0.84 0.00 0.00 0.00 0.10 0.06 0.00 0.00
#> TCGA.EB.A5UN.06 5 0.6104 0.6079 0.28 0.00 0.00 0.00 0.46 0.18 0.02 0.06
#> TCGA.FS.A1ZB.06 7 0.0808 0.5542 0.00 0.00 0.00 0.04 0.00 0.00 0.96 0.00
#> TCGA.D9.A3Z1.06 4 0.2623 0.6179 0.00 0.00 0.06 0.84 0.00 0.10 0.00 0.00
#> TCGA.EB.A44N.01 4 0.1557 0.7171 0.00 0.00 0.06 0.92 0.00 0.02 0.00 0.00
#> TCGA.DA.A3F8.06 3 0.3264 0.7361 0.00 0.00 0.84 0.04 0.02 0.02 0.02 0.06
#> TCGA.EE.A3JE.06 3 0.1275 0.7899 0.00 0.00 0.94 0.04 0.00 0.02 0.00 0.00
#> TCGA.W3.AA1W.06 1 0.0000 0.9180 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EB.A4IS.01 2 0.0000 0.7361 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.3N.A9WD.06 3 0.4812 0.5470 0.00 0.00 0.60 0.00 0.06 0.06 0.00 0.28
#> TCGA.WE.AA9Y.06 1 0.2623 0.8566 0.84 0.00 0.00 0.00 0.10 0.06 0.00 0.00
#> TCGA.FS.A4F8.06 5 0.2852 0.5550 0.00 0.00 0.28 0.00 0.72 0.00 0.00 0.00
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
consensus_heatmap(res, k = 7)
consensus_heatmap(res, k = 8)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
membership_heatmap(res, k = 7)
membership_heatmap(res, k = 8)
As soon as the classes for columns are determined, the signatures that are significantly different between subgroups can be looked for. Following are the heatmaps for signatures.
get_signatures(res, k = 2)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
get_signatures(res, k = 7)
get_signatures(res, k = 8)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. To get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows (which is done by automatically selecting number of clusters).If there are too many signatures, top_signatures = ... can be set to only show the
signatures with the highest FDRs:
# code only for demonstration
# e.g. to show the top 500 most significant rows
tb = get_signature(res, k = ..., top_signatures = 500)
If the signatures are defined as these which are uniquely high in current group, diff_method argument
can be set to "uniquely_high_in_one_group":
# code only for demonstration
tb = get_signature(res, k = ..., diff_method = "uniquely_high_in_one_group")
UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
dimension_reduction(res, k = 7, method = "UMAP")
dimension_reduction(res, k = 8, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
If matrix rows can be associated to genes, consider to use functional_enrichment(res,
...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.
Parent node: Node011. Child nodes: Node01111-leaf , Node01112-leaf , Node01113-leaf , Node01131-leaf , Node01132-leaf , Node01133-leaf , Node01311-leaf , Node01312-leaf , Node02121-leaf , Node02122-leaf , Node02123-leaf , Node03111-leaf , Node03112-leaf , Node03113-leaf , Node03221-leaf , Node03222-leaf , Node03231-leaf , Node03232-leaf , Node03233-leaf , Node03234-leaf , Node04111-leaf , Node04112-leaf , Node04121-leaf , Node04122-leaf , Node04421-leaf , Node04422-leaf , Node04423-leaf , Node04424-leaf , Node05111-leaf , Node05112-leaf , Node05113-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 14 columns.
#> Top rows (1000) are extracted by 'ATC' method.
#> Subgroups are detected by 'skmeans' method.
#> Performed in total 350 partitions by row resampling.
#> Best k for subgroups seems to be 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 0.3633 0.637 0.637
#> 3 3 1.000 0.994 0.993 0.7253 0.736 0.586
#> 4 4 0.714 0.844 0.910 0.2070 0.868 0.647
#> 5 5 0.780 0.765 0.904 0.0636 0.945 0.773
#> 6 6 0.846 0.727 0.927 0.0574 0.956 0.765
#> 7 7 0.890 0.596 0.903 0.0286 0.989 0.923
#> 8 8 0.890 0.547 0.930 0.0259 0.978 0.833
suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:
suggest_best_k(res)
#> [1] 3
#> attr(,"optional")
#> [1] 2
There is also optional best \(k\) = 2 that is worth to check.
Following is the table of the partitions (You need to click the show/hide
code output link to see it). The membership matrix (columns with name p*)
is inferred by
clue::cl_consensus()
function with the SE method. Basically the value in the membership matrix
represents the probability to belong to a certain group. The finall subgroup
label for an item is determined with the group with highest probability it
belongs to.
In get_classes() function, the entropy is calculated from the membership
matrix and the silhouette score is calculated from the consensus matrix.
cbind(get_classes(res, k = 2), get_membership(res, k = 2))
#> class entropy silhouette p1 p2
#> TCGA.EE.A183.06 2 0 1 0 1
#> TCGA.EE.A2MR.06 2 0 1 0 1
#> TCGA.BF.A1PX.01 2 0 1 0 1
#> TCGA.GN.A269.01 2 0 1 0 1
#> TCGA.EE.A2MH.06 2 0 1 0 1
#> TCGA.EE.A2ME.06 2 0 1 0 1
#> TCGA.EE.A3AA.06 2 0 1 0 1
#> TCGA.D3.A3CB.06 1 0 1 1 0
#> TCGA.RP.A693.06 1 0 1 1 0
#> TCGA.GN.A26C.01 2 0 1 0 1
#> TCGA.EB.A5UN.06 2 0 1 0 1
#> TCGA.W3.AA1W.06 1 0 1 1 0
#> TCGA.WE.AA9Y.06 2 0 1 0 1
#> TCGA.FS.A4F8.06 2 0 1 0 1
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.EE.A183.06 2 0.0000 0.985 0 1.00 0.00
#> TCGA.EE.A2MR.06 2 0.0000 0.985 0 1.00 0.00
#> TCGA.BF.A1PX.01 2 0.0892 0.991 0 0.98 0.02
#> TCGA.GN.A269.01 3 0.0000 1.000 0 0.00 1.00
#> TCGA.EE.A2MH.06 2 0.0892 0.991 0 0.98 0.02
#> TCGA.EE.A2ME.06 2 0.0892 0.991 0 0.98 0.02
#> TCGA.EE.A3AA.06 2 0.0892 0.991 0 0.98 0.02
#> TCGA.D3.A3CB.06 1 0.0000 1.000 1 0.00 0.00
#> TCGA.RP.A693.06 1 0.0000 1.000 1 0.00 0.00
#> TCGA.GN.A26C.01 2 0.0000 0.985 0 1.00 0.00
#> TCGA.EB.A5UN.06 3 0.0000 1.000 0 0.00 1.00
#> TCGA.W3.AA1W.06 1 0.0000 1.000 1 0.00 0.00
#> TCGA.WE.AA9Y.06 3 0.0000 1.000 0 0.00 1.00
#> TCGA.FS.A4F8.06 2 0.0892 0.991 0 0.98 0.02
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> TCGA.EE.A183.06 2 0.398 0.559 0 0.76 0.00 0.24
#> TCGA.EE.A2MR.06 4 0.317 0.793 0 0.16 0.00 0.84
#> TCGA.BF.A1PX.01 2 0.292 0.761 0 0.86 0.00 0.14
#> TCGA.GN.A269.01 3 0.000 1.000 0 0.00 1.00 0.00
#> TCGA.EE.A2MH.06 2 0.385 0.650 0 0.82 0.02 0.16
#> TCGA.EE.A2ME.06 2 0.292 0.761 0 0.86 0.00 0.14
#> TCGA.EE.A3AA.06 2 0.164 0.753 0 0.94 0.00 0.06
#> TCGA.D3.A3CB.06 1 0.000 1.000 1 0.00 0.00 0.00
#> TCGA.RP.A693.06 1 0.000 1.000 1 0.00 0.00 0.00
#> TCGA.GN.A26C.01 4 0.441 0.757 0 0.30 0.00 0.70
#> TCGA.EB.A5UN.06 3 0.000 1.000 0 0.00 1.00 0.00
#> TCGA.W3.AA1W.06 1 0.000 1.000 1 0.00 0.00 0.00
#> TCGA.WE.AA9Y.06 3 0.000 1.000 0 0.00 1.00 0.00
#> TCGA.FS.A4F8.06 2 0.121 0.781 0 0.96 0.00 0.04
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> TCGA.EE.A183.06 5 0.4227 0.000 0 0.42 0.00 0.00 0.58
#> TCGA.EE.A2MR.06 4 0.0000 0.731 0 0.00 0.00 1.00 0.00
#> TCGA.BF.A1PX.01 2 0.2020 0.769 0 0.90 0.00 0.10 0.00
#> TCGA.GN.A269.01 3 0.0000 0.976 0 0.00 1.00 0.00 0.00
#> TCGA.EE.A2MH.06 2 0.3796 0.363 0 0.70 0.00 0.00 0.30
#> TCGA.EE.A2ME.06 2 0.2020 0.764 0 0.90 0.00 0.10 0.00
#> TCGA.EE.A3AA.06 2 0.0609 0.713 0 0.98 0.00 0.00 0.02
#> TCGA.D3.A3CB.06 1 0.0000 1.000 1 0.00 0.00 0.00 0.00
#> TCGA.RP.A693.06 1 0.0000 1.000 1 0.00 0.00 0.00 0.00
#> TCGA.GN.A26C.01 4 0.4676 0.698 0 0.12 0.00 0.74 0.14
#> TCGA.EB.A5UN.06 3 0.0000 0.976 0 0.00 1.00 0.00 0.00
#> TCGA.W3.AA1W.06 1 0.0000 1.000 1 0.00 0.00 0.00 0.00
#> TCGA.WE.AA9Y.06 3 0.1410 0.951 0 0.00 0.94 0.00 0.06
#> TCGA.FS.A4F8.06 2 0.1732 0.775 0 0.92 0.00 0.08 0.00
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> TCGA.EE.A183.06 5 0.0937 0.000 0 0.04 0.00 0.00 0.96 0.00
#> TCGA.EE.A2MR.06 4 0.0547 0.575 0 0.02 0.00 0.98 0.00 0.00
#> TCGA.BF.A1PX.01 2 0.0547 0.858 0 0.98 0.00 0.00 0.02 0.00
#> TCGA.GN.A269.01 3 0.0547 0.933 0 0.00 0.98 0.00 0.00 0.02
#> TCGA.EE.A2MH.06 6 0.2454 0.000 0 0.16 0.00 0.00 0.00 0.84
#> TCGA.EE.A2ME.06 2 0.0547 0.866 0 0.98 0.00 0.00 0.02 0.00
#> TCGA.EE.A3AA.06 2 0.3315 0.684 0 0.78 0.00 0.00 0.02 0.20
#> TCGA.D3.A3CB.06 1 0.0000 1.000 1 0.00 0.00 0.00 0.00 0.00
#> TCGA.RP.A693.06 1 0.0000 1.000 1 0.00 0.00 0.00 0.00 0.00
#> TCGA.GN.A26C.01 4 0.4864 0.574 0 0.26 0.00 0.66 0.02 0.06
#> TCGA.EB.A5UN.06 3 0.0547 0.932 0 0.02 0.98 0.00 0.00 0.00
#> TCGA.W3.AA1W.06 1 0.0000 1.000 1 0.00 0.00 0.00 0.00 0.00
#> TCGA.WE.AA9Y.06 3 0.2094 0.899 0 0.00 0.90 0.00 0.02 0.08
#> TCGA.FS.A4F8.06 2 0.1267 0.859 0 0.94 0.00 0.00 0.00 0.06
cbind(get_classes(res, k = 7), get_membership(res, k = 7))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7
#> TCGA.EE.A183.06 5 0.0000 0.000 0 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.EE.A2MR.06 4 0.3985 0.000 0 0.00 0.00 0.52 0.00 0.02 0.46
#> TCGA.BF.A1PX.01 2 0.0000 0.893 0 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.GN.A269.01 3 0.3968 0.748 0 0.00 0.54 0.44 0.00 0.02 0.00
#> TCGA.EE.A2MH.06 6 0.1671 0.000 0 0.10 0.00 0.00 0.00 0.90 0.00
#> TCGA.EE.A2ME.06 2 0.0504 0.886 0 0.98 0.00 0.00 0.02 0.00 0.00
#> TCGA.EE.A3AA.06 2 0.3186 0.680 0 0.76 0.00 0.02 0.00 0.22 0.00
#> TCGA.D3.A3CB.06 1 0.0000 1.000 1 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.RP.A693.06 1 0.0000 1.000 1 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.GN.A26C.01 7 0.1166 0.000 0 0.06 0.00 0.00 0.00 0.00 0.94
#> TCGA.EB.A5UN.06 3 0.4278 0.738 0 0.00 0.50 0.46 0.00 0.04 0.00
#> TCGA.W3.AA1W.06 1 0.0000 1.000 1 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.WE.AA9Y.06 3 0.0000 0.505 0 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.FS.A4F8.06 2 0.0504 0.891 0 0.98 0.00 0.00 0.00 0.02 0.00
cbind(get_classes(res, k = 8), get_membership(res, k = 8))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7 p8
#> TCGA.EE.A183.06 5 0.0000 0.000 0 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.EE.A2MR.06 4 0.0000 0.000 0 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.BF.A1PX.01 2 0.0941 0.845 0 0.96 0.00 0.00 0.00 0.02 0.02 0.00
#> TCGA.GN.A269.01 3 0.1765 0.723 0 0.00 0.88 0.00 0.00 0.00 0.00 0.12
#> TCGA.EE.A2MH.06 6 0.0471 0.000 0 0.02 0.00 0.00 0.00 0.98 0.00 0.00
#> TCGA.EE.A2ME.06 2 0.0941 0.845 0 0.96 0.00 0.00 0.02 0.00 0.02 0.00
#> TCGA.EE.A3AA.06 2 0.4720 0.662 0 0.70 0.00 0.00 0.02 0.12 0.06 0.10
#> TCGA.D3.A3CB.06 1 0.0000 1.000 1 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.RP.A693.06 1 0.0000 1.000 1 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.GN.A26C.01 7 0.2404 0.000 0 0.02 0.00 0.14 0.00 0.00 0.84 0.00
#> TCGA.EB.A5UN.06 3 0.2265 0.739 0 0.00 0.88 0.00 0.00 0.02 0.08 0.02
#> TCGA.W3.AA1W.06 1 0.0000 1.000 1 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.WE.AA9Y.06 8 0.1563 0.000 0 0.00 0.10 0.00 0.00 0.00 0.00 0.90
#> TCGA.FS.A4F8.06 2 0.1741 0.844 0 0.92 0.00 0.00 0.00 0.02 0.02 0.04
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
consensus_heatmap(res, k = 7)
consensus_heatmap(res, k = 8)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
membership_heatmap(res, k = 7)
membership_heatmap(res, k = 8)
As soon as the classes for columns are determined, the signatures that are significantly different between subgroups can be looked for. Following are the heatmaps for signatures.
get_signatures(res, k = 2)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
get_signatures(res, k = 7)
get_signatures(res, k = 8)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. To get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows (which is done by automatically selecting number of clusters).If there are too many signatures, top_signatures = ... can be set to only show the
signatures with the highest FDRs:
# code only for demonstration
# e.g. to show the top 500 most significant rows
tb = get_signature(res, k = ..., top_signatures = 500)
If the signatures are defined as these which are uniquely high in current group, diff_method argument
can be set to "uniquely_high_in_one_group":
# code only for demonstration
tb = get_signature(res, k = ..., diff_method = "uniquely_high_in_one_group")
UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
dimension_reduction(res, k = 7, method = "UMAP")
dimension_reduction(res, k = 8, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
If matrix rows can be associated to genes, consider to use functional_enrichment(res,
...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.
Parent node: Node011. Child nodes: Node01111-leaf , Node01112-leaf , Node01113-leaf , Node01131-leaf , Node01132-leaf , Node01133-leaf , Node01311-leaf , Node01312-leaf , Node02121-leaf , Node02122-leaf , Node02123-leaf , Node03111-leaf , Node03112-leaf , Node03113-leaf , Node03221-leaf , Node03222-leaf , Node03231-leaf , Node03232-leaf , Node03233-leaf , Node03234-leaf , Node04111-leaf , Node04112-leaf , Node04121-leaf , Node04122-leaf , Node04421-leaf , Node04422-leaf , Node04423-leaf , Node04424-leaf , Node05111-leaf , Node05112-leaf , Node05113-leaf .
The object with results only for a single top-value method and a single partitioning method can be extracted as:
res = res_rh["0113"]
A summary of res and all the functions that can be applied to it:
res
#> A 'ConsensusPartition' object with k = 2, 3, 4, 5, 6, 7, 8.
#> On a matrix with 30000 rows and 16 columns.
#> Top rows (1000) are extracted by 'ATC' method.
#> Subgroups are detected by 'skmeans' method.
#> Performed in total 350 partitions by row resampling.
#> Best k for subgroups seems to be 3.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_partitions"
#> [7] "compare_signatures" "consensus_heatmap" "dimension_reduction"
#> [10] "functional_enrichment" "get_anno_col" "get_anno"
#> [13] "get_classes" "get_consensus" "get_matrix"
#> [16] "get_membership" "get_param" "get_signatures"
#> [19] "get_stats" "is_best_k" "is_stable_k"
#> [22] "membership_heatmap" "ncol" "nrow"
#> [25] "plot_ecdf" "predict_classes" "rownames"
#> [28] "select_partition_number" "show" "suggest_best_k"
#> [31] "test_to_known_factors" "top_rows_heatmap"
collect_plots() function collects all the plots made from res for all k (number of subgroups)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
The plots are:
k and the heatmap of
predicted classes for each k.k.k.k.All the plots in panels can be made by individual functions and they are plotted later in this section.
select_partition_number() produces several plots showing different
statistics for choosing “optimized” k. There are following statistics:
k;k, the area increased is defined as \(A_k - A_{k-1}\).The detailed explanations of these statistics can be found in the cola vignette.
Generally speaking, higher 1-PAC score, higher mean silhouette score or higher
concordance corresponds to better partition. Rand index and Jaccard index
measure how similar the current partition is compared to partition with k-1.
If they are too similar, we won't accept k is better than k-1.
select_partition_number(res)
The numeric values for all these statistics can be obtained by get_stats().
get_stats(res)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> 2 2 0.875 0.908 0.964 0.2830 0.767 0.767
#> 3 3 1.000 0.997 0.999 1.2401 0.600 0.478
#> 4 4 0.850 0.881 0.946 0.2067 0.792 0.479
#> 5 5 0.783 0.546 0.833 0.0579 0.900 0.625
#> 6 6 0.750 0.592 0.841 0.0404 0.900 0.571
#> 7 7 0.767 0.577 0.873 0.0299 0.967 0.789
#> 8 8 0.800 0.510 0.854 0.0256 0.975 0.800
suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:
suggest_best_k(res)
#> [1] 3
Following is the table of the partitions (You need to click the show/hide
code output link to see it). The membership matrix (columns with name p*)
is inferred by
clue::cl_consensus()
function with the SE method. Basically the value in the membership matrix
represents the probability to belong to a certain group. The finall subgroup
label for an item is determined with the group with highest probability it
belongs to.
In get_classes() function, the entropy is calculated from the membership
matrix and the silhouette score is calculated from the consensus matrix.
cbind(get_classes(res, k = 2), get_membership(res, k = 2))
#> class entropy silhouette p1 p2
#> TCGA.GN.A4U8.11 2 0.000 0.955 0.00 1.00
#> TCGA.ER.A42L.06 2 0.141 0.947 0.02 0.98
#> TCGA.FR.A8YE.06 2 0.000 0.955 0.00 1.00
#> TCGA.EE.A29N.06 2 0.141 0.947 0.02 0.98
#> TCGA.EE.A29G.06 1 0.000 1.000 1.00 0.00
#> TCGA.D3.A2J7.06 2 0.327 0.914 0.06 0.94
#> TCGA.D3.A2J9.06 2 0.000 0.955 0.00 1.00
#> TCGA.EE.A2MJ.06 2 0.000 0.955 0.00 1.00
#> TCGA.GN.A265.06 2 0.000 0.955 0.00 1.00
#> TCGA.EE.A2MU.06 2 0.141 0.947 0.02 0.98
#> TCGA.GF.A6C9.06 2 0.000 0.955 0.00 1.00
#> TCGA.D9.A3Z1.06 2 0.000 0.955 0.00 1.00
#> TCGA.EB.A44N.01 2 0.995 0.185 0.46 0.54
#> TCGA.DA.A3F8.06 2 0.000 0.955 0.00 1.00
#> TCGA.EE.A3JE.06 2 0.000 0.955 0.00 1.00
#> TCGA.3N.A9WD.06 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.GN.A4U8.11 2 0.0000 0.997 0 1.00 0.00
#> TCGA.ER.A42L.06 3 0.0000 1.000 0 0.00 1.00
#> TCGA.FR.A8YE.06 2 0.0000 0.997 0 1.00 0.00
#> TCGA.EE.A29N.06 3 0.0000 1.000 0 0.00 1.00
#> TCGA.EE.A29G.06 1 0.0000 1.000 1 0.00 0.00
#> TCGA.D3.A2J7.06 3 0.0000 1.000 0 0.00 1.00
#> TCGA.D3.A2J9.06 2 0.0000 0.997 0 1.00 0.00
#> TCGA.EE.A2MJ.06 2 0.0892 0.976 0 0.98 0.02
#> TCGA.GN.A265.06 2 0.0000 0.997 0 1.00 0.00
#> TCGA.EE.A2MU.06 3 0.0000 1.000 0 0.00 1.00
#> TCGA.GF.A6C9.06 2 0.0000 0.997 0 1.00 0.00
#> TCGA.D9.A3Z1.06 3 0.0000 1.000 0 0.00 1.00
#> TCGA.EB.A44N.01 3 0.0000 1.000 0 0.00 1.00
#> TCGA.DA.A3F8.06 2 0.0000 0.997 0 1.00 0.00
#> TCGA.EE.A3JE.06 2 0.0000 0.997 0 1.00 0.00
#> TCGA.3N.A9WD.06 1 0.0000 1.000 1 0.00 0.00
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> TCGA.GN.A4U8.11 2 0.0000 0.837 0 1.00 0.00 0.00
#> TCGA.ER.A42L.06 3 0.0707 0.969 0 0.00 0.98 0.02
#> TCGA.FR.A8YE.06 2 0.0000 0.837 0 1.00 0.00 0.00
#> TCGA.EE.A29N.06 3 0.1637 0.961 0 0.00 0.94 0.06
#> TCGA.EE.A29G.06 1 0.0000 1.000 1 0.00 0.00 0.00
#> TCGA.D3.A2J7.06 3 0.0000 0.966 0 0.00 1.00 0.00
#> TCGA.D3.A2J9.06 2 0.0000 0.837 0 1.00 0.00 0.00
#> TCGA.EE.A2MJ.06 4 0.0000 0.895 0 0.00 0.00 1.00
#> TCGA.GN.A265.06 4 0.2647 0.901 0 0.12 0.00 0.88
#> TCGA.EE.A2MU.06 3 0.1637 0.961 0 0.00 0.94 0.06
#> TCGA.GF.A6C9.06 2 0.4790 0.271 0 0.62 0.00 0.38
#> TCGA.D9.A3Z1.06 4 0.0000 0.895 0 0.00 0.00 1.00
#> TCGA.EB.A44N.01 3 0.0000 0.966 0 0.00 1.00 0.00
#> TCGA.DA.A3F8.06 4 0.2011 0.913 0 0.08 0.00 0.92
#> TCGA.EE.A3JE.06 4 0.2921 0.883 0 0.14 0.00 0.86
#> TCGA.3N.A9WD.06 1 0.0000 1.000 1 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.GN.A4U8.11 2 0.0000 1.000 0.00 1.00 0.00 0.00 0.00
#> TCGA.ER.A42L.06 3 0.1732 0.512 0.00 0.00 0.92 0.00 0.08
#> TCGA.FR.A8YE.06 2 0.0000 1.000 0.00 1.00 0.00 0.00 0.00
#> TCGA.EE.A29N.06 5 0.4307 0.000 0.00 0.00 0.50 0.00 0.50
#> TCGA.EE.A29G.06 1 0.4060 0.757 0.64 0.00 0.00 0.00 0.36
#> TCGA.D3.A2J7.06 3 0.0609 0.570 0.00 0.00 0.98 0.00 0.02
#> TCGA.D3.A2J9.06 2 0.0000 1.000 0.00 1.00 0.00 0.00 0.00
#> TCGA.EE.A2MJ.06 4 0.2516 0.717 0.00 0.00 0.00 0.86 0.14
#> TCGA.GN.A265.06 4 0.0609 0.763 0.00 0.02 0.00 0.98 0.00
#> TCGA.EE.A2MU.06 3 0.4307 -1.000 0.00 0.00 0.50 0.00 0.50
#> TCGA.GF.A6C9.06 4 0.4227 0.241 0.00 0.42 0.00 0.58 0.00
#> TCGA.D9.A3Z1.06 4 0.4287 0.345 0.00 0.00 0.00 0.54 0.46
#> TCGA.EB.A44N.01 3 0.1043 0.556 0.00 0.00 0.96 0.00 0.04
#> TCGA.DA.A3F8.06 4 0.0000 0.761 0.00 0.00 0.00 1.00 0.00
#> TCGA.EE.A3JE.06 4 0.1043 0.759 0.00 0.04 0.00 0.96 0.00
#> TCGA.3N.A9WD.06 1 0.0000 0.757 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.GN.A4U8.11 2 0.0000 1.000 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.ER.A42L.06 3 0.3828 0.369 0.00 0.00 0.56 0.00 0.44 0.00
#> TCGA.FR.A8YE.06 2 0.0000 1.000 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.EE.A29N.06 5 0.2981 0.505 0.00 0.00 0.16 0.00 0.82 0.02
#> TCGA.EE.A29G.06 1 0.0000 0.000 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D3.A2J7.06 3 0.2454 0.689 0.00 0.00 0.84 0.00 0.16 0.00
#> TCGA.D3.A2J9.06 2 0.0000 1.000 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.EE.A2MJ.06 4 0.5012 0.463 0.00 0.00 0.00 0.60 0.10 0.30
#> TCGA.GN.A265.06 4 0.0547 0.787 0.00 0.02 0.00 0.98 0.00 0.00
#> TCGA.EE.A2MU.06 5 0.1556 0.555 0.00 0.00 0.08 0.00 0.92 0.00
#> TCGA.GF.A6C9.06 4 0.3821 0.653 0.00 0.22 0.00 0.74 0.00 0.04
#> TCGA.D9.A3Z1.06 5 0.4482 0.271 0.00 0.00 0.00 0.36 0.60 0.04
#> TCGA.EB.A44N.01 3 0.0000 0.652 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.DA.A3F8.06 4 0.2581 0.746 0.00 0.00 0.00 0.86 0.02 0.12
#> TCGA.EE.A3JE.06 4 0.0547 0.787 0.00 0.02 0.00 0.98 0.00 0.00
#> TCGA.3N.A9WD.06 6 0.3828 0.000 0.44 0.00 0.00 0.00 0.00 0.56
cbind(get_classes(res, k = 7), get_membership(res, k = 7))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7
#> TCGA.GN.A4U8.11 2 0.0000 1.000 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.ER.A42L.06 3 0.5212 0.206 0.00 0.00 0.48 0.00 0.42 0.06 0.04
#> TCGA.FR.A8YE.06 2 0.0000 1.000 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EE.A29N.06 5 0.2213 0.671 0.00 0.00 0.04 0.00 0.90 0.04 0.02
#> TCGA.EE.A29G.06 1 0.0000 0.000 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D3.A2J7.06 3 0.3186 0.578 0.00 0.00 0.76 0.00 0.22 0.02 0.00
#> TCGA.D3.A2J9.06 2 0.0000 1.000 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EE.A2MJ.06 7 0.2572 0.000 0.00 0.00 0.00 0.20 0.00 0.00 0.80
#> TCGA.GN.A265.06 4 0.0863 0.817 0.00 0.04 0.00 0.96 0.00 0.00 0.00
#> TCGA.EE.A2MU.06 5 0.0000 0.708 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.GF.A6C9.06 4 0.2708 0.696 0.00 0.22 0.00 0.78 0.00 0.00 0.00
#> TCGA.D9.A3Z1.06 5 0.4309 0.494 0.00 0.00 0.00 0.20 0.68 0.00 0.12
#> TCGA.EB.A44N.01 3 0.0000 0.557 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DA.A3F8.06 4 0.3199 0.682 0.00 0.00 0.00 0.80 0.00 0.06 0.14
#> TCGA.EE.A3JE.06 4 0.0863 0.817 0.00 0.04 0.00 0.96 0.00 0.00 0.00
#> TCGA.3N.A9WD.06 6 0.2259 0.000 0.16 0.00 0.00 0.00 0.00 0.84 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.GN.A4U8.11 2 0.0000 1.000 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.ER.A42L.06 3 0.5917 0.222 0.00 0.00 0.44 0.02 0.36 0.00 0.06 0.12
#> TCGA.FR.A8YE.06 2 0.0000 1.000 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EE.A29N.06 5 0.4881 0.496 0.04 0.00 0.00 0.04 0.68 0.00 0.08 0.16
#> TCGA.EE.A29G.06 1 0.0808 0.000 0.96 0.00 0.00 0.00 0.00 0.04 0.00 0.00
#> TCGA.D3.A2J7.06 3 0.3763 0.588 0.02 0.00 0.78 0.02 0.08 0.00 0.00 0.10
#> TCGA.D3.A2J9.06 2 0.0000 1.000 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EE.A2MJ.06 7 0.2114 0.000 0.00 0.00 0.00 0.16 0.00 0.00 0.84 0.00
#> TCGA.GN.A265.06 4 0.1091 0.793 0.00 0.06 0.00 0.94 0.00 0.00 0.00 0.00
#> TCGA.EE.A2MU.06 5 0.0000 0.617 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.GF.A6C9.06 4 0.3095 0.625 0.00 0.24 0.00 0.74 0.00 0.00 0.02 0.00
#> TCGA.D9.A3Z1.06 5 0.3774 0.456 0.00 0.00 0.00 0.22 0.70 0.00 0.08 0.00
#> TCGA.EB.A44N.01 3 0.0471 0.573 0.00 0.00 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.DA.A3F8.06 8 0.3015 0.000 0.00 0.00 0.00 0.32 0.00 0.00 0.00 0.68
#> TCGA.EE.A3JE.06 4 0.1341 0.797 0.00 0.08 0.00 0.92 0.00 0.00 0.00 0.00
#> TCGA.3N.A9WD.06 6 0.0000 0.000 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: Node01. Child nodes: Node0111 , Node0112-leaf , Node0113 , Node0121-leaf , Node0122-leaf , Node0123-leaf , Node0124-leaf , Node0125-leaf , Node0131 , Node0132-leaf , Node0133-leaf , Node0211-leaf , Node0212 , Node0221-leaf , Node0222-leaf , Node0311 , Node0312-leaf , Node0321-leaf , Node0322 , Node0323 , Node0411 , Node0412 , Node0413-leaf , Node0421-leaf , Node0422-leaf , Node0423-leaf , Node0431-leaf , Node0432-leaf , Node0433-leaf , Node0441-leaf , Node0442 , Node0443-leaf , Node0511 , Node0512-leaf , Node0513-leaf , Node0521-leaf , Node0522-leaf , Node0523-leaf , Node0524-leaf .
The object with results only for a single top-value method and a single partitioning method can be extracted as:
res = res_rh["012"]
A summary of res and all the functions that can be applied to it:
res
#> A 'ConsensusPartition' object with k = 2, 3, 4, 5, 6, 7, 8.
#> On a matrix with 30000 rows and 31 columns.
#> Top rows (1000) are extracted by 'ATC' method.
#> Subgroups are detected by 'skmeans' method.
#> Performed in total 350 partitions by row resampling.
#> Best k for subgroups seems to be 5.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_partitions"
#> [7] "compare_signatures" "consensus_heatmap" "dimension_reduction"
#> [10] "functional_enrichment" "get_anno_col" "get_anno"
#> [13] "get_classes" "get_consensus" "get_matrix"
#> [16] "get_membership" "get_param" "get_signatures"
#> [19] "get_stats" "is_best_k" "is_stable_k"
#> [22] "membership_heatmap" "ncol" "nrow"
#> [25] "plot_ecdf" "predict_classes" "rownames"
#> [28] "select_partition_number" "show" "suggest_best_k"
#> [31] "test_to_known_factors" "top_rows_heatmap"
collect_plots() function collects all the plots made from res for all k (number of subgroups)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
The plots are:
k and the heatmap of
predicted classes for each k.k.k.k.All the plots in panels can be made by individual functions and they are plotted later in this section.
select_partition_number() produces several plots showing different
statistics for choosing “optimized” k. There are following statistics:
k;k, the area increased is defined as \(A_k - A_{k-1}\).The detailed explanations of these statistics can be found in the cola vignette.
Generally speaking, higher 1-PAC score, higher mean silhouette score or higher
concordance corresponds to better partition. Rand index and Jaccard index
measure how similar the current partition is compared to partition with k-1.
If they are too similar, we won't accept k is better than k-1.
select_partition_number(res)
The numeric values for all these statistics can be obtained by get_stats().
get_stats(res)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> 2 2 1.000 0.992 0.996 0.5022 0.497 0.497
#> 3 3 0.842 0.841 0.928 0.3067 0.665 0.441
#> 4 4 1.000 0.982 0.986 0.1567 0.834 0.572
#> 5 5 0.948 0.952 0.965 0.0531 0.955 0.812
#> 6 6 0.914 0.846 0.912 0.0249 1.000 1.000
#> 7 7 0.874 0.778 0.895 0.0161 0.957 0.794
#> 8 8 0.882 0.708 0.887 0.0141 0.966 0.818
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.D3.A8GO.06 1 0.000 1.000 1.00 0.00
#> TCGA.EB.A550.01 2 0.000 0.990 0.00 1.00
#> TCGA.EB.A5VV.06 1 0.000 1.000 1.00 0.00
#> TCGA.EE.A2M8.06 1 0.000 1.000 1.00 0.00
#> TCGA.DA.A1I5.06 1 0.000 1.000 1.00 0.00
#> TCGA.ER.A19D.06 2 0.000 0.990 0.00 1.00
#> TCGA.ER.A196.01 1 0.000 1.000 1.00 0.00
#> TCGA.D3.A2JB.06 1 0.000 1.000 1.00 0.00
#> TCGA.FR.A7U9.06 1 0.000 1.000 1.00 0.00
#> TCGA.ER.A19Q.06 1 0.000 1.000 1.00 0.00
#> TCGA.GN.A261.06 2 0.000 0.990 0.00 1.00
#> TCGA.D3.A1QB.06 1 0.000 1.000 1.00 0.00
#> TCGA.EE.A29M.06 1 0.000 1.000 1.00 0.00
#> TCGA.D3.A1Q4.06 2 0.000 0.990 0.00 1.00
#> TCGA.FS.A1Z0.06 2 0.000 0.990 0.00 1.00
#> TCGA.EE.A2GK.06 1 0.000 1.000 1.00 0.00
#> TCGA.EB.A5SF.01 2 0.000 0.990 0.00 1.00
#> TCGA.BF.AAP7.01 1 0.000 1.000 1.00 0.00
#> TCGA.FW.A3TV.06 2 0.000 0.990 0.00 1.00
#> TCGA.XV.AAZV.01 1 0.000 1.000 1.00 0.00
#> TCGA.RP.A690.06 2 0.000 0.990 0.00 1.00
#> TCGA.D3.A3CF.06 1 0.000 1.000 1.00 0.00
#> TCGA.EB.A3XD.01 2 0.000 0.990 0.00 1.00
#> TCGA.HR.A2OG.06 1 0.000 1.000 1.00 0.00
#> TCGA.D9.A3Z3.06 2 0.529 0.864 0.12 0.88
#> TCGA.XV.A9VZ.01 2 0.000 0.990 0.00 1.00
#> TCGA.Z2.AA3V.06 1 0.000 1.000 1.00 0.00
#> TCGA.EB.A4OZ.01 1 0.000 1.000 1.00 0.00
#> TCGA.EB.A4OY.01 2 0.000 0.990 0.00 1.00
#> TCGA.BF.AAP0.06 1 0.000 1.000 1.00 0.00
#> TCGA.BF.A3DL.01 2 0.000 0.990 0.00 1.00
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.D3.A8GO.06 1 0.000 0.8299 1.00 0.00 0.00
#> TCGA.EB.A550.01 2 0.000 1.0000 0.00 1.00 0.00
#> TCGA.EB.A5VV.06 3 0.000 0.9854 0.00 0.00 1.00
#> TCGA.EE.A2M8.06 3 0.000 0.9854 0.00 0.00 1.00
#> TCGA.DA.A1I5.06 1 0.604 0.5045 0.62 0.00 0.38
#> TCGA.ER.A19D.06 2 0.000 1.0000 0.00 1.00 0.00
#> TCGA.ER.A196.01 1 0.000 0.8299 1.00 0.00 0.00
#> TCGA.D3.A2JB.06 3 0.000 0.9854 0.00 0.00 1.00
#> TCGA.FR.A7U9.06 1 0.000 0.8299 1.00 0.00 0.00
#> TCGA.ER.A19Q.06 1 0.571 0.6068 0.68 0.00 0.32
#> TCGA.GN.A261.06 2 0.000 1.0000 0.00 1.00 0.00
#> TCGA.D3.A1QB.06 1 0.000 0.8299 1.00 0.00 0.00
#> TCGA.EE.A29M.06 1 0.571 0.6068 0.68 0.00 0.32
#> TCGA.D3.A1Q4.06 2 0.000 1.0000 0.00 1.00 0.00
#> TCGA.FS.A1Z0.06 2 0.000 1.0000 0.00 1.00 0.00
#> TCGA.EE.A2GK.06 3 0.000 0.9854 0.00 0.00 1.00
#> TCGA.EB.A5SF.01 2 0.000 1.0000 0.00 1.00 0.00
#> TCGA.BF.AAP7.01 1 0.000 0.8299 1.00 0.00 0.00
#> TCGA.FW.A3TV.06 1 0.000 0.8299 1.00 0.00 0.00
#> TCGA.XV.AAZV.01 1 0.000 0.8299 1.00 0.00 0.00
#> TCGA.RP.A690.06 2 0.000 1.0000 0.00 1.00 0.00
#> TCGA.D3.A3CF.06 3 0.207 0.9224 0.06 0.00 0.94
#> TCGA.EB.A3XD.01 1 0.628 0.0474 0.54 0.46 0.00
#> TCGA.HR.A2OG.06 1 0.000 0.8299 1.00 0.00 0.00
#> TCGA.D9.A3Z3.06 1 0.000 0.8299 1.00 0.00 0.00
#> TCGA.XV.A9VZ.01 2 0.000 1.0000 0.00 1.00 0.00
#> TCGA.Z2.AA3V.06 1 0.571 0.6068 0.68 0.00 0.32
#> TCGA.EB.A4OZ.01 1 0.571 0.6068 0.68 0.00 0.32
#> TCGA.EB.A4OY.01 2 0.000 1.0000 0.00 1.00 0.00
#> TCGA.BF.AAP0.06 3 0.000 0.9854 0.00 0.00 1.00
#> TCGA.BF.A3DL.01 1 0.207 0.7875 0.94 0.06 0.00
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> TCGA.D3.A8GO.06 4 0.000 1.000 0.00 0 0.00 1.00
#> TCGA.EB.A550.01 2 0.000 1.000 0.00 1 0.00 0.00
#> TCGA.EB.A5VV.06 3 0.000 1.000 0.00 0 1.00 0.00
#> TCGA.EE.A2M8.06 3 0.000 1.000 0.00 0 1.00 0.00
#> TCGA.DA.A1I5.06 1 0.000 0.953 1.00 0 0.00 0.00
#> TCGA.ER.A19D.06 2 0.000 1.000 0.00 1 0.00 0.00
#> TCGA.ER.A196.01 4 0.000 1.000 0.00 0 0.00 1.00
#> TCGA.D3.A2JB.06 3 0.000 1.000 0.00 0 1.00 0.00
#> TCGA.FR.A7U9.06 1 0.121 0.960 0.96 0 0.00 0.04
#> TCGA.ER.A19Q.06 1 0.000 0.953 1.00 0 0.00 0.00
#> TCGA.GN.A261.06 2 0.000 1.000 0.00 1 0.00 0.00
#> TCGA.D3.A1QB.06 4 0.000 1.000 0.00 0 0.00 1.00
#> TCGA.EE.A29M.06 1 0.141 0.962 0.96 0 0.02 0.02
#> TCGA.D3.A1Q4.06 2 0.000 1.000 0.00 1 0.00 0.00
#> TCGA.FS.A1Z0.06 2 0.000 1.000 0.00 1 0.00 0.00
#> TCGA.EE.A2GK.06 3 0.000 1.000 0.00 0 1.00 0.00
#> TCGA.EB.A5SF.01 2 0.000 1.000 0.00 1 0.00 0.00
#> TCGA.BF.AAP7.01 1 0.121 0.960 0.96 0 0.00 0.04
#> TCGA.FW.A3TV.06 4 0.000 1.000 0.00 0 0.00 1.00
#> TCGA.XV.AAZV.01 1 0.121 0.960 0.96 0 0.00 0.04
#> TCGA.RP.A690.06 2 0.000 1.000 0.00 1 0.00 0.00
#> TCGA.D3.A3CF.06 1 0.164 0.937 0.94 0 0.06 0.00
#> TCGA.EB.A3XD.01 4 0.000 1.000 0.00 0 0.00 1.00
#> TCGA.HR.A2OG.06 1 0.292 0.831 0.86 0 0.00 0.14
#> TCGA.D9.A3Z3.06 4 0.000 1.000 0.00 0 0.00 1.00
#> TCGA.XV.A9VZ.01 2 0.000 1.000 0.00 1 0.00 0.00
#> TCGA.Z2.AA3V.06 1 0.141 0.962 0.96 0 0.02 0.02
#> TCGA.EB.A4OZ.01 1 0.141 0.962 0.96 0 0.02 0.02
#> TCGA.EB.A4OY.01 2 0.000 1.000 0.00 1 0.00 0.00
#> TCGA.BF.AAP0.06 3 0.000 1.000 0.00 0 1.00 0.00
#> TCGA.BF.A3DL.01 4 0.000 1.000 0.00 0 0.00 1.00
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> TCGA.D3.A8GO.06 4 0.0609 0.935 0.00 0 0.00 0.98 0.02
#> TCGA.EB.A550.01 2 0.0000 1.000 0.00 1 0.00 0.00 0.00
#> TCGA.EB.A5VV.06 3 0.0000 1.000 0.00 0 1.00 0.00 0.00
#> TCGA.EE.A2M8.06 3 0.0000 1.000 0.00 0 1.00 0.00 0.00
#> TCGA.DA.A1I5.06 5 0.2732 0.933 0.16 0 0.00 0.00 0.84
#> TCGA.ER.A19D.06 2 0.0000 1.000 0.00 1 0.00 0.00 0.00
#> TCGA.ER.A196.01 4 0.3424 0.667 0.24 0 0.00 0.76 0.00
#> TCGA.D3.A2JB.06 3 0.0000 1.000 0.00 0 1.00 0.00 0.00
#> TCGA.FR.A7U9.06 1 0.2012 0.922 0.92 0 0.00 0.02 0.06
#> TCGA.ER.A19Q.06 5 0.2732 0.933 0.16 0 0.00 0.00 0.84
#> TCGA.GN.A261.06 2 0.0000 1.000 0.00 1 0.00 0.00 0.00
#> TCGA.D3.A1QB.06 4 0.0000 0.948 0.00 0 0.00 1.00 0.00
#> TCGA.EE.A29M.06 1 0.2020 0.873 0.90 0 0.00 0.00 0.10
#> TCGA.D3.A1Q4.06 2 0.0000 1.000 0.00 1 0.00 0.00 0.00
#> TCGA.FS.A1Z0.06 2 0.0000 1.000 0.00 1 0.00 0.00 0.00
#> TCGA.EE.A2GK.06 3 0.0000 1.000 0.00 0 1.00 0.00 0.00
#> TCGA.EB.A5SF.01 2 0.0000 1.000 0.00 1 0.00 0.00 0.00
#> TCGA.BF.AAP7.01 1 0.1732 0.895 0.92 0 0.00 0.08 0.00
#> TCGA.FW.A3TV.06 4 0.0000 0.948 0.00 0 0.00 1.00 0.00
#> TCGA.XV.AAZV.01 1 0.1216 0.939 0.96 0 0.00 0.02 0.02
#> TCGA.RP.A690.06 2 0.0000 1.000 0.00 1 0.00 0.00 0.00
#> TCGA.D3.A3CF.06 1 0.1043 0.921 0.96 0 0.04 0.00 0.00
#> TCGA.EB.A3XD.01 4 0.0000 0.948 0.00 0 0.00 1.00 0.00
#> TCGA.HR.A2OG.06 5 0.3110 0.872 0.08 0 0.00 0.06 0.86
#> TCGA.D9.A3Z3.06 4 0.0000 0.948 0.00 0 0.00 1.00 0.00
#> TCGA.XV.A9VZ.01 2 0.0000 1.000 0.00 1 0.00 0.00 0.00
#> TCGA.Z2.AA3V.06 1 0.0609 0.942 0.98 0 0.00 0.02 0.00
#> TCGA.EB.A4OZ.01 1 0.0609 0.942 0.98 0 0.00 0.02 0.00
#> TCGA.EB.A4OY.01 2 0.0000 1.000 0.00 1 0.00 0.00 0.00
#> TCGA.BF.AAP0.06 3 0.0000 1.000 0.00 0 1.00 0.00 0.00
#> TCGA.BF.A3DL.01 4 0.0000 0.948 0.00 0 0.00 1.00 0.00
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> TCGA.D3.A8GO.06 4 0.1814 0.79475 0.00 0.00 0.00 0.90 0.10 0.00
#> TCGA.EB.A550.01 2 0.0547 0.98866 0.00 0.98 0.00 0.00 0.02 0.00
#> TCGA.EB.A5VV.06 3 0.0000 1.00000 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.EE.A2M8.06 3 0.0000 1.00000 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.DA.A1I5.06 6 0.1480 0.82824 0.04 0.00 0.00 0.00 0.02 0.94
#> TCGA.ER.A19D.06 2 0.0000 0.99094 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.ER.A196.01 4 0.4902 -0.00668 0.46 0.00 0.00 0.48 0.06 0.00
#> TCGA.D3.A2JB.06 3 0.0000 1.00000 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.FR.A7U9.06 1 0.1267 0.80897 0.94 0.00 0.00 0.00 0.06 0.00
#> TCGA.ER.A19Q.06 6 0.0937 0.83121 0.04 0.00 0.00 0.00 0.00 0.96
#> TCGA.GN.A261.06 2 0.0000 0.99094 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.D3.A1QB.06 4 0.1807 0.80677 0.06 0.00 0.00 0.92 0.02 0.00
#> TCGA.EE.A29M.06 1 0.3864 0.43599 0.52 0.00 0.00 0.00 0.48 0.00
#> TCGA.D3.A1Q4.06 2 0.0547 0.98866 0.00 0.98 0.00 0.00 0.02 0.00
#> TCGA.FS.A1Z0.06 2 0.0547 0.98866 0.00 0.98 0.00 0.00 0.02 0.00
#> TCGA.EE.A2GK.06 3 0.0000 1.00000 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.EB.A5SF.01 2 0.0000 0.99094 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.BF.AAP7.01 1 0.3163 0.75206 0.82 0.00 0.00 0.04 0.14 0.00
#> TCGA.FW.A3TV.06 4 0.0937 0.82725 0.00 0.00 0.00 0.96 0.04 0.00
#> TCGA.XV.AAZV.01 1 0.3045 0.76632 0.84 0.00 0.00 0.00 0.10 0.06
#> TCGA.RP.A690.06 2 0.0000 0.99094 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.D3.A3CF.06 1 0.3045 0.78384 0.84 0.00 0.06 0.00 0.10 0.00
#> TCGA.EB.A3XD.01 4 0.0547 0.82710 0.00 0.00 0.00 0.98 0.02 0.00
#> TCGA.HR.A2OG.06 6 0.5945 0.64169 0.10 0.00 0.00 0.06 0.26 0.58
#> TCGA.D9.A3Z3.06 4 0.0547 0.82991 0.00 0.00 0.00 0.98 0.02 0.00
#> TCGA.XV.A9VZ.01 2 0.0000 0.99094 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.Z2.AA3V.06 1 0.1267 0.80957 0.94 0.00 0.00 0.00 0.06 0.00
#> TCGA.EB.A4OZ.01 1 0.1556 0.80493 0.92 0.00 0.00 0.00 0.08 0.00
#> TCGA.EB.A4OY.01 2 0.0547 0.98866 0.00 0.98 0.00 0.00 0.02 0.00
#> TCGA.BF.AAP0.06 3 0.0000 1.00000 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.BF.A3DL.01 4 0.2790 0.76903 0.00 0.00 0.00 0.84 0.14 0.02
cbind(get_classes(res, k = 7), get_membership(res, k = 7))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7
#> TCGA.D3.A8GO.06 4 0.3687 0.733 0.12 0 0.0 0.76 0.00 0.00 0.12
#> TCGA.EB.A550.01 2 0.0000 1.000 0.00 1 0.0 0.00 0.00 0.00 0.00
#> TCGA.EB.A5VV.06 3 0.0000 1.000 0.00 0 1.0 0.00 0.00 0.00 0.00
#> TCGA.EE.A2M8.06 3 0.0000 1.000 0.00 0 1.0 0.00 0.00 0.00 0.00
#> TCGA.DA.A1I5.06 6 0.1166 0.909 0.06 0 0.0 0.00 0.00 0.94 0.00
#> TCGA.ER.A19D.06 2 0.0000 1.000 0.00 1 0.0 0.00 0.00 0.00 0.00
#> TCGA.ER.A196.01 1 0.4681 0.293 0.58 0 0.0 0.32 0.00 0.00 0.10
#> TCGA.D3.A2JB.06 3 0.0000 1.000 0.00 0 1.0 0.00 0.00 0.00 0.00
#> TCGA.FR.A7U9.06 1 0.4242 0.574 0.72 0 0.0 0.00 0.18 0.02 0.08
#> TCGA.ER.A19Q.06 6 0.0504 0.909 0.02 0 0.0 0.00 0.00 0.98 0.00
#> TCGA.GN.A261.06 2 0.0000 1.000 0.00 1 0.0 0.00 0.00 0.00 0.00
#> TCGA.D3.A1QB.06 4 0.3086 0.742 0.16 0 0.0 0.80 0.00 0.00 0.04
#> TCGA.EE.A29M.06 5 0.1886 0.000 0.12 0 0.0 0.00 0.88 0.00 0.00
#> TCGA.D3.A1Q4.06 2 0.0000 1.000 0.00 1 0.0 0.00 0.00 0.00 0.00
#> TCGA.FS.A1Z0.06 2 0.0000 1.000 0.00 1 0.0 0.00 0.00 0.00 0.00
#> TCGA.EE.A2GK.06 3 0.0000 1.000 0.00 0 1.0 0.00 0.00 0.00 0.00
#> TCGA.EB.A5SF.01 2 0.0000 1.000 0.00 1 0.0 0.00 0.00 0.00 0.00
#> TCGA.BF.AAP7.01 1 0.3000 0.594 0.84 0 0.0 0.04 0.02 0.00 0.10
#> TCGA.FW.A3TV.06 4 0.1664 0.802 0.00 0 0.0 0.92 0.02 0.00 0.06
#> TCGA.XV.AAZV.01 1 0.5506 0.488 0.60 0 0.0 0.02 0.22 0.02 0.14
#> TCGA.RP.A690.06 2 0.0000 1.000 0.00 1 0.0 0.00 0.00 0.00 0.00
#> TCGA.D3.A3CF.06 1 0.3284 0.576 0.80 0 0.1 0.00 0.10 0.00 0.00
#> TCGA.EB.A3XD.01 4 0.1006 0.817 0.02 0 0.0 0.96 0.00 0.00 0.02
#> TCGA.HR.A2OG.06 7 0.4832 0.000 0.04 0 0.0 0.04 0.00 0.34 0.58
#> TCGA.D9.A3Z3.06 4 0.1664 0.814 0.02 0 0.0 0.92 0.00 0.00 0.06
#> TCGA.XV.A9VZ.01 2 0.0000 1.000 0.00 1 0.0 0.00 0.00 0.00 0.00
#> TCGA.Z2.AA3V.06 1 0.2708 0.577 0.78 0 0.0 0.00 0.22 0.00 0.00
#> TCGA.EB.A4OZ.01 1 0.0504 0.645 0.98 0 0.0 0.00 0.00 0.00 0.02
#> TCGA.EB.A4OY.01 2 0.0000 1.000 0.00 1 0.0 0.00 0.00 0.00 0.00
#> TCGA.BF.AAP0.06 3 0.0000 1.000 0.00 0 1.0 0.00 0.00 0.00 0.00
#> TCGA.BF.A3DL.01 4 0.3745 0.639 0.00 0 0.0 0.70 0.04 0.00 0.26
cbind(get_classes(res, k = 8), get_membership(res, k = 8))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7 p8
#> TCGA.D3.A8GO.06 4 0.2859 0.568 0.02 0.00 0.00 0.82 0.00 0.00 0.14 0.02
#> TCGA.EB.A550.01 2 0.1275 0.955 0.00 0.94 0.00 0.00 0.02 0.00 0.00 0.04
#> TCGA.EB.A5VV.06 3 0.0000 0.967 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EE.A2M8.06 3 0.1275 0.950 0.02 0.00 0.94 0.00 0.00 0.00 0.04 0.00
#> TCGA.DA.A1I5.06 6 0.2350 0.831 0.10 0.00 0.00 0.00 0.00 0.86 0.00 0.04
#> TCGA.ER.A19D.06 2 0.0471 0.960 0.00 0.98 0.00 0.00 0.00 0.00 0.00 0.02
#> TCGA.ER.A196.01 4 0.3991 0.216 0.32 0.00 0.00 0.62 0.00 0.00 0.00 0.06
#> TCGA.D3.A2JB.06 3 0.1275 0.950 0.02 0.00 0.94 0.00 0.00 0.00 0.04 0.00
#> TCGA.FR.A7U9.06 1 0.5081 0.602 0.66 0.00 0.00 0.02 0.12 0.02 0.02 0.16
#> TCGA.ER.A19Q.06 6 0.0941 0.828 0.02 0.00 0.00 0.00 0.00 0.96 0.02 0.00
#> TCGA.GN.A261.06 2 0.0471 0.960 0.00 0.98 0.00 0.00 0.00 0.00 0.00 0.02
#> TCGA.D3.A1QB.06 4 0.0941 0.624 0.02 0.00 0.00 0.96 0.00 0.00 0.00 0.02
#> TCGA.EE.A29M.06 5 0.0471 0.000 0.02 0.00 0.00 0.00 0.98 0.00 0.00 0.00
#> TCGA.D3.A1Q4.06 2 0.1275 0.955 0.00 0.94 0.00 0.00 0.02 0.00 0.00 0.04
#> TCGA.FS.A1Z0.06 2 0.1275 0.955 0.00 0.94 0.00 0.00 0.02 0.00 0.00 0.04
#> TCGA.EE.A2GK.06 3 0.0000 0.967 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EB.A5SF.01 2 0.0000 0.961 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BF.AAP7.01 1 0.3744 0.602 0.74 0.00 0.00 0.18 0.00 0.00 0.06 0.02
#> TCGA.FW.A3TV.06 4 0.2406 0.448 0.00 0.00 0.00 0.80 0.00 0.00 0.00 0.20
#> TCGA.XV.AAZV.01 1 0.5013 0.590 0.66 0.00 0.00 0.00 0.04 0.04 0.08 0.18
#> TCGA.RP.A690.06 2 0.0471 0.960 0.00 0.98 0.00 0.00 0.00 0.00 0.00 0.02
#> TCGA.D3.A3CF.06 1 0.2914 0.659 0.84 0.00 0.08 0.00 0.04 0.00 0.04 0.00
#> TCGA.EB.A3XD.01 4 0.0941 0.627 0.00 0.00 0.00 0.96 0.02 0.00 0.00 0.02
#> TCGA.HR.A2OG.06 7 0.1563 0.000 0.00 0.00 0.00 0.00 0.00 0.10 0.90 0.00
#> TCGA.D9.A3Z3.06 4 0.3054 0.559 0.00 0.00 0.00 0.80 0.00 0.00 0.08 0.12
#> TCGA.XV.A9VZ.01 2 0.0471 0.960 0.00 0.98 0.00 0.00 0.00 0.00 0.00 0.02
#> TCGA.Z2.AA3V.06 1 0.2404 0.674 0.84 0.00 0.00 0.00 0.14 0.00 0.00 0.02
#> TCGA.EB.A4OZ.01 1 0.1887 0.706 0.90 0.00 0.00 0.06 0.00 0.00 0.04 0.00
#> TCGA.EB.A4OY.01 2 0.1275 0.955 0.00 0.94 0.00 0.00 0.02 0.00 0.00 0.04
#> TCGA.BF.AAP0.06 3 0.0000 0.967 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BF.A3DL.01 8 0.3142 0.000 0.00 0.00 0.00 0.36 0.00 0.00 0.00 0.64
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
consensus_heatmap(res, k = 7)
consensus_heatmap(res, k = 8)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
membership_heatmap(res, k = 7)
membership_heatmap(res, k = 8)
As soon as the classes for columns are determined, the signatures that are significantly different between subgroups can be looked for. Following are the heatmaps for signatures.
get_signatures(res, k = 2)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
get_signatures(res, k = 7)
get_signatures(res, k = 8)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. To get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows (which is done by automatically selecting number of clusters).If there are too many signatures, top_signatures = ... can be set to only show the
signatures with the highest FDRs:
# code only for demonstration
# e.g. to show the top 500 most significant rows
tb = get_signature(res, k = ..., top_signatures = 500)
If the signatures are defined as these which are uniquely high in current group, diff_method argument
can be set to "uniquely_high_in_one_group":
# code only for demonstration
tb = get_signature(res, k = ..., diff_method = "uniquely_high_in_one_group")
UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
dimension_reduction(res, k = 7, method = "UMAP")
dimension_reduction(res, k = 8, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
If matrix rows can be associated to genes, consider to use functional_enrichment(res,
...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.
Parent node: Node01. Child nodes: Node0111 , Node0112-leaf , Node0113 , Node0121-leaf , Node0122-leaf , Node0123-leaf , Node0124-leaf , Node0125-leaf , Node0131 , Node0132-leaf , Node0133-leaf , Node0211-leaf , Node0212 , Node0221-leaf , Node0222-leaf , Node0311 , Node0312-leaf , Node0321-leaf , Node0322 , Node0323 , Node0411 , Node0412 , Node0413-leaf , Node0421-leaf , Node0422-leaf , Node0423-leaf , Node0431-leaf , Node0432-leaf , Node0433-leaf , Node0441-leaf , Node0442 , Node0443-leaf , Node0511 , Node0512-leaf , Node0513-leaf , Node0521-leaf , Node0522-leaf , Node0523-leaf , Node0524-leaf .
The object with results only for a single top-value method and a single partitioning method can be extracted as:
res = res_rh["013"]
A summary of res and all the functions that can be applied to it:
res
#> A 'ConsensusPartition' object with k = 2, 3, 4, 5, 6, 7, 8.
#> On a matrix with 30000 rows and 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 0.995 0.997 0.5025 0.497 0.497
#> 3 3 1.000 0.992 0.996 0.2636 0.766 0.573
#> 4 4 0.958 0.944 0.964 0.0686 0.948 0.859
#> 5 5 0.877 0.721 0.857 0.0210 0.955 0.867
#> 6 6 0.890 0.699 0.870 0.0330 0.951 0.853
#> 7 7 0.783 0.646 0.850 0.0301 0.942 0.816
#> 8 8 0.741 0.654 0.843 0.0463 0.974 0.909
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.D3.A8GB.06 1 0.000 1.000 1.00 0.00
#> TCGA.EB.A6QY.01 2 0.000 0.993 0.00 1.00
#> TCGA.EB.A6L9.06 1 0.000 1.000 1.00 0.00
#> TCGA.EB.A430.01 2 0.000 0.993 0.00 1.00
#> TCGA.D3.A8GE.06 1 0.000 1.000 1.00 0.00
#> TCGA.W3.A828.06 2 0.000 0.993 0.00 1.00
#> TCGA.FS.A1Z4.06 1 0.000 1.000 1.00 0.00
#> TCGA.ER.A2NF.01 2 0.242 0.962 0.04 0.96
#> TCGA.GN.A263.01 2 0.000 0.993 0.00 1.00
#> TCGA.EE.A2MG.06 1 0.000 1.000 1.00 0.00
#> TCGA.EE.A2MC.06 1 0.000 1.000 1.00 0.00
#> TCGA.EE.A2A1.06 1 0.000 1.000 1.00 0.00
#> TCGA.ER.A1A1.06 1 0.000 1.000 1.00 0.00
#> TCGA.D3.A3BZ.06 1 0.000 1.000 1.00 0.00
#> TCGA.ER.A19A.06 1 0.000 1.000 1.00 0.00
#> TCGA.D3.A2J8.06 1 0.000 1.000 1.00 0.00
#> TCGA.EB.A1NK.01 2 0.000 0.993 0.00 1.00
#> TCGA.EE.A29E.06 2 0.000 0.993 0.00 1.00
#> TCGA.ER.A195.06 2 0.000 0.993 0.00 1.00
#> TCGA.ER.A2NF.06 2 0.000 0.993 0.00 1.00
#> TCGA.FW.A3R5.11 2 0.242 0.962 0.04 0.96
#> TCGA.EE.A29C.06 2 0.000 0.993 0.00 1.00
#> TCGA.DA.A1I4.06 1 0.000 1.000 1.00 0.00
#> TCGA.EE.A2GT.06 1 0.000 1.000 1.00 0.00
#> TCGA.D3.A2JA.06 2 0.000 0.993 0.00 1.00
#> TCGA.QB.A6FS.06 1 0.000 1.000 1.00 0.00
#> TCGA.FS.A1ZT.06 2 0.000 0.993 0.00 1.00
#> TCGA.EE.A3JD.06 1 0.000 1.000 1.00 0.00
#> TCGA.D3.A51F.06 1 0.000 1.000 1.00 0.00
#> TCGA.DA.A3F2.06 1 0.000 1.000 1.00 0.00
#> TCGA.D3.A51H.06 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.D3.A8GB.06 1 0.000 1.000 1 0.00 0.00
#> TCGA.EB.A6QY.01 3 0.000 0.990 0 0.00 1.00
#> TCGA.EB.A6L9.06 1 0.000 1.000 1 0.00 0.00
#> TCGA.EB.A430.01 3 0.000 0.990 0 0.00 1.00
#> TCGA.D3.A8GE.06 2 0.000 0.992 0 1.00 0.00
#> TCGA.W3.A828.06 3 0.153 0.958 0 0.04 0.96
#> TCGA.FS.A1Z4.06 1 0.000 1.000 1 0.00 0.00
#> TCGA.ER.A2NF.01 2 0.000 0.992 0 1.00 0.00
#> TCGA.GN.A263.01 2 0.000 0.992 0 1.00 0.00
#> TCGA.EE.A2MG.06 1 0.000 1.000 1 0.00 0.00
#> TCGA.EE.A2MC.06 1 0.000 1.000 1 0.00 0.00
#> TCGA.EE.A2A1.06 1 0.000 1.000 1 0.00 0.00
#> TCGA.ER.A1A1.06 1 0.000 1.000 1 0.00 0.00
#> TCGA.D3.A3BZ.06 1 0.000 1.000 1 0.00 0.00
#> TCGA.ER.A19A.06 1 0.000 1.000 1 0.00 0.00
#> TCGA.D3.A2J8.06 1 0.000 1.000 1 0.00 0.00
#> TCGA.EB.A1NK.01 3 0.000 0.990 0 0.00 1.00
#> TCGA.EE.A29E.06 3 0.000 0.990 0 0.00 1.00
#> TCGA.ER.A195.06 2 0.000 0.992 0 1.00 0.00
#> TCGA.ER.A2NF.06 2 0.000 0.992 0 1.00 0.00
#> TCGA.FW.A3R5.11 2 0.000 0.992 0 1.00 0.00
#> TCGA.EE.A29C.06 2 0.254 0.912 0 0.92 0.08
#> TCGA.DA.A1I4.06 2 0.000 0.992 0 1.00 0.00
#> TCGA.EE.A2GT.06 1 0.000 1.000 1 0.00 0.00
#> TCGA.D3.A2JA.06 2 0.000 0.992 0 1.00 0.00
#> TCGA.QB.A6FS.06 2 0.000 0.992 0 1.00 0.00
#> TCGA.FS.A1ZT.06 2 0.000 0.992 0 1.00 0.00
#> TCGA.EE.A3JD.06 1 0.000 1.000 1 0.00 0.00
#> TCGA.D3.A51F.06 1 0.000 1.000 1 0.00 0.00
#> TCGA.DA.A3F2.06 1 0.000 1.000 1 0.00 0.00
#> TCGA.D3.A51H.06 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.D3.A8GB.06 1 0.0000 1.000 1 0.00 0.00 0.00
#> TCGA.EB.A6QY.01 3 0.1637 0.916 0 0.06 0.94 0.00
#> TCGA.EB.A6L9.06 1 0.0000 1.000 1 0.00 0.00 0.00
#> TCGA.EB.A430.01 3 0.1637 0.916 0 0.06 0.94 0.00
#> TCGA.D3.A8GE.06 2 0.2011 0.909 0 0.92 0.00 0.08
#> TCGA.W3.A828.06 3 0.3975 0.721 0 0.24 0.76 0.00
#> TCGA.FS.A1Z4.06 1 0.0000 1.000 1 0.00 0.00 0.00
#> TCGA.ER.A2NF.01 4 0.2647 0.875 0 0.12 0.00 0.88
#> TCGA.GN.A263.01 2 0.0000 0.947 0 1.00 0.00 0.00
#> TCGA.EE.A2MG.06 1 0.0000 1.000 1 0.00 0.00 0.00
#> TCGA.EE.A2MC.06 1 0.0000 1.000 1 0.00 0.00 0.00
#> TCGA.EE.A2A1.06 1 0.0000 1.000 1 0.00 0.00 0.00
#> TCGA.ER.A1A1.06 1 0.0000 1.000 1 0.00 0.00 0.00
#> TCGA.D3.A3BZ.06 1 0.0000 1.000 1 0.00 0.00 0.00
#> TCGA.ER.A19A.06 1 0.0000 1.000 1 0.00 0.00 0.00
#> TCGA.D3.A2J8.06 1 0.0000 1.000 1 0.00 0.00 0.00
#> TCGA.EB.A1NK.01 3 0.1637 0.916 0 0.06 0.94 0.00
#> TCGA.EE.A29E.06 3 0.0707 0.858 0 0.00 0.98 0.02
#> TCGA.ER.A195.06 2 0.0000 0.947 0 1.00 0.00 0.00
#> TCGA.ER.A2NF.06 4 0.1637 0.826 0 0.06 0.00 0.94
#> TCGA.FW.A3R5.11 4 0.3801 0.795 0 0.22 0.00 0.78
#> TCGA.EE.A29C.06 2 0.1637 0.898 0 0.94 0.06 0.00
#> TCGA.DA.A1I4.06 2 0.1637 0.924 0 0.94 0.00 0.06
#> TCGA.EE.A2GT.06 1 0.0000 1.000 1 0.00 0.00 0.00
#> TCGA.D3.A2JA.06 2 0.0707 0.934 0 0.98 0.02 0.00
#> TCGA.QB.A6FS.06 2 0.1637 0.924 0 0.94 0.00 0.06
#> TCGA.FS.A1ZT.06 2 0.0000 0.947 0 1.00 0.00 0.00
#> TCGA.EE.A3JD.06 1 0.0000 1.000 1 0.00 0.00 0.00
#> TCGA.D3.A51F.06 1 0.0000 1.000 1 0.00 0.00 0.00
#> TCGA.DA.A3F2.06 1 0.0000 1.000 1 0.00 0.00 0.00
#> TCGA.D3.A51H.06 1 0.0000 1.000 1 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.D3.A8GB.06 1 0.000 1.000 1.00 0.00 0.00 0.00 0.00
#> TCGA.EB.A6QY.01 3 0.000 0.742 0.00 0.00 1.00 0.00 0.00
#> TCGA.EB.A6L9.06 1 0.000 1.000 1.00 0.00 0.00 0.00 0.00
#> TCGA.EB.A430.01 3 0.000 0.742 0.00 0.00 1.00 0.00 0.00
#> TCGA.D3.A8GE.06 2 0.311 0.415 0.00 0.84 0.00 0.02 0.14
#> TCGA.W3.A828.06 3 0.339 0.638 0.00 0.06 0.84 0.00 0.10
#> TCGA.FS.A1Z4.06 1 0.000 1.000 1.00 0.00 0.00 0.00 0.00
#> TCGA.ER.A2NF.01 4 0.473 0.348 0.00 0.40 0.00 0.58 0.02
#> TCGA.GN.A263.01 2 0.521 0.564 0.00 0.68 0.20 0.00 0.12
#> TCGA.EE.A2MG.06 1 0.000 1.000 1.00 0.00 0.00 0.00 0.00
#> TCGA.EE.A2MC.06 1 0.000 1.000 1.00 0.00 0.00 0.00 0.00
#> TCGA.EE.A2A1.06 1 0.000 1.000 1.00 0.00 0.00 0.00 0.00
#> TCGA.ER.A1A1.06 1 0.000 1.000 1.00 0.00 0.00 0.00 0.00
#> TCGA.D3.A3BZ.06 1 0.000 1.000 1.00 0.00 0.00 0.00 0.00
#> TCGA.ER.A19A.06 1 0.000 1.000 1.00 0.00 0.00 0.00 0.00
#> TCGA.D3.A2J8.06 1 0.000 1.000 1.00 0.00 0.00 0.00 0.00
#> TCGA.EB.A1NK.01 3 0.000 0.742 0.00 0.00 1.00 0.00 0.00
#> TCGA.EE.A29E.06 3 0.431 0.230 0.00 0.00 0.50 0.00 0.50
#> TCGA.ER.A195.06 2 0.487 0.595 0.00 0.72 0.16 0.00 0.12
#> TCGA.ER.A2NF.06 4 0.000 0.525 0.00 0.00 0.00 1.00 0.00
#> TCGA.FW.A3R5.11 2 0.618 -0.175 0.00 0.48 0.00 0.14 0.38
#> TCGA.EE.A29C.06 3 0.586 0.107 0.00 0.32 0.56 0.00 0.12
#> TCGA.DA.A1I4.06 2 0.262 0.452 0.00 0.88 0.00 0.02 0.10
#> TCGA.EE.A2GT.06 1 0.000 1.000 1.00 0.00 0.00 0.00 0.00
#> TCGA.D3.A2JA.06 2 0.586 0.392 0.00 0.56 0.32 0.00 0.12
#> TCGA.QB.A6FS.06 2 0.122 0.511 0.02 0.96 0.00 0.00 0.02
#> TCGA.FS.A1ZT.06 2 0.660 0.527 0.00 0.60 0.22 0.06 0.12
#> TCGA.EE.A3JD.06 1 0.000 1.000 1.00 0.00 0.00 0.00 0.00
#> TCGA.D3.A51F.06 1 0.000 1.000 1.00 0.00 0.00 0.00 0.00
#> TCGA.DA.A3F2.06 1 0.000 1.000 1.00 0.00 0.00 0.00 0.00
#> TCGA.D3.A51H.06 1 0.000 1.000 1.00 0.00 0.00 0.00 0.00
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> TCGA.D3.A8GB.06 1 0.0000 0.9842 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EB.A6QY.01 3 0.0547 0.8150 0.00 0.02 0.98 0.00 0.00 0.00
#> TCGA.EB.A6L9.06 1 0.0000 0.9842 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EB.A430.01 3 0.0000 0.8154 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.D3.A8GE.06 2 0.5922 0.1043 0.00 0.44 0.00 0.00 0.22 0.34
#> TCGA.W3.A828.06 3 0.3711 0.5539 0.00 0.26 0.72 0.00 0.02 0.00
#> TCGA.FS.A1Z4.06 1 0.0000 0.9842 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.ER.A2NF.01 4 0.5480 0.5338 0.00 0.10 0.00 0.66 0.18 0.06
#> TCGA.GN.A263.01 2 0.1814 0.6135 0.00 0.90 0.10 0.00 0.00 0.00
#> TCGA.EE.A2MG.06 1 0.0000 0.9842 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EE.A2MC.06 1 0.1865 0.9264 0.92 0.04 0.00 0.00 0.04 0.00
#> TCGA.EE.A2A1.06 1 0.1480 0.9423 0.94 0.04 0.00 0.00 0.02 0.00
#> TCGA.ER.A1A1.06 1 0.0000 0.9842 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D3.A3BZ.06 1 0.0000 0.9842 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.ER.A19A.06 1 0.0000 0.9842 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D3.A2J8.06 1 0.0000 0.9842 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EB.A1NK.01 3 0.0000 0.8154 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.EE.A29E.06 5 0.3499 0.0000 0.00 0.00 0.32 0.00 0.68 0.00
#> TCGA.ER.A195.06 2 0.1556 0.6152 0.00 0.92 0.08 0.00 0.00 0.00
#> TCGA.ER.A2NF.06 4 0.0000 0.5584 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.FW.A3R5.11 6 0.0000 0.0000 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.EE.A29C.06 2 0.4801 -0.0706 0.00 0.50 0.46 0.02 0.02 0.00
#> TCGA.DA.A1I4.06 2 0.5876 0.1972 0.00 0.48 0.00 0.00 0.26 0.26
#> TCGA.EE.A2GT.06 1 0.1865 0.9264 0.92 0.04 0.00 0.00 0.04 0.00
#> TCGA.D3.A2JA.06 2 0.2631 0.5584 0.00 0.82 0.18 0.00 0.00 0.00
#> TCGA.QB.A6FS.06 2 0.4172 0.4044 0.00 0.68 0.00 0.00 0.28 0.04
#> TCGA.FS.A1ZT.06 2 0.4879 0.5391 0.00 0.72 0.12 0.12 0.04 0.00
#> TCGA.EE.A3JD.06 1 0.0000 0.9842 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D3.A51F.06 1 0.0000 0.9842 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DA.A3F2.06 1 0.0000 0.9842 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D3.A51H.06 1 0.0000 0.9842 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.D3.A8GB.06 1 0.1671 0.9025 0.90 0.10 0.00 0.00 0.00 0.00 0.00
#> TCGA.EB.A6QY.01 3 0.0504 0.7508 0.00 0.02 0.98 0.00 0.00 0.00 0.00
#> TCGA.EB.A6L9.06 1 0.0000 0.9411 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EB.A430.01 3 0.0504 0.7407 0.00 0.02 0.98 0.00 0.00 0.00 0.00
#> TCGA.D3.A8GE.06 7 0.4993 0.4469 0.00 0.24 0.00 0.00 0.02 0.12 0.62
#> TCGA.W3.A828.06 3 0.4001 0.6197 0.00 0.18 0.74 0.00 0.06 0.02 0.00
#> TCGA.FS.A1Z4.06 1 0.0000 0.9411 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.ER.A2NF.01 7 0.3985 -0.0103 0.00 0.02 0.00 0.46 0.00 0.00 0.52
#> TCGA.GN.A263.01 2 0.4998 0.6971 0.00 0.54 0.14 0.00 0.00 0.00 0.32
#> TCGA.EE.A2MG.06 1 0.0863 0.9289 0.96 0.04 0.00 0.00 0.00 0.00 0.00
#> TCGA.EE.A2MC.06 1 0.3086 0.8320 0.80 0.16 0.00 0.00 0.00 0.00 0.04
#> TCGA.EE.A2A1.06 1 0.3526 0.7947 0.76 0.18 0.00 0.00 0.00 0.00 0.06
#> TCGA.ER.A1A1.06 1 0.0000 0.9411 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D3.A3BZ.06 1 0.1433 0.9128 0.92 0.08 0.00 0.00 0.00 0.00 0.00
#> TCGA.ER.A19A.06 1 0.0000 0.9411 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D3.A2J8.06 1 0.0000 0.9411 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EB.A1NK.01 3 0.0000 0.7519 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.EE.A29E.06 5 0.1433 0.0000 0.00 0.00 0.08 0.00 0.92 0.00 0.00
#> TCGA.ER.A195.06 2 0.5047 0.6696 0.00 0.52 0.14 0.00 0.00 0.00 0.34
#> TCGA.ER.A2NF.06 4 0.0000 0.0000 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.FW.A3R5.11 6 0.0000 0.0000 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.EE.A29C.06 3 0.5812 -0.2549 0.00 0.36 0.48 0.02 0.02 0.00 0.12
#> TCGA.DA.A1I4.06 7 0.1928 0.4882 0.00 0.08 0.00 0.00 0.00 0.02 0.90
#> TCGA.EE.A2GT.06 1 0.3244 0.8162 0.78 0.18 0.00 0.00 0.00 0.00 0.04
#> TCGA.D3.A2JA.06 2 0.5402 0.6409 0.00 0.48 0.28 0.00 0.00 0.00 0.24
#> TCGA.QB.A6FS.06 7 0.2422 0.3990 0.00 0.18 0.00 0.00 0.00 0.00 0.82
#> TCGA.FS.A1ZT.06 2 0.6211 0.4383 0.00 0.42 0.18 0.06 0.00 0.00 0.34
#> TCGA.EE.A3JD.06 1 0.0000 0.9411 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D3.A51F.06 1 0.0000 0.9411 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DA.A3F2.06 1 0.0000 0.9411 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D3.A51H.06 1 0.0000 0.9411 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.D3.A8GB.06 1 0.2650 0.773 0.76 0.00 0.00 0.00 0.24 0 0.00 0.00
#> TCGA.EB.A6QY.01 3 0.0471 0.810 0.00 0.02 0.98 0.00 0.00 0 0.00 0.00
#> TCGA.EB.A6L9.06 1 0.0000 0.864 1.00 0.00 0.00 0.00 0.00 0 0.00 0.00
#> TCGA.EB.A430.01 3 0.0471 0.811 0.00 0.00 0.98 0.00 0.02 0 0.00 0.00
#> TCGA.D3.A8GE.06 7 0.3299 0.516 0.00 0.18 0.00 0.00 0.06 0 0.76 0.00
#> TCGA.W3.A828.06 3 0.5541 0.409 0.00 0.16 0.52 0.00 0.26 0 0.06 0.00
#> TCGA.FS.A1Z4.06 1 0.0471 0.864 0.98 0.00 0.00 0.00 0.02 0 0.00 0.00
#> TCGA.ER.A2NF.01 4 0.3845 0.509 0.00 0.06 0.00 0.66 0.00 0 0.28 0.00
#> TCGA.GN.A263.01 2 0.0941 0.642 0.00 0.96 0.00 0.00 0.02 0 0.02 0.00
#> TCGA.EE.A2MG.06 1 0.1341 0.849 0.92 0.00 0.00 0.00 0.08 0 0.00 0.00
#> TCGA.EE.A2MC.06 1 0.3658 0.621 0.58 0.00 0.00 0.00 0.40 0 0.02 0.00
#> TCGA.EE.A2A1.06 1 0.3658 0.623 0.58 0.00 0.00 0.00 0.40 0 0.02 0.00
#> TCGA.ER.A1A1.06 1 0.0000 0.864 1.00 0.00 0.00 0.00 0.00 0 0.00 0.00
#> TCGA.D3.A3BZ.06 1 0.2756 0.761 0.74 0.00 0.00 0.00 0.26 0 0.00 0.00
#> TCGA.ER.A19A.06 1 0.0471 0.864 0.98 0.00 0.00 0.00 0.02 0 0.00 0.00
#> TCGA.D3.A2J8.06 1 0.0808 0.861 0.96 0.00 0.00 0.00 0.04 0 0.00 0.00
#> TCGA.EB.A1NK.01 3 0.0000 0.816 0.00 0.00 1.00 0.00 0.00 0 0.00 0.00
#> TCGA.EE.A29E.06 8 0.0808 0.000 0.00 0.00 0.04 0.00 0.00 0 0.00 0.96
#> TCGA.ER.A195.06 2 0.1557 0.669 0.00 0.92 0.02 0.00 0.06 0 0.00 0.00
#> TCGA.ER.A2NF.06 4 0.0000 0.564 0.00 0.00 0.00 1.00 0.00 0 0.00 0.00
#> TCGA.FW.A3R5.11 6 0.0000 0.000 0.00 0.00 0.00 0.00 0.00 1 0.00 0.00
#> TCGA.EE.A29C.06 2 0.4642 0.449 0.00 0.60 0.30 0.00 0.06 0 0.04 0.00
#> TCGA.DA.A1I4.06 7 0.4134 0.608 0.00 0.30 0.00 0.00 0.08 0 0.62 0.00
#> TCGA.EE.A2GT.06 1 0.3714 0.568 0.54 0.00 0.00 0.00 0.44 0 0.02 0.00
#> TCGA.D3.A2JA.06 2 0.2025 0.670 0.00 0.88 0.10 0.00 0.02 0 0.00 0.00
#> TCGA.QB.A6FS.06 7 0.5190 0.470 0.00 0.26 0.00 0.00 0.32 0 0.42 0.00
#> TCGA.FS.A1ZT.06 2 0.5785 0.374 0.00 0.58 0.02 0.02 0.16 0 0.18 0.04
#> TCGA.EE.A3JD.06 1 0.0000 0.864 1.00 0.00 0.00 0.00 0.00 0 0.00 0.00
#> TCGA.D3.A51F.06 1 0.0000 0.864 1.00 0.00 0.00 0.00 0.00 0 0.00 0.00
#> TCGA.DA.A3F2.06 1 0.0000 0.864 1.00 0.00 0.00 0.00 0.00 0 0.00 0.00
#> TCGA.D3.A51H.06 1 0.0000 0.864 1.00 0.00 0.00 0.00 0.00 0 0.00 0.00
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
consensus_heatmap(res, k = 7)
consensus_heatmap(res, k = 8)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
membership_heatmap(res, k = 7)
membership_heatmap(res, k = 8)
As soon as the classes for columns are determined, the signatures that are significantly different between subgroups can be looked for. Following are the heatmaps for signatures.
get_signatures(res, k = 2)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
get_signatures(res, k = 7)
get_signatures(res, k = 8)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. To get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows (which is done by automatically selecting number of clusters).If there are too many signatures, top_signatures = ... can be set to only show the
signatures with the highest FDRs:
# code only for demonstration
# e.g. to show the top 500 most significant rows
tb = get_signature(res, k = ..., top_signatures = 500)
If the signatures are defined as these which are uniquely high in current group, diff_method argument
can be set to "uniquely_high_in_one_group":
# code only for demonstration
tb = get_signature(res, k = ..., diff_method = "uniquely_high_in_one_group")
UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
dimension_reduction(res, k = 7, method = "UMAP")
dimension_reduction(res, k = 8, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
If matrix rows can be associated to genes, consider to use functional_enrichment(res,
...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.
Parent node: Node013. Child nodes: Node01111-leaf , Node01112-leaf , Node01113-leaf , Node01131-leaf , Node01132-leaf , Node01133-leaf , Node01311-leaf , Node01312-leaf , Node02121-leaf , Node02122-leaf , Node02123-leaf , Node03111-leaf , Node03112-leaf , Node03113-leaf , Node03221-leaf , Node03222-leaf , Node03231-leaf , Node03232-leaf , Node03233-leaf , Node03234-leaf , Node04111-leaf , Node04112-leaf , Node04121-leaf , Node04122-leaf , Node04421-leaf , Node04422-leaf , Node04423-leaf , Node04424-leaf , Node05111-leaf , Node05112-leaf , Node05113-leaf .
The object with results only for a single top-value method and a single partitioning method can be extracted as:
res = res_rh["0131"]
A summary of res and all the functions that can be applied to it:
res
#> A 'ConsensusPartition' object with k = 2, 3, 4, 5, 6, 7, 8.
#> On a matrix with 30000 rows and 15 columns.
#> Top rows (1000) are extracted by 'ATC' method.
#> Subgroups are detected by 'kmeans' method.
#> Performed in total 350 partitions by row resampling.
#> Best k for subgroups seems to be 8.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_partitions"
#> [7] "compare_signatures" "consensus_heatmap" "dimension_reduction"
#> [10] "functional_enrichment" "get_anno_col" "get_anno"
#> [13] "get_classes" "get_consensus" "get_matrix"
#> [16] "get_membership" "get_param" "get_signatures"
#> [19] "get_stats" "is_best_k" "is_stable_k"
#> [22] "membership_heatmap" "ncol" "nrow"
#> [25] "plot_ecdf" "predict_classes" "rownames"
#> [28] "select_partition_number" "show" "suggest_best_k"
#> [31] "test_to_known_factors" "top_rows_heatmap"
collect_plots() function collects all the plots made from res for all k (number of subgroups)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
The plots are:
k and the heatmap of
predicted classes for each k.k.k.k.All the plots in panels can be made by individual functions and they are plotted later in this section.
select_partition_number() produces several plots showing different
statistics for choosing “optimized” k. There are following statistics:
k;k, the area increased is defined as \(A_k - A_{k-1}\).The detailed explanations of these statistics can be found in the cola vignette.
Generally speaking, higher 1-PAC score, higher mean silhouette score or higher
concordance corresponds to better partition. Rand index and Jaccard index
measure how similar the current partition is compared to partition with k-1.
If they are too similar, we won't accept k is better than k-1.
select_partition_number(res)
The numeric values for all these statistics can be obtained by get_stats().
get_stats(res)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> 2 2 1.000 1.000 1.000 0.2484 0.752 0.752
#> 3 3 0.581 0.932 0.917 1.4286 0.600 0.468
#> 4 4 1.000 0.915 0.992 0.1704 0.924 0.789
#> 5 5 1.000 0.839 0.984 0.1009 0.810 0.459
#> 6 6 1.000 0.795 0.995 0.0305 0.981 0.913
#> 7 7 0.867 0.693 0.935 0.0695 0.943 0.714
#> 8 8 0.943 0.671 0.973 0.0378 0.924 0.529
suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:
suggest_best_k(res)
#> [1] 8
#> attr(,"optional")
#> [1] 2 4 5
There is also optional best \(k\) = 2 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.D3.A8GB.06 1 0 1 1 0
#> TCGA.EB.A6L9.06 1 0 1 1 0
#> TCGA.FS.A1Z4.06 1 0 1 1 0
#> TCGA.EE.A2MG.06 1 0 1 1 0
#> TCGA.EE.A2MC.06 2 0 1 0 1
#> TCGA.EE.A2A1.06 1 0 1 1 0
#> TCGA.ER.A1A1.06 1 0 1 1 0
#> TCGA.D3.A3BZ.06 1 0 1 1 0
#> TCGA.ER.A19A.06 1 0 1 1 0
#> TCGA.D3.A2J8.06 1 0 1 1 0
#> TCGA.EE.A2GT.06 2 0 1 0 1
#> TCGA.EE.A3JD.06 1 0 1 1 0
#> TCGA.D3.A51F.06 1 0 1 1 0
#> TCGA.DA.A3F2.06 1 0 1 1 0
#> TCGA.D3.A51H.06 1 0 1 1 0
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.D3.A8GB.06 1 0.455 0.923 0.80 0.0 0.20
#> TCGA.EB.A6L9.06 1 0.455 0.923 0.80 0.0 0.20
#> TCGA.FS.A1Z4.06 1 0.455 0.923 0.80 0.0 0.20
#> TCGA.EE.A2MG.06 1 0.334 0.899 0.88 0.0 0.12
#> TCGA.EE.A2MC.06 2 0.455 0.864 0.20 0.8 0.00
#> TCGA.EE.A2A1.06 1 0.000 0.752 1.00 0.0 0.00
#> TCGA.ER.A1A1.06 3 0.000 1.000 0.00 0.0 1.00
#> TCGA.D3.A3BZ.06 1 0.334 0.899 0.88 0.0 0.12
#> TCGA.ER.A19A.06 3 0.000 1.000 0.00 0.0 1.00
#> TCGA.D3.A2J8.06 1 0.455 0.923 0.80 0.0 0.20
#> TCGA.EE.A2GT.06 2 0.000 0.870 0.00 1.0 0.00
#> TCGA.EE.A3JD.06 3 0.000 1.000 0.00 0.0 1.00
#> TCGA.D3.A51F.06 3 0.000 1.000 0.00 0.0 1.00
#> TCGA.DA.A3F2.06 3 0.000 1.000 0.00 0.0 1.00
#> TCGA.D3.A51H.06 3 0.000 1.000 0.00 0.0 1.00
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> TCGA.D3.A8GB.06 1 0.0000 0.991 1.00 0.00 0.00 0.00
#> TCGA.EB.A6L9.06 1 0.0000 0.991 1.00 0.00 0.00 0.00
#> TCGA.FS.A1Z4.06 1 0.0000 0.991 1.00 0.00 0.00 0.00
#> TCGA.EE.A2MG.06 1 0.0707 0.983 0.98 0.02 0.00 0.00
#> TCGA.EE.A2MC.06 2 0.0707 0.974 0.00 0.98 0.00 0.02
#> TCGA.EE.A2A1.06 2 0.0000 0.974 0.00 1.00 0.00 0.00
#> TCGA.ER.A1A1.06 3 0.0000 0.985 0.00 0.00 1.00 0.00
#> TCGA.D3.A3BZ.06 1 0.0707 0.983 0.98 0.02 0.00 0.00
#> TCGA.ER.A19A.06 3 0.1637 0.922 0.06 0.00 0.94 0.00
#> TCGA.D3.A2J8.06 1 0.0000 0.991 1.00 0.00 0.00 0.00
#> TCGA.EE.A2GT.06 4 0.0000 0.000 0.00 0.00 0.00 1.00
#> TCGA.EE.A3JD.06 3 0.0000 0.985 0.00 0.00 1.00 0.00
#> TCGA.D3.A51F.06 3 0.0000 0.985 0.00 0.00 1.00 0.00
#> TCGA.DA.A3F2.06 3 0.0000 0.985 0.00 0.00 1.00 0.00
#> TCGA.D3.A51H.06 3 0.0000 0.985 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.D3.A8GB.06 1 0.0609 0.964 0.98 0.00 0.00 0.02 0.00
#> TCGA.EB.A6L9.06 1 0.0000 0.974 1.00 0.00 0.00 0.00 0.00
#> TCGA.FS.A1Z4.06 1 0.0000 0.974 1.00 0.00 0.00 0.00 0.00
#> TCGA.EE.A2MG.06 5 0.1732 0.934 0.08 0.00 0.00 0.00 0.92
#> TCGA.EE.A2MC.06 2 0.0000 0.000 0.00 1.00 0.00 0.00 0.00
#> TCGA.EE.A2A1.06 5 0.0000 0.907 0.00 0.00 0.00 0.00 1.00
#> TCGA.ER.A1A1.06 3 0.0000 1.000 0.00 0.00 1.00 0.00 0.00
#> TCGA.D3.A3BZ.06 5 0.1410 0.945 0.06 0.00 0.00 0.00 0.94
#> TCGA.ER.A19A.06 1 0.1410 0.912 0.94 0.00 0.06 0.00 0.00
#> TCGA.D3.A2J8.06 1 0.0000 0.974 1.00 0.00 0.00 0.00 0.00
#> TCGA.EE.A2GT.06 4 0.0609 0.000 0.00 0.02 0.00 0.98 0.00
#> TCGA.EE.A3JD.06 3 0.0000 1.000 0.00 0.00 1.00 0.00 0.00
#> TCGA.D3.A51F.06 3 0.0000 1.000 0.00 0.00 1.00 0.00 0.00
#> TCGA.DA.A3F2.06 3 0.0000 1.000 0.00 0.00 1.00 0.00 0.00
#> TCGA.D3.A51H.06 3 0.0000 1.000 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.D3.A8GB.06 1 0.0937 0.962 0.96 0 0 0 0.00 0.04
#> TCGA.EB.A6L9.06 1 0.0000 0.991 1.00 0 0 0 0.00 0.00
#> TCGA.FS.A1Z4.06 1 0.0000 0.991 1.00 0 0 0 0.00 0.00
#> TCGA.EE.A2MG.06 5 0.0000 1.000 0.00 0 0 0 1.00 0.00
#> TCGA.EE.A2MC.06 2 0.0000 0.000 0.00 1 0 0 0.00 0.00
#> TCGA.EE.A2A1.06 6 0.0937 0.000 0.00 0 0 0 0.04 0.96
#> TCGA.ER.A1A1.06 3 0.0000 1.000 0.00 0 1 0 0.00 0.00
#> TCGA.D3.A3BZ.06 5 0.0000 1.000 0.00 0 0 0 1.00 0.00
#> TCGA.ER.A19A.06 1 0.0000 0.991 1.00 0 0 0 0.00 0.00
#> TCGA.D3.A2J8.06 1 0.0000 0.991 1.00 0 0 0 0.00 0.00
#> TCGA.EE.A2GT.06 4 0.0000 0.000 0.00 0 0 1 0.00 0.00
#> TCGA.EE.A3JD.06 3 0.0000 1.000 0.00 0 1 0 0.00 0.00
#> TCGA.D3.A51F.06 3 0.0000 1.000 0.00 0 1 0 0.00 0.00
#> TCGA.DA.A3F2.06 3 0.0000 1.000 0.00 0 1 0 0.00 0.00
#> TCGA.D3.A51H.06 3 0.0000 1.000 0.00 0 1 0 0.00 0.00
cbind(get_classes(res, k = 7), get_membership(res, k = 7))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7
#> TCGA.D3.A8GB.06 1 0.2708 0.471 0.78 0 0.00 0 0.00 0 0.22
#> TCGA.EB.A6L9.06 1 0.2708 0.753 0.78 0 0.00 0 0.00 0 0.22
#> TCGA.FS.A1Z4.06 7 0.0863 0.972 0.00 0 0.00 0 0.04 0 0.96
#> TCGA.EE.A2MG.06 5 0.0000 1.000 0.00 0 0.00 0 1.00 0 0.00
#> TCGA.EE.A2MC.06 2 0.0000 0.000 0.00 1 0.00 0 0.00 0 0.00
#> TCGA.EE.A2A1.06 6 0.0000 0.000 0.00 0 0.00 0 0.00 1 0.00
#> TCGA.ER.A1A1.06 3 0.0000 0.939 0.00 0 1.00 0 0.00 0 0.00
#> TCGA.D3.A3BZ.06 5 0.0000 1.000 0.00 0 0.00 0 1.00 0 0.00
#> TCGA.ER.A19A.06 1 0.2708 0.753 0.78 0 0.00 0 0.00 0 0.22
#> TCGA.D3.A2J8.06 7 0.1166 0.972 0.00 0 0.00 0 0.06 0 0.94
#> TCGA.EE.A2GT.06 4 0.0000 0.000 0.00 0 0.00 1 0.00 0 0.00
#> TCGA.EE.A3JD.06 3 0.2708 0.727 0.22 0 0.78 0 0.00 0 0.00
#> TCGA.D3.A51F.06 3 0.0000 0.939 0.00 0 1.00 0 0.00 0 0.00
#> TCGA.DA.A3F2.06 3 0.0000 0.939 0.00 0 1.00 0 0.00 0 0.00
#> TCGA.D3.A51H.06 3 0.0000 0.939 0.00 0 1.00 0 0.00 0 0.00
cbind(get_classes(res, k = 8), get_membership(res, k = 8))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7 p8
#> TCGA.D3.A8GB.06 8 0.0471 0.000 0.02 0 0.0 0 0.00 0 0.00 0.98
#> TCGA.EB.A6L9.06 1 0.0000 0.784 1.00 0 0.0 0 0.00 0 0.00 0.00
#> TCGA.FS.A1Z4.06 7 0.0471 1.000 0.02 0 0.0 0 0.00 0 0.98 0.00
#> TCGA.EE.A2MG.06 5 0.0000 0.967 0.00 0 0.0 0 1.00 0 0.00 0.00
#> TCGA.EE.A2MC.06 2 0.0000 0.000 0.00 1 0.0 0 0.00 0 0.00 0.00
#> TCGA.EE.A2A1.06 6 0.0000 0.000 0.00 0 0.0 0 0.00 1 0.00 0.00
#> TCGA.ER.A1A1.06 3 0.0000 1.000 0.00 0 1.0 0 0.00 0 0.00 0.00
#> TCGA.D3.A3BZ.06 5 0.0941 0.967 0.00 0 0.0 0 0.96 0 0.02 0.02
#> TCGA.ER.A19A.06 1 0.0000 0.784 1.00 0 0.0 0 0.00 0 0.00 0.00
#> TCGA.D3.A2J8.06 7 0.0471 1.000 0.02 0 0.0 0 0.00 0 0.98 0.00
#> TCGA.EE.A2GT.06 4 0.0000 0.000 0.00 0 0.0 1 0.00 0 0.00 0.00
#> TCGA.EE.A3JD.06 1 0.2938 0.562 0.70 0 0.3 0 0.00 0 0.00 0.00
#> TCGA.D3.A51F.06 3 0.0000 1.000 0.00 0 1.0 0 0.00 0 0.00 0.00
#> TCGA.DA.A3F2.06 3 0.0000 1.000 0.00 0 1.0 0 0.00 0 0.00 0.00
#> TCGA.D3.A51H.06 3 0.0000 1.000 0.00 0 1.0 0 0.00 0 0.00 0.00
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
consensus_heatmap(res, k = 7)
consensus_heatmap(res, k = 8)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
membership_heatmap(res, k = 7)
membership_heatmap(res, k = 8)
As soon as the classes for columns are determined, the signatures that are significantly different between subgroups can be looked for. Following are the heatmaps for signatures.
get_signatures(res, k = 2)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
get_signatures(res, k = 7)
get_signatures(res, k = 8)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. To get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows (which is done by automatically selecting number of clusters).If there are too many signatures, top_signatures = ... can be set to only show the
signatures with the highest FDRs:
# code only for demonstration
# e.g. to show the top 500 most significant rows
tb = get_signature(res, k = ..., top_signatures = 500)
If the signatures are defined as these which are uniquely high in current group, diff_method argument
can be set to "uniquely_high_in_one_group":
# code only for demonstration
tb = get_signature(res, k = ..., diff_method = "uniquely_high_in_one_group")
UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
dimension_reduction(res, k = 7, method = "UMAP")
dimension_reduction(res, k = 8, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
If matrix rows can be associated to genes, consider to use functional_enrichment(res,
...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.
Parent node: Node0. Child nodes: Node011 , Node012 , Node013 , Node014-leaf , Node021 , Node022 , Node023-leaf , Node031 , Node032 , Node041 , Node042 , Node043 , Node044 , Node051 , Node052 .
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 70 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 0.997 0.999 0.4927 0.508 0.508
#> 3 3 0.856 0.952 0.971 0.3411 0.760 0.555
#> 4 4 0.724 0.675 0.841 0.0967 0.986 0.958
#> 5 5 0.710 0.711 0.833 0.0619 0.886 0.661
#> 6 6 0.751 0.593 0.796 0.0497 0.899 0.619
#> 7 7 0.734 0.613 0.784 0.0296 0.937 0.687
#> 8 8 0.765 0.532 0.767 0.0225 0.959 0.768
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.FR.A8YC.06 2 0.000 0.998 0.00 1.00
#> TCGA.DA.A95X.06 1 0.000 0.999 1.00 0.00
#> TCGA.WE.A8JZ.06 1 0.000 0.999 1.00 0.00
#> TCGA.EE.A3JI.06 2 0.000 0.998 0.00 1.00
#> TCGA.OD.A75X.06 1 0.000 0.999 1.00 0.00
#> TCGA.DA.A960.01 1 0.000 0.999 1.00 0.00
#> TCGA.D3.A8GV.06 1 0.000 0.999 1.00 0.00
#> TCGA.DA.A95Z.06 2 0.000 0.998 0.00 1.00
#> TCGA.EB.A6QZ.01 1 0.000 0.999 1.00 0.00
#> TCGA.FW.A3I3.06 1 0.000 0.999 1.00 0.00
#> TCGA.D3.A8GP.06 2 0.000 0.998 0.00 1.00
#> TCGA.EB.A42Z.01 1 0.000 0.999 1.00 0.00
#> TCGA.GN.A4U4.06 1 0.000 0.999 1.00 0.00
#> TCGA.DA.A95W.06 2 0.000 0.998 0.00 1.00
#> TCGA.FW.A5DX.01 1 0.000 0.999 1.00 0.00
#> TCGA.WE.A8ZY.06 1 0.000 0.999 1.00 0.00
#> TCGA.D9.A6EG.06 2 0.000 0.998 0.00 1.00
#> TCGA.GF.A769.01 1 0.000 0.999 1.00 0.00
#> TCGA.EE.A180.06 2 0.000 0.998 0.00 1.00
#> TCGA.WE.A8K5.06 1 0.242 0.958 0.96 0.04
#> TCGA.GN.A8LN.01 1 0.000 0.999 1.00 0.00
#> TCGA.EE.A2MF.06 2 0.000 0.998 0.00 1.00
#> TCGA.EB.A42Y.01 1 0.000 0.999 1.00 0.00
#> TCGA.D3.A8GL.06 2 0.000 0.998 0.00 1.00
#> TCGA.D3.A3MU.06 2 0.000 0.998 0.00 1.00
#> TCGA.FS.A4F0.06 2 0.000 0.998 0.00 1.00
#> TCGA.EB.A41A.01 2 0.000 0.998 0.00 1.00
#> TCGA.D3.A1QA.06 1 0.000 0.999 1.00 0.00
#> TCGA.EB.A5KH.06 1 0.000 0.999 1.00 0.00
#> TCGA.FS.A1ZY.06 1 0.000 0.999 1.00 0.00
#> TCGA.EE.A184.06 2 0.327 0.936 0.06 0.94
#> TCGA.FS.A1ZZ.06 2 0.000 0.998 0.00 1.00
#> TCGA.EE.A3AD.06 1 0.000 0.999 1.00 0.00
#> TCGA.EE.A3AH.06 1 0.000 0.999 1.00 0.00
#> TCGA.FR.A7U8.06 2 0.000 0.998 0.00 1.00
#> TCGA.ER.A19J.06 1 0.000 0.999 1.00 0.00
#> TCGA.EB.A82C.01 1 0.000 0.999 1.00 0.00
#> TCGA.EB.A5FP.01 1 0.000 0.999 1.00 0.00
#> TCGA.EE.A29L.06 1 0.000 0.999 1.00 0.00
#> TCGA.FS.A1ZN.01 1 0.000 0.999 1.00 0.00
#> TCGA.EE.A20C.06 1 0.000 0.999 1.00 0.00
#> TCGA.GN.A268.06 2 0.000 0.998 0.00 1.00
#> TCGA.FS.A1ZG.06 2 0.000 0.998 0.00 1.00
#> TCGA.FS.A1ZE.06 2 0.000 0.998 0.00 1.00
#> TCGA.GN.A264.06 1 0.000 0.999 1.00 0.00
#> TCGA.FS.A1YW.06 1 0.000 0.999 1.00 0.00
#> TCGA.GN.A262.06 1 0.000 0.999 1.00 0.00
#> TCGA.EE.A29A.06 2 0.000 0.998 0.00 1.00
#> TCGA.FS.A1ZC.06 1 0.000 0.999 1.00 0.00
#> TCGA.EE.A2GO.06 1 0.000 0.999 1.00 0.00
#> TCGA.EE.A29R.06 1 0.000 0.999 1.00 0.00
#> TCGA.D9.A1X3.06 2 0.000 0.998 0.00 1.00
#> TCGA.ER.A2NE.06 1 0.000 0.999 1.00 0.00
#> TCGA.EE.A185.06 1 0.000 0.999 1.00 0.00
#> TCGA.EE.A2M6.06 1 0.000 0.999 1.00 0.00
#> TCGA.BF.AAP2.01 1 0.000 0.999 1.00 0.00
#> TCGA.EE.A2GM.06 1 0.000 0.999 1.00 0.00
#> TCGA.D9.A6EC.06 1 0.000 0.999 1.00 0.00
#> TCGA.EB.A5SE.01 2 0.000 0.998 0.00 1.00
#> TCGA.D9.A6EA.06 2 0.000 0.998 0.00 1.00
#> TCGA.EE.A29D.06 2 0.000 0.998 0.00 1.00
#> TCGA.BF.AAP1.01 2 0.000 0.998 0.00 1.00
#> TCGA.LH.A9QB.06 2 0.000 0.998 0.00 1.00
#> TCGA.EB.A97M.01 2 0.000 0.998 0.00 1.00
#> TCGA.W3.AA21.06 1 0.000 0.999 1.00 0.00
#> TCGA.Z2.AA3S.06 2 0.000 0.998 0.00 1.00
#> TCGA.FS.A4F5.06 2 0.000 0.998 0.00 1.00
#> TCGA.D9.A4Z5.01 1 0.000 0.999 1.00 0.00
#> TCGA.3N.A9WB.06 2 0.000 0.998 0.00 1.00
#> TCGA.EE.A3J8.06 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.FR.A8YC.06 2 0.000 0.975 0.00 1.00 0.00
#> TCGA.DA.A95X.06 1 0.000 1.000 1.00 0.00 0.00
#> TCGA.WE.A8JZ.06 1 0.000 1.000 1.00 0.00 0.00
#> TCGA.EE.A3JI.06 2 0.000 0.975 0.00 1.00 0.00
#> TCGA.OD.A75X.06 3 0.000 0.909 0.00 0.00 1.00
#> TCGA.DA.A960.01 1 0.000 1.000 1.00 0.00 0.00
#> TCGA.D3.A8GV.06 1 0.000 1.000 1.00 0.00 0.00
#> TCGA.DA.A95Z.06 2 0.000 0.975 0.00 1.00 0.00
#> TCGA.EB.A6QZ.01 1 0.000 1.000 1.00 0.00 0.00
#> TCGA.FW.A3I3.06 3 0.540 0.715 0.28 0.00 0.72
#> TCGA.D3.A8GP.06 2 0.000 0.975 0.00 1.00 0.00
#> TCGA.EB.A42Z.01 3 0.429 0.844 0.18 0.00 0.82
#> TCGA.GN.A4U4.06 1 0.000 1.000 1.00 0.00 0.00
#> TCGA.DA.A95W.06 2 0.000 0.975 0.00 1.00 0.00
#> TCGA.FW.A5DX.01 1 0.000 1.000 1.00 0.00 0.00
#> TCGA.WE.A8ZY.06 1 0.000 1.000 1.00 0.00 0.00
#> TCGA.D9.A6EG.06 2 0.000 0.975 0.00 1.00 0.00
#> TCGA.GF.A769.01 1 0.000 1.000 1.00 0.00 0.00
#> TCGA.EE.A180.06 2 0.000 0.975 0.00 1.00 0.00
#> TCGA.WE.A8K5.06 3 0.000 0.909 0.00 0.00 1.00
#> TCGA.GN.A8LN.01 1 0.000 1.000 1.00 0.00 0.00
#> TCGA.EE.A2MF.06 2 0.429 0.824 0.00 0.82 0.18
#> TCGA.EB.A42Y.01 1 0.000 1.000 1.00 0.00 0.00
#> TCGA.D3.A8GL.06 2 0.000 0.975 0.00 1.00 0.00
#> TCGA.D3.A3MU.06 2 0.429 0.824 0.00 0.82 0.18
#> TCGA.FS.A4F0.06 2 0.000 0.975 0.00 1.00 0.00
#> TCGA.EB.A41A.01 2 0.000 0.975 0.00 1.00 0.00
#> TCGA.D3.A1QA.06 1 0.000 1.000 1.00 0.00 0.00
#> TCGA.EB.A5KH.06 1 0.000 1.000 1.00 0.00 0.00
#> TCGA.FS.A1ZY.06 1 0.000 1.000 1.00 0.00 0.00
#> TCGA.EE.A184.06 3 0.000 0.909 0.00 0.00 1.00
#> TCGA.FS.A1ZZ.06 3 0.000 0.909 0.00 0.00 1.00
#> TCGA.EE.A3AD.06 1 0.000 1.000 1.00 0.00 0.00
#> TCGA.EE.A3AH.06 1 0.000 1.000 1.00 0.00 0.00
#> TCGA.FR.A7U8.06 3 0.000 0.909 0.00 0.00 1.00
#> TCGA.ER.A19J.06 3 0.429 0.844 0.18 0.00 0.82
#> TCGA.EB.A82C.01 3 0.000 0.909 0.00 0.00 1.00
#> TCGA.EB.A5FP.01 1 0.000 1.000 1.00 0.00 0.00
#> TCGA.EE.A29L.06 1 0.000 1.000 1.00 0.00 0.00
#> TCGA.FS.A1ZN.01 1 0.000 1.000 1.00 0.00 0.00
#> TCGA.EE.A20C.06 3 0.400 0.859 0.16 0.00 0.84
#> TCGA.GN.A268.06 2 0.000 0.975 0.00 1.00 0.00
#> TCGA.FS.A1ZG.06 2 0.153 0.947 0.00 0.96 0.04
#> TCGA.FS.A1ZE.06 2 0.429 0.824 0.00 0.82 0.18
#> TCGA.GN.A264.06 3 0.000 0.909 0.00 0.00 1.00
#> TCGA.FS.A1YW.06 3 0.369 0.870 0.14 0.00 0.86
#> TCGA.GN.A262.06 1 0.000 1.000 1.00 0.00 0.00
#> TCGA.EE.A29A.06 2 0.000 0.975 0.00 1.00 0.00
#> TCGA.FS.A1ZC.06 1 0.000 1.000 1.00 0.00 0.00
#> TCGA.EE.A2GO.06 3 0.480 0.801 0.22 0.00 0.78
#> TCGA.EE.A29R.06 3 0.296 0.888 0.10 0.00 0.90
#> TCGA.D9.A1X3.06 2 0.000 0.975 0.00 1.00 0.00
#> TCGA.ER.A2NE.06 1 0.000 1.000 1.00 0.00 0.00
#> TCGA.EE.A185.06 1 0.000 1.000 1.00 0.00 0.00
#> TCGA.EE.A2M6.06 1 0.000 1.000 1.00 0.00 0.00
#> TCGA.BF.AAP2.01 1 0.000 1.000 1.00 0.00 0.00
#> TCGA.EE.A2GM.06 1 0.000 1.000 1.00 0.00 0.00
#> TCGA.D9.A6EC.06 3 0.429 0.844 0.18 0.00 0.82
#> TCGA.EB.A5SE.01 2 0.000 0.975 0.00 1.00 0.00
#> TCGA.D9.A6EA.06 2 0.000 0.975 0.00 1.00 0.00
#> TCGA.EE.A29D.06 2 0.000 0.975 0.00 1.00 0.00
#> TCGA.BF.AAP1.01 3 0.000 0.909 0.00 0.00 1.00
#> TCGA.LH.A9QB.06 3 0.000 0.909 0.00 0.00 1.00
#> TCGA.EB.A97M.01 2 0.000 0.975 0.00 1.00 0.00
#> TCGA.W3.AA21.06 1 0.000 1.000 1.00 0.00 0.00
#> TCGA.Z2.AA3S.06 2 0.000 0.975 0.00 1.00 0.00
#> TCGA.FS.A4F5.06 3 0.000 0.909 0.00 0.00 1.00
#> TCGA.D9.A4Z5.01 3 0.000 0.909 0.00 0.00 1.00
#> TCGA.3N.A9WB.06 2 0.000 0.975 0.00 1.00 0.00
#> TCGA.EE.A3J8.06 1 0.000 1.000 1.00 0.00 0.00
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> TCGA.FR.A8YC.06 2 0.0707 0.8392 0.00 0.98 0.00 0.02
#> TCGA.DA.A95X.06 1 0.0000 0.9132 1.00 0.00 0.00 0.00
#> TCGA.WE.A8JZ.06 1 0.0000 0.9132 1.00 0.00 0.00 0.00
#> TCGA.EE.A3JI.06 2 0.0707 0.8392 0.00 0.98 0.00 0.02
#> TCGA.OD.A75X.06 3 0.5000 -0.0504 0.00 0.00 0.50 0.50
#> TCGA.DA.A960.01 1 0.0000 0.9132 1.00 0.00 0.00 0.00
#> TCGA.D3.A8GV.06 1 0.0000 0.9132 1.00 0.00 0.00 0.00
#> TCGA.DA.A95Z.06 2 0.0000 0.8401 0.00 1.00 0.00 0.00
#> TCGA.EB.A6QZ.01 1 0.2011 0.8936 0.92 0.00 0.00 0.08
#> TCGA.FW.A3I3.06 3 0.6510 0.0295 0.08 0.00 0.54 0.38
#> TCGA.D3.A8GP.06 2 0.4088 0.8075 0.00 0.82 0.04 0.14
#> TCGA.EB.A42Z.01 4 0.5173 0.5026 0.02 0.00 0.32 0.66
#> TCGA.GN.A4U4.06 1 0.2647 0.8777 0.88 0.00 0.00 0.12
#> TCGA.DA.A95W.06 2 0.0707 0.8392 0.00 0.98 0.00 0.02
#> TCGA.FW.A5DX.01 1 0.0000 0.9132 1.00 0.00 0.00 0.00
#> TCGA.WE.A8ZY.06 1 0.0000 0.9132 1.00 0.00 0.00 0.00
#> TCGA.D9.A6EG.06 2 0.4406 0.7343 0.00 0.70 0.00 0.30
#> TCGA.GF.A769.01 1 0.2647 0.8419 0.88 0.00 0.00 0.12
#> TCGA.EE.A180.06 2 0.0707 0.8392 0.00 0.98 0.00 0.02
#> TCGA.WE.A8K5.06 3 0.4790 0.3322 0.00 0.00 0.62 0.38
#> TCGA.GN.A8LN.01 1 0.0000 0.9132 1.00 0.00 0.00 0.00
#> TCGA.EE.A2MF.06 2 0.6988 0.5125 0.00 0.50 0.38 0.12
#> TCGA.EB.A42Y.01 1 0.0000 0.9132 1.00 0.00 0.00 0.00
#> TCGA.D3.A8GL.06 2 0.0707 0.8392 0.00 0.98 0.00 0.02
#> TCGA.D3.A3MU.06 2 0.6988 0.4890 0.00 0.50 0.38 0.12
#> TCGA.FS.A4F0.06 2 0.0000 0.8401 0.00 1.00 0.00 0.00
#> TCGA.EB.A41A.01 2 0.1211 0.8385 0.00 0.96 0.00 0.04
#> TCGA.D3.A1QA.06 1 0.4134 0.7502 0.74 0.00 0.00 0.26
#> TCGA.EB.A5KH.06 1 0.2647 0.8777 0.88 0.00 0.00 0.12
#> TCGA.FS.A1ZY.06 1 0.3172 0.7983 0.84 0.00 0.00 0.16
#> TCGA.EE.A184.06 3 0.1211 0.3856 0.00 0.00 0.96 0.04
#> TCGA.FS.A1ZZ.06 3 0.0707 0.3781 0.00 0.00 0.98 0.02
#> TCGA.EE.A3AD.06 1 0.0000 0.9132 1.00 0.00 0.00 0.00
#> TCGA.EE.A3AH.06 1 0.0000 0.9132 1.00 0.00 0.00 0.00
#> TCGA.FR.A7U8.06 3 0.3975 0.1917 0.00 0.00 0.76 0.24
#> TCGA.ER.A19J.06 4 0.4642 0.5814 0.02 0.00 0.24 0.74
#> TCGA.EB.A82C.01 3 0.2647 0.4033 0.00 0.00 0.88 0.12
#> TCGA.EB.A5FP.01 1 0.2647 0.8777 0.88 0.00 0.00 0.12
#> TCGA.EE.A29L.06 1 0.4134 0.7502 0.74 0.00 0.00 0.26
#> TCGA.FS.A1ZN.01 1 0.4522 0.5437 0.68 0.00 0.00 0.32
#> TCGA.EE.A20C.06 3 0.5355 0.2962 0.02 0.00 0.62 0.36
#> TCGA.GN.A268.06 2 0.0000 0.8401 0.00 1.00 0.00 0.00
#> TCGA.FS.A1ZG.06 2 0.7745 0.4593 0.00 0.42 0.34 0.24
#> TCGA.FS.A1ZE.06 2 0.6988 0.5125 0.00 0.50 0.38 0.12
#> TCGA.GN.A264.06 3 0.4907 0.2860 0.00 0.00 0.58 0.42
#> TCGA.FS.A1YW.06 3 0.5428 0.2546 0.02 0.00 0.60 0.38
#> TCGA.GN.A262.06 1 0.2647 0.8419 0.88 0.00 0.00 0.12
#> TCGA.EE.A29A.06 2 0.5512 0.7137 0.00 0.66 0.04 0.30
#> TCGA.FS.A1ZC.06 1 0.0000 0.9132 1.00 0.00 0.00 0.00
#> TCGA.EE.A2GO.06 3 0.5860 0.1957 0.04 0.00 0.58 0.38
#> TCGA.EE.A29R.06 3 0.4713 0.3319 0.00 0.00 0.64 0.36
#> TCGA.D9.A1X3.06 2 0.0707 0.8392 0.00 0.98 0.00 0.02
#> TCGA.ER.A2NE.06 1 0.2921 0.8395 0.86 0.00 0.00 0.14
#> TCGA.EE.A185.06 1 0.3172 0.8541 0.84 0.00 0.00 0.16
#> TCGA.EE.A2M6.06 1 0.0000 0.9132 1.00 0.00 0.00 0.00
#> TCGA.BF.AAP2.01 1 0.0000 0.9132 1.00 0.00 0.00 0.00
#> TCGA.EE.A2GM.06 1 0.2647 0.8777 0.88 0.00 0.00 0.12
#> TCGA.D9.A6EC.06 3 0.5428 0.2546 0.02 0.00 0.60 0.38
#> TCGA.EB.A5SE.01 2 0.4134 0.7479 0.00 0.74 0.00 0.26
#> TCGA.D9.A6EA.06 2 0.1211 0.8385 0.00 0.96 0.00 0.04
#> TCGA.EE.A29D.06 2 0.3975 0.7718 0.00 0.76 0.00 0.24
#> TCGA.BF.AAP1.01 3 0.2647 0.3983 0.00 0.00 0.88 0.12
#> TCGA.LH.A9QB.06 3 0.3801 0.1962 0.00 0.00 0.78 0.22
#> TCGA.EB.A97M.01 2 0.0000 0.8401 0.00 1.00 0.00 0.00
#> TCGA.W3.AA21.06 1 0.0000 0.9132 1.00 0.00 0.00 0.00
#> TCGA.Z2.AA3S.06 2 0.2011 0.8348 0.00 0.92 0.00 0.08
#> TCGA.FS.A4F5.06 3 0.1637 0.3594 0.00 0.00 0.94 0.06
#> TCGA.D9.A4Z5.01 3 0.4855 0.3183 0.00 0.00 0.60 0.40
#> TCGA.3N.A9WB.06 2 0.3975 0.7718 0.00 0.76 0.00 0.24
#> TCGA.EE.A3J8.06 1 0.3975 0.7717 0.76 0.00 0.00 0.24
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> TCGA.FR.A8YC.06 2 0.1043 0.8475 0.00 0.96 0.00 0.00 0.04
#> TCGA.DA.A95X.06 1 0.0000 0.8185 1.00 0.00 0.00 0.00 0.00
#> TCGA.WE.A8JZ.06 1 0.0609 0.8106 0.98 0.00 0.02 0.00 0.00
#> TCGA.EE.A3JI.06 2 0.1043 0.8475 0.00 0.96 0.00 0.00 0.04
#> TCGA.OD.A75X.06 4 0.5156 0.0376 0.00 0.00 0.32 0.62 0.06
#> TCGA.DA.A960.01 1 0.0000 0.8185 1.00 0.00 0.00 0.00 0.00
#> TCGA.D3.A8GV.06 1 0.0000 0.8185 1.00 0.00 0.00 0.00 0.00
#> TCGA.DA.A95Z.06 2 0.0000 0.8472 0.00 1.00 0.00 0.00 0.00
#> TCGA.EB.A6QZ.01 1 0.3291 0.7543 0.84 0.00 0.12 0.04 0.00
#> TCGA.FW.A3I3.06 3 0.1043 0.8451 0.04 0.00 0.96 0.00 0.00
#> TCGA.D3.A8GP.06 2 0.6037 0.6896 0.00 0.62 0.02 0.12 0.24
#> TCGA.EB.A42Z.01 3 0.4876 0.6053 0.00 0.00 0.70 0.22 0.08
#> TCGA.GN.A4U4.06 1 0.3641 0.7431 0.82 0.00 0.12 0.06 0.00
#> TCGA.DA.A95W.06 2 0.1043 0.8475 0.00 0.96 0.00 0.00 0.04
#> TCGA.FW.A5DX.01 1 0.0000 0.8185 1.00 0.00 0.00 0.00 0.00
#> TCGA.WE.A8ZY.06 1 0.0000 0.8185 1.00 0.00 0.00 0.00 0.00
#> TCGA.D9.A6EG.06 2 0.6148 0.6859 0.00 0.60 0.02 0.26 0.12
#> TCGA.GF.A769.01 1 0.3895 0.5832 0.68 0.00 0.32 0.00 0.00
#> TCGA.EE.A180.06 2 0.1043 0.8475 0.00 0.96 0.00 0.00 0.04
#> TCGA.WE.A8K5.06 3 0.5273 0.5142 0.00 0.00 0.68 0.16 0.16
#> TCGA.GN.A8LN.01 1 0.0000 0.8185 1.00 0.00 0.00 0.00 0.00
#> TCGA.EE.A2MF.06 5 0.2331 0.7348 0.00 0.08 0.00 0.02 0.90
#> TCGA.EB.A42Y.01 1 0.0000 0.8185 1.00 0.00 0.00 0.00 0.00
#> TCGA.D3.A8GL.06 2 0.1043 0.8475 0.00 0.96 0.00 0.00 0.04
#> TCGA.D3.A3MU.06 5 0.3697 0.7462 0.00 0.10 0.00 0.08 0.82
#> TCGA.FS.A4F0.06 2 0.0000 0.8472 0.00 1.00 0.00 0.00 0.00
#> TCGA.EB.A41A.01 2 0.3463 0.8153 0.00 0.84 0.02 0.12 0.02
#> TCGA.D3.A1QA.06 4 0.4126 0.5748 0.38 0.00 0.00 0.62 0.00
#> TCGA.EB.A5KH.06 1 0.3641 0.7431 0.82 0.00 0.12 0.06 0.00
#> TCGA.FS.A1ZY.06 1 0.4126 0.4911 0.62 0.00 0.38 0.00 0.00
#> TCGA.EE.A184.06 5 0.4558 0.7161 0.00 0.00 0.18 0.08 0.74
#> TCGA.FS.A1ZZ.06 5 0.4558 0.7201 0.00 0.00 0.18 0.08 0.74
#> TCGA.EE.A3AD.06 1 0.0000 0.8185 1.00 0.00 0.00 0.00 0.00
#> TCGA.EE.A3AH.06 1 0.0000 0.8185 1.00 0.00 0.00 0.00 0.00
#> TCGA.FR.A7U8.06 5 0.2012 0.7542 0.00 0.00 0.06 0.02 0.92
#> TCGA.ER.A19J.06 4 0.3684 0.2373 0.00 0.00 0.28 0.72 0.00
#> TCGA.EB.A82C.01 5 0.5457 0.2868 0.00 0.00 0.46 0.06 0.48
#> TCGA.EB.A5FP.01 1 0.3946 0.7264 0.80 0.00 0.12 0.08 0.00
#> TCGA.EE.A29L.06 4 0.4126 0.5748 0.38 0.00 0.00 0.62 0.00
#> TCGA.FS.A1ZN.01 1 0.4307 0.2506 0.50 0.00 0.50 0.00 0.00
#> TCGA.EE.A20C.06 3 0.0609 0.8521 0.02 0.00 0.98 0.00 0.00
#> TCGA.GN.A268.06 2 0.0000 0.8472 0.00 1.00 0.00 0.00 0.00
#> TCGA.FS.A1ZG.06 5 0.4794 0.5380 0.00 0.10 0.02 0.12 0.76
#> TCGA.FS.A1ZE.06 5 0.2331 0.7348 0.00 0.08 0.00 0.02 0.90
#> TCGA.GN.A264.06 3 0.3274 0.7314 0.00 0.00 0.78 0.22 0.00
#> TCGA.FS.A1YW.06 3 0.0609 0.8521 0.02 0.00 0.98 0.00 0.00
#> TCGA.GN.A262.06 1 0.3796 0.6086 0.70 0.00 0.30 0.00 0.00
#> TCGA.EE.A29A.06 2 0.6282 0.6852 0.00 0.60 0.02 0.22 0.16
#> TCGA.FS.A1ZC.06 1 0.0000 0.8185 1.00 0.00 0.00 0.00 0.00
#> TCGA.EE.A2GO.06 3 0.1043 0.8451 0.04 0.00 0.96 0.00 0.00
#> TCGA.EE.A29R.06 3 0.1216 0.8461 0.02 0.00 0.96 0.02 0.00
#> TCGA.D9.A1X3.06 2 0.1043 0.8475 0.00 0.96 0.00 0.00 0.04
#> TCGA.ER.A2NE.06 1 0.3895 0.5832 0.68 0.00 0.32 0.00 0.00
#> TCGA.EE.A185.06 1 0.5382 0.4191 0.64 0.00 0.10 0.26 0.00
#> TCGA.EE.A2M6.06 1 0.0000 0.8185 1.00 0.00 0.00 0.00 0.00
#> TCGA.BF.AAP2.01 1 0.0609 0.8106 0.98 0.00 0.02 0.00 0.00
#> TCGA.EE.A2GM.06 1 0.3697 0.7411 0.82 0.00 0.10 0.08 0.00
#> TCGA.D9.A6EC.06 3 0.1043 0.8451 0.04 0.00 0.96 0.00 0.00
#> TCGA.EB.A5SE.01 2 0.5934 0.6985 0.00 0.62 0.02 0.26 0.10
#> TCGA.D9.A6EA.06 2 0.2873 0.8209 0.00 0.86 0.02 0.12 0.00
#> TCGA.EE.A29D.06 2 0.5771 0.7516 0.00 0.66 0.02 0.12 0.20
#> TCGA.BF.AAP1.01 5 0.5157 0.3580 0.00 0.00 0.44 0.04 0.52
#> TCGA.LH.A9QB.06 5 0.1410 0.7557 0.00 0.00 0.06 0.00 0.94
#> TCGA.EB.A97M.01 2 0.0000 0.8472 0.00 1.00 0.00 0.00 0.00
#> TCGA.W3.AA21.06 1 0.0000 0.8185 1.00 0.00 0.00 0.00 0.00
#> TCGA.Z2.AA3S.06 2 0.3109 0.7676 0.00 0.80 0.00 0.00 0.20
#> TCGA.FS.A4F5.06 5 0.4170 0.7432 0.00 0.00 0.14 0.08 0.78
#> TCGA.D9.A4Z5.01 3 0.3291 0.7671 0.00 0.00 0.84 0.12 0.04
#> TCGA.3N.A9WB.06 2 0.6282 0.6852 0.00 0.60 0.02 0.22 0.16
#> TCGA.EE.A3J8.06 4 0.4302 0.3968 0.48 0.00 0.00 0.52 0.00
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> TCGA.FR.A8YC.06 2 0.0547 0.80125 0.00 0.98 0.00 0.00 0.00 0.02
#> TCGA.DA.A95X.06 1 0.0547 0.84247 0.98 0.00 0.00 0.02 0.00 0.00
#> TCGA.WE.A8JZ.06 1 0.0937 0.81639 0.96 0.00 0.04 0.00 0.00 0.00
#> TCGA.EE.A3JI.06 2 0.0000 0.81060 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.OD.A75X.06 4 0.5930 0.00916 0.00 0.00 0.14 0.58 0.24 0.04
#> TCGA.DA.A960.01 1 0.1267 0.82347 0.94 0.00 0.00 0.06 0.00 0.00
#> TCGA.D3.A8GV.06 1 0.0000 0.84862 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DA.A95Z.06 2 0.0547 0.80775 0.00 0.98 0.00 0.00 0.00 0.02
#> TCGA.EB.A6QZ.01 1 0.4962 0.62953 0.70 0.00 0.04 0.18 0.00 0.08
#> TCGA.FW.A3I3.06 3 0.0000 0.64312 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.D3.A8GP.06 2 0.5957 -0.31065 0.00 0.40 0.00 0.00 0.22 0.38
#> TCGA.EB.A42Z.01 6 0.5882 -0.22677 0.00 0.00 0.38 0.20 0.00 0.42
#> TCGA.GN.A4U4.06 1 0.5106 0.60718 0.68 0.00 0.04 0.20 0.00 0.08
#> TCGA.DA.A95W.06 2 0.0000 0.81060 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.FW.A5DX.01 1 0.0000 0.84862 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.WE.A8ZY.06 1 0.0000 0.84862 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D9.A6EG.06 6 0.4067 0.65096 0.00 0.26 0.00 0.04 0.00 0.70
#> TCGA.GF.A769.01 3 0.5037 0.39730 0.38 0.00 0.54 0.00 0.00 0.08
#> TCGA.EE.A180.06 2 0.0000 0.81060 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.WE.A8K5.06 5 0.6750 0.31880 0.00 0.00 0.36 0.14 0.42 0.08
#> TCGA.GN.A8LN.01 1 0.0000 0.84862 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EE.A2MF.06 5 0.3156 0.63149 0.00 0.02 0.00 0.00 0.80 0.18
#> TCGA.EB.A42Y.01 1 0.0000 0.84862 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D3.A8GL.06 2 0.0000 0.81060 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.D3.A3MU.06 5 0.3544 0.65476 0.00 0.00 0.00 0.12 0.80 0.08
#> TCGA.FS.A4F0.06 2 0.0547 0.80775 0.00 0.98 0.00 0.00 0.00 0.02
#> TCGA.EB.A41A.01 2 0.3499 0.34023 0.00 0.68 0.00 0.00 0.00 0.32
#> TCGA.D3.A1QA.06 4 0.3076 0.63945 0.24 0.00 0.00 0.76 0.00 0.00
#> TCGA.EB.A5KH.06 1 0.5106 0.60718 0.68 0.00 0.04 0.20 0.00 0.08
#> TCGA.FS.A1ZY.06 3 0.4700 0.47373 0.34 0.00 0.60 0.00 0.00 0.06
#> TCGA.EE.A184.06 5 0.4088 0.63859 0.00 0.00 0.10 0.10 0.78 0.02
#> TCGA.FS.A1ZZ.06 5 0.3846 0.64416 0.00 0.00 0.08 0.10 0.80 0.02
#> TCGA.EE.A3AD.06 1 0.0000 0.84862 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EE.A3AH.06 1 0.0000 0.84862 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FR.A7U8.06 5 0.3156 0.63903 0.00 0.00 0.00 0.02 0.80 0.18
#> TCGA.ER.A19J.06 4 0.1807 0.47381 0.00 0.00 0.02 0.92 0.00 0.06
#> TCGA.EB.A82C.01 5 0.5626 0.47539 0.00 0.00 0.34 0.10 0.54 0.02
#> TCGA.EB.A5FP.01 1 0.5106 0.60718 0.68 0.00 0.04 0.20 0.00 0.08
#> TCGA.EE.A29L.06 4 0.3076 0.63945 0.24 0.00 0.00 0.76 0.00 0.00
#> TCGA.FS.A1ZN.01 3 0.4462 0.52314 0.28 0.00 0.66 0.00 0.00 0.06
#> TCGA.EE.A20C.06 3 0.0547 0.64109 0.00 0.00 0.98 0.00 0.00 0.02
#> TCGA.GN.A268.06 2 0.0547 0.80775 0.00 0.98 0.00 0.00 0.00 0.02
#> TCGA.FS.A1ZG.06 5 0.4310 0.29344 0.00 0.02 0.00 0.00 0.54 0.44
#> TCGA.FS.A1ZE.06 5 0.3156 0.63149 0.00 0.02 0.00 0.00 0.80 0.18
#> TCGA.GN.A264.06 3 0.6678 0.09164 0.00 0.00 0.52 0.22 0.16 0.10
#> TCGA.FS.A1YW.06 3 0.0000 0.64312 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.GN.A262.06 3 0.4806 0.41316 0.38 0.00 0.56 0.00 0.00 0.06
#> TCGA.EE.A29A.06 6 0.3198 0.65707 0.00 0.26 0.00 0.00 0.00 0.74
#> TCGA.FS.A1ZC.06 1 0.0000 0.84862 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EE.A2GO.06 3 0.0547 0.64109 0.00 0.00 0.98 0.00 0.00 0.02
#> TCGA.EE.A29R.06 3 0.0000 0.64312 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.D9.A1X3.06 2 0.0000 0.81060 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.ER.A2NE.06 3 0.5037 0.39564 0.38 0.00 0.54 0.00 0.00 0.08
#> TCGA.EE.A185.06 1 0.5797 0.20293 0.52 0.00 0.04 0.36 0.00 0.08
#> TCGA.EE.A2M6.06 1 0.0000 0.84862 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BF.AAP2.01 1 0.0937 0.81639 0.96 0.00 0.04 0.00 0.00 0.00
#> TCGA.EE.A2GM.06 1 0.5106 0.60718 0.68 0.00 0.04 0.20 0.00 0.08
#> TCGA.D9.A6EC.06 3 0.0000 0.64312 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.EB.A5SE.01 6 0.4420 0.54915 0.00 0.34 0.00 0.04 0.00 0.62
#> TCGA.D9.A6EA.06 2 0.3499 0.34023 0.00 0.68 0.00 0.00 0.00 0.32
#> TCGA.EE.A29D.06 6 0.5432 0.28220 0.00 0.40 0.00 0.00 0.12 0.48
#> TCGA.BF.AAP1.01 5 0.6457 0.52295 0.00 0.00 0.28 0.10 0.52 0.10
#> TCGA.LH.A9QB.06 5 0.3315 0.63473 0.00 0.00 0.00 0.02 0.78 0.20
#> TCGA.EB.A97M.01 2 0.0547 0.80775 0.00 0.98 0.00 0.00 0.00 0.02
#> TCGA.W3.AA21.06 1 0.0937 0.83553 0.96 0.00 0.00 0.04 0.00 0.00
#> TCGA.Z2.AA3S.06 2 0.4890 0.30066 0.00 0.66 0.00 0.00 0.18 0.16
#> TCGA.FS.A4F5.06 5 0.4162 0.63032 0.00 0.00 0.06 0.12 0.78 0.04
#> TCGA.D9.A4Z5.01 3 0.6250 0.13340 0.00 0.00 0.58 0.16 0.18 0.08
#> TCGA.3N.A9WB.06 6 0.3198 0.65707 0.00 0.26 0.00 0.00 0.00 0.74
#> TCGA.EE.A3J8.06 4 0.3706 0.37298 0.38 0.00 0.00 0.62 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.FR.A8YC.06 2 0.1433 0.84107 0.00 0.92 0.00 0.00 0.00 0.08 0.00
#> TCGA.DA.A95X.06 1 0.0504 0.81562 0.98 0.00 0.00 0.02 0.00 0.00 0.00
#> TCGA.WE.A8JZ.06 1 0.0504 0.81108 0.98 0.00 0.02 0.00 0.00 0.00 0.00
#> TCGA.EE.A3JI.06 2 0.0000 0.94118 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.OD.A75X.06 4 0.5166 0.02603 0.00 0.00 0.06 0.52 0.04 0.00 0.38
#> TCGA.DA.A960.01 1 0.0504 0.81562 0.98 0.00 0.00 0.02 0.00 0.00 0.00
#> TCGA.D3.A8GV.06 1 0.0000 0.82522 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DA.A95Z.06 2 0.0000 0.94118 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EB.A6QZ.01 1 0.6612 0.40448 0.56 0.00 0.12 0.14 0.00 0.10 0.08
#> TCGA.FW.A3I3.06 3 0.0504 0.55530 0.00 0.00 0.98 0.00 0.00 0.00 0.02
#> TCGA.D3.A8GP.06 6 0.5410 0.57052 0.00 0.26 0.00 0.00 0.26 0.48 0.00
#> TCGA.EB.A42Z.01 7 0.6867 0.13868 0.00 0.00 0.22 0.08 0.02 0.28 0.40
#> TCGA.GN.A4U4.06 1 0.6863 0.36045 0.52 0.00 0.12 0.18 0.00 0.10 0.08
#> TCGA.DA.A95W.06 2 0.0000 0.94118 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FW.A5DX.01 1 0.0000 0.82522 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.WE.A8ZY.06 1 0.0504 0.81717 0.98 0.00 0.00 0.00 0.00 0.02 0.00
#> TCGA.D9.A6EG.06 6 0.5423 0.64737 0.00 0.16 0.00 0.04 0.04 0.66 0.10
#> TCGA.GF.A769.01 3 0.5917 0.38903 0.34 0.00 0.48 0.00 0.00 0.10 0.08
#> TCGA.EE.A180.06 2 0.0000 0.94118 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.WE.A8K5.06 7 0.4033 0.56977 0.00 0.00 0.22 0.00 0.08 0.00 0.70
#> TCGA.GN.A8LN.01 1 0.0000 0.82522 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EE.A2MF.06 5 0.1433 0.67084 0.00 0.00 0.00 0.00 0.92 0.08 0.00
#> TCGA.EB.A42Y.01 1 0.0000 0.82522 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D3.A8GL.06 2 0.0000 0.94118 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D3.A3MU.06 5 0.4348 0.57864 0.00 0.00 0.00 0.00 0.68 0.14 0.18
#> TCGA.FS.A4F0.06 2 0.0000 0.94118 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EB.A41A.01 6 0.3546 0.47095 0.00 0.46 0.00 0.00 0.00 0.54 0.00
#> TCGA.D3.A1QA.06 4 0.2081 0.65758 0.14 0.00 0.00 0.86 0.00 0.00 0.00
#> TCGA.EB.A5KH.06 1 0.6863 0.36045 0.52 0.00 0.12 0.18 0.00 0.10 0.08
#> TCGA.FS.A1ZY.06 3 0.4797 0.57934 0.26 0.00 0.64 0.00 0.00 0.04 0.06
#> TCGA.EE.A184.06 5 0.5169 0.49266 0.00 0.00 0.02 0.06 0.58 0.02 0.32
#> TCGA.FS.A1ZZ.06 5 0.3519 0.55815 0.00 0.00 0.00 0.04 0.74 0.00 0.22
#> TCGA.EE.A3AD.06 1 0.0000 0.82522 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EE.A3AH.06 1 0.0000 0.82522 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FR.A7U8.06 5 0.2769 0.66202 0.00 0.00 0.00 0.02 0.86 0.04 0.08
#> TCGA.ER.A19J.06 4 0.3417 0.42431 0.00 0.00 0.02 0.72 0.00 0.00 0.26
#> TCGA.EB.A82C.01 7 0.6828 0.00538 0.00 0.00 0.26 0.06 0.32 0.02 0.34
#> TCGA.EB.A5FP.01 1 0.6863 0.36045 0.52 0.00 0.12 0.18 0.00 0.10 0.08
#> TCGA.EE.A29L.06 4 0.2081 0.65758 0.14 0.00 0.00 0.86 0.00 0.00 0.00
#> TCGA.FS.A1ZN.01 3 0.4589 0.58446 0.22 0.00 0.68 0.00 0.00 0.04 0.06
#> TCGA.EE.A20C.06 3 0.2563 0.52801 0.00 0.00 0.88 0.04 0.00 0.04 0.04
#> TCGA.GN.A268.06 2 0.0000 0.94118 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FS.A1ZG.06 6 0.4421 0.02502 0.00 0.00 0.00 0.02 0.46 0.50 0.02
#> TCGA.FS.A1ZE.06 5 0.1433 0.67084 0.00 0.00 0.00 0.00 0.92 0.08 0.00
#> TCGA.GN.A264.06 7 0.3417 0.60217 0.00 0.00 0.26 0.00 0.00 0.02 0.72
#> TCGA.FS.A1YW.06 3 0.2213 0.52097 0.00 0.00 0.90 0.04 0.00 0.02 0.04
#> TCGA.GN.A262.06 3 0.5027 0.50872 0.32 0.00 0.58 0.00 0.00 0.04 0.06
#> TCGA.EE.A29A.06 6 0.4016 0.67580 0.00 0.14 0.00 0.00 0.06 0.76 0.04
#> TCGA.FS.A1ZC.06 1 0.0000 0.82522 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EE.A2GO.06 3 0.2563 0.52985 0.00 0.00 0.88 0.04 0.00 0.04 0.04
#> TCGA.EE.A29R.06 3 0.0504 0.55530 0.00 0.00 0.98 0.00 0.00 0.00 0.02
#> TCGA.D9.A1X3.06 2 0.0000 0.94118 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.ER.A2NE.06 3 0.5876 0.43856 0.32 0.00 0.50 0.00 0.00 0.10 0.08
#> TCGA.EE.A185.06 4 0.6781 0.23998 0.30 0.00 0.06 0.46 0.00 0.10 0.08
#> TCGA.EE.A2M6.06 1 0.0000 0.82522 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BF.AAP2.01 1 0.0504 0.81108 0.98 0.00 0.02 0.00 0.00 0.00 0.00
#> TCGA.EE.A2GM.06 1 0.6863 0.36045 0.52 0.00 0.12 0.18 0.00 0.10 0.08
#> TCGA.D9.A6EC.06 3 0.0504 0.55530 0.00 0.00 0.98 0.00 0.00 0.00 0.02
#> TCGA.EB.A5SE.01 6 0.4908 0.65582 0.00 0.20 0.00 0.04 0.00 0.66 0.10
#> TCGA.D9.A6EA.06 6 0.3546 0.47095 0.00 0.46 0.00 0.00 0.00 0.54 0.00
#> TCGA.EE.A29D.06 6 0.4615 0.64140 0.00 0.30 0.00 0.00 0.10 0.60 0.00
#> TCGA.BF.AAP1.01 7 0.5848 0.34580 0.00 0.00 0.16 0.02 0.20 0.04 0.58
#> TCGA.LH.A9QB.06 5 0.2769 0.66202 0.00 0.00 0.00 0.02 0.86 0.04 0.08
#> TCGA.EB.A97M.01 2 0.0000 0.94118 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.W3.AA21.06 1 0.0504 0.81562 0.98 0.00 0.00 0.02 0.00 0.00 0.00
#> TCGA.Z2.AA3S.06 2 0.4248 0.37747 0.00 0.66 0.00 0.00 0.26 0.08 0.00
#> TCGA.FS.A4F5.06 5 0.3994 0.10856 0.00 0.00 0.02 0.00 0.50 0.00 0.48
#> TCGA.D9.A4Z5.01 7 0.4146 0.59918 0.00 0.00 0.32 0.00 0.02 0.02 0.64
#> TCGA.3N.A9WB.06 6 0.2745 0.69981 0.00 0.16 0.00 0.00 0.02 0.82 0.00
#> TCGA.EE.A3J8.06 4 0.2832 0.61696 0.24 0.00 0.00 0.76 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.FR.A8YC.06 2 0.1275 0.7954 0.00 0.94 0.00 0.00 0.00 0.04 0.00 0.02
#> TCGA.DA.A95X.06 1 0.1408 0.7750 0.94 0.00 0.00 0.02 0.00 0.02 0.00 0.02
#> TCGA.WE.A8JZ.06 1 0.0000 0.8068 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EE.A3JI.06 2 0.0000 0.8351 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.OD.A75X.06 4 0.5926 -0.1009 0.00 0.00 0.02 0.42 0.00 0.04 0.36 0.16
#> TCGA.DA.A960.01 1 0.2071 0.7555 0.90 0.00 0.00 0.04 0.00 0.02 0.00 0.04
#> TCGA.D3.A8GV.06 1 0.0000 0.8068 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DA.A95Z.06 2 0.0471 0.8317 0.00 0.98 0.00 0.00 0.00 0.02 0.00 0.00
#> TCGA.EB.A6QZ.01 1 0.5401 0.3209 0.48 0.00 0.04 0.14 0.00 0.00 0.00 0.34
#> TCGA.FW.A3I3.06 3 0.0471 0.6749 0.00 0.00 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.D3.A8GP.06 5 0.6429 -0.0982 0.00 0.34 0.00 0.00 0.36 0.20 0.02 0.08
#> TCGA.EB.A42Z.01 8 0.6450 0.0000 0.00 0.00 0.18 0.00 0.02 0.14 0.20 0.46
#> TCGA.GN.A4U4.06 1 0.5511 0.2893 0.46 0.00 0.04 0.16 0.00 0.00 0.00 0.34
#> TCGA.DA.A95W.06 2 0.0000 0.8351 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FW.A5DX.01 1 0.0000 0.8068 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.WE.A8ZY.06 1 0.0000 0.8068 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D9.A6EG.06 6 0.3314 0.7660 0.00 0.10 0.00 0.00 0.02 0.80 0.00 0.08
#> TCGA.GF.A769.01 3 0.4921 0.3729 0.22 0.00 0.52 0.00 0.00 0.00 0.00 0.26
#> TCGA.EE.A180.06 2 0.0000 0.8351 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.WE.A8K5.06 7 0.1557 0.4698 0.00 0.00 0.06 0.00 0.00 0.00 0.92 0.02
#> TCGA.GN.A8LN.01 1 0.0000 0.8068 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EE.A2MF.06 5 0.4745 0.4110 0.00 0.02 0.00 0.00 0.64 0.02 0.08 0.24
#> TCGA.EB.A42Y.01 1 0.0000 0.8068 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D3.A8GL.06 2 0.0000 0.8351 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D3.A3MU.06 7 0.5925 0.0396 0.00 0.00 0.00 0.00 0.28 0.06 0.42 0.24
#> TCGA.FS.A4F0.06 2 0.0471 0.8317 0.00 0.98 0.00 0.00 0.00 0.02 0.00 0.00
#> TCGA.EB.A41A.01 2 0.3729 -0.0388 0.00 0.52 0.00 0.00 0.00 0.46 0.00 0.02
#> TCGA.D3.A1QA.06 4 0.1563 0.6042 0.10 0.00 0.00 0.90 0.00 0.00 0.00 0.00
#> TCGA.EB.A5KH.06 1 0.5535 0.2556 0.44 0.00 0.04 0.16 0.00 0.00 0.00 0.36
#> TCGA.FS.A1ZY.06 3 0.3729 0.6028 0.18 0.00 0.72 0.00 0.00 0.00 0.00 0.10
#> TCGA.EE.A184.06 5 0.6949 -0.0553 0.00 0.00 0.02 0.10 0.42 0.04 0.26 0.16
#> TCGA.FS.A1ZZ.06 7 0.6322 0.1128 0.00 0.00 0.00 0.04 0.26 0.04 0.42 0.24
#> TCGA.EE.A3AD.06 1 0.0000 0.8068 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EE.A3AH.06 1 0.0000 0.8068 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FR.A7U8.06 5 0.1741 0.4539 0.00 0.00 0.00 0.00 0.92 0.02 0.02 0.04
#> TCGA.ER.A19J.06 4 0.4211 0.3523 0.00 0.00 0.00 0.68 0.00 0.02 0.22 0.08
#> TCGA.EB.A82C.01 5 0.7613 -0.2085 0.00 0.00 0.16 0.06 0.34 0.04 0.26 0.14
#> TCGA.EB.A5FP.01 1 0.5535 0.2556 0.44 0.00 0.04 0.16 0.00 0.00 0.00 0.36
#> TCGA.EE.A29L.06 4 0.1563 0.6042 0.10 0.00 0.00 0.90 0.00 0.00 0.00 0.00
#> TCGA.FS.A1ZN.01 3 0.3785 0.6042 0.14 0.00 0.72 0.00 0.00 0.00 0.00 0.14
#> TCGA.EE.A20C.06 3 0.0941 0.6642 0.00 0.00 0.96 0.00 0.02 0.02 0.00 0.00
#> TCGA.GN.A268.06 2 0.0471 0.8317 0.00 0.98 0.00 0.00 0.00 0.02 0.00 0.00
#> TCGA.FS.A1ZG.06 5 0.3735 0.3755 0.00 0.02 0.00 0.00 0.72 0.22 0.00 0.04
#> TCGA.FS.A1ZE.06 5 0.4745 0.4110 0.00 0.02 0.00 0.00 0.64 0.02 0.08 0.24
#> TCGA.GN.A264.06 7 0.4180 0.3104 0.00 0.00 0.06 0.00 0.00 0.04 0.70 0.20
#> TCGA.FS.A1YW.06 3 0.0941 0.6642 0.00 0.00 0.96 0.00 0.02 0.02 0.00 0.00
#> TCGA.GN.A262.06 3 0.4033 0.5695 0.20 0.00 0.68 0.00 0.00 0.00 0.00 0.12
#> TCGA.EE.A29A.06 6 0.2165 0.7620 0.00 0.06 0.00 0.00 0.06 0.88 0.00 0.00
#> TCGA.FS.A1ZC.06 1 0.0000 0.8068 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EE.A2GO.06 3 0.0941 0.6642 0.00 0.00 0.96 0.00 0.02 0.02 0.00 0.00
#> TCGA.EE.A29R.06 3 0.0808 0.6585 0.00 0.00 0.96 0.00 0.00 0.00 0.00 0.04
#> TCGA.D9.A1X3.06 2 0.0000 0.8351 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.ER.A2NE.06 3 0.4799 0.4033 0.18 0.00 0.54 0.00 0.00 0.00 0.00 0.28
#> TCGA.EE.A185.06 4 0.5101 0.3151 0.16 0.00 0.00 0.54 0.00 0.02 0.00 0.28
#> TCGA.EE.A2M6.06 1 0.0000 0.8068 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BF.AAP2.01 1 0.0000 0.8068 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EE.A2GM.06 1 0.5877 0.2899 0.46 0.00 0.04 0.16 0.00 0.02 0.00 0.32
#> TCGA.D9.A6EC.06 3 0.0471 0.6749 0.00 0.00 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.EB.A5SE.01 6 0.2818 0.7692 0.00 0.12 0.00 0.00 0.00 0.82 0.00 0.06
#> TCGA.D9.A6EA.06 2 0.3729 -0.0388 0.00 0.52 0.00 0.00 0.00 0.46 0.00 0.02
#> TCGA.EE.A29D.06 6 0.5308 0.3540 0.00 0.32 0.00 0.00 0.18 0.48 0.00 0.02
#> TCGA.BF.AAP1.01 7 0.5158 0.3921 0.00 0.00 0.02 0.00 0.30 0.02 0.56 0.10
#> TCGA.LH.A9QB.06 5 0.0941 0.4563 0.00 0.00 0.00 0.00 0.96 0.00 0.02 0.02
#> TCGA.EB.A97M.01 2 0.0471 0.8317 0.00 0.98 0.00 0.00 0.00 0.02 0.00 0.00
#> TCGA.W3.AA21.06 1 0.2071 0.7555 0.90 0.00 0.00 0.04 0.00 0.02 0.00 0.04
#> TCGA.Z2.AA3S.06 2 0.4340 0.1483 0.00 0.54 0.00 0.00 0.38 0.00 0.00 0.08
#> TCGA.FS.A4F5.06 7 0.2680 0.5016 0.00 0.00 0.00 0.00 0.12 0.02 0.84 0.02
#> TCGA.D9.A4Z5.01 7 0.3314 0.4264 0.00 0.00 0.08 0.00 0.00 0.02 0.80 0.10
#> TCGA.3N.A9WB.06 6 0.2025 0.7887 0.00 0.10 0.00 0.00 0.02 0.88 0.00 0.00
#> TCGA.EE.A3J8.06 4 0.3879 0.5416 0.14 0.00 0.00 0.74 0.00 0.02 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-leaf , Node0113 , Node0121-leaf , Node0122-leaf , Node0123-leaf , Node0124-leaf , Node0125-leaf , Node0131 , Node0132-leaf , Node0133-leaf , Node0211-leaf , Node0212 , Node0221-leaf , Node0222-leaf , Node0311 , Node0312-leaf , Node0321-leaf , Node0322 , Node0323 , Node0411 , Node0412 , Node0413-leaf , Node0421-leaf , Node0422-leaf , Node0423-leaf , Node0431-leaf , Node0432-leaf , Node0433-leaf , Node0441-leaf , Node0442 , Node0443-leaf , Node0511 , Node0512-leaf , Node0513-leaf , Node0521-leaf , Node0522-leaf , Node0523-leaf , Node0524-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 28 columns.
#> Top rows (1000) are extracted by 'ATC' method.
#> Subgroups are detected by 'kmeans' method.
#> Performed in total 350 partitions by row resampling.
#> Best k for subgroups seems to be 6.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_partitions"
#> [7] "compare_signatures" "consensus_heatmap" "dimension_reduction"
#> [10] "functional_enrichment" "get_anno_col" "get_anno"
#> [13] "get_classes" "get_consensus" "get_matrix"
#> [16] "get_membership" "get_param" "get_signatures"
#> [19] "get_stats" "is_best_k" "is_stable_k"
#> [22] "membership_heatmap" "ncol" "nrow"
#> [25] "plot_ecdf" "predict_classes" "rownames"
#> [28] "select_partition_number" "show" "suggest_best_k"
#> [31] "test_to_known_factors" "top_rows_heatmap"
collect_plots() function collects all the plots made from res for all k (number of subgroups)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
The plots are:
k and the heatmap of
predicted classes for each k.k.k.k.All the plots in panels can be made by individual functions and they are plotted later in this section.
select_partition_number() produces several plots showing different
statistics for choosing “optimized” k. There are following statistics:
k;k, the area increased is defined as \(A_k - A_{k-1}\).The detailed explanations of these statistics can be found in the cola vignette.
Generally speaking, higher 1-PAC score, higher mean silhouette score or higher
concordance corresponds to better partition. Rand index and Jaccard index
measure how similar the current partition is compared to partition with k-1.
If they are too similar, we won't accept k is better than k-1.
select_partition_number(res)
The numeric values for all these statistics can be obtained by get_stats().
get_stats(res)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> 2 2 1.000 1.000 1.000 0.3499 0.651 0.651
#> 3 3 1.000 0.991 0.996 0.9123 0.680 0.508
#> 4 4 0.828 0.840 0.906 0.1219 0.889 0.674
#> 5 5 0.960 0.901 0.954 0.0691 0.915 0.673
#> 6 6 0.942 0.916 0.949 0.0252 0.976 0.878
#> 7 7 0.886 0.851 0.907 0.0175 1.000 1.000
#> 8 8 0.870 0.766 0.894 0.0109 0.992 0.955
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 5
There is also optional best \(k\) = 2 3 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.DA.A95X.06 1 0 1 1 0
#> TCGA.WE.A8JZ.06 2 0 1 0 1
#> TCGA.DA.A960.01 1 0 1 1 0
#> TCGA.D3.A8GV.06 2 0 1 0 1
#> TCGA.EB.A6QZ.01 2 0 1 0 1
#> TCGA.GN.A4U4.06 2 0 1 0 1
#> TCGA.FW.A5DX.01 2 0 1 0 1
#> TCGA.WE.A8ZY.06 2 0 1 0 1
#> TCGA.GF.A769.01 2 0 1 0 1
#> TCGA.GN.A8LN.01 2 0 1 0 1
#> TCGA.EB.A42Y.01 2 0 1 0 1
#> TCGA.D3.A1QA.06 1 0 1 1 0
#> TCGA.EB.A5KH.06 2 0 1 0 1
#> TCGA.FS.A1ZY.06 2 0 1 0 1
#> TCGA.EE.A3AD.06 2 0 1 0 1
#> TCGA.EE.A3AH.06 2 0 1 0 1
#> TCGA.EB.A5FP.01 2 0 1 0 1
#> TCGA.EE.A29L.06 1 0 1 1 0
#> TCGA.FS.A1ZN.01 2 0 1 0 1
#> TCGA.GN.A262.06 2 0 1 0 1
#> TCGA.FS.A1ZC.06 2 0 1 0 1
#> TCGA.ER.A2NE.06 2 0 1 0 1
#> TCGA.EE.A185.06 2 0 1 0 1
#> TCGA.EE.A2M6.06 2 0 1 0 1
#> TCGA.BF.AAP2.01 2 0 1 0 1
#> TCGA.EE.A2GM.06 2 0 1 0 1
#> TCGA.W3.AA21.06 1 0 1 1 0
#> TCGA.EE.A3J8.06 1 0 1 1 0
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.DA.A95X.06 1 0.000 1.000 1 0.00 0.00
#> TCGA.WE.A8JZ.06 2 0.207 0.937 0 0.94 0.06
#> TCGA.DA.A960.01 1 0.000 1.000 1 0.00 0.00
#> TCGA.D3.A8GV.06 3 0.000 1.000 0 0.00 1.00
#> TCGA.EB.A6QZ.01 3 0.000 1.000 0 0.00 1.00
#> TCGA.GN.A4U4.06 2 0.000 0.986 0 1.00 0.00
#> TCGA.FW.A5DX.01 2 0.000 0.986 0 1.00 0.00
#> TCGA.WE.A8ZY.06 2 0.000 0.986 0 1.00 0.00
#> TCGA.GF.A769.01 3 0.000 1.000 0 0.00 1.00
#> TCGA.GN.A8LN.01 3 0.000 1.000 0 0.00 1.00
#> TCGA.EB.A42Y.01 2 0.000 0.986 0 1.00 0.00
#> TCGA.D3.A1QA.06 1 0.000 1.000 1 0.00 0.00
#> TCGA.EB.A5KH.06 2 0.000 0.986 0 1.00 0.00
#> TCGA.FS.A1ZY.06 3 0.000 1.000 0 0.00 1.00
#> TCGA.EE.A3AD.06 3 0.000 1.000 0 0.00 1.00
#> TCGA.EE.A3AH.06 3 0.000 1.000 0 0.00 1.00
#> TCGA.EB.A5FP.01 2 0.000 0.986 0 1.00 0.00
#> TCGA.EE.A29L.06 1 0.000 1.000 1 0.00 0.00
#> TCGA.FS.A1ZN.01 3 0.000 1.000 0 0.00 1.00
#> TCGA.GN.A262.06 3 0.000 1.000 0 0.00 1.00
#> TCGA.FS.A1ZC.06 3 0.000 1.000 0 0.00 1.00
#> TCGA.ER.A2NE.06 3 0.000 1.000 0 0.00 1.00
#> TCGA.EE.A185.06 2 0.000 0.986 0 1.00 0.00
#> TCGA.EE.A2M6.06 2 0.000 0.986 0 1.00 0.00
#> TCGA.BF.AAP2.01 2 0.207 0.937 0 0.94 0.06
#> TCGA.EE.A2GM.06 2 0.000 0.986 0 1.00 0.00
#> TCGA.W3.AA21.06 1 0.000 1.000 1 0.00 0.00
#> TCGA.EE.A3J8.06 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.DA.A95X.06 1 0.000 0.957 1.00 0.00 0.00 0.00
#> TCGA.WE.A8JZ.06 4 0.511 0.703 0.00 0.24 0.04 0.72
#> TCGA.DA.A960.01 1 0.000 0.957 1.00 0.00 0.00 0.00
#> TCGA.D3.A8GV.06 3 0.164 0.924 0.00 0.00 0.94 0.06
#> TCGA.EB.A6QZ.01 3 0.000 0.992 0.00 0.00 1.00 0.00
#> TCGA.GN.A4U4.06 2 0.485 0.633 0.00 0.60 0.00 0.40
#> TCGA.FW.A5DX.01 4 0.464 0.689 0.00 0.24 0.02 0.74
#> TCGA.WE.A8ZY.06 2 0.380 0.724 0.00 0.78 0.00 0.22
#> TCGA.GF.A769.01 3 0.000 0.992 0.00 0.00 1.00 0.00
#> TCGA.GN.A8LN.01 3 0.000 0.992 0.00 0.00 1.00 0.00
#> TCGA.EB.A42Y.01 2 0.000 0.782 0.00 1.00 0.00 0.00
#> TCGA.D3.A1QA.06 1 0.000 0.957 1.00 0.00 0.00 0.00
#> TCGA.EB.A5KH.06 2 0.000 0.782 0.00 1.00 0.00 0.00
#> TCGA.FS.A1ZY.06 3 0.000 0.992 0.00 0.00 1.00 0.00
#> TCGA.EE.A3AD.06 3 0.000 0.992 0.00 0.00 1.00 0.00
#> TCGA.EE.A3AH.06 3 0.000 0.992 0.00 0.00 1.00 0.00
#> TCGA.EB.A5FP.01 2 0.234 0.688 0.00 0.90 0.00 0.10
#> TCGA.EE.A29L.06 1 0.000 0.957 1.00 0.00 0.00 0.00
#> TCGA.FS.A1ZN.01 3 0.000 0.992 0.00 0.00 1.00 0.00
#> TCGA.GN.A262.06 3 0.000 0.992 0.00 0.00 1.00 0.00
#> TCGA.FS.A1ZC.06 4 0.536 0.489 0.00 0.02 0.36 0.62
#> TCGA.ER.A2NE.06 3 0.000 0.992 0.00 0.00 1.00 0.00
#> TCGA.EE.A185.06 2 0.000 0.782 0.00 1.00 0.00 0.00
#> TCGA.EE.A2M6.06 4 0.000 0.540 0.00 0.00 0.00 1.00
#> TCGA.BF.AAP2.01 4 0.659 0.686 0.00 0.24 0.14 0.62
#> TCGA.EE.A2GM.06 2 0.485 0.633 0.00 0.60 0.00 0.40
#> TCGA.W3.AA21.06 1 0.380 0.759 0.78 0.00 0.00 0.22
#> TCGA.EE.A3J8.06 1 0.000 0.957 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.DA.A95X.06 1 0.0000 0.899 1.00 0.00 0.00 0.00 0.00
#> TCGA.WE.A8JZ.06 4 0.1410 0.873 0.00 0.00 0.00 0.94 0.06
#> TCGA.DA.A960.01 1 0.0000 0.899 1.00 0.00 0.00 0.00 0.00
#> TCGA.D3.A8GV.06 4 0.3424 0.700 0.00 0.00 0.24 0.76 0.00
#> TCGA.EB.A6QZ.01 3 0.0000 1.000 0.00 0.00 1.00 0.00 0.00
#> TCGA.GN.A4U4.06 5 0.0000 0.902 0.00 0.00 0.00 0.00 1.00
#> TCGA.FW.A5DX.01 4 0.1410 0.873 0.00 0.00 0.00 0.94 0.06
#> TCGA.WE.A8ZY.06 5 0.2280 0.823 0.00 0.12 0.00 0.00 0.88
#> TCGA.GF.A769.01 3 0.0000 1.000 0.00 0.00 1.00 0.00 0.00
#> TCGA.GN.A8LN.01 3 0.0000 1.000 0.00 0.00 1.00 0.00 0.00
#> TCGA.EB.A42Y.01 2 0.0000 0.994 0.00 1.00 0.00 0.00 0.00
#> TCGA.D3.A1QA.06 1 0.0000 0.899 1.00 0.00 0.00 0.00 0.00
#> TCGA.EB.A5KH.06 2 0.0000 0.994 0.00 1.00 0.00 0.00 0.00
#> TCGA.FS.A1ZY.06 3 0.0000 1.000 0.00 0.00 1.00 0.00 0.00
#> TCGA.EE.A3AD.06 3 0.0000 1.000 0.00 0.00 1.00 0.00 0.00
#> TCGA.EE.A3AH.06 3 0.0000 1.000 0.00 0.00 1.00 0.00 0.00
#> TCGA.EB.A5FP.01 2 0.0000 0.994 0.00 1.00 0.00 0.00 0.00
#> TCGA.EE.A29L.06 1 0.0000 0.899 1.00 0.00 0.00 0.00 0.00
#> TCGA.FS.A1ZN.01 3 0.0000 1.000 0.00 0.00 1.00 0.00 0.00
#> TCGA.GN.A262.06 3 0.0000 1.000 0.00 0.00 1.00 0.00 0.00
#> TCGA.FS.A1ZC.06 4 0.1410 0.883 0.00 0.00 0.06 0.94 0.00
#> TCGA.ER.A2NE.06 3 0.0000 1.000 0.00 0.00 1.00 0.00 0.00
#> TCGA.EE.A185.06 2 0.0609 0.983 0.00 0.98 0.00 0.02 0.00
#> TCGA.EE.A2M6.06 5 0.2929 0.803 0.00 0.00 0.00 0.18 0.82
#> TCGA.BF.AAP2.01 4 0.1648 0.885 0.00 0.02 0.04 0.94 0.00
#> TCGA.EE.A2GM.06 5 0.0000 0.902 0.00 0.00 0.00 0.00 1.00
#> TCGA.W3.AA21.06 1 0.5157 0.111 0.52 0.00 0.00 0.04 0.44
#> TCGA.EE.A3J8.06 1 0.0000 0.899 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.DA.A95X.06 1 0.0547 0.979 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.WE.A8JZ.06 4 0.0000 0.926 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.DA.A960.01 1 0.0000 0.986 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D3.A8GV.06 4 0.3163 0.738 0.00 0.00 0.14 0.82 0.00 0.04
#> TCGA.EB.A6QZ.01 3 0.0000 0.985 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.GN.A4U4.06 5 0.2260 0.890 0.00 0.00 0.00 0.00 0.86 0.14
#> TCGA.FW.A5DX.01 4 0.0000 0.926 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.WE.A8ZY.06 5 0.0547 0.790 0.00 0.02 0.00 0.00 0.98 0.00
#> TCGA.GF.A769.01 3 0.0000 0.985 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.GN.A8LN.01 3 0.0937 0.971 0.00 0.00 0.96 0.00 0.00 0.04
#> TCGA.EB.A42Y.01 2 0.1556 0.896 0.00 0.92 0.00 0.00 0.08 0.00
#> TCGA.D3.A1QA.06 1 0.0000 0.986 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EB.A5KH.06 2 0.0000 0.933 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.FS.A1ZY.06 3 0.0000 0.985 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.EE.A3AD.06 3 0.0937 0.971 0.00 0.00 0.96 0.00 0.00 0.04
#> TCGA.EE.A3AH.06 3 0.0937 0.971 0.00 0.00 0.96 0.00 0.00 0.04
#> TCGA.EB.A5FP.01 2 0.0000 0.933 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.EE.A29L.06 1 0.0000 0.986 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FS.A1ZN.01 3 0.0000 0.985 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.GN.A262.06 3 0.0000 0.985 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.FS.A1ZC.06 4 0.0000 0.926 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.ER.A2NE.06 3 0.0000 0.985 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.EE.A185.06 2 0.2260 0.865 0.00 0.86 0.00 0.00 0.00 0.14
#> TCGA.EE.A2M6.06 6 0.4094 0.625 0.00 0.00 0.00 0.08 0.18 0.74
#> TCGA.BF.AAP2.01 4 0.0937 0.904 0.00 0.04 0.00 0.96 0.00 0.00
#> TCGA.EE.A2GM.06 5 0.2260 0.890 0.00 0.00 0.00 0.00 0.86 0.14
#> TCGA.W3.AA21.06 6 0.3829 0.665 0.18 0.00 0.00 0.00 0.06 0.76
#> TCGA.EE.A3J8.06 1 0.0937 0.968 0.96 0.00 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.DA.A95X.06 1 0.0504 0.980 0.98 0.00 0.00 0.00 0.00 0.02 0.00
#> TCGA.WE.A8JZ.06 4 0.0504 0.811 0.00 0.02 0.00 0.98 0.00 0.00 0.00
#> TCGA.DA.A960.01 1 0.0000 0.987 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D3.A8GV.06 4 0.4429 0.630 0.00 0.00 0.12 0.66 0.00 0.00 0.22
#> TCGA.EB.A6QZ.01 3 0.0504 0.935 0.00 0.00 0.98 0.00 0.00 0.00 0.02
#> TCGA.GN.A4U4.06 5 0.2259 0.867 0.00 0.00 0.00 0.00 0.84 0.16 0.00
#> TCGA.FW.A5DX.01 4 0.0504 0.811 0.00 0.02 0.00 0.98 0.00 0.00 0.00
#> TCGA.WE.A8ZY.06 5 0.1433 0.738 0.00 0.00 0.00 0.00 0.92 0.00 0.08
#> TCGA.GF.A769.01 3 0.0000 0.946 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.GN.A8LN.01 3 0.1671 0.904 0.00 0.00 0.90 0.00 0.00 0.00 0.10
#> TCGA.EB.A42Y.01 2 0.2572 0.798 0.00 0.80 0.00 0.00 0.00 0.00 0.20
#> TCGA.D3.A1QA.06 1 0.0000 0.987 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EB.A5KH.06 2 0.0000 0.830 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FS.A1ZY.06 3 0.0000 0.946 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.EE.A3AD.06 3 0.1671 0.904 0.00 0.00 0.90 0.00 0.00 0.00 0.10
#> TCGA.EE.A3AH.06 3 0.2708 0.793 0.00 0.00 0.78 0.00 0.00 0.00 0.22
#> TCGA.EB.A5FP.01 2 0.0000 0.830 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EE.A29L.06 1 0.0000 0.987 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FS.A1ZN.01 3 0.0000 0.946 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.GN.A262.06 3 0.0000 0.946 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.FS.A1ZC.06 4 0.2376 0.780 0.00 0.00 0.02 0.86 0.00 0.00 0.12
#> TCGA.ER.A2NE.06 3 0.0000 0.946 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.EE.A185.06 2 0.3413 0.688 0.00 0.62 0.00 0.00 0.00 0.00 0.38
#> TCGA.EE.A2M6.06 6 0.4305 0.667 0.00 0.00 0.00 0.04 0.02 0.66 0.28
#> TCGA.BF.AAP2.01 4 0.3526 0.697 0.00 0.18 0.00 0.76 0.00 0.00 0.06
#> TCGA.EE.A2GM.06 5 0.2259 0.867 0.00 0.00 0.00 0.00 0.84 0.16 0.00
#> TCGA.W3.AA21.06 6 0.1363 0.653 0.04 0.00 0.00 0.00 0.02 0.94 0.00
#> TCGA.EE.A3J8.06 1 0.1006 0.970 0.96 0.00 0.00 0.02 0.00 0.02 0.00
cbind(get_classes(res, k = 8), get_membership(res, k = 8))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7 p8
#> TCGA.DA.A95X.06 1 0.0000 0.961 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.WE.A8JZ.06 4 0.0000 0.840 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DA.A960.01 1 0.0000 0.961 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D3.A8GV.06 4 0.3404 0.671 0.00 0.00 0.04 0.72 0.00 0.00 0.24 0.00
#> TCGA.EB.A6QZ.01 3 0.0808 0.905 0.00 0.00 0.96 0.00 0.00 0.00 0.04 0.00
#> TCGA.GN.A4U4.06 5 0.3272 1.000 0.00 0.00 0.00 0.00 0.58 0.00 0.00 0.42
#> TCGA.FW.A5DX.01 4 0.0000 0.840 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.WE.A8ZY.06 8 0.0000 0.000 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.GF.A769.01 3 0.0000 0.927 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.GN.A8LN.01 3 0.1947 0.866 0.00 0.00 0.86 0.00 0.00 0.00 0.14 0.00
#> TCGA.EB.A42Y.01 2 0.3002 0.757 0.00 0.82 0.00 0.00 0.12 0.00 0.02 0.04
#> TCGA.D3.A1QA.06 1 0.0000 0.961 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EB.A5KH.06 2 0.0000 0.791 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FS.A1ZY.06 3 0.0000 0.927 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EE.A3AD.06 3 0.1947 0.866 0.00 0.00 0.86 0.00 0.00 0.00 0.14 0.00
#> TCGA.EE.A3AH.06 3 0.3095 0.750 0.00 0.00 0.74 0.02 0.00 0.00 0.24 0.00
#> TCGA.EB.A5FP.01 2 0.0000 0.791 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EE.A29L.06 1 0.0000 0.961 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FS.A1ZN.01 3 0.0000 0.927 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.GN.A262.06 3 0.0000 0.927 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FS.A1ZC.06 4 0.1563 0.818 0.00 0.00 0.00 0.90 0.00 0.00 0.10 0.00
#> TCGA.ER.A2NE.06 3 0.0000 0.927 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EE.A185.06 2 0.4929 0.543 0.00 0.52 0.00 0.00 0.24 0.00 0.24 0.00
#> TCGA.EE.A2M6.06 6 0.0000 0.000 0.00 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.BF.AAP2.01 4 0.2719 0.701 0.00 0.18 0.00 0.80 0.00 0.00 0.02 0.00
#> TCGA.EE.A2GM.06 5 0.3272 1.000 0.00 0.00 0.00 0.00 0.58 0.00 0.00 0.42
#> TCGA.W3.AA21.06 7 0.5617 0.000 0.06 0.00 0.00 0.00 0.34 0.14 0.46 0.00
#> TCGA.EE.A3J8.06 1 0.2547 0.827 0.84 0.00 0.00 0.00 0.12 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-leaf , Node01112-leaf , Node01113-leaf , Node01131-leaf , Node01132-leaf , Node01133-leaf , Node01311-leaf , Node01312-leaf , Node02121-leaf , Node02122-leaf , Node02123-leaf , Node03111-leaf , Node03112-leaf , Node03113-leaf , Node03221-leaf , Node03222-leaf , Node03231-leaf , Node03232-leaf , Node03233-leaf , Node03234-leaf , Node04111-leaf , Node04112-leaf , Node04121-leaf , Node04122-leaf , Node04421-leaf , Node04422-leaf , Node04423-leaf , Node04424-leaf , Node05111-leaf , Node05112-leaf , Node05113-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 22 columns.
#> Top rows (1000) are extracted by 'ATC' method.
#> Subgroups are detected by 'skmeans' method.
#> Performed in total 350 partitions by row resampling.
#> Best k for subgroups seems to be 3.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_partitions"
#> [7] "compare_signatures" "consensus_heatmap" "dimension_reduction"
#> [10] "functional_enrichment" "get_anno_col" "get_anno"
#> [13] "get_classes" "get_consensus" "get_matrix"
#> [16] "get_membership" "get_param" "get_signatures"
#> [19] "get_stats" "is_best_k" "is_stable_k"
#> [22] "membership_heatmap" "ncol" "nrow"
#> [25] "plot_ecdf" "predict_classes" "rownames"
#> [28] "select_partition_number" "show" "suggest_best_k"
#> [31] "test_to_known_factors" "top_rows_heatmap"
collect_plots() function collects all the plots made from res for all k (number of subgroups)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
The plots are:
k and the heatmap of
predicted classes for each k.k.k.k.All the plots in panels can be made by individual functions and they are plotted later in this section.
select_partition_number() produces several plots showing different
statistics for choosing “optimized” k. There are following statistics:
k;k, the area increased is defined as \(A_k - A_{k-1}\).The detailed explanations of these statistics can be found in the cola vignette.
Generally speaking, higher 1-PAC score, higher mean silhouette score or higher
concordance corresponds to better partition. Rand index and Jaccard index
measure how similar the current partition is compared to partition with k-1.
If they are too similar, we won't accept k is better than k-1.
select_partition_number(res)
The numeric values for all these statistics can be obtained by get_stats().
get_stats(res)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> 2 2 1.000 0.964 0.983 0.4920 0.515 0.515
#> 3 3 1.000 0.984 0.986 0.3236 0.779 0.592
#> 4 4 0.632 0.495 0.757 0.1094 0.844 0.600
#> 5 5 0.653 0.626 0.710 0.0539 0.810 0.421
#> 6 6 0.653 0.652 0.814 0.0618 0.987 0.932
#> 7 7 0.700 0.450 0.716 0.0299 0.879 0.451
#> 8 8 0.719 0.484 0.728 0.0303 0.909 0.523
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.WE.A8JZ.06 1 0.000 1.000 1.00 0.00
#> TCGA.D3.A8GV.06 1 0.000 1.000 1.00 0.00
#> TCGA.EB.A6QZ.01 2 0.000 0.970 0.00 1.00
#> TCGA.GN.A4U4.06 2 0.722 0.769 0.20 0.80
#> TCGA.FW.A5DX.01 1 0.000 1.000 1.00 0.00
#> TCGA.WE.A8ZY.06 2 0.000 0.970 0.00 1.00
#> TCGA.GF.A769.01 2 0.680 0.795 0.18 0.82
#> TCGA.GN.A8LN.01 2 0.000 0.970 0.00 1.00
#> TCGA.EB.A42Y.01 2 0.000 0.970 0.00 1.00
#> TCGA.EB.A5KH.06 2 0.000 0.970 0.00 1.00
#> TCGA.FS.A1ZY.06 2 0.000 0.970 0.00 1.00
#> TCGA.EE.A3AD.06 2 0.000 0.970 0.00 1.00
#> TCGA.EE.A3AH.06 1 0.000 1.000 1.00 0.00
#> TCGA.EB.A5FP.01 2 0.000 0.970 0.00 1.00
#> TCGA.FS.A1ZN.01 2 0.000 0.970 0.00 1.00
#> TCGA.GN.A262.06 1 0.000 1.000 1.00 0.00
#> TCGA.FS.A1ZC.06 1 0.000 1.000 1.00 0.00
#> TCGA.ER.A2NE.06 2 0.000 0.970 0.00 1.00
#> TCGA.EE.A185.06 2 0.000 0.970 0.00 1.00
#> TCGA.EE.A2M6.06 1 0.000 1.000 1.00 0.00
#> TCGA.BF.AAP2.01 2 0.000 0.970 0.00 1.00
#> TCGA.EE.A2GM.06 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.WE.A8JZ.06 1 0.0000 0.971 1.00 0.00 0.00
#> TCGA.D3.A8GV.06 1 0.1529 0.985 0.96 0.00 0.04
#> TCGA.EB.A6QZ.01 2 0.0892 0.983 0.00 0.98 0.02
#> TCGA.GN.A4U4.06 3 0.0892 0.979 0.00 0.02 0.98
#> TCGA.FW.A5DX.01 1 0.1529 0.985 0.96 0.00 0.04
#> TCGA.WE.A8ZY.06 2 0.0000 0.994 0.00 1.00 0.00
#> TCGA.GF.A769.01 3 0.0892 0.979 0.00 0.02 0.98
#> TCGA.GN.A8LN.01 2 0.0892 0.983 0.00 0.98 0.02
#> TCGA.EB.A42Y.01 2 0.0000 0.994 0.00 1.00 0.00
#> TCGA.EB.A5KH.06 2 0.0000 0.994 0.00 1.00 0.00
#> TCGA.FS.A1ZY.06 3 0.1529 0.960 0.00 0.04 0.96
#> TCGA.EE.A3AD.06 2 0.0000 0.994 0.00 1.00 0.00
#> TCGA.EE.A3AH.06 1 0.1529 0.985 0.96 0.00 0.04
#> TCGA.EB.A5FP.01 2 0.0000 0.994 0.00 1.00 0.00
#> TCGA.FS.A1ZN.01 2 0.0892 0.983 0.00 0.98 0.02
#> TCGA.GN.A262.06 3 0.0000 0.973 0.00 0.00 1.00
#> TCGA.FS.A1ZC.06 1 0.0000 0.971 1.00 0.00 0.00
#> TCGA.ER.A2NE.06 2 0.0000 0.994 0.00 1.00 0.00
#> TCGA.EE.A185.06 2 0.0000 0.994 0.00 1.00 0.00
#> TCGA.EE.A2M6.06 1 0.1529 0.985 0.96 0.00 0.04
#> TCGA.BF.AAP2.01 2 0.0000 0.994 0.00 1.00 0.00
#> TCGA.EE.A2GM.06 3 0.0000 0.973 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.WE.A8JZ.06 4 0.4855 0.9653 0.40 0.00 0.00 0.60
#> TCGA.D3.A8GV.06 1 0.6110 0.4952 0.66 0.00 0.10 0.24
#> TCGA.EB.A6QZ.01 3 0.5000 -0.4493 0.00 0.50 0.50 0.00
#> TCGA.GN.A4U4.06 3 0.3801 0.4566 0.00 0.00 0.78 0.22
#> TCGA.FW.A5DX.01 1 0.0707 0.7873 0.98 0.00 0.00 0.02
#> TCGA.WE.A8ZY.06 2 0.6201 0.5708 0.00 0.62 0.30 0.08
#> TCGA.GF.A769.01 3 0.2011 0.4950 0.00 0.00 0.92 0.08
#> TCGA.GN.A8LN.01 2 0.4994 0.3330 0.00 0.52 0.48 0.00
#> TCGA.EB.A42Y.01 2 0.2921 0.6190 0.00 0.86 0.00 0.14
#> TCGA.EB.A5KH.06 2 0.0000 0.7214 0.00 1.00 0.00 0.00
#> TCGA.FS.A1ZY.06 3 0.1211 0.4460 0.00 0.04 0.96 0.00
#> TCGA.EE.A3AD.06 2 0.4713 0.5391 0.00 0.64 0.36 0.00
#> TCGA.EE.A3AH.06 1 0.1211 0.7979 0.96 0.00 0.00 0.04
#> TCGA.EB.A5FP.01 2 0.0000 0.7214 0.00 1.00 0.00 0.00
#> TCGA.FS.A1ZN.01 3 0.5000 -0.4493 0.00 0.50 0.50 0.00
#> TCGA.GN.A262.06 3 0.7198 0.1203 0.28 0.00 0.54 0.18
#> TCGA.FS.A1ZC.06 4 0.4790 0.9657 0.38 0.00 0.00 0.62
#> TCGA.ER.A2NE.06 2 0.4855 0.4901 0.00 0.60 0.40 0.00
#> TCGA.EE.A185.06 2 0.0000 0.7214 0.00 1.00 0.00 0.00
#> TCGA.EE.A2M6.06 1 0.0000 0.8014 1.00 0.00 0.00 0.00
#> TCGA.BF.AAP2.01 2 0.0000 0.7214 0.00 1.00 0.00 0.00
#> TCGA.EE.A2GM.06 3 0.7610 0.0263 0.32 0.00 0.46 0.22
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> TCGA.WE.A8JZ.06 4 0.104 0.9473 0.04 0.00 0.00 0.96 0.00
#> TCGA.D3.A8GV.06 1 0.882 0.0844 0.32 0.02 0.30 0.20 0.16
#> TCGA.EB.A6QZ.01 5 0.327 0.6929 0.00 0.22 0.00 0.00 0.78
#> TCGA.GN.A4U4.06 3 0.173 0.7122 0.00 0.00 0.92 0.00 0.08
#> TCGA.FW.A5DX.01 1 0.173 0.6908 0.92 0.00 0.00 0.08 0.00
#> TCGA.WE.A8ZY.06 5 0.569 0.1777 0.00 0.46 0.08 0.00 0.46
#> TCGA.GF.A769.01 3 0.423 0.5252 0.00 0.00 0.58 0.00 0.42
#> TCGA.GN.A8LN.01 5 0.342 0.6797 0.00 0.24 0.00 0.00 0.76
#> TCGA.EB.A42Y.01 2 0.182 0.5183 0.00 0.94 0.02 0.02 0.02
#> TCGA.EB.A5KH.06 2 0.389 0.7623 0.00 0.68 0.00 0.00 0.32
#> TCGA.FS.A1ZY.06 5 0.380 0.0192 0.00 0.00 0.30 0.00 0.70
#> TCGA.EE.A3AD.06 5 0.389 0.5303 0.00 0.32 0.00 0.00 0.68
#> TCGA.EE.A3AH.06 1 0.122 0.7040 0.96 0.02 0.00 0.00 0.02
#> TCGA.EB.A5FP.01 2 0.380 0.7944 0.00 0.70 0.00 0.00 0.30
#> TCGA.FS.A1ZN.01 5 0.311 0.6923 0.00 0.20 0.00 0.00 0.80
#> TCGA.GN.A262.06 3 0.482 0.6747 0.18 0.00 0.72 0.00 0.10
#> TCGA.FS.A1ZC.06 4 0.173 0.9463 0.08 0.00 0.00 0.92 0.00
#> TCGA.ER.A2NE.06 5 0.342 0.6717 0.00 0.24 0.00 0.00 0.76
#> TCGA.EE.A185.06 2 0.380 0.7944 0.00 0.70 0.00 0.00 0.30
#> TCGA.EE.A2M6.06 1 0.104 0.7129 0.96 0.00 0.00 0.04 0.00
#> TCGA.BF.AAP2.01 2 0.327 0.7618 0.00 0.78 0.00 0.00 0.22
#> TCGA.EE.A2GM.06 3 0.273 0.6704 0.16 0.00 0.84 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.WE.A8JZ.06 4 0.0000 1.000 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.D3.A8GV.06 6 0.5000 0.000 0.06 0.00 0.18 0.06 0.00 0.70
#> TCGA.EB.A6QZ.01 5 0.1480 0.708 0.00 0.04 0.00 0.00 0.94 0.02
#> TCGA.GN.A4U4.06 3 0.4097 0.594 0.02 0.02 0.80 0.00 0.10 0.06
#> TCGA.FW.A5DX.01 1 0.1480 0.922 0.94 0.00 0.02 0.04 0.00 0.00
#> TCGA.WE.A8ZY.06 5 0.6516 0.157 0.00 0.26 0.08 0.00 0.52 0.14
#> TCGA.GF.A769.01 3 0.4873 0.383 0.00 0.00 0.60 0.00 0.32 0.08
#> TCGA.GN.A8LN.01 5 0.3483 0.654 0.00 0.12 0.02 0.00 0.82 0.04
#> TCGA.EB.A42Y.01 2 0.3795 0.431 0.00 0.80 0.06 0.00 0.02 0.12
#> TCGA.EB.A5KH.06 2 0.3499 0.792 0.00 0.68 0.00 0.00 0.32 0.00
#> TCGA.FS.A1ZY.06 5 0.4348 0.249 0.00 0.00 0.32 0.00 0.64 0.04
#> TCGA.EE.A3AD.06 5 0.3163 0.637 0.00 0.14 0.00 0.00 0.82 0.04
#> TCGA.EE.A3AH.06 1 0.1556 0.866 0.92 0.00 0.00 0.00 0.00 0.08
#> TCGA.EB.A5FP.01 2 0.3409 0.813 0.00 0.70 0.00 0.00 0.30 0.00
#> TCGA.FS.A1ZN.01 5 0.0547 0.719 0.00 0.02 0.00 0.00 0.98 0.00
#> TCGA.GN.A262.06 3 0.2794 0.613 0.08 0.00 0.86 0.00 0.00 0.06
#> TCGA.FS.A1ZC.06 4 0.0000 1.000 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.ER.A2NE.06 5 0.1807 0.702 0.00 0.06 0.00 0.00 0.92 0.02
#> TCGA.EE.A185.06 2 0.3409 0.813 0.00 0.70 0.00 0.00 0.30 0.00
#> TCGA.EE.A2M6.06 1 0.0937 0.925 0.96 0.00 0.00 0.04 0.00 0.00
#> TCGA.BF.AAP2.01 2 0.3460 0.773 0.00 0.76 0.02 0.00 0.22 0.00
#> TCGA.EE.A2GM.06 3 0.3318 0.595 0.14 0.02 0.82 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.WE.A8JZ.06 4 0.0000 0.9573 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.D3.A8GV.06 6 0.2572 0.0000 0.08 0.00 0.00 0.06 0.00 0.86 0.00
#> TCGA.EB.A6QZ.01 5 0.4657 0.3526 0.00 0.40 0.02 0.00 0.54 0.00 0.04
#> TCGA.GN.A4U4.06 3 0.2509 0.7102 0.00 0.00 0.88 0.00 0.06 0.02 0.04
#> TCGA.FW.A5DX.01 1 0.1860 0.8757 0.92 0.00 0.00 0.04 0.02 0.02 0.00
#> TCGA.WE.A8ZY.06 7 0.6794 -0.0531 0.00 0.24 0.06 0.00 0.32 0.02 0.36
#> TCGA.GF.A769.01 5 0.5083 -0.2127 0.00 0.00 0.34 0.00 0.56 0.06 0.04
#> TCGA.GN.A8LN.01 5 0.6218 0.3497 0.00 0.24 0.02 0.00 0.54 0.08 0.12
#> TCGA.EB.A42Y.01 7 0.3459 0.0114 0.00 0.40 0.00 0.00 0.00 0.00 0.60
#> TCGA.EB.A5KH.06 2 0.0504 0.6207 0.00 0.98 0.00 0.00 0.02 0.00 0.00
#> TCGA.FS.A1ZY.06 5 0.4617 0.3834 0.00 0.10 0.14 0.00 0.72 0.02 0.02
#> TCGA.EE.A3AD.06 2 0.4869 -0.2178 0.00 0.54 0.02 0.00 0.38 0.00 0.06
#> TCGA.EE.A3AH.06 1 0.1718 0.8743 0.92 0.00 0.00 0.00 0.00 0.04 0.04
#> TCGA.EB.A5FP.01 2 0.0000 0.6281 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FS.A1ZN.01 5 0.3358 0.4348 0.00 0.36 0.00 0.00 0.64 0.00 0.00
#> TCGA.GN.A262.06 3 0.5484 0.6207 0.08 0.00 0.66 0.00 0.16 0.04 0.06
#> TCGA.FS.A1ZC.06 4 0.1006 0.9576 0.02 0.00 0.00 0.96 0.00 0.00 0.02
#> TCGA.ER.A2NE.06 5 0.3558 0.2941 0.00 0.48 0.00 0.00 0.52 0.00 0.00
#> TCGA.EE.A185.06 2 0.0000 0.6281 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EE.A2M6.06 1 0.0863 0.8940 0.96 0.00 0.00 0.00 0.00 0.00 0.04
#> TCGA.BF.AAP2.01 2 0.5240 0.0583 0.00 0.58 0.00 0.00 0.14 0.02 0.26
#> TCGA.EE.A2GM.06 3 0.1928 0.7296 0.08 0.00 0.90 0.00 0.00 0.02 0.00
cbind(get_classes(res, k = 8), get_membership(res, k = 8))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7 p8
#> TCGA.WE.A8JZ.06 4 0.0471 0.824 0.00 0.00 0.00 0.98 0.00 0.02 0.00 0.00
#> TCGA.D3.A8GV.06 6 0.1557 0.000 0.00 0.00 0.02 0.06 0.00 0.92 0.00 0.00
#> TCGA.EB.A6QZ.01 5 0.2725 0.530 0.00 0.14 0.00 0.00 0.82 0.00 0.00 0.04
#> TCGA.GN.A4U4.06 3 0.2623 0.576 0.00 0.00 0.84 0.00 0.00 0.00 0.06 0.10
#> TCGA.FW.A5DX.01 1 0.0941 0.896 0.96 0.00 0.00 0.02 0.00 0.00 0.02 0.00
#> TCGA.WE.A8ZY.06 5 0.6459 0.120 0.00 0.04 0.02 0.00 0.48 0.04 0.22 0.20
#> TCGA.GF.A769.01 8 0.5624 0.000 0.00 0.00 0.18 0.00 0.36 0.04 0.00 0.42
#> TCGA.GN.A8LN.01 5 0.4211 0.423 0.00 0.08 0.02 0.00 0.68 0.00 0.00 0.22
#> TCGA.EB.A42Y.01 7 0.3374 0.000 0.00 0.30 0.00 0.00 0.02 0.00 0.68 0.00
#> TCGA.EB.A5KH.06 2 0.1765 0.821 0.00 0.88 0.00 0.00 0.12 0.00 0.00 0.00
#> TCGA.FS.A1ZY.06 5 0.4050 -0.453 0.00 0.00 0.06 0.00 0.60 0.00 0.00 0.34
#> TCGA.EE.A3AD.06 5 0.5491 0.441 0.00 0.20 0.00 0.00 0.56 0.00 0.08 0.16
#> TCGA.EE.A3AH.06 1 0.2940 0.829 0.84 0.02 0.00 0.00 0.00 0.10 0.02 0.02
#> TCGA.EB.A5FP.01 2 0.1341 0.836 0.00 0.92 0.00 0.00 0.08 0.00 0.00 0.00
#> TCGA.FS.A1ZN.01 5 0.3170 0.511 0.00 0.20 0.00 0.00 0.76 0.00 0.00 0.04
#> TCGA.GN.A262.06 3 0.5259 0.148 0.00 0.00 0.52 0.00 0.02 0.10 0.02 0.34
#> TCGA.FS.A1ZC.06 4 0.3131 0.827 0.04 0.02 0.00 0.84 0.00 0.00 0.04 0.06
#> TCGA.ER.A2NE.06 5 0.2938 0.507 0.00 0.30 0.00 0.00 0.70 0.00 0.00 0.00
#> TCGA.EE.A185.06 2 0.1341 0.836 0.00 0.92 0.00 0.00 0.08 0.00 0.00 0.00
#> TCGA.EE.A2M6.06 1 0.0000 0.905 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BF.AAP2.01 2 0.5114 0.503 0.00 0.66 0.00 0.00 0.12 0.02 0.08 0.12
#> TCGA.EE.A2GM.06 3 0.1341 0.571 0.08 0.00 0.92 0.00 0.00 0.00 0.00 0.00
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
consensus_heatmap(res, k = 7)
consensus_heatmap(res, k = 8)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
membership_heatmap(res, k = 7)
membership_heatmap(res, k = 8)
As soon as the classes for columns are determined, the signatures that are significantly different between subgroups can be looked for. Following are the heatmaps for signatures.
get_signatures(res, k = 2)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
get_signatures(res, k = 7)
get_signatures(res, k = 8)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. To get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows (which is done by automatically selecting number of clusters).If there are too many signatures, top_signatures = ... can be set to only show the
signatures with the highest FDRs:
# code only for demonstration
# e.g. to show the top 500 most significant rows
tb = get_signature(res, k = ..., top_signatures = 500)
If the signatures are defined as these which are uniquely high in current group, diff_method argument
can be set to "uniquely_high_in_one_group":
# code only for demonstration
tb = get_signature(res, k = ..., diff_method = "uniquely_high_in_one_group")
UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
dimension_reduction(res, k = 7, method = "UMAP")
dimension_reduction(res, k = 8, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
If matrix rows can be associated to genes, consider to use functional_enrichment(res,
...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.
Parent node: Node02. Child nodes: Node0111 , Node0112-leaf , Node0113 , Node0121-leaf , Node0122-leaf , Node0123-leaf , Node0124-leaf , Node0125-leaf , Node0131 , Node0132-leaf , Node0133-leaf , Node0211-leaf , Node0212 , Node0221-leaf , Node0222-leaf , Node0311 , Node0312-leaf , Node0321-leaf , Node0322 , Node0323 , Node0411 , Node0412 , Node0413-leaf , Node0421-leaf , Node0422-leaf , Node0423-leaf , Node0431-leaf , Node0432-leaf , Node0433-leaf , Node0441-leaf , Node0442 , Node0443-leaf , Node0511 , Node0512-leaf , Node0513-leaf , Node0521-leaf , Node0522-leaf , Node0523-leaf , Node0524-leaf .
The object with results only for a single top-value method and a single partitioning method can be extracted as:
res = res_rh["022"]
A summary of res and all the functions that can be applied to it:
res
#> A 'ConsensusPartition' object with k = 2, 3, 4, 5, 6, 7, 8.
#> On a matrix with 30000 rows and 23 columns.
#> Top rows (1000) are extracted by 'SD' method.
#> Subgroups are detected by 'kmeans' method.
#> Performed in total 350 partitions by row resampling.
#> Best k for subgroups seems to be 2.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_partitions"
#> [7] "compare_signatures" "consensus_heatmap" "dimension_reduction"
#> [10] "functional_enrichment" "get_anno_col" "get_anno"
#> [13] "get_classes" "get_consensus" "get_matrix"
#> [16] "get_membership" "get_param" "get_signatures"
#> [19] "get_stats" "is_best_k" "is_stable_k"
#> [22] "membership_heatmap" "ncol" "nrow"
#> [25] "plot_ecdf" "predict_classes" "rownames"
#> [28] "select_partition_number" "show" "suggest_best_k"
#> [31] "test_to_known_factors" "top_rows_heatmap"
collect_plots() function collects all the plots made from res for all k (number of subgroups)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
The plots are:
k and the heatmap of
predicted classes for each k.k.k.k.All the plots in panels can be made by individual functions and they are plotted later in this section.
select_partition_number() produces several plots showing different
statistics for choosing “optimized” k. There are following statistics:
k;k, the area increased is defined as \(A_k - A_{k-1}\).The detailed explanations of these statistics can be found in the cola vignette.
Generally speaking, higher 1-PAC score, higher mean silhouette score or higher
concordance corresponds to better partition. Rand index and Jaccard index
measure how similar the current partition is compared to partition with k-1.
If they are too similar, we won't accept k is better than k-1.
select_partition_number(res)
The numeric values for all these statistics can be obtained by get_stats().
get_stats(res)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> 2 2 1.000 0.972 0.987 0.5113 0.486 0.486
#> 3 3 0.557 0.634 0.834 0.3277 0.700 0.449
#> 4 4 0.567 0.472 0.667 0.1319 0.858 0.576
#> 5 5 0.676 0.594 0.797 0.0637 0.881 0.545
#> 6 6 0.738 0.351 0.670 0.0424 0.850 0.356
#> 7 7 0.767 0.575 0.644 0.0271 0.945 0.641
#> 8 8 0.838 0.638 0.817 0.0262 0.976 0.806
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.FR.A8YC.06 1 0.000 0.977 1.00 0.00
#> TCGA.EE.A3JI.06 1 0.000 0.977 1.00 0.00
#> TCGA.DA.A95Z.06 1 0.000 0.977 1.00 0.00
#> TCGA.D3.A8GP.06 2 0.242 0.963 0.04 0.96
#> TCGA.DA.A95W.06 1 0.000 0.977 1.00 0.00
#> TCGA.D9.A6EG.06 2 0.000 0.991 0.00 1.00
#> TCGA.EE.A180.06 2 0.000 0.991 0.00 1.00
#> TCGA.EE.A2MF.06 2 0.141 0.979 0.02 0.98
#> TCGA.D3.A8GL.06 1 0.000 0.977 1.00 0.00
#> TCGA.D3.A3MU.06 1 0.000 0.977 1.00 0.00
#> TCGA.FS.A4F0.06 1 0.000 0.977 1.00 0.00
#> TCGA.EB.A41A.01 2 0.000 0.991 0.00 1.00
#> TCGA.GN.A268.06 1 0.000 0.977 1.00 0.00
#> TCGA.FS.A1ZG.06 2 0.000 0.991 0.00 1.00
#> TCGA.FS.A1ZE.06 2 0.000 0.991 0.00 1.00
#> TCGA.EE.A29A.06 1 0.722 0.745 0.80 0.20
#> TCGA.D9.A1X3.06 1 0.000 0.977 1.00 0.00
#> TCGA.EB.A5SE.01 2 0.000 0.991 0.00 1.00
#> TCGA.D9.A6EA.06 2 0.000 0.991 0.00 1.00
#> TCGA.EE.A29D.06 2 0.000 0.991 0.00 1.00
#> TCGA.EB.A97M.01 2 0.000 0.991 0.00 1.00
#> TCGA.Z2.AA3S.06 2 0.242 0.963 0.04 0.96
#> TCGA.3N.A9WB.06 2 0.000 0.991 0.00 1.00
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.FR.A8YC.06 1 0.3340 0.87074 0.88 0.00 0.12
#> TCGA.EE.A3JI.06 1 0.0000 0.96351 1.00 0.00 0.00
#> TCGA.DA.A95Z.06 1 0.0892 0.95720 0.98 0.00 0.02
#> TCGA.D3.A8GP.06 3 0.3686 0.53073 0.00 0.14 0.86
#> TCGA.DA.A95W.06 1 0.2066 0.93375 0.94 0.00 0.06
#> TCGA.D9.A6EG.06 2 0.0892 0.80762 0.00 0.98 0.02
#> TCGA.EE.A180.06 2 0.2066 0.78839 0.00 0.94 0.06
#> TCGA.EE.A2MF.06 3 0.4291 0.55055 0.00 0.18 0.82
#> TCGA.D3.A8GL.06 1 0.0000 0.96351 1.00 0.00 0.00
#> TCGA.D3.A3MU.06 3 0.5948 0.32173 0.36 0.00 0.64
#> TCGA.FS.A4F0.06 1 0.0000 0.96351 1.00 0.00 0.00
#> TCGA.EB.A41A.01 2 0.4796 0.71175 0.00 0.78 0.22
#> TCGA.GN.A268.06 1 0.0000 0.96351 1.00 0.00 0.00
#> TCGA.FS.A1ZG.06 2 0.0892 0.80762 0.00 0.98 0.02
#> TCGA.FS.A1ZE.06 3 0.6309 -0.05435 0.00 0.50 0.50
#> TCGA.EE.A29A.06 3 0.7144 0.51277 0.22 0.08 0.70
#> TCGA.D9.A1X3.06 3 0.6758 0.33162 0.36 0.02 0.62
#> TCGA.EB.A5SE.01 2 0.4002 0.73395 0.00 0.84 0.16
#> TCGA.D9.A6EA.06 3 0.6309 -0.20412 0.00 0.50 0.50
#> TCGA.EE.A29D.06 2 0.6302 -0.00489 0.00 0.52 0.48
#> TCGA.EB.A97M.01 2 0.2066 0.78839 0.00 0.94 0.06
#> TCGA.Z2.AA3S.06 3 0.4291 0.55055 0.00 0.18 0.82
#> TCGA.3N.A9WB.06 2 0.2066 0.79956 0.00 0.94 0.06
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> TCGA.FR.A8YC.06 1 0.4522 0.57616 0.68 0.00 0.32 0.00
#> TCGA.EE.A3JI.06 1 0.0000 0.86123 1.00 0.00 0.00 0.00
#> TCGA.DA.A95Z.06 1 0.2345 0.82722 0.90 0.00 0.10 0.00
#> TCGA.D3.A8GP.06 3 0.0707 0.54952 0.00 0.02 0.98 0.00
#> TCGA.DA.A95W.06 1 0.3801 0.72151 0.78 0.00 0.22 0.00
#> TCGA.D9.A6EG.06 2 0.2345 0.66151 0.00 0.90 0.10 0.00
#> TCGA.EE.A180.06 2 0.2011 0.63763 0.00 0.92 0.00 0.08
#> TCGA.EE.A2MF.06 4 0.5570 -0.05924 0.00 0.02 0.44 0.54
#> TCGA.D3.A8GL.06 1 0.0000 0.86123 1.00 0.00 0.00 0.00
#> TCGA.D3.A3MU.06 3 0.3172 0.57285 0.16 0.00 0.84 0.00
#> TCGA.FS.A4F0.06 1 0.0707 0.85643 0.98 0.00 0.00 0.02
#> TCGA.EB.A41A.01 4 0.7748 -0.07770 0.00 0.28 0.28 0.44
#> TCGA.GN.A268.06 1 0.0707 0.85643 0.98 0.00 0.00 0.02
#> TCGA.FS.A1ZG.06 2 0.2345 0.66151 0.00 0.90 0.10 0.00
#> TCGA.FS.A1ZE.06 4 0.3611 0.33843 0.00 0.08 0.06 0.86
#> TCGA.EE.A29A.06 3 0.4296 0.56764 0.08 0.02 0.84 0.06
#> TCGA.D9.A1X3.06 3 0.8434 0.08366 0.28 0.02 0.36 0.34
#> TCGA.EB.A5SE.01 2 0.7544 0.29105 0.00 0.46 0.34 0.20
#> TCGA.D9.A6EA.06 4 0.6449 0.22161 0.00 0.14 0.22 0.64
#> TCGA.EE.A29D.06 4 0.6453 -0.00651 0.00 0.36 0.08 0.56
#> TCGA.EB.A97M.01 2 0.4939 0.56920 0.00 0.74 0.04 0.22
#> TCGA.Z2.AA3S.06 4 0.5570 -0.05924 0.00 0.02 0.44 0.54
#> TCGA.3N.A9WB.06 2 0.5793 0.33320 0.00 0.60 0.04 0.36
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> TCGA.FR.A8YC.06 1 0.5599 0.604 0.62 0.00 0.26 0.12 0.00
#> TCGA.EE.A3JI.06 1 0.0000 0.796 1.00 0.00 0.00 0.00 0.00
#> TCGA.DA.A95Z.06 1 0.4075 0.743 0.78 0.00 0.16 0.06 0.00
#> TCGA.D3.A8GP.06 3 0.1732 0.674 0.00 0.00 0.92 0.08 0.00
#> TCGA.DA.A95W.06 1 0.4728 0.688 0.70 0.00 0.24 0.06 0.00
#> TCGA.D9.A6EG.06 2 0.0609 0.766 0.00 0.98 0.00 0.00 0.02
#> TCGA.EE.A180.06 2 0.1410 0.751 0.00 0.94 0.00 0.00 0.06
#> TCGA.EE.A2MF.06 4 0.4389 0.705 0.00 0.04 0.06 0.80 0.10
#> TCGA.D3.A8GL.06 1 0.0000 0.796 1.00 0.00 0.00 0.00 0.00
#> TCGA.D3.A3MU.06 3 0.1410 0.680 0.00 0.00 0.94 0.06 0.00
#> TCGA.FS.A4F0.06 1 0.2331 0.762 0.90 0.00 0.02 0.08 0.00
#> TCGA.EB.A41A.01 5 0.6156 0.384 0.00 0.12 0.20 0.04 0.64
#> TCGA.GN.A268.06 1 0.2331 0.762 0.90 0.00 0.02 0.08 0.00
#> TCGA.FS.A1ZG.06 2 0.0609 0.766 0.00 0.98 0.00 0.00 0.02
#> TCGA.FS.A1ZE.06 4 0.5048 0.423 0.00 0.04 0.00 0.58 0.38
#> TCGA.EE.A29A.06 3 0.0000 0.678 0.00 0.00 1.00 0.00 0.00
#> TCGA.D9.A1X3.06 4 0.5681 0.478 0.24 0.00 0.06 0.66 0.04
#> TCGA.EB.A5SE.01 3 0.7288 -0.292 0.00 0.34 0.34 0.02 0.30
#> TCGA.D9.A6EA.06 5 0.2610 0.587 0.00 0.02 0.02 0.06 0.90
#> TCGA.EE.A29D.06 5 0.4653 0.588 0.00 0.16 0.02 0.06 0.76
#> TCGA.EB.A97M.01 2 0.6038 0.271 0.00 0.56 0.08 0.02 0.34
#> TCGA.Z2.AA3S.06 4 0.3700 0.703 0.00 0.02 0.06 0.84 0.08
#> TCGA.3N.A9WB.06 5 0.4262 0.344 0.00 0.44 0.00 0.00 0.56
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> TCGA.FR.A8YC.06 6 0.0000 0.8807 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.EE.A3JI.06 1 0.3828 0.6126 0.56 0.00 0.00 0.00 0.00 0.44
#> TCGA.DA.A95Z.06 6 0.2260 0.7194 0.14 0.00 0.00 0.00 0.00 0.86
#> TCGA.D3.A8GP.06 3 0.6991 -0.4288 0.00 0.00 0.34 0.34 0.06 0.26
#> TCGA.DA.A95W.06 6 0.0000 0.8807 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.D9.A6EG.06 2 0.0000 0.7609 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.EE.A180.06 2 0.4144 0.3659 0.00 0.62 0.36 0.00 0.02 0.00
#> TCGA.EE.A2MF.06 4 0.4711 0.1158 0.28 0.00 0.00 0.64 0.08 0.00
#> TCGA.D3.A8GL.06 1 0.3851 0.5822 0.54 0.00 0.00 0.00 0.00 0.46
#> TCGA.D3.A3MU.06 4 0.7013 -0.1031 0.00 0.00 0.32 0.34 0.06 0.28
#> TCGA.FS.A4F0.06 1 0.3578 0.6733 0.66 0.00 0.00 0.00 0.00 0.34
#> TCGA.EB.A41A.01 5 0.4337 0.0943 0.00 0.02 0.48 0.00 0.50 0.00
#> TCGA.GN.A268.06 1 0.3578 0.6733 0.66 0.00 0.00 0.00 0.00 0.34
#> TCGA.FS.A1ZG.06 2 0.0000 0.7609 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.FS.A1ZE.06 5 0.5285 0.0503 0.10 0.00 0.00 0.42 0.48 0.00
#> TCGA.EE.A29A.06 4 0.6991 -0.1058 0.00 0.00 0.34 0.34 0.06 0.26
#> TCGA.D9.A1X3.06 1 0.2454 0.1859 0.84 0.00 0.00 0.16 0.00 0.00
#> TCGA.EB.A5SE.01 3 0.3688 0.1937 0.00 0.14 0.80 0.02 0.04 0.00
#> TCGA.D9.A6EA.06 5 0.0000 0.5580 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.EE.A29D.06 5 0.0937 0.5628 0.00 0.04 0.00 0.00 0.96 0.00
#> TCGA.EB.A97M.01 3 0.4078 -0.2187 0.00 0.34 0.64 0.00 0.02 0.00
#> TCGA.Z2.AA3S.06 4 0.6308 0.1415 0.28 0.00 0.02 0.56 0.06 0.08
#> TCGA.3N.A9WB.06 5 0.4328 0.1240 0.00 0.46 0.02 0.00 0.52 0.00
cbind(get_classes(res, k = 7), get_membership(res, k = 7))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7
#> TCGA.FR.A8YC.06 6 0.5511 0.7271 0.14 0.00 0.00 0.20 0.00 0.60 0.06
#> TCGA.EE.A3JI.06 1 0.2421 0.6527 0.88 0.00 0.02 0.00 0.02 0.08 0.00
#> TCGA.DA.A95Z.06 6 0.4461 0.5547 0.40 0.00 0.00 0.06 0.00 0.54 0.00
#> TCGA.D3.A8GP.06 4 0.1718 0.9365 0.00 0.00 0.00 0.92 0.00 0.04 0.04
#> TCGA.DA.A95W.06 6 0.4763 0.7823 0.20 0.00 0.00 0.18 0.00 0.62 0.00
#> TCGA.D9.A6EG.06 2 0.0000 0.6908 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EE.A180.06 2 0.3994 -0.0975 0.00 0.50 0.48 0.00 0.00 0.02 0.00
#> TCGA.EE.A2MF.06 7 0.0000 0.6635 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.D3.A8GL.06 1 0.2654 0.6306 0.86 0.00 0.02 0.00 0.02 0.10 0.00
#> TCGA.D3.A3MU.06 4 0.1718 0.9365 0.00 0.00 0.00 0.92 0.00 0.04 0.04
#> TCGA.FS.A4F0.06 1 0.0000 0.6929 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EB.A41A.01 5 0.4692 0.1393 0.00 0.00 0.42 0.00 0.50 0.08 0.00
#> TCGA.GN.A268.06 1 0.0000 0.6929 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FS.A1ZG.06 2 0.0000 0.6908 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FS.A1ZE.06 7 0.6137 0.2445 0.00 0.00 0.06 0.00 0.36 0.16 0.42
#> TCGA.EE.A29A.06 4 0.0504 0.8747 0.00 0.00 0.02 0.98 0.00 0.00 0.00
#> TCGA.D9.A1X3.06 1 0.7255 -0.1163 0.36 0.00 0.14 0.00 0.04 0.14 0.32
#> TCGA.EB.A5SE.01 3 0.5070 0.6096 0.00 0.08 0.64 0.24 0.02 0.02 0.00
#> TCGA.D9.A6EA.06 5 0.1166 0.6271 0.00 0.00 0.06 0.00 0.94 0.00 0.00
#> TCGA.EE.A29D.06 5 0.1928 0.6207 0.00 0.08 0.00 0.00 0.90 0.02 0.00
#> TCGA.EB.A97M.01 3 0.3617 0.5617 0.00 0.16 0.76 0.00 0.08 0.00 0.00
#> TCGA.Z2.AA3S.06 7 0.1928 0.6476 0.00 0.00 0.00 0.02 0.00 0.08 0.90
#> TCGA.3N.A9WB.06 5 0.4328 0.4530 0.00 0.34 0.00 0.00 0.60 0.06 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.FR.A8YC.06 6 0.0471 0.935 0.00 0.00 0.00 0.02 0.00 0.98 0.00 0.00
#> TCGA.EE.A3JI.06 1 0.5331 0.557 0.60 0.00 0.04 0.00 0.08 0.24 0.00 0.04
#> TCGA.DA.A95Z.06 6 0.1091 0.902 0.06 0.00 0.00 0.00 0.00 0.94 0.00 0.00
#> TCGA.D3.A8GP.06 4 0.0808 0.944 0.00 0.00 0.00 0.96 0.00 0.04 0.00 0.00
#> TCGA.DA.A95W.06 6 0.0000 0.944 0.00 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.D9.A6EG.06 2 0.0000 1.000 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EE.A180.06 3 0.3971 0.210 0.00 0.42 0.54 0.00 0.04 0.00 0.00 0.00
#> TCGA.EE.A2MF.06 7 0.0000 0.879 0.00 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.D3.A8GL.06 1 0.5414 0.534 0.58 0.00 0.04 0.00 0.08 0.26 0.00 0.04
#> TCGA.D3.A3MU.06 4 0.0808 0.944 0.00 0.00 0.00 0.96 0.00 0.04 0.00 0.00
#> TCGA.FS.A4F0.06 1 0.0808 0.681 0.96 0.00 0.00 0.00 0.00 0.04 0.00 0.00
#> TCGA.EB.A41A.01 5 0.3514 0.199 0.02 0.00 0.34 0.00 0.64 0.00 0.00 0.00
#> TCGA.GN.A268.06 1 0.0808 0.681 0.96 0.00 0.00 0.00 0.00 0.04 0.00 0.00
#> TCGA.FS.A1ZG.06 2 0.0000 1.000 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FS.A1ZE.06 8 0.4314 0.000 0.00 0.00 0.02 0.00 0.08 0.00 0.24 0.66
#> TCGA.EE.A29A.06 4 0.1741 0.884 0.00 0.00 0.04 0.92 0.02 0.00 0.00 0.02
#> TCGA.D9.A1X3.06 1 0.5385 0.292 0.58 0.00 0.02 0.00 0.04 0.00 0.12 0.24
#> TCGA.EB.A5SE.01 3 0.4562 0.515 0.02 0.02 0.72 0.14 0.08 0.00 0.00 0.02
#> TCGA.D9.A6EA.06 5 0.3237 0.361 0.00 0.00 0.00 0.00 0.60 0.00 0.00 0.40
#> TCGA.EE.A29D.06 5 0.3690 0.337 0.00 0.02 0.00 0.00 0.56 0.00 0.00 0.42
#> TCGA.EB.A97M.01 3 0.1765 0.607 0.00 0.12 0.88 0.00 0.00 0.00 0.00 0.00
#> TCGA.Z2.AA3S.06 7 0.1557 0.883 0.00 0.00 0.00 0.02 0.00 0.06 0.92 0.00
#> TCGA.3N.A9WB.06 5 0.2852 0.384 0.00 0.28 0.00 0.00 0.72 0.00 0.00 0.00
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
consensus_heatmap(res, k = 7)
consensus_heatmap(res, k = 8)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
membership_heatmap(res, k = 7)
membership_heatmap(res, k = 8)
As soon as the classes for columns are determined, the signatures that are significantly different between subgroups can be looked for. Following are the heatmaps for signatures.
get_signatures(res, k = 2)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
get_signatures(res, k = 7)
get_signatures(res, k = 8)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. To get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows (which is done by automatically selecting number of clusters).If there are too many signatures, top_signatures = ... can be set to only show the
signatures with the highest FDRs:
# code only for demonstration
# e.g. to show the top 500 most significant rows
tb = get_signature(res, k = ..., top_signatures = 500)
If the signatures are defined as these which are uniquely high in current group, diff_method argument
can be set to "uniquely_high_in_one_group":
# code only for demonstration
tb = get_signature(res, k = ..., diff_method = "uniquely_high_in_one_group")
UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
dimension_reduction(res, k = 7, method = "UMAP")
dimension_reduction(res, k = 8, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
If matrix rows can be associated to genes, consider to use functional_enrichment(res,
...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.
Parent node: Node0. Child nodes: Node011 , Node012 , Node013 , Node014-leaf , Node021 , Node022 , Node023-leaf , Node031 , Node032 , Node041 , Node042 , Node043 , Node044 , Node051 , Node052 .
The object with results only for a single top-value method and a single partitioning method can be extracted as:
res = res_rh["03"]
A summary of res and all the functions that can be applied to it:
res
#> A 'ConsensusPartition' object with k = 2, 3, 4, 5, 6, 7, 8.
#> On a matrix with 30000 rows and 73 columns.
#> Top rows (1000) are extracted by 'ATC' method.
#> Subgroups are detected by 'skmeans' method.
#> Performed in total 350 partitions by row resampling.
#> Best k for subgroups seems to be 2.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_partitions"
#> [7] "compare_signatures" "consensus_heatmap" "dimension_reduction"
#> [10] "functional_enrichment" "get_anno_col" "get_anno"
#> [13] "get_classes" "get_consensus" "get_matrix"
#> [16] "get_membership" "get_param" "get_signatures"
#> [19] "get_stats" "is_best_k" "is_stable_k"
#> [22] "membership_heatmap" "ncol" "nrow"
#> [25] "plot_ecdf" "predict_classes" "rownames"
#> [28] "select_partition_number" "show" "suggest_best_k"
#> [31] "test_to_known_factors" "top_rows_heatmap"
collect_plots() function collects all the plots made from res for all k (number of subgroups)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
The plots are:
k and the heatmap of
predicted classes for each k.k.k.k.All the plots in panels can be made by individual functions and they are plotted later in this section.
select_partition_number() produces several plots showing different
statistics for choosing “optimized” k. There are following statistics:
k;k, the area increased is defined as \(A_k - A_{k-1}\).The detailed explanations of these statistics can be found in the cola vignette.
Generally speaking, higher 1-PAC score, higher mean silhouette score or higher
concordance corresponds to better partition. Rand index and Jaccard index
measure how similar the current partition is compared to partition with k-1.
If they are too similar, we won't accept k is better than k-1.
select_partition_number(res)
The numeric values for all these statistics can be obtained by get_stats().
get_stats(res)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> 2 2 1.000 0.990 0.995 0.4665 0.535 0.535
#> 3 3 0.363 0.494 0.737 0.3902 0.777 0.592
#> 4 4 0.408 0.466 0.730 0.1039 0.731 0.384
#> 5 5 0.463 0.504 0.566 0.0710 0.819 0.442
#> 6 6 0.492 0.360 0.683 0.0337 0.818 0.375
#> 7 7 0.521 0.379 0.608 0.0275 0.897 0.576
#> 8 8 0.542 0.355 0.655 0.0150 0.951 0.748
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.GN.A8LL.06 1 0.000 0.996 1.00 0.00
#> TCGA.ER.A42K.06 2 0.000 0.994 0.00 1.00
#> TCGA.FS.A4F2.06 2 0.242 0.959 0.04 0.96
#> TCGA.WE.A8ZT.06 1 0.000 0.996 1.00 0.00
#> TCGA.DA.A95Y.06 1 0.000 0.996 1.00 0.00
#> TCGA.WE.A8K6.06 2 0.000 0.994 0.00 1.00
#> TCGA.GN.A4U3.06 1 0.000 0.996 1.00 0.00
#> TCGA.Z2.A8RT.06 2 0.000 0.994 0.00 1.00
#> TCGA.EB.A41B.01 2 0.000 0.994 0.00 1.00
#> TCGA.EB.A6R0.01 2 0.000 0.994 0.00 1.00
#> TCGA.D9.A4Z2.01 2 0.000 0.994 0.00 1.00
#> TCGA.D3.A3MV.06 2 0.000 0.994 0.00 1.00
#> TCGA.GN.A4U7.06 1 0.000 0.996 1.00 0.00
#> TCGA.BF.A5EP.01 1 0.000 0.996 1.00 0.00
#> TCGA.D3.A5GL.06 1 0.000 0.996 1.00 0.00
#> TCGA.FS.A1YY.06 1 0.000 0.996 1.00 0.00
#> TCGA.EE.A2MK.06 1 0.000 0.996 1.00 0.00
#> TCGA.EE.A3AE.06 1 0.402 0.913 0.92 0.08
#> TCGA.EB.A51B.01 1 0.000 0.996 1.00 0.00
#> TCGA.FS.A1ZQ.06 2 0.000 0.994 0.00 1.00
#> TCGA.D3.A2JG.06 1 0.000 0.996 1.00 0.00
#> TCGA.ER.A19F.06 2 0.000 0.994 0.00 1.00
#> TCGA.EE.A3AG.06 2 0.000 0.994 0.00 1.00
#> TCGA.ER.A19B.06 2 0.000 0.994 0.00 1.00
#> TCGA.D3.A5GN.06 2 0.000 0.994 0.00 1.00
#> TCGA.EB.A4XL.01 1 0.000 0.996 1.00 0.00
#> TCGA.EE.A2GB.06 2 0.000 0.994 0.00 1.00
#> TCGA.FS.A1Z3.06 2 0.000 0.994 0.00 1.00
#> TCGA.DA.A1I8.06 2 0.000 0.994 0.00 1.00
#> TCGA.D3.A5GS.06 2 0.000 0.994 0.00 1.00
#> TCGA.EE.A2GS.06 2 0.000 0.994 0.00 1.00
#> TCGA.D3.A5GO.06 2 0.000 0.994 0.00 1.00
#> TCGA.EE.A29Q.06 2 0.000 0.994 0.00 1.00
#> TCGA.BF.A1PZ.01 2 0.000 0.994 0.00 1.00
#> TCGA.D9.A1JX.06 2 0.000 0.994 0.00 1.00
#> TCGA.FS.A1ZF.06 2 0.000 0.994 0.00 1.00
#> TCGA.EE.A29W.06 2 0.000 0.994 0.00 1.00
#> TCGA.DA.A1HV.06 2 0.000 0.994 0.00 1.00
#> TCGA.EE.A17X.06 1 0.000 0.996 1.00 0.00
#> TCGA.EE.A3AF.06 1 0.000 0.996 1.00 0.00
#> TCGA.ER.A19H.06 2 0.000 0.994 0.00 1.00
#> TCGA.DA.A1HY.06 2 0.000 0.994 0.00 1.00
#> TCGA.D3.A3C7.06 2 0.000 0.994 0.00 1.00
#> TCGA.EE.A2MP.06 2 0.000 0.994 0.00 1.00
#> TCGA.EE.A29H.06 1 0.000 0.996 1.00 0.00
#> TCGA.XV.AB01.01 1 0.000 0.996 1.00 0.00
#> TCGA.ER.A19G.06 2 0.000 0.994 0.00 1.00
#> TCGA.EB.A3XC.01 1 0.000 0.996 1.00 0.00
#> TCGA.FR.A69P.06 2 0.000 0.994 0.00 1.00
#> TCGA.D3.A3C6.06 2 0.469 0.891 0.10 0.90
#> TCGA.EE.A2A2.06 2 0.242 0.959 0.04 0.96
#> TCGA.BF.AAP6.01 2 0.327 0.939 0.06 0.94
#> TCGA.FR.A3R1.01 1 0.000 0.996 1.00 0.00
#> TCGA.EB.A299.01 2 0.000 0.994 0.00 1.00
#> TCGA.EB.A3XF.01 1 0.000 0.996 1.00 0.00
#> TCGA.D3.A2JF.06 2 0.000 0.994 0.00 1.00
#> TCGA.XV.AAZW.01 1 0.141 0.978 0.98 0.02
#> TCGA.FR.A3YN.06 2 0.000 0.994 0.00 1.00
#> TCGA.QB.AA9O.06 1 0.000 0.996 1.00 0.00
#> TCGA.BF.A3DJ.01 1 0.000 0.996 1.00 0.00
#> TCGA.EE.A3J3.06 2 0.000 0.994 0.00 1.00
#> TCGA.D3.A51G.06 2 0.000 0.994 0.00 1.00
#> TCGA.EB.A4P0.01 1 0.000 0.996 1.00 0.00
#> TCGA.D3.A51R.06 2 0.000 0.994 0.00 1.00
#> TCGA.FS.A4FB.06 1 0.000 0.996 1.00 0.00
#> TCGA.BF.A3DM.01 2 0.000 0.994 0.00 1.00
#> TCGA.W3.AA1R.06 2 0.000 0.994 0.00 1.00
#> TCGA.EE.A3JA.06 2 0.000 0.994 0.00 1.00
#> TCGA.FS.A4F4.06 1 0.000 0.996 1.00 0.00
#> TCGA.BF.A3DN.01 2 0.000 0.994 0.00 1.00
#> TCGA.D3.A51E.06 2 0.000 0.994 0.00 1.00
#> TCGA.DA.A3F3.06 2 0.000 0.994 0.00 1.00
#> TCGA.D3.A51T.06 2 0.141 0.978 0.02 0.98
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.GN.A8LL.06 1 0.8859 0.3942 0.48 0.40 0.12
#> TCGA.ER.A42K.06 2 0.5948 0.6187 0.00 0.64 0.36
#> TCGA.FS.A4F2.06 3 0.8869 0.1019 0.28 0.16 0.56
#> TCGA.WE.A8ZT.06 1 0.5835 0.6028 0.66 0.34 0.00
#> TCGA.DA.A95Y.06 1 0.0892 0.7417 0.98 0.00 0.02
#> TCGA.WE.A8K6.06 2 0.5948 0.6187 0.00 0.64 0.36
#> TCGA.GN.A4U3.06 1 0.0892 0.7417 0.98 0.00 0.02
#> TCGA.Z2.A8RT.06 2 0.5948 0.6187 0.00 0.64 0.36
#> TCGA.EB.A41B.01 2 0.5948 0.6187 0.00 0.64 0.36
#> TCGA.EB.A6R0.01 3 0.3686 0.6127 0.00 0.14 0.86
#> TCGA.D9.A4Z2.01 2 0.5397 0.0393 0.00 0.72 0.28
#> TCGA.D3.A3MV.06 2 0.5948 -0.1269 0.00 0.64 0.36
#> TCGA.GN.A4U7.06 1 0.2959 0.7388 0.90 0.10 0.00
#> TCGA.BF.A5EP.01 1 0.0000 0.7429 1.00 0.00 0.00
#> TCGA.D3.A5GL.06 1 0.0000 0.7429 1.00 0.00 0.00
#> TCGA.FS.A1YY.06 1 0.0892 0.7417 0.98 0.00 0.02
#> TCGA.EE.A2MK.06 1 0.7310 0.5637 0.60 0.36 0.04
#> TCGA.EE.A3AE.06 1 0.8271 0.3138 0.52 0.08 0.40
#> TCGA.EB.A51B.01 1 0.8587 0.4250 0.50 0.40 0.10
#> TCGA.FS.A1ZQ.06 3 0.6309 0.2510 0.00 0.50 0.50
#> TCGA.D3.A2JG.06 1 0.0892 0.7417 0.98 0.00 0.02
#> TCGA.ER.A19F.06 2 0.6309 -0.3367 0.00 0.50 0.50
#> TCGA.EE.A3AG.06 3 0.5397 0.6086 0.00 0.28 0.72
#> TCGA.ER.A19B.06 2 0.4002 0.2796 0.00 0.84 0.16
#> TCGA.D3.A5GN.06 2 0.6309 -0.3149 0.00 0.50 0.50
#> TCGA.EB.A4XL.01 1 0.0000 0.7429 1.00 0.00 0.00
#> TCGA.EE.A2GB.06 3 0.5397 0.6086 0.00 0.28 0.72
#> TCGA.FS.A1Z3.06 2 0.5948 0.6187 0.00 0.64 0.36
#> TCGA.DA.A1I8.06 3 0.5948 0.5331 0.00 0.36 0.64
#> TCGA.D3.A5GS.06 2 0.3415 0.4816 0.02 0.90 0.08
#> TCGA.EE.A2GS.06 2 0.5948 0.6187 0.00 0.64 0.36
#> TCGA.D3.A5GO.06 3 0.3340 0.4739 0.00 0.12 0.88
#> TCGA.EE.A29Q.06 3 0.6192 0.2577 0.00 0.42 0.58
#> TCGA.BF.A1PZ.01 2 0.5948 0.6187 0.00 0.64 0.36
#> TCGA.D9.A1JX.06 2 0.5948 -0.1497 0.00 0.64 0.36
#> TCGA.FS.A1ZF.06 2 0.5835 -0.1028 0.00 0.66 0.34
#> TCGA.EE.A29W.06 2 0.5948 0.6187 0.00 0.64 0.36
#> TCGA.DA.A1HV.06 3 0.1529 0.5408 0.00 0.04 0.96
#> TCGA.EE.A17X.06 1 0.0000 0.7429 1.00 0.00 0.00
#> TCGA.EE.A3AF.06 1 0.8199 0.5801 0.64 0.16 0.20
#> TCGA.ER.A19H.06 2 0.4291 0.2483 0.00 0.82 0.18
#> TCGA.DA.A1HY.06 3 0.5397 0.6086 0.00 0.28 0.72
#> TCGA.D3.A3C7.06 2 0.5948 0.6187 0.00 0.64 0.36
#> TCGA.EE.A2MP.06 2 0.3340 0.3621 0.00 0.88 0.12
#> TCGA.EE.A29H.06 1 0.9270 0.4182 0.52 0.28 0.20
#> TCGA.XV.AB01.01 1 0.0892 0.7417 0.98 0.00 0.02
#> TCGA.ER.A19G.06 3 0.5560 0.5947 0.00 0.30 0.70
#> TCGA.EB.A3XC.01 1 0.6500 0.6647 0.76 0.10 0.14
#> TCGA.FR.A69P.06 2 0.5948 0.6187 0.00 0.64 0.36
#> TCGA.D3.A3C6.06 2 0.5817 0.4680 0.10 0.80 0.10
#> TCGA.EE.A2A2.06 3 0.6922 0.3377 0.20 0.08 0.72
#> TCGA.BF.AAP6.01 2 0.3832 0.3672 0.02 0.88 0.10
#> TCGA.FR.A3R1.01 1 0.7825 0.5062 0.62 0.08 0.30
#> TCGA.EB.A299.01 2 0.5835 0.6114 0.00 0.66 0.34
#> TCGA.EB.A3XF.01 1 0.5560 0.6353 0.70 0.30 0.00
#> TCGA.D3.A2JF.06 3 0.3340 0.4925 0.00 0.12 0.88
#> TCGA.XV.AAZW.01 2 0.8033 0.3039 0.24 0.64 0.12
#> TCGA.FR.A3YN.06 2 0.5948 0.6187 0.00 0.64 0.36
#> TCGA.QB.AA9O.06 1 0.7884 0.5604 0.64 0.10 0.26
#> TCGA.BF.A3DJ.01 1 0.5706 0.6173 0.68 0.32 0.00
#> TCGA.EE.A3J3.06 2 0.5948 0.6187 0.00 0.64 0.36
#> TCGA.D3.A51G.06 3 0.6053 0.1643 0.02 0.26 0.72
#> TCGA.EB.A4P0.01 1 0.4796 0.6843 0.78 0.22 0.00
#> TCGA.D3.A51R.06 3 0.5397 0.6086 0.00 0.28 0.72
#> TCGA.FS.A4FB.06 1 0.5835 0.6028 0.66 0.34 0.00
#> TCGA.BF.A3DM.01 2 0.5948 0.6187 0.00 0.64 0.36
#> TCGA.W3.AA1R.06 3 0.0000 0.5709 0.00 0.00 1.00
#> TCGA.EE.A3JA.06 3 0.4002 0.6179 0.00 0.16 0.84
#> TCGA.FS.A4F4.06 1 0.0892 0.7417 0.98 0.00 0.02
#> TCGA.BF.A3DN.01 2 0.5835 0.6114 0.00 0.66 0.34
#> TCGA.D3.A51E.06 2 0.5397 0.5427 0.00 0.72 0.28
#> TCGA.DA.A3F3.06 3 0.4796 0.6201 0.00 0.22 0.78
#> TCGA.D3.A51T.06 3 0.5780 0.4163 0.12 0.08 0.80
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> TCGA.GN.A8LL.06 2 0.3801 0.50561 0.22 0.78 0.00 0.00
#> TCGA.ER.A42K.06 2 0.4894 0.59271 0.00 0.78 0.12 0.10
#> TCGA.FS.A4F2.06 3 0.6797 0.35091 0.16 0.24 0.60 0.00
#> TCGA.WE.A8ZT.06 2 0.5713 0.34899 0.34 0.62 0.00 0.04
#> TCGA.DA.A95Y.06 1 0.0707 0.84695 0.98 0.00 0.02 0.00
#> TCGA.WE.A8K6.06 2 0.4894 0.59271 0.00 0.78 0.12 0.10
#> TCGA.GN.A4U3.06 1 0.0707 0.84695 0.98 0.00 0.02 0.00
#> TCGA.Z2.A8RT.06 2 0.4894 0.59271 0.00 0.78 0.12 0.10
#> TCGA.EB.A41B.01 2 0.4894 0.59271 0.00 0.78 0.12 0.10
#> TCGA.EB.A6R0.01 3 0.6286 0.50386 0.00 0.14 0.66 0.20
#> TCGA.D9.A4Z2.01 4 0.1211 0.62639 0.00 0.04 0.00 0.96
#> TCGA.D3.A3MV.06 4 0.1913 0.62558 0.00 0.04 0.02 0.94
#> TCGA.GN.A4U7.06 2 0.4977 0.13600 0.46 0.54 0.00 0.00
#> TCGA.BF.A5EP.01 1 0.1913 0.84491 0.94 0.04 0.02 0.00
#> TCGA.D3.A5GL.06 1 0.1913 0.84437 0.94 0.04 0.02 0.00
#> TCGA.FS.A1YY.06 1 0.2335 0.83694 0.92 0.02 0.06 0.00
#> TCGA.EE.A2MK.06 2 0.4406 0.43010 0.30 0.70 0.00 0.00
#> TCGA.EE.A3AE.06 1 0.7179 0.06848 0.48 0.14 0.38 0.00
#> TCGA.EB.A51B.01 2 0.3801 0.50561 0.22 0.78 0.00 0.00
#> TCGA.FS.A1ZQ.06 4 0.6723 0.34349 0.00 0.14 0.26 0.60
#> TCGA.D3.A2JG.06 1 0.4227 0.77544 0.82 0.06 0.12 0.00
#> TCGA.ER.A19F.06 4 0.5512 0.36104 0.00 0.04 0.30 0.66
#> TCGA.EE.A3AG.06 3 0.6201 0.32734 0.00 0.08 0.62 0.30
#> TCGA.ER.A19B.06 4 0.2706 0.63072 0.00 0.08 0.02 0.90
#> TCGA.D3.A5GN.06 4 0.7198 0.24031 0.00 0.18 0.28 0.54
#> TCGA.EB.A4XL.01 1 0.2335 0.82372 0.92 0.06 0.02 0.00
#> TCGA.EE.A2GB.06 4 0.6843 -0.02756 0.00 0.10 0.44 0.46
#> TCGA.FS.A1Z3.06 2 0.4894 0.59271 0.00 0.78 0.12 0.10
#> TCGA.DA.A1I8.06 4 0.4079 0.50595 0.00 0.02 0.18 0.80
#> TCGA.D3.A5GS.06 4 0.5000 0.00548 0.00 0.50 0.00 0.50
#> TCGA.EE.A2GS.06 2 0.4894 0.59271 0.00 0.78 0.12 0.10
#> TCGA.D3.A5GO.06 3 0.4491 0.57684 0.00 0.14 0.80 0.06
#> TCGA.EE.A29Q.06 4 0.7414 0.08615 0.00 0.18 0.34 0.48
#> TCGA.BF.A1PZ.01 2 0.4894 0.59271 0.00 0.78 0.12 0.10
#> TCGA.D9.A1JX.06 4 0.0707 0.60964 0.00 0.00 0.02 0.98
#> TCGA.FS.A1ZF.06 4 0.3198 0.59543 0.00 0.08 0.04 0.88
#> TCGA.EE.A29W.06 2 0.4894 0.59271 0.00 0.78 0.12 0.10
#> TCGA.DA.A1HV.06 3 0.2830 0.56523 0.00 0.06 0.90 0.04
#> TCGA.EE.A17X.06 1 0.1211 0.84218 0.96 0.04 0.00 0.00
#> TCGA.EE.A3AF.06 2 0.7775 -0.09371 0.38 0.38 0.24 0.00
#> TCGA.ER.A19H.06 4 0.2647 0.60844 0.00 0.12 0.00 0.88
#> TCGA.DA.A1HY.06 3 0.6714 0.22487 0.00 0.10 0.54 0.36
#> TCGA.D3.A3C7.06 2 0.5383 0.54653 0.00 0.74 0.16 0.10
#> TCGA.EE.A2MP.06 4 0.5106 0.53602 0.00 0.24 0.04 0.72
#> TCGA.EE.A29H.06 2 0.7497 0.19344 0.26 0.50 0.24 0.00
#> TCGA.XV.AB01.01 1 0.0707 0.84695 0.98 0.00 0.02 0.00
#> TCGA.ER.A19G.06 3 0.5915 0.24875 0.00 0.04 0.56 0.40
#> TCGA.EB.A3XC.01 1 0.7583 0.29814 0.48 0.28 0.24 0.00
#> TCGA.FR.A69P.06 2 0.4894 0.59271 0.00 0.78 0.12 0.10
#> TCGA.D3.A3C6.06 2 0.5956 0.40984 0.10 0.68 0.00 0.22
#> TCGA.EE.A2A2.06 3 0.4227 0.51896 0.12 0.06 0.82 0.00
#> TCGA.BF.AAP6.01 4 0.4624 0.41958 0.00 0.34 0.00 0.66
#> TCGA.FR.A3R1.01 3 0.7220 -0.23231 0.42 0.14 0.44 0.00
#> TCGA.EB.A299.01 2 0.0707 0.58825 0.00 0.98 0.02 0.00
#> TCGA.EB.A3XF.01 2 0.4790 0.31655 0.38 0.62 0.00 0.00
#> TCGA.D3.A2JF.06 3 0.4491 0.57684 0.00 0.14 0.80 0.06
#> TCGA.XV.AAZW.01 2 0.3610 0.52071 0.20 0.80 0.00 0.00
#> TCGA.FR.A3YN.06 2 0.6104 0.52781 0.00 0.68 0.18 0.14
#> TCGA.QB.AA9O.06 3 0.7344 -0.18390 0.38 0.16 0.46 0.00
#> TCGA.BF.A3DJ.01 2 0.4713 0.35323 0.36 0.64 0.00 0.00
#> TCGA.EE.A3J3.06 2 0.4894 0.59271 0.00 0.78 0.12 0.10
#> TCGA.D3.A51G.06 3 0.7146 0.48787 0.04 0.20 0.64 0.12
#> TCGA.EB.A4P0.01 2 0.4855 0.27569 0.40 0.60 0.00 0.00
#> TCGA.D3.A51R.06 3 0.6554 0.08358 0.00 0.08 0.52 0.40
#> TCGA.FS.A4FB.06 2 0.4713 0.35238 0.36 0.64 0.00 0.00
#> TCGA.BF.A3DM.01 2 0.4894 0.59271 0.00 0.78 0.12 0.10
#> TCGA.W3.AA1R.06 3 0.3522 0.55962 0.02 0.06 0.88 0.04
#> TCGA.EE.A3JA.06 3 0.5657 0.51982 0.00 0.12 0.72 0.16
#> TCGA.FS.A4F4.06 1 0.2011 0.82734 0.92 0.00 0.08 0.00
#> TCGA.BF.A3DN.01 2 0.1637 0.59410 0.00 0.94 0.06 0.00
#> TCGA.D3.A51E.06 2 0.7653 0.03721 0.00 0.46 0.24 0.30
#> TCGA.DA.A3F3.06 3 0.6594 0.42018 0.00 0.14 0.62 0.24
#> TCGA.D3.A51T.06 3 0.5255 0.50742 0.12 0.08 0.78 0.02
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> TCGA.GN.A8LL.06 5 0.4637 0.5314 0.10 0.16 0.00 0.00 0.74
#> TCGA.ER.A42K.06 2 0.4182 0.6178 0.00 0.60 0.00 0.00 0.40
#> TCGA.FS.A4F2.06 3 0.4094 0.6124 0.02 0.18 0.78 0.00 0.02
#> TCGA.WE.A8ZT.06 5 0.3513 0.6858 0.18 0.00 0.00 0.02 0.80
#> TCGA.DA.A95Y.06 1 0.0609 0.8910 0.98 0.00 0.00 0.00 0.02
#> TCGA.WE.A8K6.06 2 0.4182 0.6178 0.00 0.60 0.00 0.00 0.40
#> TCGA.GN.A4U3.06 1 0.2012 0.8934 0.92 0.02 0.00 0.00 0.06
#> TCGA.Z2.A8RT.06 2 0.4182 0.6178 0.00 0.60 0.00 0.00 0.40
#> TCGA.EB.A41B.01 2 0.4990 0.5913 0.00 0.60 0.00 0.04 0.36
#> TCGA.EB.A6R0.01 3 0.7204 0.3221 0.00 0.28 0.48 0.20 0.04
#> TCGA.D9.A4Z2.01 4 0.2873 0.6756 0.00 0.12 0.00 0.86 0.02
#> TCGA.D3.A3MV.06 4 0.3561 0.6647 0.00 0.26 0.00 0.74 0.00
#> TCGA.GN.A4U7.06 5 0.5631 0.3028 0.40 0.04 0.02 0.00 0.54
#> TCGA.BF.A5EP.01 1 0.3209 0.8841 0.86 0.02 0.02 0.00 0.10
#> TCGA.D3.A5GL.06 1 0.3463 0.8691 0.84 0.02 0.02 0.00 0.12
#> TCGA.FS.A1YY.06 1 0.3110 0.8715 0.86 0.00 0.06 0.00 0.08
#> TCGA.EE.A2MK.06 5 0.3319 0.6894 0.16 0.02 0.00 0.00 0.82
#> TCGA.EE.A3AE.06 3 0.7995 0.3318 0.34 0.20 0.36 0.00 0.10
#> TCGA.EB.A51B.01 5 0.4170 0.5734 0.08 0.14 0.00 0.00 0.78
#> TCGA.FS.A1ZQ.06 4 0.5828 0.5706 0.00 0.38 0.10 0.52 0.00
#> TCGA.D3.A2JG.06 1 0.5440 0.7034 0.70 0.02 0.12 0.00 0.16
#> TCGA.ER.A19F.06 4 0.7531 0.5084 0.02 0.30 0.22 0.44 0.02
#> TCGA.EE.A3AG.06 2 0.7899 -0.4309 0.02 0.40 0.22 0.32 0.04
#> TCGA.ER.A19B.06 4 0.3690 0.6548 0.00 0.20 0.00 0.78 0.02
#> TCGA.D3.A5GN.06 4 0.6017 0.5213 0.00 0.42 0.04 0.50 0.04
#> TCGA.EB.A4XL.01 1 0.2020 0.8519 0.90 0.00 0.00 0.00 0.10
#> TCGA.EE.A2GB.06 4 0.6564 0.4671 0.02 0.40 0.12 0.46 0.00
#> TCGA.FS.A1Z3.06 2 0.4182 0.6178 0.00 0.60 0.00 0.00 0.40
#> TCGA.DA.A1I8.06 4 0.4794 0.5601 0.00 0.12 0.10 0.76 0.02
#> TCGA.D3.A5GS.06 5 0.5700 0.3109 0.00 0.12 0.00 0.28 0.60
#> TCGA.EE.A2GS.06 2 0.4182 0.6178 0.00 0.60 0.00 0.00 0.40
#> TCGA.D3.A5GO.06 3 0.5727 0.5350 0.00 0.20 0.68 0.06 0.06
#> TCGA.EE.A29Q.06 2 0.6400 -0.3040 0.00 0.54 0.12 0.32 0.02
#> TCGA.BF.A1PZ.01 2 0.4182 0.6178 0.00 0.60 0.00 0.00 0.40
#> TCGA.D9.A1JX.06 4 0.2438 0.6571 0.00 0.06 0.00 0.90 0.04
#> TCGA.FS.A1ZF.06 4 0.4075 0.6306 0.00 0.06 0.00 0.78 0.16
#> TCGA.EE.A29W.06 2 0.4182 0.6178 0.00 0.60 0.00 0.00 0.40
#> TCGA.DA.A1HV.06 3 0.2020 0.6198 0.00 0.10 0.90 0.00 0.00
#> TCGA.EE.A17X.06 1 0.2331 0.8934 0.90 0.02 0.00 0.00 0.08
#> TCGA.EE.A3AF.06 5 0.8284 -0.0497 0.16 0.18 0.32 0.00 0.34
#> TCGA.ER.A19H.06 4 0.4216 0.6630 0.00 0.12 0.00 0.78 0.10
#> TCGA.DA.A1HY.06 4 0.7754 0.2839 0.00 0.30 0.26 0.38 0.06
#> TCGA.D3.A3C7.06 2 0.4990 0.5879 0.00 0.60 0.04 0.00 0.36
#> TCGA.EE.A2MP.06 4 0.6308 0.5076 0.00 0.20 0.02 0.60 0.18
#> TCGA.EE.A29H.06 3 0.8119 0.2226 0.08 0.18 0.44 0.02 0.28
#> TCGA.XV.AB01.01 1 0.0609 0.8892 0.98 0.00 0.02 0.00 0.00
#> TCGA.ER.A19G.06 4 0.7001 0.1651 0.00 0.10 0.40 0.44 0.06
#> TCGA.EB.A3XC.01 3 0.8430 -0.0331 0.24 0.16 0.32 0.00 0.28
#> TCGA.FR.A69P.06 2 0.4182 0.6178 0.00 0.60 0.00 0.00 0.40
#> TCGA.D3.A3C6.06 5 0.4932 0.5442 0.04 0.08 0.00 0.12 0.76
#> TCGA.EE.A2A2.06 3 0.2616 0.6307 0.02 0.10 0.88 0.00 0.00
#> TCGA.BF.AAP6.01 4 0.6115 0.5012 0.00 0.06 0.06 0.62 0.26
#> TCGA.FR.A3R1.01 3 0.6156 0.5252 0.20 0.12 0.64 0.00 0.04
#> TCGA.EB.A299.01 5 0.3895 0.0560 0.00 0.32 0.00 0.00 0.68
#> TCGA.EB.A3XF.01 5 0.2929 0.6958 0.18 0.00 0.00 0.00 0.82
#> TCGA.D3.A2JF.06 3 0.5293 0.5765 0.00 0.24 0.68 0.02 0.06
#> TCGA.XV.AAZW.01 5 0.2873 0.5688 0.02 0.12 0.00 0.00 0.86
#> TCGA.FR.A3YN.06 2 0.5770 0.5476 0.00 0.60 0.04 0.04 0.32
#> TCGA.QB.AA9O.06 3 0.6381 0.5373 0.18 0.16 0.62 0.00 0.04
#> TCGA.BF.A3DJ.01 5 0.2929 0.6947 0.18 0.00 0.00 0.00 0.82
#> TCGA.EE.A3J3.06 2 0.4182 0.6178 0.00 0.60 0.00 0.00 0.40
#> TCGA.D3.A51G.06 3 0.7515 0.1971 0.02 0.34 0.42 0.02 0.20
#> TCGA.EB.A4P0.01 5 0.3684 0.5715 0.28 0.00 0.00 0.00 0.72
#> TCGA.D3.A51R.06 2 0.7926 -0.4564 0.02 0.36 0.22 0.36 0.04
#> TCGA.FS.A4FB.06 5 0.3319 0.7016 0.16 0.00 0.00 0.02 0.82
#> TCGA.BF.A3DM.01 2 0.4182 0.6178 0.00 0.60 0.00 0.00 0.40
#> TCGA.W3.AA1R.06 3 0.2331 0.6033 0.00 0.08 0.90 0.02 0.00
#> TCGA.EE.A3JA.06 3 0.6792 0.3015 0.00 0.28 0.54 0.14 0.04
#> TCGA.FS.A4F4.06 1 0.0609 0.8892 0.98 0.00 0.02 0.00 0.00
#> TCGA.BF.A3DN.01 2 0.4302 0.4583 0.00 0.52 0.00 0.00 0.48
#> TCGA.D3.A51E.06 2 0.8300 -0.2219 0.00 0.36 0.24 0.26 0.14
#> TCGA.DA.A3F3.06 2 0.7619 -0.3487 0.00 0.38 0.36 0.20 0.06
#> TCGA.D3.A51T.06 3 0.2873 0.6306 0.02 0.12 0.86 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.GN.A8LL.06 2 0.5841 -0.2573 0.30 0.48 0.00 0.00 0.22 0.00
#> TCGA.ER.A42K.06 2 0.0000 0.6790 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.FS.A4F2.06 3 0.3258 0.5597 0.00 0.06 0.86 0.02 0.04 0.02
#> TCGA.WE.A8ZT.06 1 0.6430 0.1780 0.44 0.12 0.00 0.06 0.38 0.00
#> TCGA.DA.A95Y.06 1 0.4392 0.4732 0.76 0.00 0.02 0.02 0.16 0.04
#> TCGA.WE.A8K6.06 2 0.0000 0.6790 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.GN.A4U3.06 1 0.2581 0.5398 0.86 0.00 0.00 0.02 0.12 0.00
#> TCGA.Z2.A8RT.06 2 0.0000 0.6790 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.EB.A41B.01 2 0.1865 0.6215 0.00 0.92 0.00 0.04 0.04 0.00
#> TCGA.EB.A6R0.01 6 0.8246 0.4404 0.00 0.20 0.28 0.08 0.10 0.34
#> TCGA.D9.A4Z2.01 4 0.4238 0.5424 0.00 0.16 0.00 0.76 0.04 0.04
#> TCGA.D3.A3MV.06 4 0.4462 0.5026 0.00 0.28 0.00 0.66 0.00 0.06
#> TCGA.GN.A4U7.06 1 0.5438 0.3142 0.56 0.16 0.00 0.00 0.28 0.00
#> TCGA.BF.A5EP.01 1 0.1556 0.5596 0.92 0.00 0.08 0.00 0.00 0.00
#> TCGA.D3.A5GL.06 1 0.2350 0.5578 0.88 0.00 0.02 0.00 0.10 0.00
#> TCGA.FS.A1YY.06 1 0.3475 0.5257 0.80 0.00 0.14 0.00 0.06 0.00
#> TCGA.EE.A2MK.06 1 0.6070 0.0469 0.40 0.28 0.00 0.00 0.32 0.00
#> TCGA.EE.A3AE.06 3 0.9158 -0.0290 0.16 0.16 0.30 0.02 0.16 0.20
#> TCGA.EB.A51B.01 2 0.6077 -0.3388 0.30 0.40 0.00 0.00 0.30 0.00
#> TCGA.FS.A1ZQ.06 2 0.7020 -0.3102 0.00 0.42 0.04 0.32 0.02 0.20
#> TCGA.D3.A2JG.06 1 0.4608 0.4226 0.68 0.00 0.22 0.00 0.10 0.00
#> TCGA.ER.A19F.06 4 0.8309 0.1215 0.00 0.20 0.08 0.38 0.14 0.20
#> TCGA.EE.A3AG.06 6 0.4221 0.5197 0.00 0.04 0.02 0.08 0.06 0.80
#> TCGA.ER.A19B.06 4 0.5363 0.4577 0.00 0.32 0.00 0.58 0.02 0.08
#> TCGA.D3.A5GN.06 2 0.6215 -0.2211 0.00 0.48 0.02 0.30 0.00 0.20
#> TCGA.EB.A4XL.01 1 0.4708 0.4886 0.72 0.00 0.02 0.02 0.20 0.04
#> TCGA.EE.A2GB.06 6 0.7418 0.3597 0.00 0.14 0.10 0.24 0.04 0.48
#> TCGA.FS.A1Z3.06 2 0.0000 0.6790 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DA.A1I8.06 4 0.5570 0.0370 0.00 0.06 0.00 0.54 0.04 0.36
#> TCGA.D3.A5GS.06 4 0.6984 -0.4187 0.02 0.30 0.04 0.44 0.20 0.00
#> TCGA.EE.A2GS.06 2 0.0000 0.6790 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.D3.A5GO.06 6 0.6918 0.3042 0.00 0.10 0.36 0.02 0.08 0.44
#> TCGA.EE.A29Q.06 2 0.5691 0.0645 0.00 0.58 0.02 0.26 0.00 0.14
#> TCGA.BF.A1PZ.01 2 0.0000 0.6790 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.D9.A1JX.06 4 0.4221 0.4675 0.00 0.08 0.02 0.80 0.06 0.04
#> TCGA.FS.A1ZF.06 4 0.4444 0.3695 0.00 0.08 0.00 0.74 0.16 0.02
#> TCGA.EE.A29W.06 2 0.0000 0.6790 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DA.A1HV.06 3 0.3318 0.4442 0.00 0.02 0.82 0.02 0.00 0.14
#> TCGA.EE.A17X.06 1 0.1267 0.5557 0.94 0.00 0.00 0.00 0.06 0.00
#> TCGA.EE.A3AF.06 3 0.7137 0.1346 0.32 0.12 0.40 0.00 0.16 0.00
#> TCGA.ER.A19H.06 4 0.4392 0.5168 0.00 0.16 0.02 0.76 0.04 0.02
#> TCGA.DA.A1HY.06 6 0.6193 0.4998 0.00 0.10 0.10 0.22 0.00 0.58
#> TCGA.D3.A3C7.06 2 0.0547 0.6630 0.00 0.98 0.02 0.00 0.00 0.00
#> TCGA.EE.A2MP.06 4 0.4637 0.4278 0.00 0.36 0.02 0.60 0.00 0.02
#> TCGA.EE.A29H.06 3 0.5730 0.5056 0.08 0.10 0.64 0.00 0.18 0.00
#> TCGA.XV.AB01.01 1 0.4822 0.4860 0.74 0.00 0.10 0.02 0.12 0.02
#> TCGA.ER.A19G.06 6 0.8369 0.4300 0.00 0.14 0.16 0.22 0.10 0.38
#> TCGA.EB.A3XC.01 3 0.7241 0.2410 0.28 0.10 0.46 0.00 0.14 0.02
#> TCGA.FR.A69P.06 2 0.0000 0.6790 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.D3.A3C6.06 5 0.7727 0.0000 0.10 0.26 0.00 0.30 0.32 0.02
#> TCGA.EE.A2A2.06 3 0.1480 0.5411 0.00 0.02 0.94 0.00 0.00 0.04
#> TCGA.BF.AAP6.01 4 0.6793 0.1519 0.00 0.14 0.16 0.52 0.18 0.00
#> TCGA.FR.A3R1.01 3 0.3572 0.5540 0.10 0.02 0.82 0.00 0.06 0.00
#> TCGA.EB.A299.01 2 0.2981 0.4607 0.00 0.82 0.00 0.02 0.16 0.00
#> TCGA.EB.A3XF.01 1 0.5682 0.2478 0.46 0.16 0.00 0.00 0.38 0.00
#> TCGA.D3.A2JF.06 3 0.6022 -0.0259 0.00 0.14 0.56 0.00 0.04 0.26
#> TCGA.XV.AAZW.01 2 0.6566 -0.3804 0.20 0.44 0.00 0.04 0.32 0.00
#> TCGA.FR.A3YN.06 2 0.3572 0.5372 0.00 0.82 0.02 0.10 0.06 0.00
#> TCGA.QB.AA9O.06 3 0.4055 0.5577 0.14 0.04 0.78 0.00 0.04 0.00
#> TCGA.BF.A3DJ.01 1 0.5844 0.3014 0.50 0.12 0.00 0.02 0.36 0.00
#> TCGA.EE.A3J3.06 2 0.0000 0.6790 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.D3.A51G.06 2 0.8350 -0.3608 0.00 0.38 0.20 0.10 0.12 0.20
#> TCGA.EB.A4P0.01 1 0.5896 0.2580 0.46 0.12 0.00 0.02 0.40 0.00
#> TCGA.D3.A51R.06 6 0.5394 0.5288 0.00 0.06 0.04 0.08 0.10 0.72
#> TCGA.FS.A4FB.06 1 0.5906 0.2377 0.44 0.12 0.00 0.02 0.42 0.00
#> TCGA.BF.A3DM.01 2 0.0000 0.6790 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.W3.AA1R.06 3 0.3318 0.4403 0.00 0.00 0.82 0.02 0.02 0.14
#> TCGA.EE.A3JA.06 6 0.6651 0.5728 0.00 0.16 0.12 0.06 0.06 0.60
#> TCGA.FS.A4F4.06 1 0.4380 0.3697 0.70 0.00 0.22 0.00 0.08 0.00
#> TCGA.BF.A3DN.01 2 0.0937 0.6384 0.00 0.96 0.00 0.00 0.04 0.00
#> TCGA.D3.A51E.06 3 0.7437 -0.0488 0.00 0.28 0.36 0.22 0.14 0.00
#> TCGA.DA.A3F3.06 6 0.6358 0.5397 0.00 0.22 0.06 0.08 0.04 0.60
#> TCGA.D3.A51T.06 3 0.2175 0.5525 0.00 0.02 0.92 0.02 0.02 0.02
cbind(get_classes(res, k = 7), get_membership(res, k = 7))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7
#> TCGA.GN.A8LL.06 2 0.5016 -0.46220 0.12 0.46 0.00 0.00 0.42 0.00 0.00
#> TCGA.ER.A42K.06 2 0.0000 0.74576 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FS.A4F2.06 7 0.3542 0.53397 0.04 0.04 0.02 0.02 0.04 0.00 0.84
#> TCGA.WE.A8ZT.06 5 0.5232 0.64573 0.12 0.12 0.02 0.06 0.68 0.00 0.00
#> TCGA.DA.A95Y.06 1 0.3745 0.55234 0.70 0.00 0.26 0.00 0.04 0.00 0.00
#> TCGA.WE.A8K6.06 2 0.0000 0.74576 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.GN.A4U3.06 1 0.4773 0.55908 0.66 0.00 0.20 0.00 0.12 0.02 0.00
#> TCGA.Z2.A8RT.06 2 0.0000 0.74576 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EB.A41B.01 2 0.2512 0.63741 0.00 0.86 0.00 0.10 0.00 0.04 0.00
#> TCGA.EB.A6R0.01 7 0.7877 0.00128 0.00 0.18 0.12 0.16 0.00 0.18 0.36
#> TCGA.D9.A4Z2.01 4 0.3680 0.42013 0.00 0.14 0.00 0.78 0.06 0.02 0.00
#> TCGA.D3.A3MV.06 4 0.5130 0.26264 0.00 0.14 0.00 0.64 0.00 0.18 0.04
#> TCGA.GN.A4U7.06 1 0.6667 -0.10049 0.40 0.12 0.10 0.00 0.36 0.00 0.02
#> TCGA.BF.A5EP.01 1 0.4311 0.59081 0.76 0.00 0.06 0.00 0.12 0.02 0.04
#> TCGA.D3.A5GL.06 1 0.3055 0.56878 0.82 0.00 0.02 0.00 0.14 0.00 0.02
#> TCGA.FS.A1YY.06 1 0.3058 0.58562 0.82 0.00 0.00 0.00 0.10 0.00 0.08
#> TCGA.EE.A2MK.06 5 0.5669 0.60897 0.20 0.28 0.02 0.00 0.50 0.00 0.00
#> TCGA.EE.A3AE.06 7 0.8837 0.22348 0.14 0.20 0.18 0.02 0.08 0.06 0.32
#> TCGA.EB.A51B.01 2 0.4875 -0.46828 0.10 0.46 0.00 0.00 0.44 0.00 0.00
#> TCGA.FS.A1ZQ.06 4 0.7389 0.00175 0.00 0.24 0.04 0.40 0.04 0.24 0.04
#> TCGA.D3.A2JG.06 1 0.5199 0.51956 0.64 0.00 0.08 0.00 0.08 0.00 0.20
#> TCGA.ER.A19F.06 6 0.8394 0.01270 0.00 0.16 0.08 0.26 0.06 0.32 0.12
#> TCGA.EE.A3AG.06 6 0.4565 0.44402 0.00 0.00 0.08 0.16 0.02 0.72 0.02
#> TCGA.ER.A19B.06 4 0.5477 0.33446 0.00 0.26 0.02 0.60 0.08 0.04 0.00
#> TCGA.D3.A5GN.06 2 0.6153 -0.29293 0.00 0.42 0.00 0.36 0.02 0.18 0.02
#> TCGA.EB.A4XL.01 1 0.5997 0.25178 0.38 0.02 0.28 0.00 0.32 0.00 0.00
#> TCGA.EE.A2GB.06 6 0.7501 0.25087 0.00 0.12 0.14 0.28 0.04 0.40 0.02
#> TCGA.FS.A1Z3.06 2 0.0000 0.74576 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DA.A1I8.06 4 0.5279 -0.16209 0.00 0.04 0.00 0.56 0.04 0.34 0.02
#> TCGA.D3.A5GS.06 4 0.6577 0.16253 0.00 0.20 0.10 0.40 0.30 0.00 0.00
#> TCGA.EE.A2GS.06 2 0.0000 0.74576 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D3.A5GO.06 7 0.6758 0.37865 0.00 0.14 0.14 0.02 0.02 0.14 0.54
#> TCGA.EE.A29Q.06 2 0.7281 -0.10087 0.00 0.46 0.02 0.20 0.06 0.20 0.06
#> TCGA.BF.A1PZ.01 2 0.0000 0.74576 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D9.A1JX.06 4 0.4079 0.30528 0.00 0.04 0.12 0.76 0.00 0.08 0.00
#> TCGA.FS.A1ZF.06 4 0.6367 0.34259 0.00 0.04 0.10 0.60 0.16 0.08 0.02
#> TCGA.EE.A29W.06 2 0.0000 0.74576 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DA.A1HV.06 7 0.2159 0.55737 0.00 0.06 0.00 0.02 0.00 0.02 0.90
#> TCGA.EE.A17X.06 1 0.3867 0.56551 0.74 0.00 0.12 0.00 0.14 0.00 0.00
#> TCGA.EE.A3AF.06 1 0.7594 0.16582 0.34 0.16 0.08 0.00 0.12 0.00 0.30
#> TCGA.ER.A19H.06 4 0.4875 0.42543 0.00 0.08 0.02 0.72 0.14 0.02 0.02
#> TCGA.DA.A1HY.06 6 0.6033 0.42888 0.00 0.10 0.02 0.24 0.02 0.58 0.04
#> TCGA.D3.A3C7.06 2 0.1006 0.71470 0.00 0.96 0.00 0.00 0.00 0.02 0.02
#> TCGA.EE.A2MP.06 4 0.5474 0.31776 0.00 0.32 0.00 0.56 0.06 0.04 0.02
#> TCGA.EE.A29H.06 7 0.7047 0.06278 0.22 0.10 0.02 0.04 0.12 0.00 0.50
#> TCGA.XV.AB01.01 1 0.4797 0.55569 0.64 0.00 0.26 0.00 0.06 0.00 0.04
#> TCGA.ER.A19G.06 7 0.8128 -0.13597 0.00 0.06 0.12 0.28 0.04 0.18 0.32
#> TCGA.EB.A3XC.01 1 0.6956 0.23941 0.46 0.06 0.08 0.00 0.14 0.00 0.26
#> TCGA.FR.A69P.06 2 0.0000 0.74576 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D3.A3C6.06 5 0.6857 0.31594 0.02 0.12 0.04 0.22 0.54 0.02 0.04
#> TCGA.EE.A2A2.06 7 0.0863 0.56218 0.00 0.04 0.00 0.00 0.00 0.00 0.96
#> TCGA.BF.AAP6.01 4 0.6866 0.30830 0.00 0.04 0.10 0.50 0.26 0.02 0.08
#> TCGA.FR.A3R1.01 7 0.5477 0.30902 0.26 0.04 0.08 0.00 0.02 0.00 0.60
#> TCGA.EB.A299.01 2 0.3863 0.42401 0.00 0.74 0.04 0.02 0.20 0.00 0.00
#> TCGA.EB.A3XF.01 5 0.4970 0.64524 0.24 0.18 0.00 0.00 0.58 0.00 0.00
#> TCGA.D3.A2JF.06 7 0.6398 0.34026 0.00 0.24 0.04 0.02 0.06 0.08 0.56
#> TCGA.XV.AAZW.01 5 0.4421 0.35673 0.02 0.46 0.00 0.02 0.50 0.00 0.00
#> TCGA.FR.A3YN.06 2 0.6939 0.17726 0.00 0.54 0.08 0.14 0.06 0.16 0.02
#> TCGA.QB.AA9O.06 7 0.5854 0.33958 0.22 0.04 0.06 0.00 0.08 0.00 0.60
#> TCGA.BF.A3DJ.01 5 0.5814 0.66294 0.22 0.14 0.04 0.02 0.58 0.00 0.00
#> TCGA.EE.A3J3.06 2 0.0000 0.74576 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D3.A51G.06 2 0.8489 -0.17271 0.02 0.36 0.04 0.06 0.16 0.16 0.20
#> TCGA.EB.A4P0.01 5 0.5051 0.63231 0.20 0.10 0.02 0.02 0.66 0.00 0.00
#> TCGA.D3.A51R.06 6 0.4357 0.43071 0.00 0.00 0.08 0.10 0.04 0.76 0.02
#> TCGA.FS.A4FB.06 5 0.4824 0.69760 0.12 0.16 0.00 0.04 0.68 0.00 0.00
#> TCGA.BF.A3DM.01 2 0.0000 0.74576 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.W3.AA1R.06 7 0.2706 0.55448 0.00 0.04 0.02 0.02 0.00 0.04 0.88
#> TCGA.EE.A3JA.06 7 0.7348 -0.02304 0.00 0.18 0.20 0.02 0.00 0.28 0.32
#> TCGA.FS.A4F4.06 1 0.5051 0.53522 0.66 0.00 0.10 0.00 0.02 0.02 0.20
#> TCGA.BF.A3DN.01 2 0.1166 0.68870 0.00 0.94 0.00 0.00 0.06 0.00 0.00
#> TCGA.D3.A51E.06 4 0.8023 0.08233 0.00 0.22 0.02 0.30 0.10 0.08 0.28
#> TCGA.DA.A3F3.06 6 0.7452 0.28731 0.00 0.22 0.14 0.08 0.00 0.42 0.14
#> TCGA.D3.A51T.06 7 0.2355 0.55977 0.00 0.04 0.02 0.02 0.02 0.00 0.90
cbind(get_classes(res, k = 8), get_membership(res, k = 8))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7 p8
#> TCGA.GN.A8LL.06 2 0.3142 0.1344 0.00 0.64 0.00 0.00 0.36 0.00 0.00 0.00
#> TCGA.ER.A42K.06 2 0.0000 0.7351 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FS.A4F2.06 7 0.2348 0.4964 0.04 0.00 0.02 0.00 0.00 0.00 0.88 0.06
#> TCGA.WE.A8ZT.06 5 0.4464 0.6017 0.12 0.10 0.00 0.02 0.72 0.00 0.00 0.04
#> TCGA.DA.A95Y.06 1 0.3847 0.6705 0.78 0.00 0.10 0.00 0.06 0.00 0.02 0.04
#> TCGA.WE.A8K6.06 2 0.0000 0.7351 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.GN.A4U3.06 1 0.4282 0.6740 0.74 0.00 0.10 0.00 0.10 0.00 0.02 0.04
#> TCGA.Z2.A8RT.06 2 0.0000 0.7351 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EB.A41B.01 2 0.5457 0.4370 0.00 0.66 0.00 0.02 0.06 0.10 0.04 0.12
#> TCGA.EB.A6R0.01 7 0.8126 -0.3576 0.02 0.20 0.16 0.06 0.00 0.24 0.28 0.04
#> TCGA.D9.A4Z2.01 4 0.3185 0.3904 0.00 0.06 0.00 0.82 0.04 0.08 0.00 0.00
#> TCGA.D3.A3MV.06 4 0.5072 0.2093 0.00 0.16 0.00 0.62 0.02 0.18 0.00 0.02
#> TCGA.GN.A4U7.06 5 0.6476 0.3788 0.28 0.16 0.00 0.00 0.42 0.00 0.02 0.12
#> TCGA.BF.A5EP.01 1 0.3891 0.6803 0.76 0.00 0.02 0.00 0.14 0.00 0.06 0.02
#> TCGA.D3.A5GL.06 1 0.3928 0.6436 0.74 0.00 0.02 0.00 0.18 0.00 0.02 0.04
#> TCGA.FS.A1YY.06 1 0.4846 0.6865 0.70 0.00 0.06 0.00 0.10 0.00 0.10 0.04
#> TCGA.EE.A2MK.06 5 0.5040 0.6128 0.10 0.24 0.00 0.00 0.60 0.00 0.00 0.06
#> TCGA.EE.A3AE.06 3 0.8683 0.0959 0.16 0.14 0.24 0.00 0.12 0.04 0.24 0.06
#> TCGA.EB.A51B.01 2 0.3318 -0.1850 0.00 0.54 0.00 0.00 0.46 0.00 0.00 0.00
#> TCGA.FS.A1ZQ.06 4 0.7538 -0.3098 0.00 0.26 0.02 0.28 0.00 0.26 0.08 0.10
#> TCGA.D3.A2JG.06 1 0.5281 0.5057 0.56 0.00 0.00 0.00 0.12 0.00 0.26 0.06
#> TCGA.ER.A19F.06 8 0.8145 0.0000 0.00 0.10 0.10 0.18 0.00 0.22 0.10 0.30
#> TCGA.EE.A3AG.06 6 0.4914 0.2768 0.00 0.06 0.04 0.06 0.00 0.68 0.00 0.16
#> TCGA.ER.A19B.06 4 0.6377 0.3333 0.00 0.14 0.04 0.58 0.08 0.08 0.00 0.08
#> TCGA.D3.A5GN.06 2 0.7252 -0.4844 0.00 0.32 0.02 0.30 0.00 0.22 0.06 0.08
#> TCGA.EB.A4XL.01 1 0.6173 0.5218 0.54 0.02 0.16 0.00 0.20 0.00 0.04 0.04
#> TCGA.EE.A2GB.06 6 0.7725 -0.0899 0.00 0.10 0.06 0.12 0.00 0.40 0.16 0.16
#> TCGA.FS.A1Z3.06 2 0.0000 0.7351 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DA.A1I8.06 4 0.5256 0.1628 0.00 0.00 0.02 0.62 0.02 0.24 0.04 0.06
#> TCGA.D3.A5GS.06 5 0.7517 -0.0393 0.02 0.20 0.04 0.30 0.32 0.00 0.02 0.10
#> TCGA.EE.A2GS.06 2 0.0000 0.7351 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D3.A5GO.06 7 0.7322 -0.0230 0.06 0.08 0.22 0.00 0.02 0.12 0.46 0.04
#> TCGA.EE.A29Q.06 2 0.7524 -0.3901 0.00 0.38 0.04 0.16 0.00 0.24 0.10 0.08
#> TCGA.BF.A1PZ.01 2 0.0000 0.7351 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D9.A1JX.06 4 0.4662 0.3322 0.00 0.02 0.06 0.74 0.04 0.06 0.00 0.08
#> TCGA.FS.A1ZF.06 4 0.6336 0.2230 0.00 0.04 0.16 0.58 0.06 0.02 0.02 0.12
#> TCGA.EE.A29W.06 2 0.0000 0.7351 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DA.A1HV.06 7 0.3048 0.4373 0.00 0.02 0.04 0.00 0.00 0.08 0.84 0.02
#> TCGA.EE.A17X.06 1 0.3002 0.6801 0.82 0.00 0.04 0.00 0.12 0.00 0.00 0.02
#> TCGA.EE.A3AF.06 7 0.7478 0.1176 0.10 0.22 0.00 0.00 0.18 0.00 0.30 0.20
#> TCGA.ER.A19H.06 4 0.4134 0.3959 0.00 0.08 0.02 0.76 0.06 0.00 0.00 0.08
#> TCGA.DA.A1HY.06 6 0.7589 -0.0554 0.00 0.12 0.04 0.24 0.00 0.38 0.12 0.10
#> TCGA.D3.A3C7.06 2 0.1557 0.6792 0.00 0.92 0.00 0.00 0.02 0.00 0.06 0.00
#> TCGA.EE.A2MP.06 4 0.6436 0.1536 0.00 0.32 0.00 0.46 0.10 0.04 0.04 0.04
#> TCGA.EE.A29H.06 7 0.7011 0.2131 0.08 0.18 0.02 0.02 0.06 0.00 0.50 0.14
#> TCGA.XV.AB01.01 1 0.4345 0.6565 0.74 0.00 0.12 0.00 0.06 0.00 0.04 0.04
#> TCGA.ER.A19G.06 3 0.7596 0.0260 0.00 0.04 0.36 0.24 0.02 0.14 0.18 0.02
#> TCGA.EB.A3XC.01 1 0.7148 0.0947 0.34 0.14 0.00 0.00 0.22 0.00 0.24 0.06
#> TCGA.FR.A69P.06 2 0.0000 0.7351 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D3.A3C6.06 5 0.7070 0.3509 0.02 0.22 0.06 0.20 0.44 0.02 0.00 0.04
#> TCGA.EE.A2A2.06 7 0.0471 0.5025 0.00 0.02 0.00 0.00 0.00 0.00 0.98 0.00
#> TCGA.BF.AAP6.01 4 0.6602 0.1744 0.02 0.06 0.00 0.48 0.26 0.00 0.12 0.06
#> TCGA.FR.A3R1.01 7 0.4538 0.4458 0.16 0.02 0.02 0.00 0.04 0.00 0.72 0.04
#> TCGA.EB.A299.01 2 0.3537 0.3955 0.00 0.72 0.02 0.00 0.24 0.00 0.00 0.02
#> TCGA.EB.A3XF.01 5 0.4144 0.5823 0.22 0.12 0.00 0.00 0.66 0.00 0.00 0.00
#> TCGA.D3.A2JF.06 7 0.6404 0.0403 0.00 0.16 0.14 0.00 0.00 0.12 0.52 0.06
#> TCGA.XV.AAZW.01 5 0.3299 0.3315 0.00 0.44 0.00 0.00 0.56 0.00 0.00 0.00
#> TCGA.FR.A3YN.06 2 0.5958 0.3168 0.00 0.60 0.00 0.02 0.04 0.10 0.08 0.16
#> TCGA.QB.AA9O.06 7 0.4590 0.4535 0.10 0.04 0.00 0.00 0.04 0.00 0.72 0.10
#> TCGA.BF.A3DJ.01 5 0.4031 0.6572 0.10 0.16 0.00 0.00 0.72 0.00 0.00 0.02
#> TCGA.EE.A3J3.06 2 0.0000 0.7351 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D3.A51G.06 2 0.8588 -0.3731 0.06 0.28 0.10 0.00 0.04 0.14 0.22 0.16
#> TCGA.EB.A4P0.01 5 0.3758 0.5896 0.14 0.06 0.00 0.00 0.76 0.00 0.00 0.04
#> TCGA.D3.A51R.06 6 0.3771 0.2480 0.02 0.02 0.06 0.08 0.00 0.80 0.00 0.02
#> TCGA.FS.A4FB.06 5 0.3710 0.6452 0.10 0.12 0.00 0.02 0.76 0.00 0.00 0.00
#> TCGA.BF.A3DM.01 2 0.0000 0.7351 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.W3.AA1R.06 7 0.2914 0.4444 0.00 0.00 0.04 0.00 0.00 0.08 0.84 0.04
#> TCGA.EE.A3JA.06 3 0.5563 0.3637 0.00 0.10 0.56 0.00 0.00 0.18 0.16 0.00
#> TCGA.FS.A4F4.06 1 0.3494 0.6704 0.78 0.00 0.04 0.00 0.00 0.00 0.14 0.04
#> TCGA.BF.A3DN.01 2 0.0808 0.7012 0.00 0.96 0.00 0.00 0.04 0.00 0.00 0.00
#> TCGA.D3.A51E.06 7 0.8747 -0.3202 0.00 0.16 0.04 0.14 0.12 0.08 0.28 0.18
#> TCGA.DA.A3F3.06 3 0.6233 0.2967 0.00 0.14 0.52 0.04 0.00 0.20 0.10 0.00
#> TCGA.D3.A51T.06 7 0.1408 0.4954 0.00 0.00 0.00 0.02 0.02 0.00 0.94 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: Node03. Child nodes: Node0111 , Node0112-leaf , Node0113 , Node0121-leaf , Node0122-leaf , Node0123-leaf , Node0124-leaf , Node0125-leaf , Node0131 , Node0132-leaf , Node0133-leaf , Node0211-leaf , Node0212 , Node0221-leaf , Node0222-leaf , Node0311 , Node0312-leaf , Node0321-leaf , Node0322 , Node0323 , Node0411 , Node0412 , Node0413-leaf , Node0421-leaf , Node0422-leaf , Node0423-leaf , Node0431-leaf , Node0432-leaf , Node0433-leaf , Node0441-leaf , Node0442 , Node0443-leaf , Node0511 , Node0512-leaf , Node0513-leaf , Node0521-leaf , Node0522-leaf , Node0523-leaf , Node0524-leaf .
The object with results only for a single top-value method and a single partitioning method can be extracted as:
res = res_rh["031"]
A summary of res and all the functions that can be applied to it:
res
#> A 'ConsensusPartition' object with k = 2, 3, 4, 5, 6, 7, 8.
#> On a matrix with 30000 rows and 26 columns.
#> Top rows (1000) are extracted by 'ATC' method.
#> Subgroups are detected by 'kmeans' method.
#> Performed in total 350 partitions by row resampling.
#> Best k for subgroups seems to be 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 0.995 0.998 0.4697 0.529 0.529
#> 3 3 0.797 0.864 0.936 0.3769 0.748 0.554
#> 4 4 0.713 0.938 0.942 0.1266 0.723 0.379
#> 5 5 0.855 0.624 0.791 0.0915 0.969 0.884
#> 6 6 0.859 0.733 0.858 0.0443 0.914 0.650
#> 7 7 0.826 0.622 0.835 0.0287 0.951 0.733
#> 8 8 0.851 0.622 0.812 0.0204 0.972 0.824
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.GN.A8LL.06 1 0.000 1.000 1.00 0.00
#> TCGA.WE.A8ZT.06 1 0.000 1.000 1.00 0.00
#> TCGA.DA.A95Y.06 1 0.000 1.000 1.00 0.00
#> TCGA.GN.A4U3.06 1 0.000 1.000 1.00 0.00
#> TCGA.GN.A4U7.06 1 0.000 1.000 1.00 0.00
#> TCGA.BF.A5EP.01 2 0.000 0.992 0.00 1.00
#> TCGA.D3.A5GL.06 2 0.000 0.992 0.00 1.00
#> TCGA.FS.A1YY.06 2 0.000 0.992 0.00 1.00
#> TCGA.EE.A2MK.06 1 0.000 1.000 1.00 0.00
#> TCGA.EE.A3AE.06 1 0.000 1.000 1.00 0.00
#> TCGA.EB.A51B.01 2 0.327 0.936 0.06 0.94
#> TCGA.D3.A2JG.06 2 0.000 0.992 0.00 1.00
#> TCGA.EB.A4XL.01 1 0.000 1.000 1.00 0.00
#> TCGA.EE.A17X.06 1 0.000 1.000 1.00 0.00
#> TCGA.EE.A3AF.06 2 0.000 0.992 0.00 1.00
#> TCGA.EE.A29H.06 2 0.000 0.992 0.00 1.00
#> TCGA.XV.AB01.01 2 0.000 0.992 0.00 1.00
#> TCGA.EB.A3XC.01 1 0.000 1.000 1.00 0.00
#> TCGA.FR.A3R1.01 2 0.000 0.992 0.00 1.00
#> TCGA.EB.A3XF.01 1 0.000 1.000 1.00 0.00
#> TCGA.XV.AAZW.01 1 0.000 1.000 1.00 0.00
#> TCGA.QB.AA9O.06 1 0.000 1.000 1.00 0.00
#> TCGA.BF.A3DJ.01 1 0.000 1.000 1.00 0.00
#> TCGA.EB.A4P0.01 1 0.000 1.000 1.00 0.00
#> TCGA.FS.A4FB.06 1 0.000 1.000 1.00 0.00
#> TCGA.FS.A4F4.06 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.GN.A8LL.06 1 0.000 0.900 1.00 0.00 0.00
#> TCGA.WE.A8ZT.06 1 0.000 0.900 1.00 0.00 0.00
#> TCGA.DA.A95Y.06 1 0.153 0.899 0.96 0.00 0.04
#> TCGA.GN.A4U3.06 1 0.153 0.899 0.96 0.00 0.04
#> TCGA.GN.A4U7.06 1 0.000 0.900 1.00 0.00 0.00
#> TCGA.BF.A5EP.01 3 0.000 0.895 0.00 0.00 1.00
#> TCGA.D3.A5GL.06 3 0.153 0.859 0.00 0.04 0.96
#> TCGA.FS.A1YY.06 2 0.000 0.979 0.00 1.00 0.00
#> TCGA.EE.A2MK.06 1 0.153 0.899 0.96 0.00 0.04
#> TCGA.EE.A3AE.06 1 0.153 0.899 0.96 0.00 0.04
#> TCGA.EB.A51B.01 3 0.000 0.895 0.00 0.00 1.00
#> TCGA.D3.A2JG.06 2 0.000 0.979 0.00 1.00 0.00
#> TCGA.EB.A4XL.01 1 0.000 0.900 1.00 0.00 0.00
#> TCGA.EE.A17X.06 3 0.334 0.905 0.12 0.00 0.88
#> TCGA.EE.A3AF.06 2 0.000 0.979 0.00 1.00 0.00
#> TCGA.EE.A29H.06 2 0.334 0.889 0.00 0.88 0.12
#> TCGA.XV.AB01.01 2 0.000 0.979 0.00 1.00 0.00
#> TCGA.EB.A3XC.01 1 0.619 0.280 0.58 0.00 0.42
#> TCGA.FR.A3R1.01 2 0.000 0.979 0.00 1.00 0.00
#> TCGA.EB.A3XF.01 3 0.334 0.905 0.12 0.00 0.88
#> TCGA.XV.AAZW.01 3 0.254 0.915 0.08 0.00 0.92
#> TCGA.QB.AA9O.06 1 0.000 0.900 1.00 0.00 0.00
#> TCGA.BF.A3DJ.01 1 0.624 0.219 0.56 0.00 0.44
#> TCGA.EB.A4P0.01 1 0.153 0.899 0.96 0.00 0.04
#> TCGA.FS.A4FB.06 1 0.000 0.900 1.00 0.00 0.00
#> TCGA.FS.A4F4.06 3 0.334 0.905 0.12 0.00 0.88
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> TCGA.GN.A8LL.06 4 0.000 1.000 0.00 0.00 0.00 1.00
#> TCGA.WE.A8ZT.06 4 0.000 1.000 0.00 0.00 0.00 1.00
#> TCGA.DA.A95Y.06 1 0.317 0.911 0.84 0.00 0.00 0.16
#> TCGA.GN.A4U3.06 1 0.317 0.911 0.84 0.00 0.00 0.16
#> TCGA.GN.A4U7.06 4 0.000 1.000 0.00 0.00 0.00 1.00
#> TCGA.BF.A5EP.01 3 0.265 0.949 0.12 0.00 0.88 0.00
#> TCGA.D3.A5GL.06 3 0.265 0.949 0.12 0.00 0.88 0.00
#> TCGA.FS.A1YY.06 2 0.000 0.974 0.00 1.00 0.00 0.00
#> TCGA.EE.A2MK.06 1 0.317 0.911 0.84 0.00 0.00 0.16
#> TCGA.EE.A3AE.06 1 0.317 0.911 0.84 0.00 0.00 0.16
#> TCGA.EB.A51B.01 3 0.265 0.949 0.12 0.00 0.88 0.00
#> TCGA.D3.A2JG.06 2 0.265 0.891 0.00 0.88 0.12 0.00
#> TCGA.EB.A4XL.01 4 0.000 1.000 0.00 0.00 0.00 1.00
#> TCGA.EE.A17X.06 1 0.000 0.875 1.00 0.00 0.00 0.00
#> TCGA.EE.A3AF.06 2 0.000 0.974 0.00 1.00 0.00 0.00
#> TCGA.EE.A29H.06 3 0.121 0.835 0.00 0.04 0.96 0.00
#> TCGA.XV.AB01.01 2 0.000 0.974 0.00 1.00 0.00 0.00
#> TCGA.EB.A3XC.01 1 0.265 0.921 0.88 0.00 0.00 0.12
#> TCGA.FR.A3R1.01 2 0.000 0.974 0.00 1.00 0.00 0.00
#> TCGA.EB.A3XF.01 1 0.000 0.875 1.00 0.00 0.00 0.00
#> TCGA.XV.AAZW.01 1 0.000 0.875 1.00 0.00 0.00 0.00
#> TCGA.QB.AA9O.06 4 0.000 1.000 0.00 0.00 0.00 1.00
#> TCGA.BF.A3DJ.01 1 0.265 0.921 0.88 0.00 0.00 0.12
#> TCGA.EB.A4P0.01 1 0.265 0.921 0.88 0.00 0.00 0.12
#> TCGA.FS.A4FB.06 4 0.000 1.000 0.00 0.00 0.00 1.00
#> TCGA.FS.A4F4.06 1 0.000 0.875 1.00 0.00 0.00 0.00
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> TCGA.GN.A8LL.06 4 0.0000 1.000 0.00 0.00 0.00 1.00 0.00
#> TCGA.WE.A8ZT.06 4 0.0000 1.000 0.00 0.00 0.00 1.00 0.00
#> TCGA.DA.A95Y.06 1 0.5425 -0.393 0.52 0.00 0.00 0.06 0.42
#> TCGA.GN.A4U3.06 1 0.5673 -0.390 0.50 0.00 0.00 0.08 0.42
#> TCGA.GN.A4U7.06 4 0.0000 1.000 0.00 0.00 0.00 1.00 0.00
#> TCGA.BF.A5EP.01 3 0.0609 0.840 0.02 0.00 0.98 0.00 0.00
#> TCGA.D3.A5GL.06 3 0.0609 0.840 0.02 0.00 0.98 0.00 0.00
#> TCGA.FS.A1YY.06 2 0.0000 0.949 0.00 1.00 0.00 0.00 0.00
#> TCGA.EE.A2MK.06 1 0.1732 0.560 0.92 0.00 0.00 0.08 0.00
#> TCGA.EE.A3AE.06 1 0.1732 0.560 0.92 0.00 0.00 0.08 0.00
#> TCGA.EB.A51B.01 3 0.3852 0.712 0.02 0.00 0.76 0.00 0.22
#> TCGA.D3.A2JG.06 2 0.3690 0.773 0.00 0.78 0.02 0.00 0.20
#> TCGA.EB.A4XL.01 4 0.0000 1.000 0.00 0.00 0.00 1.00 0.00
#> TCGA.EE.A17X.06 5 0.3983 0.000 0.34 0.00 0.00 0.00 0.66
#> TCGA.EE.A3AF.06 2 0.0000 0.949 0.00 1.00 0.00 0.00 0.00
#> TCGA.EE.A29H.06 3 0.4433 0.697 0.00 0.06 0.74 0.00 0.20
#> TCGA.XV.AB01.01 2 0.0000 0.949 0.00 1.00 0.00 0.00 0.00
#> TCGA.EB.A3XC.01 1 0.4767 -0.414 0.56 0.00 0.00 0.02 0.42
#> TCGA.FR.A3R1.01 2 0.0000 0.949 0.00 1.00 0.00 0.00 0.00
#> TCGA.EB.A3XF.01 1 0.3109 0.490 0.80 0.00 0.00 0.00 0.20
#> TCGA.XV.AAZW.01 1 0.3109 0.490 0.80 0.00 0.00 0.00 0.20
#> TCGA.QB.AA9O.06 4 0.0000 1.000 0.00 0.00 0.00 1.00 0.00
#> TCGA.BF.A3DJ.01 1 0.0609 0.573 0.98 0.00 0.00 0.02 0.00
#> TCGA.EB.A4P0.01 1 0.0609 0.573 0.98 0.00 0.00 0.02 0.00
#> TCGA.FS.A4FB.06 4 0.0000 1.000 0.00 0.00 0.00 1.00 0.00
#> TCGA.FS.A4F4.06 1 0.2732 0.513 0.84 0.00 0.00 0.00 0.16
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> TCGA.GN.A8LL.06 4 0.0000 1.0000 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.WE.A8ZT.06 4 0.0000 1.0000 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.DA.A95Y.06 5 0.2094 0.6736 0.00 0.00 0.00 0.02 0.90 0.08
#> TCGA.GN.A4U3.06 5 0.3045 0.6530 0.02 0.00 0.00 0.06 0.86 0.06
#> TCGA.GN.A4U7.06 4 0.0000 1.0000 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.BF.A5EP.01 3 0.0000 0.7880 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.D3.A5GL.06 3 0.0937 0.7849 0.04 0.00 0.96 0.00 0.00 0.00
#> TCGA.FS.A1YY.06 2 0.0000 0.8912 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.EE.A2MK.06 6 0.5835 0.3289 0.06 0.00 0.00 0.06 0.36 0.52
#> TCGA.EE.A3AE.06 5 0.5788 0.0219 0.06 0.00 0.00 0.06 0.54 0.34
#> TCGA.EB.A51B.01 3 0.3679 0.7028 0.04 0.00 0.76 0.00 0.00 0.20
#> TCGA.D3.A2JG.06 2 0.3828 0.4691 0.44 0.56 0.00 0.00 0.00 0.00
#> TCGA.EB.A4XL.01 4 0.0000 1.0000 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.EE.A17X.06 5 0.5095 0.2738 0.42 0.00 0.00 0.00 0.50 0.08
#> TCGA.EE.A3AF.06 2 0.0547 0.8843 0.00 0.98 0.00 0.00 0.02 0.00
#> TCGA.EE.A29H.06 3 0.4310 0.5278 0.44 0.02 0.54 0.00 0.00 0.00
#> TCGA.XV.AB01.01 2 0.0000 0.8912 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.EB.A3XC.01 5 0.2094 0.6736 0.00 0.00 0.00 0.02 0.90 0.08
#> TCGA.FR.A3R1.01 2 0.0000 0.8912 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.EB.A3XF.01 6 0.0937 0.7183 0.00 0.00 0.00 0.00 0.04 0.96
#> TCGA.XV.AAZW.01 6 0.0547 0.6766 0.02 0.00 0.00 0.00 0.00 0.98
#> TCGA.QB.AA9O.06 4 0.0000 1.0000 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.BF.A3DJ.01 6 0.2631 0.7538 0.00 0.00 0.00 0.00 0.18 0.82
#> TCGA.EB.A4P0.01 6 0.4105 0.6925 0.02 0.00 0.00 0.02 0.24 0.72
#> TCGA.FS.A4FB.06 4 0.0000 1.0000 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.FS.A4F4.06 6 0.3660 0.7516 0.06 0.00 0.00 0.00 0.16 0.78
cbind(get_classes(res, k = 7), get_membership(res, k = 7))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7
#> TCGA.GN.A8LL.06 4 0.0000 1.000 0.00 0.00 0.00 1 0.00 0.00 0.00
#> TCGA.WE.A8ZT.06 4 0.0000 1.000 0.00 0.00 0.00 1 0.00 0.00 0.00
#> TCGA.DA.A95Y.06 5 0.4016 0.568 0.04 0.00 0.00 0 0.76 0.06 0.14
#> TCGA.GN.A4U3.06 5 0.2572 0.588 0.06 0.00 0.00 0 0.86 0.08 0.00
#> TCGA.GN.A4U7.06 4 0.0000 1.000 0.00 0.00 0.00 1 0.00 0.00 0.00
#> TCGA.BF.A5EP.01 3 0.3968 0.431 0.44 0.00 0.54 0 0.00 0.00 0.02
#> TCGA.D3.A5GL.06 3 0.4514 0.399 0.46 0.00 0.48 0 0.00 0.00 0.06
#> TCGA.FS.A1YY.06 2 0.0000 0.858 0.00 1.00 0.00 0 0.00 0.00 0.00
#> TCGA.EE.A2MK.06 5 0.3968 0.117 0.00 0.00 0.02 0 0.54 0.44 0.00
#> TCGA.EE.A3AE.06 5 0.4070 0.427 0.00 0.00 0.02 0 0.66 0.30 0.02
#> TCGA.EB.A51B.01 1 0.3867 0.000 0.74 0.00 0.14 0 0.00 0.12 0.00
#> TCGA.D3.A2JG.06 2 0.3525 0.448 0.00 0.56 0.44 0 0.00 0.00 0.00
#> TCGA.EB.A4XL.01 4 0.0000 1.000 0.00 0.00 0.00 1 0.00 0.00 0.00
#> TCGA.EE.A17X.06 7 0.2163 0.000 0.00 0.00 0.00 0 0.10 0.02 0.88
#> TCGA.EE.A3AF.06 2 0.1718 0.829 0.00 0.92 0.00 0 0.04 0.00 0.04
#> TCGA.EE.A29H.06 3 0.0504 0.273 0.00 0.02 0.98 0 0.00 0.00 0.00
#> TCGA.XV.AB01.01 2 0.0504 0.859 0.00 0.98 0.00 0 0.02 0.00 0.00
#> TCGA.EB.A3XC.01 5 0.4016 0.568 0.04 0.00 0.00 0 0.76 0.06 0.14
#> TCGA.FR.A3R1.01 2 0.0504 0.859 0.00 0.98 0.00 0 0.02 0.00 0.00
#> TCGA.EB.A3XF.01 6 0.0863 0.692 0.04 0.00 0.00 0 0.00 0.96 0.00
#> TCGA.XV.AAZW.01 6 0.2259 0.595 0.16 0.00 0.00 0 0.00 0.84 0.00
#> TCGA.QB.AA9O.06 4 0.0000 1.000 0.00 0.00 0.00 1 0.00 0.00 0.00
#> TCGA.BF.A3DJ.01 6 0.2376 0.660 0.02 0.00 0.00 0 0.12 0.86 0.00
#> TCGA.EB.A4P0.01 6 0.3186 0.564 0.00 0.00 0.02 0 0.22 0.76 0.00
#> TCGA.FS.A4FB.06 4 0.0000 1.000 0.00 0.00 0.00 1 0.00 0.00 0.00
#> TCGA.FS.A4F4.06 6 0.5760 0.431 0.28 0.00 0.02 0 0.14 0.54 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.GN.A8LL.06 4 0.0000 1.0000 0.00 0.00 0.00 1 0.00 0.00 0.00 0.00
#> TCGA.WE.A8ZT.06 4 0.0000 1.0000 0.00 0.00 0.00 1 0.00 0.00 0.00 0.00
#> TCGA.DA.A95Y.06 5 0.4897 0.4505 0.00 0.00 0.00 0 0.52 0.00 0.28 0.20
#> TCGA.GN.A4U3.06 5 0.5045 0.4674 0.06 0.00 0.00 0 0.62 0.00 0.14 0.18
#> TCGA.GN.A4U7.06 4 0.0000 1.0000 0.00 0.00 0.00 1 0.00 0.00 0.00 0.00
#> TCGA.BF.A5EP.01 3 0.2650 0.4891 0.24 0.00 0.76 0 0.00 0.00 0.00 0.00
#> TCGA.D3.A5GL.06 3 0.2406 0.4895 0.00 0.00 0.80 0 0.00 0.00 0.00 0.20
#> TCGA.FS.A1YY.06 2 0.0000 0.9508 0.00 1.00 0.00 0 0.00 0.00 0.00 0.00
#> TCGA.EE.A2MK.06 5 0.2938 -0.0586 0.00 0.00 0.00 0 0.70 0.30 0.00 0.00
#> TCGA.EE.A3AE.06 5 0.2025 0.3876 0.02 0.00 0.00 0 0.88 0.10 0.00 0.00
#> TCGA.EB.A51B.01 3 0.4799 0.4277 0.00 0.00 0.54 0 0.00 0.18 0.00 0.28
#> TCGA.D3.A2JG.06 1 0.3083 0.4100 0.66 0.34 0.00 0 0.00 0.00 0.00 0.00
#> TCGA.EB.A4XL.01 4 0.0000 1.0000 0.00 0.00 0.00 1 0.00 0.00 0.00 0.00
#> TCGA.EE.A17X.06 7 0.0471 0.0000 0.00 0.00 0.00 0 0.00 0.02 0.98 0.00
#> TCGA.EE.A3AF.06 2 0.2224 0.8429 0.00 0.86 0.00 0 0.00 0.00 0.02 0.12
#> TCGA.EE.A29H.06 1 0.1563 0.3728 0.90 0.00 0.10 0 0.00 0.00 0.00 0.00
#> TCGA.XV.AB01.01 2 0.0000 0.9508 0.00 1.00 0.00 0 0.00 0.00 0.00 0.00
#> TCGA.EB.A3XC.01 5 0.4897 0.4505 0.00 0.00 0.00 0 0.52 0.00 0.28 0.20
#> TCGA.FR.A3R1.01 2 0.0000 0.9508 0.00 1.00 0.00 0 0.00 0.00 0.00 0.00
#> TCGA.EB.A3XF.01 6 0.0471 0.6423 0.00 0.00 0.00 0 0.02 0.98 0.00 0.00
#> TCGA.XV.AAZW.01 6 0.2224 0.5427 0.00 0.00 0.00 0 0.02 0.86 0.00 0.12
#> TCGA.QB.AA9O.06 4 0.0000 1.0000 0.00 0.00 0.00 1 0.00 0.00 0.00 0.00
#> TCGA.BF.A3DJ.01 6 0.2569 0.6123 0.00 0.00 0.00 0 0.16 0.82 0.00 0.02
#> TCGA.EB.A4P0.01 6 0.3272 0.4378 0.00 0.00 0.00 0 0.42 0.58 0.00 0.00
#> TCGA.FS.A4FB.06 4 0.0000 1.0000 0.00 0.00 0.00 1 0.00 0.00 0.00 0.00
#> TCGA.FS.A4F4.06 6 0.5612 0.3447 0.02 0.00 0.00 0 0.28 0.38 0.00 0.32
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
consensus_heatmap(res, k = 7)
consensus_heatmap(res, k = 8)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
membership_heatmap(res, k = 7)
membership_heatmap(res, k = 8)
As soon as the classes for columns are determined, the signatures that are significantly different between subgroups can be looked for. Following are the heatmaps for signatures.
get_signatures(res, k = 2)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
get_signatures(res, k = 7)
get_signatures(res, k = 8)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. To get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows (which is done by automatically selecting number of clusters).If there are too many signatures, top_signatures = ... can be set to only show the
signatures with the highest FDRs:
# code only for demonstration
# e.g. to show the top 500 most significant rows
tb = get_signature(res, k = ..., top_signatures = 500)
If the signatures are defined as these which are uniquely high in current group, diff_method argument
can be set to "uniquely_high_in_one_group":
# code only for demonstration
tb = get_signature(res, k = ..., diff_method = "uniquely_high_in_one_group")
UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
dimension_reduction(res, k = 7, method = "UMAP")
dimension_reduction(res, k = 8, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
If matrix rows can be associated to genes, consider to use functional_enrichment(res,
...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.
Parent node: Node031. Child nodes: Node01111-leaf , Node01112-leaf , Node01113-leaf , Node01131-leaf , Node01132-leaf , Node01133-leaf , Node01311-leaf , Node01312-leaf , Node02121-leaf , Node02122-leaf , Node02123-leaf , Node03111-leaf , Node03112-leaf , Node03113-leaf , Node03221-leaf , Node03222-leaf , Node03231-leaf , Node03232-leaf , Node03233-leaf , Node03234-leaf , Node04111-leaf , Node04112-leaf , Node04121-leaf , Node04122-leaf , Node04421-leaf , Node04422-leaf , Node04423-leaf , Node04424-leaf , Node05111-leaf , Node05112-leaf , Node05113-leaf .
The object with results only for a single top-value method and a single partitioning method can be extracted as:
res = res_rh["0311"]
A summary of res and all the functions that can be applied to it:
res
#> A 'ConsensusPartition' object with k = 2, 3, 4, 5, 6, 7, 8.
#> On a matrix with 30000 rows and 17 columns.
#> Top rows (1000) are extracted by 'ATC' method.
#> Subgroups are detected by 'skmeans' method.
#> Performed in total 350 partitions by row resampling.
#> Best k for subgroups seems to be 3.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_partitions"
#> [7] "compare_signatures" "consensus_heatmap" "dimension_reduction"
#> [10] "functional_enrichment" "get_anno_col" "get_anno"
#> [13] "get_classes" "get_consensus" "get_matrix"
#> [16] "get_membership" "get_param" "get_signatures"
#> [19] "get_stats" "is_best_k" "is_stable_k"
#> [22] "membership_heatmap" "ncol" "nrow"
#> [25] "plot_ecdf" "predict_classes" "rownames"
#> [28] "select_partition_number" "show" "suggest_best_k"
#> [31] "test_to_known_factors" "top_rows_heatmap"
collect_plots() function collects all the plots made from res for all k (number of subgroups)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
The plots are:
k and the heatmap of
predicted classes for each k.k.k.k.All the plots in panels can be made by individual functions and they are plotted later in this section.
select_partition_number() produces several plots showing different
statistics for choosing “optimized” k. There are following statistics:
k;k, the area increased is defined as \(A_k - A_{k-1}\).The detailed explanations of these statistics can be found in the cola vignette.
Generally speaking, higher 1-PAC score, higher mean silhouette score or higher
concordance corresponds to better partition. Rand index and Jaccard index
measure how similar the current partition is compared to partition with k-1.
If they are too similar, we won't accept k is better than k-1.
select_partition_number(res)
The numeric values for all these statistics can be obtained by get_stats().
get_stats(res)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> 2 2 1.000 1.000 1.000 0.5152 0.485 0.485
#> 3 3 1.000 1.000 1.000 0.1996 0.882 0.761
#> 4 4 0.787 0.868 0.895 0.1363 0.897 0.731
#> 5 5 0.750 0.774 0.864 0.0914 1.000 1.000
#> 6 6 0.809 0.130 0.748 0.0512 0.904 0.667
#> 7 7 0.846 0.723 0.920 0.0504 0.868 0.438
#> 8 8 0.926 0.687 0.951 0.0324 0.993 0.947
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.GN.A8LL.06 2 0 1 0 1
#> TCGA.WE.A8ZT.06 2 0 1 0 1
#> TCGA.DA.A95Y.06 1 0 1 1 0
#> TCGA.GN.A4U3.06 1 0 1 1 0
#> TCGA.GN.A4U7.06 1 0 1 1 0
#> TCGA.EE.A2MK.06 2 0 1 0 1
#> TCGA.EE.A3AE.06 2 0 1 0 1
#> TCGA.EB.A4XL.01 2 0 1 0 1
#> TCGA.EE.A17X.06 1 0 1 1 0
#> TCGA.EB.A3XC.01 1 0 1 1 0
#> TCGA.EB.A3XF.01 2 0 1 0 1
#> TCGA.XV.AAZW.01 2 0 1 0 1
#> TCGA.QB.AA9O.06 1 0 1 1 0
#> TCGA.BF.A3DJ.01 2 0 1 0 1
#> TCGA.EB.A4P0.01 2 0 1 0 1
#> TCGA.FS.A4FB.06 2 0 1 0 1
#> TCGA.FS.A4F4.06 1 0 1 1 0
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.GN.A8LL.06 3 0 1 0 0 1
#> TCGA.WE.A8ZT.06 2 0 1 0 1 0
#> TCGA.DA.A95Y.06 1 0 1 1 0 0
#> TCGA.GN.A4U3.06 1 0 1 1 0 0
#> TCGA.GN.A4U7.06 3 0 1 0 0 1
#> TCGA.EE.A2MK.06 2 0 1 0 1 0
#> TCGA.EE.A3AE.06 2 0 1 0 1 0
#> TCGA.EB.A4XL.01 2 0 1 0 1 0
#> TCGA.EE.A17X.06 1 0 1 1 0 0
#> TCGA.EB.A3XC.01 1 0 1 1 0 0
#> TCGA.EB.A3XF.01 2 0 1 0 1 0
#> TCGA.XV.AAZW.01 2 0 1 0 1 0
#> TCGA.QB.AA9O.06 1 0 1 1 0 0
#> TCGA.BF.A3DJ.01 2 0 1 0 1 0
#> TCGA.EB.A4P0.01 2 0 1 0 1 0
#> TCGA.FS.A4FB.06 2 0 1 0 1 0
#> TCGA.FS.A4F4.06 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.GN.A8LL.06 3 0.380 0.860 0.00 0.00 0.78 0.22
#> TCGA.WE.A8ZT.06 2 0.000 0.849 0.00 1.00 0.00 0.00
#> TCGA.DA.A95Y.06 1 0.000 0.973 1.00 0.00 0.00 0.00
#> TCGA.GN.A4U3.06 1 0.121 0.956 0.96 0.00 0.00 0.04
#> TCGA.GN.A4U7.06 3 0.000 0.860 0.00 0.00 1.00 0.00
#> TCGA.EE.A2MK.06 2 0.000 0.849 0.00 1.00 0.00 0.00
#> TCGA.EE.A3AE.06 4 0.491 1.000 0.00 0.42 0.00 0.58
#> TCGA.EB.A4XL.01 4 0.491 1.000 0.00 0.42 0.00 0.58
#> TCGA.EE.A17X.06 1 0.000 0.973 1.00 0.00 0.00 0.00
#> TCGA.EB.A3XC.01 1 0.000 0.973 1.00 0.00 0.00 0.00
#> TCGA.EB.A3XF.01 2 0.380 0.629 0.00 0.78 0.00 0.22
#> TCGA.XV.AAZW.01 2 0.000 0.849 0.00 1.00 0.00 0.00
#> TCGA.QB.AA9O.06 1 0.000 0.973 1.00 0.00 0.00 0.00
#> TCGA.BF.A3DJ.01 2 0.121 0.821 0.00 0.96 0.00 0.04
#> TCGA.EB.A4P0.01 2 0.441 0.444 0.00 0.70 0.00 0.30
#> TCGA.FS.A4FB.06 2 0.000 0.849 0.00 1.00 0.00 0.00
#> TCGA.FS.A4F4.06 1 0.304 0.899 0.88 0.00 0.02 0.10
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> TCGA.GN.A8LL.06 3 0.526 0.746 0.00 0.00 0.66 0.24 0.10
#> TCGA.WE.A8ZT.06 2 0.499 0.812 0.00 0.60 0.00 0.36 0.04
#> TCGA.DA.A95Y.06 1 0.000 0.870 1.00 0.00 0.00 0.00 0.00
#> TCGA.GN.A4U3.06 1 0.356 0.739 0.74 0.00 0.00 0.26 0.00
#> TCGA.GN.A4U7.06 3 0.000 0.746 0.00 0.00 1.00 0.00 0.00
#> TCGA.EE.A2MK.06 2 0.499 0.812 0.00 0.60 0.00 0.36 0.04
#> TCGA.EE.A3AE.06 5 0.202 1.000 0.00 0.10 0.00 0.00 0.90
#> TCGA.EB.A4XL.01 5 0.202 1.000 0.00 0.10 0.00 0.00 0.90
#> TCGA.EE.A17X.06 1 0.000 0.870 1.00 0.00 0.00 0.00 0.00
#> TCGA.EB.A3XC.01 1 0.000 0.870 1.00 0.00 0.00 0.00 0.00
#> TCGA.EB.A3XF.01 2 0.141 0.460 0.00 0.94 0.00 0.00 0.06
#> TCGA.XV.AAZW.01 2 0.499 0.812 0.00 0.60 0.00 0.36 0.04
#> TCGA.QB.AA9O.06 1 0.000 0.870 1.00 0.00 0.00 0.00 0.00
#> TCGA.BF.A3DJ.01 2 0.454 0.798 0.00 0.64 0.00 0.34 0.02
#> TCGA.EB.A4P0.01 2 0.228 0.365 0.00 0.88 0.00 0.00 0.12
#> TCGA.FS.A4FB.06 2 0.499 0.812 0.00 0.60 0.00 0.36 0.04
#> TCGA.FS.A4F4.06 1 0.509 0.574 0.56 0.00 0.04 0.40 0.00
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> TCGA.GN.A8LL.06 3 0.0000 0.000 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.WE.A8ZT.06 2 0.3869 -1.000 0.00 0.50 0.00 0.00 0.00 0.50
#> TCGA.DA.A95Y.06 1 0.0547 0.841 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.GN.A4U3.06 1 0.3851 0.148 0.54 0.00 0.00 0.46 0.00 0.00
#> TCGA.GN.A4U7.06 4 0.6424 -0.364 0.00 0.00 0.24 0.50 0.04 0.22
#> TCGA.EE.A2MK.06 6 0.3869 0.000 0.00 0.50 0.00 0.00 0.00 0.50
#> TCGA.EE.A3AE.06 5 0.1092 1.000 0.00 0.02 0.00 0.00 0.96 0.02
#> TCGA.EB.A4XL.01 5 0.1092 1.000 0.00 0.02 0.00 0.00 0.96 0.02
#> TCGA.EE.A17X.06 1 0.0547 0.841 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.EB.A3XC.01 1 0.0000 0.841 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EB.A3XF.01 2 0.0547 0.232 0.00 0.98 0.00 0.00 0.02 0.00
#> TCGA.XV.AAZW.01 2 0.3869 -1.000 0.00 0.50 0.00 0.00 0.00 0.50
#> TCGA.QB.AA9O.06 1 0.0547 0.834 0.98 0.00 0.00 0.02 0.00 0.00
#> TCGA.BF.A3DJ.01 2 0.3409 -0.232 0.00 0.70 0.00 0.00 0.00 0.30
#> TCGA.EB.A4P0.01 2 0.2094 0.227 0.00 0.90 0.00 0.00 0.08 0.02
#> TCGA.FS.A4FB.06 2 0.3869 -1.000 0.00 0.50 0.00 0.00 0.00 0.50
#> TCGA.FS.A4F4.06 4 0.5801 -0.152 0.26 0.00 0.00 0.50 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.GN.A8LL.06 3 0.0000 0.000 0.00 0.00 1.0 0.00 0.00 0.00 0.00
#> TCGA.WE.A8ZT.06 2 0.0000 0.969 0.00 1.00 0.0 0.00 0.00 0.00 0.00
#> TCGA.DA.A95Y.06 1 0.0000 0.910 1.00 0.00 0.0 0.00 0.00 0.00 0.00
#> TCGA.GN.A4U3.06 4 0.6253 0.199 0.36 0.00 0.0 0.42 0.00 0.10 0.12
#> TCGA.GN.A4U7.06 6 0.1671 0.000 0.00 0.00 0.1 0.00 0.00 0.90 0.00
#> TCGA.EE.A2MK.06 2 0.0000 0.969 0.00 1.00 0.0 0.00 0.00 0.00 0.00
#> TCGA.EE.A3AE.06 5 0.0000 0.972 0.00 0.00 0.0 0.00 1.00 0.00 0.00
#> TCGA.EB.A4XL.01 5 0.0504 0.972 0.00 0.02 0.0 0.00 0.98 0.00 0.00
#> TCGA.EE.A17X.06 1 0.0000 0.910 1.00 0.00 0.0 0.00 0.00 0.00 0.00
#> TCGA.EB.A3XC.01 1 0.0863 0.901 0.96 0.00 0.0 0.04 0.00 0.00 0.00
#> TCGA.EB.A3XF.01 7 0.3052 0.817 0.00 0.20 0.0 0.00 0.02 0.00 0.78
#> TCGA.XV.AAZW.01 2 0.0000 0.969 0.00 1.00 0.0 0.00 0.00 0.00 0.00
#> TCGA.QB.AA9O.06 1 0.2745 0.772 0.82 0.00 0.0 0.16 0.00 0.02 0.00
#> TCGA.BF.A3DJ.01 2 0.1671 0.865 0.00 0.90 0.0 0.00 0.00 0.00 0.10
#> TCGA.EB.A4P0.01 7 0.2278 0.811 0.00 0.08 0.0 0.00 0.04 0.00 0.88
#> TCGA.FS.A4FB.06 2 0.0000 0.969 0.00 1.00 0.0 0.00 0.00 0.00 0.00
#> TCGA.FS.A4F4.06 4 0.0000 0.288 0.00 0.00 0.0 1.00 0.00 0.00 0.00
cbind(get_classes(res, k = 8), get_membership(res, k = 8))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7 p8
#> TCGA.GN.A8LL.06 3 0.0471 0.000 0.00 0.00 0.98 0.00 0.00 0.02 0.00 0.00
#> TCGA.WE.A8ZT.06 2 0.0000 0.928 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DA.A95Y.06 1 0.0000 0.929 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.GN.A4U3.06 4 0.0471 0.000 0.02 0.00 0.00 0.98 0.00 0.00 0.00 0.00
#> TCGA.GN.A4U7.06 6 0.0471 0.000 0.00 0.00 0.02 0.00 0.00 0.98 0.00 0.00
#> TCGA.EE.A2MK.06 2 0.0000 0.928 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EE.A3AE.06 5 0.1091 0.931 0.00 0.00 0.00 0.00 0.94 0.00 0.00 0.06
#> TCGA.EB.A4XL.01 5 0.0471 0.931 0.00 0.00 0.00 0.00 0.98 0.00 0.02 0.00
#> TCGA.EE.A17X.06 1 0.0808 0.915 0.96 0.00 0.00 0.04 0.00 0.00 0.00 0.00
#> TCGA.EB.A3XC.01 1 0.0471 0.930 0.98 0.00 0.00 0.02 0.00 0.00 0.00 0.00
#> TCGA.EB.A3XF.01 7 0.0941 0.920 0.00 0.02 0.00 0.00 0.02 0.00 0.96 0.00
#> TCGA.XV.AAZW.01 2 0.0000 0.928 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.QB.AA9O.06 1 0.2864 0.845 0.84 0.00 0.00 0.06 0.00 0.02 0.00 0.08
#> TCGA.BF.A3DJ.01 2 0.2756 0.650 0.00 0.74 0.00 0.00 0.00 0.00 0.26 0.00
#> TCGA.EB.A4P0.01 7 0.0941 0.919 0.00 0.00 0.02 0.00 0.00 0.00 0.96 0.02
#> TCGA.FS.A4FB.06 2 0.0000 0.928 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FS.A4F4.06 8 0.1947 0.000 0.00 0.00 0.00 0.14 0.00 0.00 0.00 0.86
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
consensus_heatmap(res, k = 7)
consensus_heatmap(res, k = 8)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
membership_heatmap(res, k = 7)
membership_heatmap(res, k = 8)
As soon as the classes for columns are determined, the signatures that are significantly different between subgroups can be looked for. Following are the heatmaps for signatures.
get_signatures(res, k = 2)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
get_signatures(res, k = 7)
get_signatures(res, k = 8)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. To get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows (which is done by automatically selecting number of clusters).If there are too many signatures, top_signatures = ... can be set to only show the
signatures with the highest FDRs:
# code only for demonstration
# e.g. to show the top 500 most significant rows
tb = get_signature(res, k = ..., top_signatures = 500)
If the signatures are defined as these which are uniquely high in current group, diff_method argument
can be set to "uniquely_high_in_one_group":
# code only for demonstration
tb = get_signature(res, k = ..., diff_method = "uniquely_high_in_one_group")
UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
dimension_reduction(res, k = 7, method = "UMAP")
dimension_reduction(res, k = 8, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
If matrix rows can be associated to genes, consider to use functional_enrichment(res,
...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.
Parent node: Node03. Child nodes: Node0111 , Node0112-leaf , Node0113 , Node0121-leaf , Node0122-leaf , Node0123-leaf , Node0124-leaf , Node0125-leaf , Node0131 , Node0132-leaf , Node0133-leaf , Node0211-leaf , Node0212 , Node0221-leaf , Node0222-leaf , Node0311 , Node0312-leaf , Node0321-leaf , Node0322 , Node0323 , Node0411 , Node0412 , Node0413-leaf , Node0421-leaf , Node0422-leaf , Node0423-leaf , Node0431-leaf , Node0432-leaf , Node0433-leaf , Node0441-leaf , Node0442 , Node0443-leaf , Node0511 , Node0512-leaf , Node0513-leaf , Node0521-leaf , Node0522-leaf , Node0523-leaf , Node0524-leaf .
The object with results only for a single top-value method and a single partitioning method can be extracted as:
res = res_rh["032"]
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 47 columns.
#> Top rows (1000) are extracted by 'ATC' method.
#> Subgroups are detected by 'kmeans' method.
#> Performed in total 350 partitions by row resampling.
#> Best k for subgroups seems to be 3.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_partitions"
#> [7] "compare_signatures" "consensus_heatmap" "dimension_reduction"
#> [10] "functional_enrichment" "get_anno_col" "get_anno"
#> [13] "get_classes" "get_consensus" "get_matrix"
#> [16] "get_membership" "get_param" "get_signatures"
#> [19] "get_stats" "is_best_k" "is_stable_k"
#> [22] "membership_heatmap" "ncol" "nrow"
#> [25] "plot_ecdf" "predict_classes" "rownames"
#> [28] "select_partition_number" "show" "suggest_best_k"
#> [31] "test_to_known_factors" "top_rows_heatmap"
collect_plots() function collects all the plots made from res for all k (number of subgroups)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
The plots are:
k and the heatmap of
predicted classes for each k.k.k.k.All the plots in panels can be made by individual functions and they are plotted later in this section.
select_partition_number() produces several plots showing different
statistics for choosing “optimized” k. There are following statistics:
k;k, the area increased is defined as \(A_k - A_{k-1}\).The detailed explanations of these statistics can be found in the cola vignette.
Generally speaking, higher 1-PAC score, higher mean silhouette score or higher
concordance corresponds to better partition. Rand index and Jaccard index
measure how similar the current partition is compared to partition with k-1.
If they are too similar, we won't accept k is better than k-1.
select_partition_number(res)
The numeric values for all these statistics can be obtained by get_stats().
get_stats(res)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> 2 2 1.000 0.993 0.996 0.4582 0.541 0.541
#> 3 3 1.000 0.992 0.995 0.4565 0.730 0.528
#> 4 4 0.809 0.887 0.923 0.1171 0.826 0.533
#> 5 5 0.882 0.888 0.925 0.0438 0.987 0.946
#> 6 6 0.868 0.817 0.885 0.0319 1.000 1.000
#> 7 7 0.850 0.693 0.840 0.0262 0.957 0.811
#> 8 8 0.879 0.683 0.840 0.0177 0.960 0.794
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.ER.A42K.06 1 0.000 0.992 1.00 0.00
#> TCGA.FS.A4F2.06 2 0.000 0.998 0.00 1.00
#> TCGA.WE.A8K6.06 1 0.000 0.992 1.00 0.00
#> TCGA.Z2.A8RT.06 1 0.000 0.992 1.00 0.00
#> TCGA.EB.A41B.01 1 0.000 0.992 1.00 0.00
#> TCGA.EB.A6R0.01 2 0.000 0.998 0.00 1.00
#> TCGA.D9.A4Z2.01 2 0.000 0.998 0.00 1.00
#> TCGA.D3.A3MV.06 2 0.000 0.998 0.00 1.00
#> TCGA.FS.A1ZQ.06 2 0.000 0.998 0.00 1.00
#> TCGA.ER.A19F.06 2 0.000 0.998 0.00 1.00
#> TCGA.EE.A3AG.06 2 0.000 0.998 0.00 1.00
#> TCGA.ER.A19B.06 2 0.000 0.998 0.00 1.00
#> TCGA.D3.A5GN.06 2 0.000 0.998 0.00 1.00
#> TCGA.EE.A2GB.06 2 0.000 0.998 0.00 1.00
#> TCGA.FS.A1Z3.06 1 0.000 0.992 1.00 0.00
#> TCGA.DA.A1I8.06 2 0.000 0.998 0.00 1.00
#> TCGA.D3.A5GS.06 2 0.000 0.998 0.00 1.00
#> TCGA.EE.A2GS.06 1 0.000 0.992 1.00 0.00
#> TCGA.D3.A5GO.06 2 0.000 0.998 0.00 1.00
#> TCGA.EE.A29Q.06 2 0.000 0.998 0.00 1.00
#> TCGA.BF.A1PZ.01 1 0.000 0.992 1.00 0.00
#> TCGA.D9.A1JX.06 2 0.000 0.998 0.00 1.00
#> TCGA.FS.A1ZF.06 2 0.000 0.998 0.00 1.00
#> TCGA.EE.A29W.06 1 0.000 0.992 1.00 0.00
#> TCGA.DA.A1HV.06 2 0.000 0.998 0.00 1.00
#> TCGA.ER.A19H.06 2 0.000 0.998 0.00 1.00
#> TCGA.DA.A1HY.06 2 0.000 0.998 0.00 1.00
#> TCGA.D3.A3C7.06 1 0.000 0.992 1.00 0.00
#> TCGA.EE.A2MP.06 2 0.000 0.998 0.00 1.00
#> TCGA.ER.A19G.06 2 0.000 0.998 0.00 1.00
#> TCGA.FR.A69P.06 1 0.000 0.992 1.00 0.00
#> TCGA.D3.A3C6.06 2 0.000 0.998 0.00 1.00
#> TCGA.EE.A2A2.06 2 0.000 0.998 0.00 1.00
#> TCGA.BF.AAP6.01 2 0.000 0.998 0.00 1.00
#> TCGA.EB.A299.01 1 0.242 0.964 0.96 0.04
#> TCGA.D3.A2JF.06 2 0.000 0.998 0.00 1.00
#> TCGA.FR.A3YN.06 1 0.242 0.964 0.96 0.04
#> TCGA.EE.A3J3.06 1 0.000 0.992 1.00 0.00
#> TCGA.D3.A51G.06 2 0.000 0.998 0.00 1.00
#> TCGA.D3.A51R.06 2 0.000 0.998 0.00 1.00
#> TCGA.BF.A3DM.01 1 0.000 0.992 1.00 0.00
#> TCGA.W3.AA1R.06 2 0.000 0.998 0.00 1.00
#> TCGA.EE.A3JA.06 2 0.327 0.935 0.06 0.94
#> TCGA.BF.A3DN.01 1 0.000 0.992 1.00 0.00
#> TCGA.D3.A51E.06 2 0.000 0.998 0.00 1.00
#> TCGA.DA.A3F3.06 1 0.242 0.964 0.96 0.04
#> TCGA.D3.A51T.06 2 0.000 0.998 0.00 1.00
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.ER.A42K.06 1 0.0000 0.999 1.00 0.00 0.00
#> TCGA.FS.A4F2.06 2 0.0000 0.996 0.00 1.00 0.00
#> TCGA.WE.A8K6.06 1 0.0000 0.999 1.00 0.00 0.00
#> TCGA.Z2.A8RT.06 1 0.0000 0.999 1.00 0.00 0.00
#> TCGA.EB.A41B.01 1 0.0892 0.982 0.98 0.00 0.02
#> TCGA.EB.A6R0.01 2 0.0000 0.996 0.00 1.00 0.00
#> TCGA.D9.A4Z2.01 2 0.0892 0.978 0.00 0.98 0.02
#> TCGA.D3.A3MV.06 2 0.2066 0.937 0.00 0.94 0.06
#> TCGA.FS.A1ZQ.06 3 0.0000 0.989 0.00 0.00 1.00
#> TCGA.ER.A19F.06 2 0.0000 0.996 0.00 1.00 0.00
#> TCGA.EE.A3AG.06 2 0.0000 0.996 0.00 1.00 0.00
#> TCGA.ER.A19B.06 3 0.0000 0.989 0.00 0.00 1.00
#> TCGA.D3.A5GN.06 3 0.0892 0.986 0.00 0.02 0.98
#> TCGA.EE.A2GB.06 2 0.0000 0.996 0.00 1.00 0.00
#> TCGA.FS.A1Z3.06 1 0.0000 0.999 1.00 0.00 0.00
#> TCGA.DA.A1I8.06 2 0.0000 0.996 0.00 1.00 0.00
#> TCGA.D3.A5GS.06 3 0.0000 0.989 0.00 0.00 1.00
#> TCGA.EE.A2GS.06 1 0.0000 0.999 1.00 0.00 0.00
#> TCGA.D3.A5GO.06 2 0.0000 0.996 0.00 1.00 0.00
#> TCGA.EE.A29Q.06 3 0.0000 0.989 0.00 0.00 1.00
#> TCGA.BF.A1PZ.01 1 0.0000 0.999 1.00 0.00 0.00
#> TCGA.D9.A1JX.06 2 0.0000 0.996 0.00 1.00 0.00
#> TCGA.FS.A1ZF.06 3 0.0892 0.986 0.00 0.02 0.98
#> TCGA.EE.A29W.06 1 0.0000 0.999 1.00 0.00 0.00
#> TCGA.DA.A1HV.06 2 0.0000 0.996 0.00 1.00 0.00
#> TCGA.ER.A19H.06 2 0.0000 0.996 0.00 1.00 0.00
#> TCGA.DA.A1HY.06 2 0.0000 0.996 0.00 1.00 0.00
#> TCGA.D3.A3C7.06 1 0.0000 0.999 1.00 0.00 0.00
#> TCGA.EE.A2MP.06 3 0.0892 0.986 0.00 0.02 0.98
#> TCGA.ER.A19G.06 2 0.0000 0.996 0.00 1.00 0.00
#> TCGA.FR.A69P.06 1 0.0000 0.999 1.00 0.00 0.00
#> TCGA.D3.A3C6.06 3 0.0892 0.986 0.00 0.02 0.98
#> TCGA.EE.A2A2.06 2 0.0000 0.996 0.00 1.00 0.00
#> TCGA.BF.AAP6.01 2 0.0000 0.996 0.00 1.00 0.00
#> TCGA.EB.A299.01 3 0.0000 0.989 0.00 0.00 1.00
#> TCGA.D3.A2JF.06 3 0.0892 0.986 0.00 0.02 0.98
#> TCGA.FR.A3YN.06 3 0.0000 0.989 0.00 0.00 1.00
#> TCGA.EE.A3J3.06 1 0.0000 0.999 1.00 0.00 0.00
#> TCGA.D3.A51G.06 3 0.0892 0.986 0.00 0.02 0.98
#> TCGA.D3.A51R.06 2 0.0000 0.996 0.00 1.00 0.00
#> TCGA.BF.A3DM.01 1 0.0000 0.999 1.00 0.00 0.00
#> TCGA.W3.AA1R.06 2 0.0000 0.996 0.00 1.00 0.00
#> TCGA.EE.A3JA.06 3 0.0000 0.989 0.00 0.00 1.00
#> TCGA.BF.A3DN.01 1 0.0000 0.999 1.00 0.00 0.00
#> TCGA.D3.A51E.06 2 0.0000 0.996 0.00 1.00 0.00
#> TCGA.DA.A3F3.06 3 0.0000 0.989 0.00 0.00 1.00
#> TCGA.D3.A51T.06 2 0.0000 0.996 0.00 1.00 0.00
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> TCGA.ER.A42K.06 1 0.0000 0.976 1.00 0.00 0.00 0.00
#> TCGA.FS.A4F2.06 2 0.0000 1.000 0.00 1.00 0.00 0.00
#> TCGA.WE.A8K6.06 1 0.0000 0.976 1.00 0.00 0.00 0.00
#> TCGA.Z2.A8RT.06 1 0.0000 0.976 1.00 0.00 0.00 0.00
#> TCGA.EB.A41B.01 3 0.4624 0.296 0.34 0.00 0.66 0.00
#> TCGA.EB.A6R0.01 4 0.4713 0.593 0.00 0.36 0.00 0.64
#> TCGA.D9.A4Z2.01 4 0.2921 0.813 0.00 0.14 0.00 0.86
#> TCGA.D3.A3MV.06 4 0.2921 0.813 0.00 0.14 0.00 0.86
#> TCGA.FS.A1ZQ.06 3 0.3400 0.870 0.00 0.00 0.82 0.18
#> TCGA.ER.A19F.06 2 0.0000 1.000 0.00 1.00 0.00 0.00
#> TCGA.EE.A3AG.06 2 0.0000 1.000 0.00 1.00 0.00 0.00
#> TCGA.ER.A19B.06 3 0.4522 0.767 0.00 0.00 0.68 0.32
#> TCGA.D3.A5GN.06 4 0.0707 0.806 0.00 0.02 0.00 0.98
#> TCGA.EE.A2GB.06 2 0.0000 1.000 0.00 1.00 0.00 0.00
#> TCGA.FS.A1Z3.06 1 0.0000 0.976 1.00 0.00 0.00 0.00
#> TCGA.DA.A1I8.06 4 0.4790 0.556 0.00 0.38 0.00 0.62
#> TCGA.D3.A5GS.06 3 0.3610 0.866 0.00 0.00 0.80 0.20
#> TCGA.EE.A2GS.06 1 0.0000 0.976 1.00 0.00 0.00 0.00
#> TCGA.D3.A5GO.06 2 0.0000 1.000 0.00 1.00 0.00 0.00
#> TCGA.EE.A29Q.06 3 0.4522 0.767 0.00 0.00 0.68 0.32
#> TCGA.BF.A1PZ.01 1 0.0000 0.976 1.00 0.00 0.00 0.00
#> TCGA.D9.A1JX.06 4 0.3610 0.787 0.00 0.20 0.00 0.80
#> TCGA.FS.A1ZF.06 4 0.0000 0.796 0.00 0.00 0.00 1.00
#> TCGA.EE.A29W.06 1 0.0000 0.976 1.00 0.00 0.00 0.00
#> TCGA.DA.A1HV.06 2 0.0000 1.000 0.00 1.00 0.00 0.00
#> TCGA.ER.A19H.06 4 0.3610 0.787 0.00 0.20 0.00 0.80
#> TCGA.DA.A1HY.06 2 0.0000 1.000 0.00 1.00 0.00 0.00
#> TCGA.D3.A3C7.06 1 0.2345 0.926 0.90 0.00 0.10 0.00
#> TCGA.EE.A2MP.06 4 0.0707 0.806 0.00 0.02 0.00 0.98
#> TCGA.ER.A19G.06 2 0.0000 1.000 0.00 1.00 0.00 0.00
#> TCGA.FR.A69P.06 1 0.2345 0.926 0.90 0.00 0.10 0.00
#> TCGA.D3.A3C6.06 4 0.0000 0.796 0.00 0.00 0.00 1.00
#> TCGA.EE.A2A2.06 2 0.0000 1.000 0.00 1.00 0.00 0.00
#> TCGA.BF.AAP6.01 2 0.0000 1.000 0.00 1.00 0.00 0.00
#> TCGA.EB.A299.01 3 0.3400 0.870 0.00 0.00 0.82 0.18
#> TCGA.D3.A2JF.06 4 0.0000 0.796 0.00 0.00 0.00 1.00
#> TCGA.FR.A3YN.06 3 0.3400 0.870 0.00 0.00 0.82 0.18
#> TCGA.EE.A3J3.06 1 0.2345 0.926 0.90 0.00 0.10 0.00
#> TCGA.D3.A51G.06 4 0.0000 0.796 0.00 0.00 0.00 1.00
#> TCGA.D3.A51R.06 2 0.0000 1.000 0.00 1.00 0.00 0.00
#> TCGA.BF.A3DM.01 1 0.0000 0.976 1.00 0.00 0.00 0.00
#> TCGA.W3.AA1R.06 2 0.0000 1.000 0.00 1.00 0.00 0.00
#> TCGA.EE.A3JA.06 3 0.2647 0.843 0.00 0.00 0.88 0.12
#> TCGA.BF.A3DN.01 1 0.0000 0.976 1.00 0.00 0.00 0.00
#> TCGA.D3.A51E.06 2 0.0000 1.000 0.00 1.00 0.00 0.00
#> TCGA.DA.A3F3.06 3 0.2647 0.843 0.00 0.00 0.88 0.12
#> TCGA.D3.A51T.06 2 0.0000 1.000 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.ER.A42K.06 1 0.0000 0.9603 1.00 0.00 0.00 0.00 0.00
#> TCGA.FS.A4F2.06 2 0.0000 0.9920 0.00 1.00 0.00 0.00 0.00
#> TCGA.WE.A8K6.06 1 0.0000 0.9603 1.00 0.00 0.00 0.00 0.00
#> TCGA.Z2.A8RT.06 1 0.0000 0.9603 1.00 0.00 0.00 0.00 0.00
#> TCGA.EB.A41B.01 3 0.5972 0.0627 0.30 0.00 0.56 0.00 0.14
#> TCGA.EB.A6R0.01 4 0.4263 0.8258 0.00 0.06 0.00 0.76 0.18
#> TCGA.D9.A4Z2.01 4 0.1732 0.8914 0.00 0.00 0.00 0.92 0.08
#> TCGA.D3.A3MV.06 4 0.1410 0.8915 0.00 0.00 0.00 0.94 0.06
#> TCGA.FS.A1ZQ.06 3 0.2020 0.7183 0.00 0.00 0.90 0.10 0.00
#> TCGA.ER.A19F.06 2 0.0000 0.9920 0.00 1.00 0.00 0.00 0.00
#> TCGA.EE.A3AG.06 2 0.0000 0.9920 0.00 1.00 0.00 0.00 0.00
#> TCGA.ER.A19B.06 3 0.3037 0.6952 0.00 0.00 0.86 0.10 0.04
#> TCGA.D3.A5GN.06 4 0.0000 0.8850 0.00 0.00 0.00 1.00 0.00
#> TCGA.EE.A2GB.06 2 0.2020 0.8882 0.00 0.90 0.00 0.00 0.10
#> TCGA.FS.A1Z3.06 1 0.0000 0.9603 1.00 0.00 0.00 0.00 0.00
#> TCGA.DA.A1I8.06 4 0.4818 0.7837 0.00 0.10 0.00 0.72 0.18
#> TCGA.D3.A5GS.06 3 0.0609 0.7155 0.00 0.00 0.98 0.02 0.00
#> TCGA.EE.A2GS.06 1 0.0000 0.9603 1.00 0.00 0.00 0.00 0.00
#> TCGA.D3.A5GO.06 2 0.0000 0.9920 0.00 1.00 0.00 0.00 0.00
#> TCGA.EE.A29Q.06 3 0.2280 0.7010 0.00 0.00 0.88 0.12 0.00
#> TCGA.BF.A1PZ.01 1 0.0000 0.9603 1.00 0.00 0.00 0.00 0.00
#> TCGA.D9.A1JX.06 4 0.3690 0.8452 0.00 0.02 0.00 0.78 0.20
#> TCGA.FS.A1ZF.06 4 0.3561 0.8469 0.00 0.00 0.00 0.74 0.26
#> TCGA.EE.A29W.06 1 0.0000 0.9603 1.00 0.00 0.00 0.00 0.00
#> TCGA.DA.A1HV.06 2 0.0000 0.9920 0.00 1.00 0.00 0.00 0.00
#> TCGA.ER.A19H.06 4 0.2012 0.8890 0.00 0.02 0.00 0.92 0.06
#> TCGA.DA.A1HY.06 2 0.0000 0.9920 0.00 1.00 0.00 0.00 0.00
#> TCGA.D3.A3C7.06 1 0.3106 0.8659 0.84 0.00 0.02 0.00 0.14
#> TCGA.EE.A2MP.06 4 0.0000 0.8850 0.00 0.00 0.00 1.00 0.00
#> TCGA.ER.A19G.06 2 0.0000 0.9920 0.00 1.00 0.00 0.00 0.00
#> TCGA.FR.A69P.06 1 0.3106 0.8659 0.84 0.00 0.02 0.00 0.14
#> TCGA.D3.A3C6.06 4 0.1732 0.8719 0.00 0.00 0.00 0.92 0.08
#> TCGA.EE.A2A2.06 2 0.0000 0.9920 0.00 1.00 0.00 0.00 0.00
#> TCGA.BF.AAP6.01 2 0.0000 0.9920 0.00 1.00 0.00 0.00 0.00
#> TCGA.EB.A299.01 3 0.0609 0.7155 0.00 0.00 0.98 0.02 0.00
#> TCGA.D3.A2JF.06 4 0.1410 0.8724 0.00 0.00 0.00 0.94 0.06
#> TCGA.FR.A3YN.06 3 0.0609 0.7155 0.00 0.00 0.98 0.02 0.00
#> TCGA.EE.A3J3.06 1 0.2873 0.8798 0.86 0.00 0.02 0.00 0.12
#> TCGA.D3.A51G.06 4 0.1410 0.8724 0.00 0.00 0.00 0.94 0.06
#> TCGA.D3.A51R.06 2 0.0000 0.9920 0.00 1.00 0.00 0.00 0.00
#> TCGA.BF.A3DM.01 1 0.0000 0.9603 1.00 0.00 0.00 0.00 0.00
#> TCGA.W3.AA1R.06 2 0.0000 0.9920 0.00 1.00 0.00 0.00 0.00
#> TCGA.EE.A3JA.06 5 0.4262 1.0000 0.00 0.00 0.44 0.00 0.56
#> TCGA.BF.A3DN.01 1 0.0000 0.9603 1.00 0.00 0.00 0.00 0.00
#> TCGA.D3.A51E.06 2 0.0000 0.9920 0.00 1.00 0.00 0.00 0.00
#> TCGA.DA.A3F3.06 5 0.4262 1.0000 0.00 0.00 0.44 0.00 0.56
#> TCGA.D3.A51T.06 2 0.0000 0.9920 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.ER.A42K.06 1 0.0000 0.897 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FS.A4F2.06 2 0.0000 0.961 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.WE.A8K6.06 1 0.0000 0.897 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.Z2.A8RT.06 1 0.0000 0.897 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EB.A41B.01 3 0.6481 0.145 0.10 0.00 0.44 0.00 0.08 0.38
#> TCGA.EB.A6R0.01 4 0.3873 0.749 0.00 0.02 0.00 0.78 0.04 0.16
#> TCGA.D9.A4Z2.01 4 0.0000 0.819 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.D3.A3MV.06 4 0.0000 0.819 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.FS.A1ZQ.06 3 0.1092 0.750 0.00 0.00 0.96 0.02 0.02 0.00
#> TCGA.ER.A19F.06 2 0.0000 0.961 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.EE.A3AG.06 2 0.2728 0.865 0.00 0.86 0.00 0.00 0.04 0.10
#> TCGA.ER.A19B.06 3 0.2474 0.713 0.00 0.00 0.88 0.00 0.08 0.04
#> TCGA.D3.A5GN.06 4 0.1092 0.816 0.00 0.00 0.02 0.96 0.02 0.00
#> TCGA.EE.A2GB.06 2 0.5100 0.665 0.00 0.70 0.00 0.08 0.06 0.16
#> TCGA.FS.A1Z3.06 1 0.0000 0.897 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DA.A1I8.06 4 0.3873 0.749 0.00 0.02 0.00 0.78 0.04 0.16
#> TCGA.D3.A5GS.06 3 0.2941 0.582 0.00 0.00 0.78 0.00 0.22 0.00
#> TCGA.EE.A2GS.06 1 0.0000 0.897 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D3.A5GO.06 2 0.0000 0.961 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.EE.A29Q.06 3 0.1092 0.750 0.00 0.00 0.96 0.02 0.02 0.00
#> TCGA.BF.A1PZ.01 1 0.0000 0.897 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D9.A1JX.06 4 0.3163 0.764 0.00 0.00 0.00 0.82 0.04 0.14
#> TCGA.FS.A1ZF.06 4 0.5354 0.685 0.00 0.00 0.00 0.58 0.26 0.16
#> TCGA.EE.A29W.06 1 0.0000 0.897 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DA.A1HV.06 2 0.0000 0.961 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.ER.A19H.06 4 0.0000 0.819 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.DA.A1HY.06 2 0.0000 0.961 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.D3.A3C7.06 1 0.3706 0.626 0.62 0.00 0.00 0.00 0.00 0.38
#> TCGA.EE.A2MP.06 4 0.1092 0.816 0.00 0.00 0.02 0.96 0.02 0.00
#> TCGA.ER.A19G.06 2 0.0000 0.961 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.FR.A69P.06 1 0.3706 0.626 0.62 0.00 0.00 0.00 0.00 0.38
#> TCGA.D3.A3C6.06 4 0.4637 0.626 0.00 0.00 0.02 0.60 0.36 0.02
#> TCGA.EE.A2A2.06 2 0.0000 0.961 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.BF.AAP6.01 2 0.0000 0.961 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.EB.A299.01 3 0.0937 0.736 0.00 0.00 0.96 0.00 0.04 0.00
#> TCGA.D3.A2JF.06 4 0.3592 0.731 0.00 0.00 0.02 0.74 0.24 0.00
#> TCGA.FR.A3YN.06 3 0.2474 0.702 0.00 0.00 0.88 0.00 0.08 0.04
#> TCGA.EE.A3J3.06 1 0.3647 0.644 0.64 0.00 0.00 0.00 0.00 0.36
#> TCGA.D3.A51G.06 4 0.4078 0.658 0.00 0.00 0.02 0.64 0.34 0.00
#> TCGA.D3.A51R.06 2 0.2094 0.894 0.00 0.90 0.00 0.00 0.02 0.08
#> TCGA.BF.A3DM.01 1 0.0000 0.897 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.W3.AA1R.06 2 0.0000 0.961 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.EE.A3JA.06 5 0.5801 1.000 0.00 0.00 0.24 0.00 0.50 0.26
#> TCGA.BF.A3DN.01 1 0.0000 0.897 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D3.A51E.06 2 0.0000 0.961 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DA.A3F3.06 5 0.5801 1.000 0.00 0.00 0.24 0.00 0.50 0.26
#> TCGA.D3.A51T.06 2 0.0000 0.961 0.00 1.00 0.00 0.00 0.00 0.00
cbind(get_classes(res, k = 7), get_membership(res, k = 7))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7
#> TCGA.ER.A42K.06 1 0.0000 0.903 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FS.A4F2.06 2 0.0000 0.893 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.WE.A8K6.06 1 0.0000 0.903 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.Z2.A8RT.06 1 0.0000 0.903 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EB.A41B.01 7 0.7101 0.000 0.06 0.00 0.36 0.00 0.14 0.08 0.36
#> TCGA.EB.A6R0.01 4 0.2422 0.580 0.00 0.00 0.00 0.82 0.00 0.00 0.18
#> TCGA.D9.A4Z2.01 4 0.2081 0.785 0.00 0.00 0.00 0.86 0.00 0.14 0.00
#> TCGA.D3.A3MV.06 4 0.2745 0.778 0.00 0.00 0.02 0.82 0.00 0.16 0.00
#> TCGA.FS.A1ZQ.06 3 0.0504 0.634 0.00 0.00 0.98 0.00 0.00 0.02 0.00
#> TCGA.ER.A19F.06 2 0.0000 0.893 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EE.A3AG.06 2 0.4505 0.413 0.00 0.50 0.00 0.00 0.06 0.00 0.44
#> TCGA.ER.A19B.06 3 0.5091 0.377 0.00 0.00 0.64 0.00 0.04 0.20 0.12
#> TCGA.D3.A5GN.06 4 0.4030 0.697 0.00 0.00 0.12 0.72 0.00 0.16 0.00
#> TCGA.EE.A2GB.06 2 0.5832 0.275 0.00 0.42 0.00 0.14 0.04 0.00 0.40
#> TCGA.FS.A1Z3.06 1 0.0000 0.903 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DA.A1I8.06 4 0.1166 0.706 0.00 0.00 0.00 0.94 0.00 0.00 0.06
#> TCGA.D3.A5GS.06 6 0.5143 -0.270 0.00 0.00 0.42 0.00 0.14 0.44 0.00
#> TCGA.EE.A2GS.06 1 0.0000 0.903 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D3.A5GO.06 2 0.0000 0.893 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EE.A29Q.06 3 0.0863 0.638 0.00 0.00 0.96 0.00 0.00 0.04 0.00
#> TCGA.BF.A1PZ.01 1 0.0000 0.903 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D9.A1JX.06 4 0.0000 0.733 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.FS.A1ZF.06 6 0.3994 0.338 0.00 0.00 0.00 0.48 0.00 0.50 0.02
#> TCGA.EE.A29W.06 1 0.0000 0.903 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DA.A1HV.06 2 0.0000 0.893 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.ER.A19H.06 4 0.2259 0.782 0.00 0.00 0.00 0.84 0.00 0.16 0.00
#> TCGA.DA.A1HY.06 2 0.0000 0.893 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D3.A3C7.06 1 0.3606 0.630 0.68 0.00 0.00 0.00 0.00 0.02 0.30
#> TCGA.EE.A2MP.06 4 0.4030 0.697 0.00 0.00 0.12 0.72 0.00 0.16 0.00
#> TCGA.ER.A19G.06 2 0.0000 0.893 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FR.A69P.06 1 0.3606 0.630 0.68 0.00 0.00 0.00 0.00 0.02 0.30
#> TCGA.D3.A3C6.06 6 0.2259 0.559 0.00 0.00 0.00 0.16 0.00 0.84 0.00
#> TCGA.EE.A2A2.06 2 0.0000 0.893 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BF.AAP6.01 2 0.0000 0.893 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EB.A299.01 3 0.2864 0.565 0.00 0.00 0.84 0.00 0.12 0.02 0.02
#> TCGA.D3.A2JF.06 6 0.4978 0.143 0.00 0.00 0.12 0.38 0.00 0.50 0.00
#> TCGA.FR.A3YN.06 3 0.5091 0.178 0.00 0.00 0.66 0.00 0.16 0.06 0.12
#> TCGA.EE.A3J3.06 1 0.3606 0.630 0.68 0.00 0.00 0.00 0.00 0.02 0.30
#> TCGA.D3.A51G.06 6 0.3526 0.548 0.00 0.00 0.06 0.18 0.00 0.76 0.00
#> TCGA.D3.A51R.06 2 0.4003 0.586 0.00 0.64 0.00 0.00 0.04 0.00 0.32
#> TCGA.BF.A3DM.01 1 0.0000 0.903 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.W3.AA1R.06 2 0.0000 0.893 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EE.A3JA.06 5 0.1886 1.000 0.00 0.00 0.12 0.00 0.88 0.00 0.00
#> TCGA.BF.A3DN.01 1 0.0000 0.903 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D3.A51E.06 2 0.0000 0.893 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DA.A3F3.06 5 0.1886 1.000 0.00 0.00 0.12 0.00 0.88 0.00 0.00
#> TCGA.D3.A51T.06 2 0.0000 0.893 0.00 1.00 0.00 0.00 0.00 0.00 0.00
cbind(get_classes(res, k = 8), get_membership(res, k = 8))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7 p8
#> TCGA.ER.A42K.06 1 0.0471 0.9830 0.98 0.00 0.00 0.00 0.00 0.00 0.00 0.02
#> TCGA.FS.A4F2.06 2 0.0000 0.8829 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.WE.A8K6.06 1 0.0000 0.9864 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.Z2.A8RT.06 1 0.0000 0.9864 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EB.A41B.01 7 0.5535 -0.2388 0.00 0.00 0.22 0.00 0.04 0.00 0.50 0.24
#> TCGA.EB.A6R0.01 4 0.5566 0.4636 0.00 0.02 0.00 0.50 0.00 0.16 0.02 0.30
#> TCGA.D9.A4Z2.01 4 0.0471 0.7400 0.00 0.00 0.00 0.98 0.00 0.02 0.00 0.00
#> TCGA.D3.A3MV.06 4 0.0471 0.7370 0.00 0.00 0.02 0.98 0.00 0.00 0.00 0.00
#> TCGA.FS.A1ZQ.06 3 0.0471 0.7635 0.00 0.00 0.98 0.00 0.00 0.02 0.00 0.00
#> TCGA.ER.A19F.06 2 0.0000 0.8829 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EE.A3AG.06 2 0.4533 -0.5433 0.00 0.50 0.00 0.00 0.02 0.02 0.02 0.44
#> TCGA.ER.A19B.06 3 0.4478 0.5794 0.00 0.00 0.68 0.00 0.04 0.02 0.22 0.04
#> TCGA.D3.A5GN.06 4 0.1275 0.7099 0.00 0.00 0.04 0.94 0.00 0.02 0.00 0.00
#> TCGA.EE.A2GB.06 8 0.4302 0.0000 0.00 0.36 0.00 0.08 0.00 0.00 0.00 0.56
#> TCGA.FS.A1Z3.06 1 0.0471 0.9830 0.98 0.00 0.00 0.00 0.00 0.00 0.00 0.02
#> TCGA.DA.A1I8.06 4 0.4934 0.6016 0.00 0.02 0.00 0.64 0.00 0.14 0.02 0.18
#> TCGA.D3.A5GS.06 6 0.4325 0.0672 0.00 0.00 0.38 0.00 0.04 0.56 0.00 0.02
#> TCGA.EE.A2GS.06 1 0.0471 0.9830 0.98 0.00 0.00 0.00 0.00 0.00 0.00 0.02
#> TCGA.D3.A5GO.06 2 0.0000 0.8829 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EE.A29Q.06 3 0.0471 0.7635 0.00 0.00 0.98 0.00 0.00 0.02 0.00 0.00
#> TCGA.BF.A1PZ.01 1 0.0000 0.9864 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D9.A1JX.06 4 0.4515 0.6049 0.00 0.00 0.00 0.66 0.00 0.16 0.02 0.16
#> TCGA.FS.A1ZF.06 6 0.4061 0.4793 0.00 0.00 0.00 0.14 0.02 0.72 0.00 0.12
#> TCGA.EE.A29W.06 1 0.0000 0.9864 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DA.A1HV.06 2 0.0000 0.8829 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.ER.A19H.06 4 0.0000 0.7395 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DA.A1HY.06 2 0.0000 0.8829 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D3.A3C7.06 7 0.4216 0.5918 0.44 0.00 0.00 0.00 0.00 0.06 0.50 0.00
#> TCGA.EE.A2MP.06 4 0.0941 0.7225 0.00 0.00 0.02 0.96 0.00 0.02 0.00 0.00
#> TCGA.ER.A19G.06 2 0.0000 0.8829 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FR.A69P.06 7 0.3299 0.5997 0.44 0.00 0.00 0.00 0.00 0.00 0.56 0.00
#> TCGA.D3.A3C6.06 6 0.2650 0.6300 0.00 0.00 0.00 0.24 0.00 0.76 0.00 0.00
#> TCGA.EE.A2A2.06 2 0.0000 0.8829 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BF.AAP6.01 2 0.0000 0.8829 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EB.A299.01 3 0.2071 0.7389 0.00 0.00 0.90 0.00 0.04 0.00 0.02 0.04
#> TCGA.D3.A2JF.06 6 0.3729 0.4661 0.00 0.00 0.02 0.46 0.00 0.52 0.00 0.00
#> TCGA.FR.A3YN.06 3 0.5351 0.4020 0.00 0.00 0.54 0.00 0.04 0.00 0.18 0.24
#> TCGA.EE.A3J3.06 7 0.3329 0.5407 0.48 0.00 0.00 0.00 0.00 0.00 0.52 0.00
#> TCGA.D3.A51G.06 6 0.3618 0.5754 0.00 0.00 0.02 0.38 0.00 0.60 0.00 0.00
#> TCGA.D3.A51R.06 2 0.3193 -0.2152 0.00 0.62 0.00 0.00 0.00 0.00 0.00 0.38
#> TCGA.BF.A3DM.01 1 0.0471 0.9830 0.98 0.00 0.00 0.00 0.00 0.00 0.00 0.02
#> TCGA.W3.AA1R.06 2 0.0000 0.8829 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EE.A3JA.06 5 0.1341 1.0000 0.00 0.00 0.08 0.00 0.92 0.00 0.00 0.00
#> TCGA.BF.A3DN.01 1 0.0000 0.9864 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D3.A51E.06 2 0.0000 0.8829 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DA.A3F3.06 5 0.1341 1.0000 0.00 0.00 0.08 0.00 0.92 0.00 0.00 0.00
#> TCGA.D3.A51T.06 2 0.0000 0.8829 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
consensus_heatmap(res, k = 7)
consensus_heatmap(res, k = 8)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
membership_heatmap(res, k = 7)
membership_heatmap(res, k = 8)
As soon as the classes for columns are determined, the signatures that are significantly different between subgroups can be looked for. Following are the heatmaps for signatures.
get_signatures(res, k = 2)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
get_signatures(res, k = 7)
get_signatures(res, k = 8)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. To get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows (which is done by automatically selecting number of clusters).If there are too many signatures, top_signatures = ... can be set to only show the
signatures with the highest FDRs:
# code only for demonstration
# e.g. to show the top 500 most significant rows
tb = get_signature(res, k = ..., top_signatures = 500)
If the signatures are defined as these which are uniquely high in current group, diff_method argument
can be set to "uniquely_high_in_one_group":
# code only for demonstration
tb = get_signature(res, k = ..., diff_method = "uniquely_high_in_one_group")
UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
dimension_reduction(res, k = 7, method = "UMAP")
dimension_reduction(res, k = 8, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
If matrix rows can be associated to genes, consider to use functional_enrichment(res,
...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.
Parent node: Node032. Child nodes: Node01111-leaf , Node01112-leaf , Node01113-leaf , Node01131-leaf , Node01132-leaf , Node01133-leaf , Node01311-leaf , Node01312-leaf , Node02121-leaf , Node02122-leaf , Node02123-leaf , Node03111-leaf , Node03112-leaf , Node03113-leaf , Node03221-leaf , Node03222-leaf , Node03231-leaf , Node03232-leaf , Node03233-leaf , Node03234-leaf , Node04111-leaf , Node04112-leaf , Node04121-leaf , Node04122-leaf , Node04421-leaf , Node04422-leaf , Node04423-leaf , Node04424-leaf , Node05111-leaf , Node05112-leaf , Node05113-leaf .
The object with results only for a single top-value method and a single partitioning method can be extracted as:
res = res_rh["0322"]
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 20 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 0.4427 0.558 0.558
#> 3 3 0.568 0.691 0.806 0.4548 0.789 0.623
#> 4 4 0.600 0.795 0.834 0.1544 0.837 0.557
#> 5 5 0.811 0.901 0.936 0.0866 0.958 0.814
#> 6 6 0.853 0.810 0.896 0.0437 1.000 1.000
#> 7 7 0.858 0.666 0.846 0.0180 0.989 0.943
#> 8 8 0.863 0.688 0.832 0.0290 0.911 0.514
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.FS.A4F2.06 1 0 1 1 0
#> TCGA.EB.A6R0.01 1 0 1 1 0
#> TCGA.D9.A4Z2.01 1 0 1 1 0
#> TCGA.D3.A3MV.06 1 0 1 1 0
#> TCGA.ER.A19F.06 1 0 1 1 0
#> TCGA.EE.A3AG.06 1 0 1 1 0
#> TCGA.EE.A2GB.06 1 0 1 1 0
#> TCGA.DA.A1I8.06 1 0 1 1 0
#> TCGA.D3.A5GO.06 1 0 1 1 0
#> TCGA.D9.A1JX.06 2 0 1 0 1
#> TCGA.DA.A1HV.06 2 0 1 0 1
#> TCGA.ER.A19H.06 1 0 1 1 0
#> TCGA.DA.A1HY.06 1 0 1 1 0
#> TCGA.ER.A19G.06 2 0 1 0 1
#> TCGA.EE.A2A2.06 2 0 1 0 1
#> TCGA.BF.AAP6.01 1 0 1 1 0
#> TCGA.D3.A51R.06 1 0 1 1 0
#> TCGA.W3.AA1R.06 2 0 1 0 1
#> TCGA.D3.A51E.06 1 0 1 1 0
#> TCGA.D3.A51T.06 2 0 1 0 1
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.FS.A4F2.06 1 0.207 0.7140 0.94 0.00 0.06
#> TCGA.EB.A6R0.01 1 0.624 -0.0656 0.56 0.00 0.44
#> TCGA.D9.A4Z2.01 3 0.556 0.8967 0.30 0.00 0.70
#> TCGA.D3.A3MV.06 3 0.556 0.8967 0.30 0.00 0.70
#> TCGA.ER.A19F.06 1 0.000 0.7407 1.00 0.00 0.00
#> TCGA.EE.A3AG.06 1 0.522 0.4444 0.74 0.00 0.26
#> TCGA.EE.A2GB.06 1 0.000 0.7407 1.00 0.00 0.00
#> TCGA.DA.A1I8.06 3 0.369 0.7274 0.14 0.00 0.86
#> TCGA.D3.A5GO.06 1 0.207 0.7140 0.94 0.00 0.06
#> TCGA.D9.A1JX.06 2 0.502 0.8281 0.00 0.76 0.24
#> TCGA.DA.A1HV.06 2 0.000 0.9510 0.00 1.00 0.00
#> TCGA.ER.A19H.06 3 0.556 0.8967 0.30 0.00 0.70
#> TCGA.DA.A1HY.06 1 0.631 -0.3555 0.50 0.00 0.50
#> TCGA.ER.A19G.06 2 0.296 0.9158 0.00 0.90 0.10
#> TCGA.EE.A2A2.06 2 0.000 0.9510 0.00 1.00 0.00
#> TCGA.BF.AAP6.01 1 0.000 0.7407 1.00 0.00 0.00
#> TCGA.D3.A51R.06 1 0.522 0.4444 0.74 0.00 0.26
#> TCGA.W3.AA1R.06 2 0.000 0.9510 0.00 1.00 0.00
#> TCGA.D3.A51E.06 1 0.000 0.7407 1.00 0.00 0.00
#> TCGA.D3.A51T.06 2 0.000 0.9510 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.FS.A4F2.06 4 0.536 0.838 0.36 0.00 0.02 0.62
#> TCGA.EB.A6R0.01 4 0.669 0.719 0.20 0.00 0.18 0.62
#> TCGA.D9.A4Z2.01 3 0.317 0.856 0.16 0.00 0.84 0.00
#> TCGA.D3.A3MV.06 3 0.317 0.856 0.16 0.00 0.84 0.00
#> TCGA.ER.A19F.06 1 0.000 0.885 1.00 0.00 0.00 0.00
#> TCGA.EE.A3AG.06 1 0.317 0.777 0.84 0.00 0.16 0.00
#> TCGA.EE.A2GB.06 1 0.000 0.885 1.00 0.00 0.00 0.00
#> TCGA.DA.A1I8.06 3 0.353 0.664 0.04 0.00 0.86 0.10
#> TCGA.D3.A5GO.06 4 0.479 0.820 0.38 0.00 0.00 0.62
#> TCGA.D9.A1JX.06 2 0.734 0.533 0.00 0.46 0.16 0.38
#> TCGA.DA.A1HV.06 2 0.000 0.855 0.00 1.00 0.00 0.00
#> TCGA.ER.A19H.06 3 0.317 0.856 0.16 0.00 0.84 0.00
#> TCGA.DA.A1HY.06 3 0.479 0.530 0.38 0.00 0.62 0.00
#> TCGA.ER.A19G.06 2 0.539 0.710 0.00 0.68 0.04 0.28
#> TCGA.EE.A2A2.06 2 0.000 0.855 0.00 1.00 0.00 0.00
#> TCGA.BF.AAP6.01 1 0.000 0.885 1.00 0.00 0.00 0.00
#> TCGA.D3.A51R.06 1 0.317 0.777 0.84 0.00 0.16 0.00
#> TCGA.W3.AA1R.06 2 0.000 0.855 0.00 1.00 0.00 0.00
#> TCGA.D3.A51E.06 1 0.000 0.885 1.00 0.00 0.00 0.00
#> TCGA.D3.A51T.06 2 0.000 0.855 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.FS.A4F2.06 4 0.1410 0.945 0.06 0.00 0.00 0.94 0.00
#> TCGA.EB.A6R0.01 4 0.2438 0.937 0.06 0.00 0.00 0.90 0.04
#> TCGA.D9.A4Z2.01 3 0.0609 0.882 0.02 0.00 0.98 0.00 0.00
#> TCGA.D3.A3MV.06 3 0.0609 0.882 0.02 0.00 0.98 0.00 0.00
#> TCGA.ER.A19F.06 1 0.0000 0.933 1.00 0.00 0.00 0.00 0.00
#> TCGA.EE.A3AG.06 1 0.2873 0.861 0.86 0.00 0.12 0.00 0.02
#> TCGA.EE.A2GB.06 1 0.0000 0.933 1.00 0.00 0.00 0.00 0.00
#> TCGA.DA.A1I8.06 3 0.2754 0.791 0.00 0.00 0.88 0.04 0.08
#> TCGA.D3.A5GO.06 4 0.2280 0.919 0.12 0.00 0.00 0.88 0.00
#> TCGA.D9.A1JX.06 5 0.1410 0.905 0.00 0.06 0.00 0.00 0.94
#> TCGA.DA.A1HV.06 2 0.1216 0.961 0.00 0.96 0.02 0.02 0.00
#> TCGA.ER.A19H.06 3 0.0609 0.882 0.02 0.00 0.98 0.00 0.00
#> TCGA.DA.A1HY.06 3 0.4728 0.605 0.24 0.00 0.70 0.00 0.06
#> TCGA.ER.A19G.06 5 0.2516 0.902 0.00 0.14 0.00 0.00 0.86
#> TCGA.EE.A2A2.06 2 0.0000 0.987 0.00 1.00 0.00 0.00 0.00
#> TCGA.BF.AAP6.01 1 0.0000 0.933 1.00 0.00 0.00 0.00 0.00
#> TCGA.D3.A51R.06 1 0.2873 0.861 0.86 0.00 0.12 0.00 0.02
#> TCGA.W3.AA1R.06 2 0.0000 0.987 0.00 1.00 0.00 0.00 0.00
#> TCGA.D3.A51E.06 1 0.0000 0.933 1.00 0.00 0.00 0.00 0.00
#> TCGA.D3.A51T.06 2 0.0000 0.987 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.FS.A4F2.06 4 0.0000 0.792 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.EB.A6R0.01 4 0.3819 0.691 0.28 0.00 0.00 0.70 0.02 0.00
#> TCGA.D9.A4Z2.01 3 0.0000 0.814 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.D3.A3MV.06 3 0.0000 0.814 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.ER.A19F.06 6 0.0000 0.848 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.EE.A3AG.06 6 0.4002 0.697 0.32 0.00 0.02 0.00 0.00 0.66
#> TCGA.EE.A2GB.06 6 0.0000 0.848 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.DA.A1I8.06 3 0.2793 0.698 0.20 0.00 0.80 0.00 0.00 0.00
#> TCGA.D3.A5GO.06 4 0.2728 0.750 0.04 0.00 0.00 0.86 0.00 0.10
#> TCGA.D9.A1JX.06 5 0.0547 1.000 0.00 0.02 0.00 0.00 0.98 0.00
#> TCGA.DA.A1HV.06 2 0.2260 0.875 0.14 0.86 0.00 0.00 0.00 0.00
#> TCGA.ER.A19H.06 3 0.0000 0.814 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.DA.A1HY.06 3 0.5115 0.312 0.46 0.00 0.46 0.00 0.00 0.08
#> TCGA.ER.A19G.06 5 0.0547 1.000 0.00 0.02 0.00 0.00 0.98 0.00
#> TCGA.EE.A2A2.06 2 0.0000 0.960 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.BF.AAP6.01 6 0.0000 0.848 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.D3.A51R.06 6 0.4002 0.697 0.32 0.00 0.02 0.00 0.00 0.66
#> TCGA.W3.AA1R.06 2 0.0000 0.960 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.D3.A51E.06 6 0.0937 0.826 0.04 0.00 0.00 0.00 0.00 0.96
#> TCGA.D3.A51T.06 2 0.0000 0.960 0.00 1.00 0.00 0.00 0.00 0.00
cbind(get_classes(res, k = 7), get_membership(res, k = 7))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7
#> TCGA.FS.A4F2.06 4 0.0504 0.612 0.00 0.00 0.00 0.98 0.00 0.02 0.00
#> TCGA.EB.A6R0.01 1 0.3909 0.000 0.58 0.00 0.00 0.40 0.00 0.02 0.00
#> TCGA.D9.A4Z2.01 3 0.0000 0.756 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.D3.A3MV.06 3 0.0000 0.756 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.ER.A19F.06 6 0.3459 0.773 0.00 0.00 0.00 0.00 0.00 0.60 0.40
#> TCGA.EE.A3AG.06 6 0.1433 0.530 0.00 0.00 0.08 0.00 0.00 0.92 0.00
#> TCGA.EE.A2GB.06 6 0.3413 0.771 0.00 0.00 0.00 0.00 0.00 0.62 0.38
#> TCGA.DA.A1I8.06 3 0.4264 0.470 0.06 0.00 0.62 0.00 0.00 0.00 0.32
#> TCGA.D3.A5GO.06 4 0.3011 0.657 0.00 0.00 0.00 0.82 0.00 0.06 0.12
#> TCGA.D9.A1JX.06 5 0.0863 0.968 0.00 0.00 0.00 0.00 0.96 0.00 0.04
#> TCGA.DA.A1HV.06 2 0.5190 0.468 0.30 0.52 0.00 0.00 0.00 0.00 0.18
#> TCGA.ER.A19H.06 3 0.0000 0.756 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DA.A1HY.06 3 0.5564 0.251 0.10 0.00 0.46 0.00 0.00 0.40 0.04
#> TCGA.ER.A19G.06 5 0.0000 0.968 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.EE.A2A2.06 2 0.0000 0.841 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BF.AAP6.01 6 0.3459 0.773 0.00 0.00 0.00 0.00 0.00 0.60 0.40
#> TCGA.D3.A51R.06 6 0.1433 0.530 0.00 0.00 0.08 0.00 0.00 0.92 0.00
#> TCGA.W3.AA1R.06 2 0.0000 0.841 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D3.A51E.06 6 0.3496 0.762 0.00 0.00 0.00 0.00 0.00 0.58 0.42
#> TCGA.D3.A51T.06 2 0.1006 0.831 0.00 0.96 0.00 0.02 0.00 0.00 0.02
cbind(get_classes(res, k = 8), get_membership(res, k = 8))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7 p8
#> TCGA.FS.A4F2.06 4 0.0000 0.654 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.EB.A6R0.01 1 0.2852 0.000 0.72 0.00 0.00 0.28 0.00 0.00 0.00 0.00
#> TCGA.D9.A4Z2.01 3 0.0000 1.000 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D3.A3MV.06 3 0.0000 1.000 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.ER.A19F.06 6 0.3193 0.940 0.00 0.00 0.00 0.00 0.00 0.62 0.00 0.38
#> TCGA.EE.A3AG.06 8 0.0000 0.587 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.EE.A2GB.06 6 0.3272 0.905 0.00 0.00 0.00 0.00 0.00 0.58 0.00 0.42
#> TCGA.DA.A1I8.06 7 0.3329 0.000 0.00 0.00 0.48 0.00 0.00 0.00 0.52 0.00
#> TCGA.D3.A5GO.06 4 0.2406 0.689 0.00 0.00 0.00 0.80 0.00 0.20 0.00 0.00
#> TCGA.D9.A1JX.06 5 0.0941 0.967 0.02 0.00 0.00 0.00 0.96 0.02 0.00 0.00
#> TCGA.DA.A1HV.06 2 0.6426 0.189 0.14 0.34 0.00 0.00 0.00 0.22 0.30 0.00
#> TCGA.ER.A19H.06 3 0.0000 1.000 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DA.A1HY.06 8 0.6767 0.202 0.08 0.00 0.22 0.00 0.00 0.08 0.18 0.44
#> TCGA.ER.A19G.06 5 0.0000 0.967 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.EE.A2A2.06 2 0.0000 0.765 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BF.AAP6.01 6 0.3193 0.940 0.00 0.00 0.00 0.00 0.00 0.62 0.00 0.38
#> TCGA.D3.A51R.06 8 0.0000 0.587 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.W3.AA1R.06 2 0.0000 0.765 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D3.A51E.06 6 0.2938 0.866 0.00 0.00 0.00 0.00 0.00 0.70 0.00 0.30
#> TCGA.D3.A51T.06 2 0.1557 0.744 0.06 0.92 0.00 0.00 0.00 0.02 0.00 0.00
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
consensus_heatmap(res, k = 7)
consensus_heatmap(res, k = 8)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
membership_heatmap(res, k = 7)
membership_heatmap(res, k = 8)
As soon as the classes for columns are determined, the signatures that are significantly different between subgroups can be looked for. Following are the heatmaps for signatures.
get_signatures(res, k = 2)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
get_signatures(res, k = 7)
get_signatures(res, k = 8)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. To get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows (which is done by automatically selecting number of clusters).If there are too many signatures, top_signatures = ... can be set to only show the
signatures with the highest FDRs:
# code only for demonstration
# e.g. to show the top 500 most significant rows
tb = get_signature(res, k = ..., top_signatures = 500)
If the signatures are defined as these which are uniquely high in current group, diff_method argument
can be set to "uniquely_high_in_one_group":
# code only for demonstration
tb = get_signature(res, k = ..., diff_method = "uniquely_high_in_one_group")
UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
dimension_reduction(res, k = 7, method = "UMAP")
dimension_reduction(res, k = 8, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
If matrix rows can be associated to genes, consider to use functional_enrichment(res,
...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.
Parent node: Node032. Child nodes: Node01111-leaf , Node01112-leaf , Node01113-leaf , Node01131-leaf , Node01132-leaf , Node01133-leaf , Node01311-leaf , Node01312-leaf , Node02121-leaf , Node02122-leaf , Node02123-leaf , Node03111-leaf , Node03112-leaf , Node03113-leaf , Node03221-leaf , Node03222-leaf , Node03231-leaf , Node03232-leaf , Node03233-leaf , Node03234-leaf , Node04111-leaf , Node04112-leaf , Node04121-leaf , Node04122-leaf , Node04421-leaf , Node04422-leaf , Node04423-leaf , Node04424-leaf , Node05111-leaf , Node05112-leaf , Node05113-leaf .
The object with results only for a single top-value method and a single partitioning method can be extracted as:
res = res_rh["0323"]
A summary of res and all the functions that can be applied to it:
res
#> A 'ConsensusPartition' object with k = 2, 3, 4, 5, 6, 7, 8.
#> On a matrix with 30000 rows and 14 columns.
#> Top rows (1000) are extracted by 'ATC' method.
#> Subgroups are detected by '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 0.2645 0.736 0.736
#> 3 3 1.000 0.997 0.986 1.2780 0.648 0.522
#> 4 4 0.934 0.962 0.963 0.0911 0.956 0.886
#> 5 5 0.714 0.465 0.844 0.1501 0.923 0.774
#> 6 6 0.736 0.531 0.837 0.0847 0.912 0.680
#> 7 7 0.846 0.725 0.870 0.0429 0.912 0.556
#> 8 8 0.857 0.615 0.914 0.0398 0.989 0.900
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.FS.A1ZQ.06 2 0 1 0 1
#> TCGA.ER.A19B.06 2 0 1 0 1
#> TCGA.D3.A5GN.06 2 0 1 0 1
#> TCGA.D3.A5GS.06 2 0 1 0 1
#> TCGA.EE.A29Q.06 2 0 1 0 1
#> TCGA.FS.A1ZF.06 2 0 1 0 1
#> TCGA.EE.A2MP.06 2 0 1 0 1
#> TCGA.D3.A3C6.06 2 0 1 0 1
#> TCGA.EB.A299.01 2 0 1 0 1
#> TCGA.D3.A2JF.06 2 0 1 0 1
#> TCGA.FR.A3YN.06 2 0 1 0 1
#> TCGA.D3.A51G.06 2 0 1 0 1
#> TCGA.EE.A3JA.06 1 0 1 1 0
#> TCGA.DA.A3F3.06 1 0 1 1 0
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.FS.A1ZQ.06 3 0.153 1.000 0.00 0.04 0.96
#> TCGA.ER.A19B.06 2 0.000 1.000 0.00 1.00 0.00
#> TCGA.D3.A5GN.06 2 0.000 1.000 0.00 1.00 0.00
#> TCGA.D3.A5GS.06 2 0.000 1.000 0.00 1.00 0.00
#> TCGA.EE.A29Q.06 2 0.000 1.000 0.00 1.00 0.00
#> TCGA.FS.A1ZF.06 2 0.000 1.000 0.00 1.00 0.00
#> TCGA.EE.A2MP.06 2 0.000 1.000 0.00 1.00 0.00
#> TCGA.D3.A3C6.06 2 0.000 1.000 0.00 1.00 0.00
#> TCGA.EB.A299.01 2 0.000 1.000 0.00 1.00 0.00
#> TCGA.D3.A2JF.06 3 0.153 1.000 0.00 0.04 0.96
#> TCGA.FR.A3YN.06 3 0.153 1.000 0.00 0.04 0.96
#> TCGA.D3.A51G.06 3 0.153 1.000 0.00 0.04 0.96
#> TCGA.EE.A3JA.06 1 0.153 0.977 0.96 0.00 0.04
#> TCGA.DA.A3F3.06 1 0.000 0.977 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.FS.A1ZQ.06 3 0.2647 1.000 0.0 0.00 0.88 0.12
#> TCGA.ER.A19B.06 2 0.0707 0.987 0.0 0.98 0.02 0.00
#> TCGA.D3.A5GN.06 2 0.0000 0.992 0.0 1.00 0.00 0.00
#> TCGA.D3.A5GS.06 2 0.0000 0.992 0.0 1.00 0.00 0.00
#> TCGA.EE.A29Q.06 2 0.0000 0.992 0.0 1.00 0.00 0.00
#> TCGA.FS.A1ZF.06 2 0.0707 0.987 0.0 0.98 0.02 0.00
#> TCGA.EE.A2MP.06 2 0.0000 0.992 0.0 1.00 0.00 0.00
#> TCGA.D3.A3C6.06 2 0.0707 0.987 0.0 0.98 0.02 0.00
#> TCGA.EB.A299.01 2 0.0000 0.992 0.0 1.00 0.00 0.00
#> TCGA.D3.A2JF.06 4 0.2647 0.842 0.0 0.00 0.12 0.88
#> TCGA.FR.A3YN.06 3 0.2647 1.000 0.0 0.00 0.88 0.12
#> TCGA.D3.A51G.06 4 0.0000 0.855 0.0 0.00 0.00 1.00
#> TCGA.EE.A3JA.06 1 0.2345 0.926 0.9 0.00 0.10 0.00
#> TCGA.DA.A3F3.06 1 0.0000 0.926 1.0 0.00 0.00 0.00
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> TCGA.FS.A1ZQ.06 3 0.000 0.7947 0.00 0.00 1.00 0.00 0.00
#> TCGA.ER.A19B.06 2 0.389 -0.2344 0.00 0.68 0.00 0.00 0.32
#> TCGA.D3.A5GN.06 2 0.000 0.6133 0.00 1.00 0.00 0.00 0.00
#> TCGA.D3.A5GS.06 2 0.000 0.6133 0.00 1.00 0.00 0.00 0.00
#> TCGA.EE.A29Q.06 2 0.413 -0.0674 0.00 0.62 0.00 0.00 0.38
#> TCGA.FS.A1ZF.06 5 0.429 0.0000 0.00 0.46 0.00 0.00 0.54
#> TCGA.EE.A2MP.06 2 0.000 0.6133 0.00 1.00 0.00 0.00 0.00
#> TCGA.D3.A3C6.06 2 0.389 -0.2344 0.00 0.68 0.00 0.00 0.32
#> TCGA.EB.A299.01 2 0.000 0.6133 0.00 1.00 0.00 0.00 0.00
#> TCGA.D3.A2JF.06 4 0.342 0.5685 0.00 0.00 0.24 0.76 0.00
#> TCGA.FR.A3YN.06 3 0.273 0.8049 0.00 0.00 0.84 0.00 0.16
#> TCGA.D3.A51G.06 4 0.293 0.6209 0.00 0.00 0.00 0.82 0.18
#> TCGA.EE.A3JA.06 1 0.000 0.9043 1.00 0.00 0.00 0.00 0.00
#> TCGA.DA.A3F3.06 1 0.228 0.9043 0.88 0.00 0.00 0.00 0.12
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> TCGA.FS.A1ZQ.06 3 0.2790 0.778 0.0 0.00 0.84 0.14 0.02 0.00
#> TCGA.ER.A19B.06 2 0.5655 0.271 0.0 0.48 0.00 0.00 0.36 0.16
#> TCGA.D3.A5GN.06 2 0.0000 0.707 0.0 1.00 0.00 0.00 0.00 0.00
#> TCGA.D3.A5GS.06 2 0.0000 0.707 0.0 1.00 0.00 0.00 0.00 0.00
#> TCGA.EE.A29Q.06 5 0.5428 0.418 0.0 0.32 0.14 0.00 0.54 0.00
#> TCGA.FS.A1ZF.06 5 0.2048 0.426 0.0 0.12 0.00 0.00 0.88 0.00
#> TCGA.EE.A2MP.06 2 0.0000 0.707 0.0 1.00 0.00 0.00 0.00 0.00
#> TCGA.D3.A3C6.06 2 0.5655 0.271 0.0 0.48 0.00 0.00 0.36 0.16
#> TCGA.EB.A299.01 2 0.0000 0.707 0.0 1.00 0.00 0.00 0.00 0.00
#> TCGA.D3.A2JF.06 4 0.0000 0.000 0.0 0.00 0.00 1.00 0.00 0.00
#> TCGA.FR.A3YN.06 3 0.0547 0.793 0.0 0.00 0.98 0.00 0.02 0.00
#> TCGA.D3.A51G.06 6 0.3309 0.000 0.0 0.00 0.00 0.28 0.00 0.72
#> TCGA.EE.A3JA.06 1 0.3544 0.828 0.8 0.00 0.00 0.00 0.08 0.12
#> TCGA.DA.A3F3.06 1 0.0000 0.828 1.0 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.FS.A1ZQ.06 3 0.3388 0.627 0.0 0.00 0.76 0.04 0.00 0.00 0.20
#> TCGA.ER.A19B.06 7 0.3413 1.000 0.0 0.38 0.00 0.00 0.00 0.00 0.62
#> TCGA.D3.A5GN.06 2 0.0000 1.000 0.0 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D3.A5GS.06 2 0.0000 1.000 0.0 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EE.A29Q.06 5 0.1433 0.707 0.0 0.08 0.00 0.00 0.92 0.00 0.00
#> TCGA.FS.A1ZF.06 5 0.3052 0.710 0.0 0.02 0.00 0.00 0.78 0.00 0.20
#> TCGA.EE.A2MP.06 2 0.0000 1.000 0.0 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D3.A3C6.06 7 0.3413 1.000 0.0 0.38 0.00 0.00 0.00 0.00 0.62
#> TCGA.EB.A299.01 2 0.0000 1.000 0.0 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D3.A2JF.06 4 0.0863 0.000 0.0 0.00 0.00 0.96 0.00 0.04 0.00
#> TCGA.FR.A3YN.06 3 0.2422 0.637 0.0 0.00 0.82 0.00 0.18 0.00 0.00
#> TCGA.D3.A51G.06 6 0.0000 0.000 0.0 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.EE.A3JA.06 1 0.0000 0.731 1.0 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DA.A3F3.06 1 0.4854 0.731 0.7 0.00 0.04 0.04 0.04 0.00 0.18
cbind(get_classes(res, k = 8), get_membership(res, k = 8))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7 p8
#> TCGA.FS.A1ZQ.06 3 0.2267 0.000 0.00 0.00 0.82 0 0.00 0 0.00 0.18
#> TCGA.ER.A19B.06 7 0.1947 1.000 0.00 0.14 0.00 0 0.00 0 0.86 0.00
#> TCGA.D3.A5GN.06 2 0.0000 0.983 0.00 1.00 0.00 0 0.00 0 0.00 0.00
#> TCGA.D3.A5GS.06 2 0.0808 0.950 0.00 0.96 0.00 0 0.00 0 0.04 0.00
#> TCGA.EE.A29Q.06 5 0.1557 0.682 0.00 0.02 0.00 0 0.92 0 0.00 0.06
#> TCGA.FS.A1ZF.06 5 0.2756 0.688 0.00 0.00 0.00 0 0.74 0 0.26 0.00
#> TCGA.EE.A2MP.06 2 0.0000 0.983 0.00 1.00 0.00 0 0.00 0 0.00 0.00
#> TCGA.D3.A3C6.06 7 0.1947 1.000 0.00 0.14 0.00 0 0.00 0 0.86 0.00
#> TCGA.EB.A299.01 2 0.0000 0.983 0.00 1.00 0.00 0 0.00 0 0.00 0.00
#> TCGA.D3.A2JF.06 4 0.0000 0.000 0.00 0.00 0.00 1 0.00 0 0.00 0.00
#> TCGA.FR.A3YN.06 8 0.0000 0.000 0.00 0.00 0.00 0 0.00 0 0.00 1.00
#> TCGA.D3.A51G.06 6 0.0000 0.000 0.00 0.00 0.00 0 0.00 1 0.00 0.00
#> TCGA.EE.A3JA.06 1 0.4937 0.672 0.64 0.00 0.18 0 0.08 0 0.10 0.00
#> TCGA.DA.A3F3.06 1 0.0000 0.672 1.00 0.00 0.00 0 0.00 0 0.00 0.00
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
consensus_heatmap(res, k = 7)
consensus_heatmap(res, k = 8)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
membership_heatmap(res, k = 7)
membership_heatmap(res, k = 8)
As soon as the classes for columns are determined, the signatures that are significantly different between subgroups can be looked for. Following are the heatmaps for signatures.
get_signatures(res, k = 2)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
get_signatures(res, k = 7)
get_signatures(res, k = 8)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. To get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows (which is done by automatically selecting number of clusters).If there are too many signatures, top_signatures = ... can be set to only show the
signatures with the highest FDRs:
# code only for demonstration
# e.g. to show the top 500 most significant rows
tb = get_signature(res, k = ..., top_signatures = 500)
If the signatures are defined as these which are uniquely high in current group, diff_method argument
can be set to "uniquely_high_in_one_group":
# code only for demonstration
tb = get_signature(res, k = ..., diff_method = "uniquely_high_in_one_group")
UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
dimension_reduction(res, k = 7, method = "UMAP")
dimension_reduction(res, k = 8, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
If matrix rows can be associated to genes, consider to use functional_enrichment(res,
...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.
Parent node: Node0. Child nodes: Node011 , Node012 , Node013 , Node014-leaf , Node021 , Node022 , Node023-leaf , Node031 , Node032 , Node041 , Node042 , Node043 , Node044 , Node051 , Node052 .
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 131 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 0.981 0.992 0.4720 0.532 0.532
#> 3 3 0.898 0.928 0.962 0.3291 0.722 0.533
#> 4 4 1.000 0.980 0.993 0.1658 0.760 0.461
#> 5 5 0.834 0.865 0.895 0.0747 0.870 0.567
#> 6 6 0.808 0.724 0.839 0.0360 0.973 0.868
#> 7 7 0.807 0.635 0.800 0.0309 0.967 0.830
#> 8 8 0.834 0.722 0.841 0.0168 0.967 0.807
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.FS.A4FC.06 2 0.000 1.000 0.00 1.00
#> TCGA.D3.A8GQ.06 1 0.000 0.988 1.00 0.00
#> TCGA.BF.A5EQ.01 2 0.000 1.000 0.00 1.00
#> TCGA.EB.A5VU.01 1 0.000 0.988 1.00 0.00
#> TCGA.D3.A8GJ.06 2 0.000 1.000 0.00 1.00
#> TCGA.WE.A8ZR.06 2 0.000 1.000 0.00 1.00
#> TCGA.DA.A95V.06 1 0.000 0.988 1.00 0.00
#> TCGA.EE.A3JB.06 1 0.000 0.988 1.00 0.00
#> TCGA.WE.A8ZX.06 1 0.000 0.988 1.00 0.00
#> TCGA.D3.A8GS.06 1 0.000 0.988 1.00 0.00
#> TCGA.GN.A4U8.06 1 0.000 0.988 1.00 0.00
#> TCGA.EB.A551.01 1 0.904 0.539 0.68 0.32
#> TCGA.D3.A8GM.06 1 0.000 0.988 1.00 0.00
#> TCGA.YD.A89C.06 1 0.000 0.988 1.00 0.00
#> TCGA.FR.A726.01 1 0.000 0.988 1.00 0.00
#> TCGA.W3.A825.06 1 0.000 0.988 1.00 0.00
#> TCGA.D3.A5GR.06 1 0.000 0.988 1.00 0.00
#> TCGA.FR.A729.06 1 0.000 0.988 1.00 0.00
#> TCGA.EE.A29P.06 1 0.000 0.988 1.00 0.00
#> TCGA.GN.A26A.06 1 0.000 0.988 1.00 0.00
#> TCGA.EE.A20I.06 1 0.000 0.988 1.00 0.00
#> TCGA.EB.A85J.01 2 0.000 1.000 0.00 1.00
#> TCGA.RP.A6K9.06 2 0.000 1.000 0.00 1.00
#> TCGA.EE.A17Y.06 1 0.000 0.988 1.00 0.00
#> TCGA.D9.A149.06 2 0.000 1.000 0.00 1.00
#> TCGA.D3.A1Q9.06 1 0.000 0.988 1.00 0.00
#> TCGA.ER.A19L.06 2 0.000 1.000 0.00 1.00
#> TCGA.ER.A19T.06 2 0.000 1.000 0.00 1.00
#> TCGA.D3.A2JC.06 1 0.000 0.988 1.00 0.00
#> TCGA.BF.A5EO.01 1 0.000 0.988 1.00 0.00
#> TCGA.EE.A2M7.06 1 0.000 0.988 1.00 0.00
#> TCGA.D3.A1Q3.06 2 0.000 1.000 0.00 1.00
#> TCGA.EB.A85I.01 2 0.000 1.000 0.00 1.00
#> TCGA.DA.A1I2.06 1 0.881 0.580 0.70 0.30
#> TCGA.DA.A1I7.06 1 0.000 0.988 1.00 0.00
#> TCGA.EE.A181.06 1 0.000 0.988 1.00 0.00
#> TCGA.FS.A1ZM.06 1 0.000 0.988 1.00 0.00
#> TCGA.D3.A2JP.06 1 0.000 0.988 1.00 0.00
#> TCGA.ER.A19C.06 1 0.000 0.988 1.00 0.00
#> TCGA.EB.A82B.01 2 0.000 1.000 0.00 1.00
#> TCGA.FS.A1ZH.06 1 0.000 0.988 1.00 0.00
#> TCGA.D3.A2J6.06 2 0.000 1.000 0.00 1.00
#> TCGA.D3.A2JO.06 1 0.000 0.988 1.00 0.00
#> TCGA.GN.A267.06 2 0.000 1.000 0.00 1.00
#> TCGA.D3.A3CC.06 2 0.000 1.000 0.00 1.00
#> TCGA.BF.A1PU.01 1 0.000 0.988 1.00 0.00
#> TCGA.D3.A1Q6.06 1 0.000 0.988 1.00 0.00
#> TCGA.EB.A24C.01 2 0.000 1.000 0.00 1.00
#> TCGA.D3.A2JL.06 1 0.000 0.988 1.00 0.00
#> TCGA.FS.A1ZS.06 2 0.000 1.000 0.00 1.00
#> TCGA.D3.A3C3.06 1 0.000 0.988 1.00 0.00
#> TCGA.D3.A1QA.07 1 0.000 0.988 1.00 0.00
#> TCGA.EE.A29S.06 1 0.000 0.988 1.00 0.00
#> TCGA.GN.A26D.06 2 0.000 1.000 0.00 1.00
#> TCGA.EE.A2M5.06 1 0.000 0.988 1.00 0.00
#> TCGA.GN.A266.06 1 0.000 0.988 1.00 0.00
#> TCGA.D3.A3C1.06 1 0.000 0.988 1.00 0.00
#> TCGA.EE.A20F.06 1 0.000 0.988 1.00 0.00
#> TCGA.ER.A193.06 2 0.000 1.000 0.00 1.00
#> TCGA.FS.A1ZW.06 1 0.000 0.988 1.00 0.00
#> TCGA.ER.A19O.06 1 0.000 0.988 1.00 0.00
#> TCGA.EE.A20B.06 1 0.000 0.988 1.00 0.00
#> TCGA.FS.A1YX.06 1 0.000 0.988 1.00 0.00
#> TCGA.ER.A194.01 1 0.000 0.988 1.00 0.00
#> TCGA.EE.A2MS.06 2 0.000 1.000 0.00 1.00
#> TCGA.EE.A29X.06 1 0.000 0.988 1.00 0.00
#> TCGA.ER.A2NC.06 1 0.000 0.988 1.00 0.00
#> TCGA.BF.A1Q0.01 2 0.000 1.000 0.00 1.00
#> TCGA.EE.A182.06 2 0.000 1.000 0.00 1.00
#> TCGA.D9.A1JW.06 2 0.000 1.000 0.00 1.00
#> TCGA.EE.A2GJ.06 2 0.000 1.000 0.00 1.00
#> TCGA.EE.A2GU.06 2 0.000 1.000 0.00 1.00
#> TCGA.FS.A1Z7.06 2 0.000 1.000 0.00 1.00
#> TCGA.ER.A19K.01 1 0.000 0.988 1.00 0.00
#> TCGA.FR.A3YO.06 1 0.000 0.988 1.00 0.00
#> TCGA.RP.A694.06 1 0.000 0.988 1.00 0.00
#> TCGA.EB.A3Y7.01 2 0.000 1.000 0.00 1.00
#> TCGA.BF.AAP8.01 2 0.000 1.000 0.00 1.00
#> TCGA.DA.A1HW.06 1 0.000 0.988 1.00 0.00
#> TCGA.GF.A6C8.06 1 0.000 0.988 1.00 0.00
#> TCGA.EE.A29V.06 1 0.000 0.988 1.00 0.00
#> TCGA.EE.A3AB.06 1 0.000 0.988 1.00 0.00
#> TCGA.EB.A5SH.06 2 0.000 1.000 0.00 1.00
#> TCGA.D9.A6E9.06 1 0.943 0.451 0.64 0.36
#> TCGA.BF.AAP4.01 1 0.000 0.988 1.00 0.00
#> TCGA.DA.A1I1.06 1 0.000 0.988 1.00 0.00
#> TCGA.EE.A2MT.06 2 0.000 1.000 0.00 1.00
#> TCGA.ER.A19M.06 1 0.000 0.988 1.00 0.00
#> TCGA.FS.A1ZA.06 1 0.000 0.988 1.00 0.00
#> TCGA.EE.A2MI.06 1 0.000 0.988 1.00 0.00
#> TCGA.D3.A3CE.06 1 0.000 0.988 1.00 0.00
#> TCGA.ER.A2NB.01 2 0.000 1.000 0.00 1.00
#> TCGA.D3.A1Q5.06 2 0.000 1.000 0.00 1.00
#> TCGA.EB.A57M.01 1 0.000 0.988 1.00 0.00
#> TCGA.EE.A2A6.06 2 0.000 1.000 0.00 1.00
#> TCGA.D3.A1Q1.06 2 0.000 1.000 0.00 1.00
#> TCGA.EB.A3Y6.01 1 0.000 0.988 1.00 0.00
#> TCGA.EB.A3XE.01 2 0.000 1.000 0.00 1.00
#> TCGA.FW.A3R5.06 2 0.000 1.000 0.00 1.00
#> TCGA.EE.A2GI.06 1 0.000 0.988 1.00 0.00
#> TCGA.EB.A3XB.01 1 0.000 0.988 1.00 0.00
#> TCGA.EE.A2MD.06 1 0.000 0.988 1.00 0.00
#> TCGA.W3.AA1V.06 1 0.000 0.988 1.00 0.00
#> TCGA.D3.A2JK.06 1 0.000 0.988 1.00 0.00
#> TCGA.EB.A5UM.01 2 0.000 1.000 0.00 1.00
#> TCGA.D9.A148.06 1 0.000 0.988 1.00 0.00
#> TCGA.EE.A2ML.06 1 0.000 0.988 1.00 0.00
#> TCGA.EB.A5UL.06 1 0.000 0.988 1.00 0.00
#> TCGA.EE.A29T.06 2 0.000 1.000 0.00 1.00
#> TCGA.ER.A3ES.06 2 0.000 1.000 0.00 1.00
#> TCGA.EB.A44Q.06 1 0.000 0.988 1.00 0.00
#> TCGA.EB.A44R.06 2 0.000 1.000 0.00 1.00
#> TCGA.D3.A51N.06 1 0.000 0.988 1.00 0.00
#> TCGA.XV.A9W5.01 1 0.000 0.988 1.00 0.00
#> TCGA.D3.A51J.06 1 0.000 0.988 1.00 0.00
#> TCGA.3N.A9WC.06 2 0.000 1.000 0.00 1.00
#> TCGA.D9.A4Z6.06 1 0.000 0.988 1.00 0.00
#> TCGA.DA.A1I0.06 1 0.000 0.988 1.00 0.00
#> TCGA.EB.A431.01 1 0.000 0.988 1.00 0.00
#> TCGA.BF.AAOX.01 1 0.000 0.988 1.00 0.00
#> TCGA.DA.A3F5.06 2 0.000 1.000 0.00 1.00
#> TCGA.YD.A9TA.06 1 0.000 0.988 1.00 0.00
#> TCGA.EB.A4IQ.01 2 0.000 1.000 0.00 1.00
#> TCGA.ER.A3EV.06 2 0.000 1.000 0.00 1.00
#> TCGA.XV.A9W2.01 2 0.141 0.979 0.02 0.98
#> TCGA.WE.AAA0.06 1 0.000 0.988 1.00 0.00
#> TCGA.EE.A3J5.06 1 0.000 0.988 1.00 0.00
#> TCGA.FS.A4FD.06 2 0.000 1.000 0.00 1.00
#> TCGA.WE.AAA3.06 2 0.000 1.000 0.00 1.00
#> TCGA.ER.A3ET.06 2 0.000 1.000 0.00 1.00
#> TCGA.YG.AA3N.01 1 0.000 0.988 1.00 0.00
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.FS.A4FC.06 2 0.2066 0.918 0.00 0.94 0.06
#> TCGA.D3.A8GQ.06 1 0.0000 0.959 1.00 0.00 0.00
#> TCGA.BF.A5EQ.01 2 0.2537 0.904 0.00 0.92 0.08
#> TCGA.EB.A5VU.01 1 0.2066 0.928 0.94 0.06 0.00
#> TCGA.D3.A8GJ.06 2 0.0000 0.944 0.00 1.00 0.00
#> TCGA.WE.A8ZR.06 3 0.0000 0.990 0.00 0.00 1.00
#> TCGA.DA.A95V.06 1 0.0000 0.959 1.00 0.00 0.00
#> TCGA.EE.A3JB.06 1 0.0000 0.959 1.00 0.00 0.00
#> TCGA.WE.A8ZX.06 1 0.0000 0.959 1.00 0.00 0.00
#> TCGA.D3.A8GS.06 1 0.4796 0.771 0.78 0.22 0.00
#> TCGA.GN.A4U8.06 1 0.0000 0.959 1.00 0.00 0.00
#> TCGA.EB.A551.01 2 0.0000 0.944 0.00 1.00 0.00
#> TCGA.D3.A8GM.06 1 0.0000 0.959 1.00 0.00 0.00
#> TCGA.YD.A89C.06 1 0.0000 0.959 1.00 0.00 0.00
#> TCGA.FR.A726.01 1 0.0000 0.959 1.00 0.00 0.00
#> TCGA.W3.A825.06 1 0.5560 0.652 0.70 0.30 0.00
#> TCGA.D3.A5GR.06 2 0.0000 0.944 0.00 1.00 0.00
#> TCGA.FR.A729.06 1 0.2066 0.928 0.94 0.06 0.00
#> TCGA.EE.A29P.06 2 0.0000 0.944 0.00 1.00 0.00
#> TCGA.GN.A26A.06 1 0.0000 0.959 1.00 0.00 0.00
#> TCGA.EE.A20I.06 1 0.0000 0.959 1.00 0.00 0.00
#> TCGA.EB.A85J.01 3 0.0000 0.990 0.00 0.00 1.00
#> TCGA.RP.A6K9.06 2 0.4796 0.764 0.00 0.78 0.22
#> TCGA.EE.A17Y.06 1 0.0000 0.959 1.00 0.00 0.00
#> TCGA.D9.A149.06 3 0.2537 0.910 0.00 0.08 0.92
#> TCGA.D3.A1Q9.06 1 0.0000 0.959 1.00 0.00 0.00
#> TCGA.ER.A19L.06 3 0.0000 0.990 0.00 0.00 1.00
#> TCGA.ER.A19T.06 3 0.0000 0.990 0.00 0.00 1.00
#> TCGA.D3.A2JC.06 2 0.0000 0.944 0.00 1.00 0.00
#> TCGA.BF.A5EO.01 1 0.0000 0.959 1.00 0.00 0.00
#> TCGA.EE.A2M7.06 1 0.2066 0.928 0.94 0.06 0.00
#> TCGA.D3.A1Q3.06 3 0.0000 0.990 0.00 0.00 1.00
#> TCGA.EB.A85I.01 2 0.2066 0.918 0.00 0.94 0.06
#> TCGA.DA.A1I2.06 2 0.0000 0.944 0.00 1.00 0.00
#> TCGA.DA.A1I7.06 2 0.0000 0.944 0.00 1.00 0.00
#> TCGA.EE.A181.06 1 0.0000 0.959 1.00 0.00 0.00
#> TCGA.FS.A1ZM.06 2 0.0000 0.944 0.00 1.00 0.00
#> TCGA.D3.A2JP.06 1 0.0000 0.959 1.00 0.00 0.00
#> TCGA.ER.A19C.06 2 0.0000 0.944 0.00 1.00 0.00
#> TCGA.EB.A82B.01 2 0.2066 0.918 0.00 0.94 0.06
#> TCGA.FS.A1ZH.06 1 0.0000 0.959 1.00 0.00 0.00
#> TCGA.D3.A2J6.06 2 0.4002 0.833 0.00 0.84 0.16
#> TCGA.D3.A2JO.06 1 0.0000 0.959 1.00 0.00 0.00
#> TCGA.GN.A267.06 3 0.0000 0.990 0.00 0.00 1.00
#> TCGA.D3.A3CC.06 2 0.4291 0.811 0.00 0.82 0.18
#> TCGA.BF.A1PU.01 2 0.0000 0.944 0.00 1.00 0.00
#> TCGA.D3.A1Q6.06 2 0.0000 0.944 0.00 1.00 0.00
#> TCGA.EB.A24C.01 3 0.0000 0.990 0.00 0.00 1.00
#> TCGA.D3.A2JL.06 1 0.0000 0.959 1.00 0.00 0.00
#> TCGA.FS.A1ZS.06 2 0.2066 0.918 0.00 0.94 0.06
#> TCGA.D3.A3C3.06 1 0.0000 0.959 1.00 0.00 0.00
#> TCGA.D3.A1QA.07 1 0.0000 0.959 1.00 0.00 0.00
#> TCGA.EE.A29S.06 1 0.4796 0.771 0.78 0.22 0.00
#> TCGA.GN.A26D.06 2 0.0000 0.944 0.00 1.00 0.00
#> TCGA.EE.A2M5.06 1 0.0000 0.959 1.00 0.00 0.00
#> TCGA.GN.A266.06 1 0.2066 0.928 0.94 0.06 0.00
#> TCGA.D3.A3C1.06 2 0.0000 0.944 0.00 1.00 0.00
#> TCGA.EE.A20F.06 1 0.0000 0.959 1.00 0.00 0.00
#> TCGA.ER.A193.06 2 0.0892 0.936 0.00 0.98 0.02
#> TCGA.FS.A1ZW.06 1 0.0000 0.959 1.00 0.00 0.00
#> TCGA.ER.A19O.06 2 0.0000 0.944 0.00 1.00 0.00
#> TCGA.EE.A20B.06 1 0.0000 0.959 1.00 0.00 0.00
#> TCGA.FS.A1YX.06 2 0.0000 0.944 0.00 1.00 0.00
#> TCGA.ER.A194.01 1 0.4555 0.794 0.80 0.20 0.00
#> TCGA.EE.A2MS.06 3 0.0000 0.990 0.00 0.00 1.00
#> TCGA.EE.A29X.06 2 0.0000 0.944 0.00 1.00 0.00
#> TCGA.ER.A2NC.06 2 0.0000 0.944 0.00 1.00 0.00
#> TCGA.BF.A1Q0.01 2 0.4796 0.764 0.00 0.78 0.22
#> TCGA.EE.A182.06 3 0.0000 0.990 0.00 0.00 1.00
#> TCGA.D9.A1JW.06 2 0.4796 0.764 0.00 0.78 0.22
#> TCGA.EE.A2GJ.06 3 0.0000 0.990 0.00 0.00 1.00
#> TCGA.EE.A2GU.06 2 0.2066 0.918 0.00 0.94 0.06
#> TCGA.FS.A1Z7.06 2 0.0000 0.944 0.00 1.00 0.00
#> TCGA.ER.A19K.01 2 0.0000 0.944 0.00 1.00 0.00
#> TCGA.FR.A3YO.06 2 0.0000 0.944 0.00 1.00 0.00
#> TCGA.RP.A694.06 1 0.5216 0.719 0.74 0.26 0.00
#> TCGA.EB.A3Y7.01 2 0.2066 0.918 0.00 0.94 0.06
#> TCGA.BF.AAP8.01 2 0.4796 0.764 0.00 0.78 0.22
#> TCGA.DA.A1HW.06 1 0.2066 0.928 0.94 0.06 0.00
#> TCGA.GF.A6C8.06 1 0.0892 0.950 0.98 0.02 0.00
#> TCGA.EE.A29V.06 1 0.0000 0.959 1.00 0.00 0.00
#> TCGA.EE.A3AB.06 1 0.0000 0.959 1.00 0.00 0.00
#> TCGA.EB.A5SH.06 3 0.0000 0.990 0.00 0.00 1.00
#> TCGA.D9.A6E9.06 2 0.0000 0.944 0.00 1.00 0.00
#> TCGA.BF.AAP4.01 1 0.4796 0.771 0.78 0.22 0.00
#> TCGA.DA.A1I1.06 1 0.0000 0.959 1.00 0.00 0.00
#> TCGA.EE.A2MT.06 3 0.0892 0.973 0.00 0.02 0.98
#> TCGA.ER.A19M.06 1 0.0000 0.959 1.00 0.00 0.00
#> TCGA.FS.A1ZA.06 1 0.0892 0.950 0.98 0.02 0.00
#> TCGA.EE.A2MI.06 1 0.5706 0.616 0.68 0.32 0.00
#> TCGA.D3.A3CE.06 1 0.2066 0.928 0.94 0.06 0.00
#> TCGA.ER.A2NB.01 2 0.4796 0.764 0.00 0.78 0.22
#> TCGA.D3.A1Q5.06 2 0.0000 0.944 0.00 1.00 0.00
#> TCGA.EB.A57M.01 1 0.0000 0.959 1.00 0.00 0.00
#> TCGA.EE.A2A6.06 2 0.0000 0.944 0.00 1.00 0.00
#> TCGA.D3.A1Q1.06 2 0.6126 0.429 0.00 0.60 0.40
#> TCGA.EB.A3Y6.01 1 0.2066 0.928 0.94 0.06 0.00
#> TCGA.EB.A3XE.01 3 0.0000 0.990 0.00 0.00 1.00
#> TCGA.FW.A3R5.06 3 0.0000 0.990 0.00 0.00 1.00
#> TCGA.EE.A2GI.06 1 0.0000 0.959 1.00 0.00 0.00
#> TCGA.EB.A3XB.01 1 0.2066 0.928 0.94 0.06 0.00
#> TCGA.EE.A2MD.06 1 0.2066 0.928 0.94 0.06 0.00
#> TCGA.W3.AA1V.06 1 0.0892 0.950 0.98 0.02 0.00
#> TCGA.D3.A2JK.06 1 0.0000 0.959 1.00 0.00 0.00
#> TCGA.EB.A5UM.01 3 0.0000 0.990 0.00 0.00 1.00
#> TCGA.D9.A148.06 1 0.0000 0.959 1.00 0.00 0.00
#> TCGA.EE.A2ML.06 1 0.0000 0.959 1.00 0.00 0.00
#> TCGA.EB.A5UL.06 1 0.0000 0.959 1.00 0.00 0.00
#> TCGA.EE.A29T.06 3 0.0000 0.990 0.00 0.00 1.00
#> TCGA.ER.A3ES.06 3 0.2537 0.910 0.00 0.08 0.92
#> TCGA.EB.A44Q.06 2 0.0000 0.944 0.00 1.00 0.00
#> TCGA.EB.A44R.06 3 0.0000 0.990 0.00 0.00 1.00
#> TCGA.D3.A51N.06 1 0.0000 0.959 1.00 0.00 0.00
#> TCGA.XV.A9W5.01 1 0.0000 0.959 1.00 0.00 0.00
#> TCGA.D3.A51J.06 1 0.2066 0.928 0.94 0.06 0.00
#> TCGA.3N.A9WC.06 2 0.2066 0.918 0.00 0.94 0.06
#> TCGA.D9.A4Z6.06 1 0.0000 0.959 1.00 0.00 0.00
#> TCGA.DA.A1I0.06 1 0.0000 0.959 1.00 0.00 0.00
#> TCGA.EB.A431.01 1 0.0000 0.959 1.00 0.00 0.00
#> TCGA.BF.AAOX.01 1 0.0000 0.959 1.00 0.00 0.00
#> TCGA.DA.A3F5.06 2 0.0000 0.944 0.00 1.00 0.00
#> TCGA.YD.A9TA.06 1 0.0000 0.959 1.00 0.00 0.00
#> TCGA.EB.A4IQ.01 3 0.0000 0.990 0.00 0.00 1.00
#> TCGA.ER.A3EV.06 3 0.0000 0.990 0.00 0.00 1.00
#> TCGA.XV.A9W2.01 2 0.0000 0.944 0.00 1.00 0.00
#> TCGA.WE.AAA0.06 1 0.0000 0.959 1.00 0.00 0.00
#> TCGA.EE.A3J5.06 1 0.0000 0.959 1.00 0.00 0.00
#> TCGA.FS.A4FD.06 2 0.0000 0.944 0.00 1.00 0.00
#> TCGA.WE.AAA3.06 2 0.0000 0.944 0.00 1.00 0.00
#> TCGA.ER.A3ET.06 2 0.1529 0.927 0.00 0.96 0.04
#> TCGA.YG.AA3N.01 2 0.0000 0.944 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.FS.A4FC.06 2 0.0000 0.995 0.00 1.00 0 0.00
#> TCGA.D3.A8GQ.06 1 0.0000 0.996 1.00 0.00 0 0.00
#> TCGA.BF.A5EQ.01 2 0.0000 0.995 0.00 1.00 0 0.00
#> TCGA.EB.A5VU.01 4 0.0000 0.980 0.00 0.00 0 1.00
#> TCGA.D3.A8GJ.06 4 0.4977 0.140 0.00 0.46 0 0.54
#> TCGA.WE.A8ZR.06 3 0.0000 1.000 0.00 0.00 1 0.00
#> TCGA.DA.A95V.06 1 0.0000 0.996 1.00 0.00 0 0.00
#> TCGA.EE.A3JB.06 1 0.0000 0.996 1.00 0.00 0 0.00
#> TCGA.WE.A8ZX.06 1 0.0000 0.996 1.00 0.00 0 0.00
#> TCGA.D3.A8GS.06 4 0.0000 0.980 0.00 0.00 0 1.00
#> TCGA.GN.A4U8.06 1 0.0000 0.996 1.00 0.00 0 0.00
#> TCGA.EB.A551.01 4 0.0000 0.980 0.00 0.00 0 1.00
#> TCGA.D3.A8GM.06 1 0.0000 0.996 1.00 0.00 0 0.00
#> TCGA.YD.A89C.06 1 0.0000 0.996 1.00 0.00 0 0.00
#> TCGA.FR.A726.01 1 0.0000 0.996 1.00 0.00 0 0.00
#> TCGA.W3.A825.06 4 0.0000 0.980 0.00 0.00 0 1.00
#> TCGA.D3.A5GR.06 4 0.0000 0.980 0.00 0.00 0 1.00
#> TCGA.FR.A729.06 4 0.0000 0.980 0.00 0.00 0 1.00
#> TCGA.EE.A29P.06 4 0.0000 0.980 0.00 0.00 0 1.00
#> TCGA.GN.A26A.06 1 0.0000 0.996 1.00 0.00 0 0.00
#> TCGA.EE.A20I.06 1 0.0000 0.996 1.00 0.00 0 0.00
#> TCGA.EB.A85J.01 3 0.0000 1.000 0.00 0.00 1 0.00
#> TCGA.RP.A6K9.06 2 0.0000 0.995 0.00 1.00 0 0.00
#> TCGA.EE.A17Y.06 1 0.0000 0.996 1.00 0.00 0 0.00
#> TCGA.D9.A149.06 2 0.0000 0.995 0.00 1.00 0 0.00
#> TCGA.D3.A1Q9.06 1 0.0000 0.996 1.00 0.00 0 0.00
#> TCGA.ER.A19L.06 3 0.0000 1.000 0.00 0.00 1 0.00
#> TCGA.ER.A19T.06 3 0.0000 1.000 0.00 0.00 1 0.00
#> TCGA.D3.A2JC.06 4 0.0000 0.980 0.00 0.00 0 1.00
#> TCGA.BF.A5EO.01 1 0.0000 0.996 1.00 0.00 0 0.00
#> TCGA.EE.A2M7.06 4 0.0000 0.980 0.00 0.00 0 1.00
#> TCGA.D3.A1Q3.06 3 0.0000 1.000 0.00 0.00 1 0.00
#> TCGA.EB.A85I.01 2 0.0000 0.995 0.00 1.00 0 0.00
#> TCGA.DA.A1I2.06 4 0.0707 0.960 0.00 0.02 0 0.98
#> TCGA.DA.A1I7.06 4 0.0000 0.980 0.00 0.00 0 1.00
#> TCGA.EE.A181.06 1 0.0000 0.996 1.00 0.00 0 0.00
#> TCGA.FS.A1ZM.06 4 0.0000 0.980 0.00 0.00 0 1.00
#> TCGA.D3.A2JP.06 1 0.0000 0.996 1.00 0.00 0 0.00
#> TCGA.ER.A19C.06 4 0.0000 0.980 0.00 0.00 0 1.00
#> TCGA.EB.A82B.01 2 0.0000 0.995 0.00 1.00 0 0.00
#> TCGA.FS.A1ZH.06 1 0.0000 0.996 1.00 0.00 0 0.00
#> TCGA.D3.A2J6.06 2 0.0000 0.995 0.00 1.00 0 0.00
#> TCGA.D3.A2JO.06 4 0.0000 0.980 0.00 0.00 0 1.00
#> TCGA.GN.A267.06 3 0.0000 1.000 0.00 0.00 1 0.00
#> TCGA.D3.A3CC.06 2 0.0000 0.995 0.00 1.00 0 0.00
#> TCGA.BF.A1PU.01 4 0.0000 0.980 0.00 0.00 0 1.00
#> TCGA.D3.A1Q6.06 4 0.0000 0.980 0.00 0.00 0 1.00
#> TCGA.EB.A24C.01 3 0.0000 1.000 0.00 0.00 1 0.00
#> TCGA.D3.A2JL.06 1 0.0000 0.996 1.00 0.00 0 0.00
#> TCGA.FS.A1ZS.06 2 0.0000 0.995 0.00 1.00 0 0.00
#> TCGA.D3.A3C3.06 1 0.0000 0.996 1.00 0.00 0 0.00
#> TCGA.D3.A1QA.07 1 0.0000 0.996 1.00 0.00 0 0.00
#> TCGA.EE.A29S.06 4 0.0000 0.980 0.00 0.00 0 1.00
#> TCGA.GN.A26D.06 2 0.0000 0.995 0.00 1.00 0 0.00
#> TCGA.EE.A2M5.06 1 0.0000 0.996 1.00 0.00 0 0.00
#> TCGA.GN.A266.06 4 0.0000 0.980 0.00 0.00 0 1.00
#> TCGA.D3.A3C1.06 4 0.0000 0.980 0.00 0.00 0 1.00
#> TCGA.EE.A20F.06 1 0.0000 0.996 1.00 0.00 0 0.00
#> TCGA.ER.A193.06 2 0.0000 0.995 0.00 1.00 0 0.00
#> TCGA.FS.A1ZW.06 1 0.0000 0.996 1.00 0.00 0 0.00
#> TCGA.ER.A19O.06 4 0.0000 0.980 0.00 0.00 0 1.00
#> TCGA.EE.A20B.06 1 0.0000 0.996 1.00 0.00 0 0.00
#> TCGA.FS.A1YX.06 4 0.0000 0.980 0.00 0.00 0 1.00
#> TCGA.ER.A194.01 4 0.0000 0.980 0.00 0.00 0 1.00
#> TCGA.EE.A2MS.06 3 0.0000 1.000 0.00 0.00 1 0.00
#> TCGA.EE.A29X.06 4 0.0000 0.980 0.00 0.00 0 1.00
#> TCGA.ER.A2NC.06 4 0.0000 0.980 0.00 0.00 0 1.00
#> TCGA.BF.A1Q0.01 2 0.0000 0.995 0.00 1.00 0 0.00
#> TCGA.EE.A182.06 3 0.0000 1.000 0.00 0.00 1 0.00
#> TCGA.D9.A1JW.06 2 0.0000 0.995 0.00 1.00 0 0.00
#> TCGA.EE.A2GJ.06 3 0.0000 1.000 0.00 0.00 1 0.00
#> TCGA.EE.A2GU.06 2 0.0000 0.995 0.00 1.00 0 0.00
#> TCGA.FS.A1Z7.06 2 0.0000 0.995 0.00 1.00 0 0.00
#> TCGA.ER.A19K.01 4 0.0000 0.980 0.00 0.00 0 1.00
#> TCGA.FR.A3YO.06 4 0.0000 0.980 0.00 0.00 0 1.00
#> TCGA.RP.A694.06 4 0.0000 0.980 0.00 0.00 0 1.00
#> TCGA.EB.A3Y7.01 2 0.0000 0.995 0.00 1.00 0 0.00
#> TCGA.BF.AAP8.01 2 0.0000 0.995 0.00 1.00 0 0.00
#> TCGA.DA.A1HW.06 4 0.0000 0.980 0.00 0.00 0 1.00
#> TCGA.GF.A6C8.06 4 0.2011 0.889 0.08 0.00 0 0.92
#> TCGA.EE.A29V.06 1 0.0000 0.996 1.00 0.00 0 0.00
#> TCGA.EE.A3AB.06 1 0.0000 0.996 1.00 0.00 0 0.00
#> TCGA.EB.A5SH.06 3 0.0000 1.000 0.00 0.00 1 0.00
#> TCGA.D9.A6E9.06 4 0.0000 0.980 0.00 0.00 0 1.00
#> TCGA.BF.AAP4.01 4 0.0000 0.980 0.00 0.00 0 1.00
#> TCGA.DA.A1I1.06 1 0.0000 0.996 1.00 0.00 0 0.00
#> TCGA.EE.A2MT.06 2 0.0000 0.995 0.00 1.00 0 0.00
#> TCGA.ER.A19M.06 1 0.0000 0.996 1.00 0.00 0 0.00
#> TCGA.FS.A1ZA.06 4 0.0000 0.980 0.00 0.00 0 1.00
#> TCGA.EE.A2MI.06 4 0.0000 0.980 0.00 0.00 0 1.00
#> TCGA.D3.A3CE.06 4 0.0000 0.980 0.00 0.00 0 1.00
#> TCGA.ER.A2NB.01 2 0.0000 0.995 0.00 1.00 0 0.00
#> TCGA.D3.A1Q5.06 2 0.0000 0.995 0.00 1.00 0 0.00
#> TCGA.EB.A57M.01 1 0.0000 0.996 1.00 0.00 0 0.00
#> TCGA.EE.A2A6.06 2 0.0000 0.995 0.00 1.00 0 0.00
#> TCGA.D3.A1Q1.06 2 0.0000 0.995 0.00 1.00 0 0.00
#> TCGA.EB.A3Y6.01 4 0.0000 0.980 0.00 0.00 0 1.00
#> TCGA.EB.A3XE.01 3 0.0000 1.000 0.00 0.00 1 0.00
#> TCGA.FW.A3R5.06 3 0.0000 1.000 0.00 0.00 1 0.00
#> TCGA.EE.A2GI.06 1 0.0000 0.996 1.00 0.00 0 0.00
#> TCGA.EB.A3XB.01 4 0.0000 0.980 0.00 0.00 0 1.00
#> TCGA.EE.A2MD.06 4 0.0000 0.980 0.00 0.00 0 1.00
#> TCGA.W3.AA1V.06 4 0.3172 0.785 0.16 0.00 0 0.84
#> TCGA.D3.A2JK.06 1 0.0000 0.996 1.00 0.00 0 0.00
#> TCGA.EB.A5UM.01 3 0.0000 1.000 0.00 0.00 1 0.00
#> TCGA.D9.A148.06 1 0.0000 0.996 1.00 0.00 0 0.00
#> TCGA.EE.A2ML.06 1 0.0000 0.996 1.00 0.00 0 0.00
#> TCGA.EB.A5UL.06 1 0.0000 0.996 1.00 0.00 0 0.00
#> TCGA.EE.A29T.06 3 0.0000 1.000 0.00 0.00 1 0.00
#> TCGA.ER.A3ES.06 2 0.0000 0.995 0.00 1.00 0 0.00
#> TCGA.EB.A44Q.06 4 0.0000 0.980 0.00 0.00 0 1.00
#> TCGA.EB.A44R.06 3 0.0000 1.000 0.00 0.00 1 0.00
#> TCGA.D3.A51N.06 1 0.0000 0.996 1.00 0.00 0 0.00
#> TCGA.XV.A9W5.01 1 0.0000 0.996 1.00 0.00 0 0.00
#> TCGA.D3.A51J.06 4 0.0000 0.980 0.00 0.00 0 1.00
#> TCGA.3N.A9WC.06 2 0.0000 0.995 0.00 1.00 0 0.00
#> TCGA.D9.A4Z6.06 1 0.2921 0.819 0.86 0.00 0 0.14
#> TCGA.DA.A1I0.06 1 0.0000 0.996 1.00 0.00 0 0.00
#> TCGA.EB.A431.01 1 0.0000 0.996 1.00 0.00 0 0.00
#> TCGA.BF.AAOX.01 1 0.0000 0.996 1.00 0.00 0 0.00
#> TCGA.DA.A3F5.06 2 0.2647 0.843 0.00 0.88 0 0.12
#> TCGA.YD.A9TA.06 1 0.0000 0.996 1.00 0.00 0 0.00
#> TCGA.EB.A4IQ.01 2 0.0000 0.995 0.00 1.00 0 0.00
#> TCGA.ER.A3EV.06 3 0.0000 1.000 0.00 0.00 1 0.00
#> TCGA.XV.A9W2.01 2 0.0000 0.995 0.00 1.00 0 0.00
#> TCGA.WE.AAA0.06 1 0.0000 0.996 1.00 0.00 0 0.00
#> TCGA.EE.A3J5.06 1 0.0000 0.996 1.00 0.00 0 0.00
#> TCGA.FS.A4FD.06 2 0.0000 0.995 0.00 1.00 0 0.00
#> TCGA.WE.AAA3.06 2 0.0000 0.995 0.00 1.00 0 0.00
#> TCGA.ER.A3ET.06 2 0.0000 0.995 0.00 1.00 0 0.00
#> TCGA.YG.AA3N.01 4 0.0000 0.980 0.00 0.00 0 1.00
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> TCGA.FS.A4FC.06 2 0.3561 0.743 0.00 0.74 0.00 0.26 0.00
#> TCGA.D3.A8GQ.06 5 0.3561 0.702 0.26 0.00 0.00 0.00 0.74
#> TCGA.BF.A5EQ.01 2 0.0000 0.900 0.00 1.00 0.00 0.00 0.00
#> TCGA.EB.A5VU.01 5 0.3037 0.795 0.04 0.00 0.00 0.10 0.86
#> TCGA.D3.A8GJ.06 4 0.2754 0.815 0.00 0.08 0.00 0.88 0.04
#> TCGA.WE.A8ZR.06 3 0.0000 0.996 0.00 0.00 1.00 0.00 0.00
#> TCGA.DA.A95V.06 5 0.4307 0.279 0.50 0.00 0.00 0.00 0.50
#> TCGA.EE.A3JB.06 1 0.0000 0.999 1.00 0.00 0.00 0.00 0.00
#> TCGA.WE.A8ZX.06 1 0.0000 0.999 1.00 0.00 0.00 0.00 0.00
#> TCGA.D3.A8GS.06 5 0.2732 0.751 0.00 0.00 0.00 0.16 0.84
#> TCGA.GN.A4U8.06 1 0.0000 0.999 1.00 0.00 0.00 0.00 0.00
#> TCGA.EB.A551.01 4 0.2020 0.898 0.00 0.00 0.00 0.90 0.10
#> TCGA.D3.A8GM.06 5 0.4060 0.589 0.36 0.00 0.00 0.00 0.64
#> TCGA.YD.A89C.06 1 0.0000 0.999 1.00 0.00 0.00 0.00 0.00
#> TCGA.FR.A726.01 5 0.4126 0.557 0.38 0.00 0.00 0.00 0.62
#> TCGA.W3.A825.06 5 0.1410 0.749 0.00 0.00 0.00 0.06 0.94
#> TCGA.D3.A5GR.06 4 0.2020 0.898 0.00 0.00 0.00 0.90 0.10
#> TCGA.FR.A729.06 5 0.3291 0.797 0.04 0.00 0.00 0.12 0.84
#> TCGA.EE.A29P.06 4 0.2020 0.898 0.00 0.00 0.00 0.90 0.10
#> TCGA.GN.A26A.06 1 0.0000 0.999 1.00 0.00 0.00 0.00 0.00
#> TCGA.EE.A20I.06 1 0.0000 0.999 1.00 0.00 0.00 0.00 0.00
#> TCGA.EB.A85J.01 3 0.0000 0.996 0.00 0.00 1.00 0.00 0.00
#> TCGA.RP.A6K9.06 2 0.0000 0.900 0.00 1.00 0.00 0.00 0.00
#> TCGA.EE.A17Y.06 1 0.0000 0.999 1.00 0.00 0.00 0.00 0.00
#> TCGA.D9.A149.06 2 0.0000 0.900 0.00 1.00 0.00 0.00 0.00
#> TCGA.D3.A1Q9.06 1 0.0000 0.999 1.00 0.00 0.00 0.00 0.00
#> TCGA.ER.A19L.06 3 0.0000 0.996 0.00 0.00 1.00 0.00 0.00
#> TCGA.ER.A19T.06 3 0.0000 0.996 0.00 0.00 1.00 0.00 0.00
#> TCGA.D3.A2JC.06 4 0.2020 0.898 0.00 0.00 0.00 0.90 0.10
#> TCGA.BF.A5EO.01 1 0.0000 0.999 1.00 0.00 0.00 0.00 0.00
#> TCGA.EE.A2M7.06 5 0.3291 0.797 0.04 0.00 0.00 0.12 0.84
#> TCGA.D3.A1Q3.06 3 0.0000 0.996 0.00 0.00 1.00 0.00 0.00
#> TCGA.EB.A85I.01 2 0.3561 0.664 0.00 0.74 0.00 0.26 0.00
#> TCGA.DA.A1I2.06 4 0.2754 0.870 0.00 0.04 0.00 0.88 0.08
#> TCGA.DA.A1I7.06 4 0.2020 0.898 0.00 0.00 0.00 0.90 0.10
#> TCGA.EE.A181.06 1 0.0000 0.999 1.00 0.00 0.00 0.00 0.00
#> TCGA.FS.A1ZM.06 4 0.2020 0.888 0.00 0.00 0.00 0.90 0.10
#> TCGA.D3.A2JP.06 1 0.0000 0.999 1.00 0.00 0.00 0.00 0.00
#> TCGA.ER.A19C.06 4 0.3895 0.733 0.00 0.00 0.00 0.68 0.32
#> TCGA.EB.A82B.01 2 0.0000 0.900 0.00 1.00 0.00 0.00 0.00
#> TCGA.FS.A1ZH.06 1 0.0000 0.999 1.00 0.00 0.00 0.00 0.00
#> TCGA.D3.A2J6.06 2 0.0000 0.900 0.00 1.00 0.00 0.00 0.00
#> TCGA.D3.A2JO.06 5 0.3291 0.797 0.04 0.00 0.00 0.12 0.84
#> TCGA.GN.A267.06 3 0.0000 0.996 0.00 0.00 1.00 0.00 0.00
#> TCGA.D3.A3CC.06 2 0.1648 0.889 0.00 0.94 0.00 0.02 0.04
#> TCGA.BF.A1PU.01 5 0.1732 0.736 0.00 0.00 0.00 0.08 0.92
#> TCGA.D3.A1Q6.06 4 0.2280 0.887 0.00 0.00 0.00 0.88 0.12
#> TCGA.EB.A24C.01 3 0.0000 0.996 0.00 0.00 1.00 0.00 0.00
#> TCGA.D3.A2JL.06 5 0.4060 0.589 0.36 0.00 0.00 0.00 0.64
#> TCGA.FS.A1ZS.06 2 0.2012 0.893 0.00 0.92 0.00 0.06 0.02
#> TCGA.D3.A3C3.06 1 0.0000 0.999 1.00 0.00 0.00 0.00 0.00
#> TCGA.D3.A1QA.07 1 0.0000 0.999 1.00 0.00 0.00 0.00 0.00
#> TCGA.EE.A29S.06 4 0.3424 0.754 0.00 0.00 0.00 0.76 0.24
#> TCGA.GN.A26D.06 2 0.4437 0.840 0.00 0.76 0.00 0.10 0.14
#> TCGA.EE.A2M5.06 1 0.0609 0.975 0.98 0.00 0.00 0.00 0.02
#> TCGA.GN.A266.06 5 0.3037 0.795 0.04 0.00 0.00 0.10 0.86
#> TCGA.D3.A3C1.06 4 0.2020 0.898 0.00 0.00 0.00 0.90 0.10
#> TCGA.EE.A20F.06 1 0.0000 0.999 1.00 0.00 0.00 0.00 0.00
#> TCGA.ER.A193.06 2 0.3561 0.664 0.00 0.74 0.00 0.26 0.00
#> TCGA.FS.A1ZW.06 1 0.0000 0.999 1.00 0.00 0.00 0.00 0.00
#> TCGA.ER.A19O.06 4 0.3684 0.704 0.00 0.00 0.00 0.72 0.28
#> TCGA.EE.A20B.06 1 0.0000 0.999 1.00 0.00 0.00 0.00 0.00
#> TCGA.FS.A1YX.06 4 0.2516 0.873 0.00 0.00 0.00 0.86 0.14
#> TCGA.ER.A194.01 5 0.2732 0.751 0.00 0.00 0.00 0.16 0.84
#> TCGA.EE.A2MS.06 3 0.0000 0.996 0.00 0.00 1.00 0.00 0.00
#> TCGA.EE.A29X.06 4 0.2020 0.898 0.00 0.00 0.00 0.90 0.10
#> TCGA.ER.A2NC.06 4 0.3895 0.733 0.00 0.00 0.00 0.68 0.32
#> TCGA.BF.A1Q0.01 2 0.1043 0.897 0.00 0.96 0.00 0.04 0.00
#> TCGA.EE.A182.06 3 0.1410 0.939 0.00 0.06 0.94 0.00 0.00
#> TCGA.D9.A1JW.06 2 0.0000 0.900 0.00 1.00 0.00 0.00 0.00
#> TCGA.EE.A2GJ.06 3 0.0000 0.996 0.00 0.00 1.00 0.00 0.00
#> TCGA.EE.A2GU.06 2 0.3561 0.743 0.00 0.74 0.00 0.26 0.00
#> TCGA.FS.A1Z7.06 4 0.2929 0.692 0.00 0.18 0.00 0.82 0.00
#> TCGA.ER.A19K.01 4 0.2020 0.898 0.00 0.00 0.00 0.90 0.10
#> TCGA.FR.A3YO.06 4 0.2020 0.898 0.00 0.00 0.00 0.90 0.10
#> TCGA.RP.A694.06 5 0.2732 0.751 0.00 0.00 0.00 0.16 0.84
#> TCGA.EB.A3Y7.01 2 0.0000 0.900 0.00 1.00 0.00 0.00 0.00
#> TCGA.BF.AAP8.01 2 0.2012 0.888 0.00 0.92 0.00 0.02 0.06
#> TCGA.DA.A1HW.06 5 0.3291 0.797 0.04 0.00 0.00 0.12 0.84
#> TCGA.GF.A6C8.06 5 0.3421 0.791 0.08 0.00 0.00 0.08 0.84
#> TCGA.EE.A29V.06 1 0.0000 0.999 1.00 0.00 0.00 0.00 0.00
#> TCGA.EE.A3AB.06 1 0.0000 0.999 1.00 0.00 0.00 0.00 0.00
#> TCGA.EB.A5SH.06 3 0.0000 0.996 0.00 0.00 1.00 0.00 0.00
#> TCGA.D9.A6E9.06 4 0.2331 0.888 0.00 0.02 0.00 0.90 0.08
#> TCGA.BF.AAP4.01 5 0.2732 0.751 0.00 0.00 0.00 0.16 0.84
#> TCGA.DA.A1I1.06 5 0.4302 0.340 0.48 0.00 0.00 0.00 0.52
#> TCGA.EE.A2MT.06 2 0.2797 0.885 0.00 0.88 0.00 0.06 0.06
#> TCGA.ER.A19M.06 5 0.4126 0.557 0.38 0.00 0.00 0.00 0.62
#> TCGA.FS.A1ZA.06 5 0.3291 0.797 0.04 0.00 0.00 0.12 0.84
#> TCGA.EE.A2MI.06 5 0.2020 0.763 0.00 0.00 0.00 0.10 0.90
#> TCGA.D3.A3CE.06 5 0.3291 0.797 0.04 0.00 0.00 0.12 0.84
#> TCGA.ER.A2NB.01 2 0.0000 0.900 0.00 1.00 0.00 0.00 0.00
#> TCGA.D3.A1Q5.06 2 0.4637 0.827 0.00 0.74 0.00 0.10 0.16
#> TCGA.EB.A57M.01 1 0.0000 0.999 1.00 0.00 0.00 0.00 0.00
#> TCGA.EE.A2A6.06 4 0.3424 0.648 0.00 0.24 0.00 0.76 0.00
#> TCGA.D3.A1Q1.06 2 0.3971 0.860 0.00 0.80 0.00 0.10 0.10
#> TCGA.EB.A3Y6.01 5 0.3291 0.797 0.04 0.00 0.00 0.12 0.84
#> TCGA.EB.A3XE.01 3 0.0000 0.996 0.00 0.00 1.00 0.00 0.00
#> TCGA.FW.A3R5.06 3 0.0000 0.996 0.00 0.00 1.00 0.00 0.00
#> TCGA.EE.A2GI.06 1 0.0000 0.999 1.00 0.00 0.00 0.00 0.00
#> TCGA.EB.A3XB.01 5 0.3291 0.797 0.04 0.00 0.00 0.12 0.84
#> TCGA.EE.A2MD.06 5 0.3291 0.797 0.04 0.00 0.00 0.12 0.84
#> TCGA.W3.AA1V.06 5 0.3390 0.796 0.06 0.00 0.00 0.10 0.84
#> TCGA.D3.A2JK.06 5 0.4287 0.394 0.46 0.00 0.00 0.00 0.54
#> TCGA.EB.A5UM.01 3 0.0000 0.996 0.00 0.00 1.00 0.00 0.00
#> TCGA.D9.A148.06 1 0.0000 0.999 1.00 0.00 0.00 0.00 0.00
#> TCGA.EE.A2ML.06 1 0.0000 0.999 1.00 0.00 0.00 0.00 0.00
#> TCGA.EB.A5UL.06 5 0.3684 0.684 0.28 0.00 0.00 0.00 0.72
#> TCGA.EE.A29T.06 3 0.0000 0.996 0.00 0.00 1.00 0.00 0.00
#> TCGA.ER.A3ES.06 2 0.2012 0.888 0.00 0.92 0.00 0.02 0.06
#> TCGA.EB.A44Q.06 4 0.2020 0.898 0.00 0.00 0.00 0.90 0.10
#> TCGA.EB.A44R.06 3 0.0000 0.996 0.00 0.00 1.00 0.00 0.00
#> TCGA.D3.A51N.06 1 0.0000 0.999 1.00 0.00 0.00 0.00 0.00
#> TCGA.XV.A9W5.01 1 0.0000 0.999 1.00 0.00 0.00 0.00 0.00
#> TCGA.D3.A51J.06 4 0.4227 0.389 0.00 0.00 0.00 0.58 0.42
#> TCGA.3N.A9WC.06 2 0.2012 0.893 0.00 0.92 0.00 0.06 0.02
#> TCGA.D9.A4Z6.06 5 0.3274 0.725 0.22 0.00 0.00 0.00 0.78
#> TCGA.DA.A1I0.06 1 0.0000 0.999 1.00 0.00 0.00 0.00 0.00
#> TCGA.EB.A431.01 1 0.0000 0.999 1.00 0.00 0.00 0.00 0.00
#> TCGA.BF.AAOX.01 1 0.0000 0.999 1.00 0.00 0.00 0.00 0.00
#> TCGA.DA.A3F5.06 4 0.2331 0.755 0.00 0.08 0.00 0.90 0.02
#> TCGA.YD.A9TA.06 1 0.0000 0.999 1.00 0.00 0.00 0.00 0.00
#> TCGA.EB.A4IQ.01 2 0.0000 0.900 0.00 1.00 0.00 0.00 0.00
#> TCGA.ER.A3EV.06 3 0.0000 0.996 0.00 0.00 1.00 0.00 0.00
#> TCGA.XV.A9W2.01 2 0.3421 0.871 0.00 0.84 0.00 0.08 0.08
#> TCGA.WE.AAA0.06 1 0.0000 0.999 1.00 0.00 0.00 0.00 0.00
#> TCGA.EE.A3J5.06 1 0.0000 0.999 1.00 0.00 0.00 0.00 0.00
#> TCGA.FS.A4FD.06 2 0.4075 0.837 0.00 0.78 0.00 0.06 0.16
#> TCGA.WE.AAA3.06 2 0.4840 0.668 0.00 0.64 0.00 0.32 0.04
#> TCGA.ER.A3ET.06 2 0.2754 0.884 0.00 0.88 0.00 0.08 0.04
#> TCGA.YG.AA3N.01 4 0.2020 0.898 0.00 0.00 0.00 0.90 0.10
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> TCGA.FS.A4FC.06 2 0.5774 0.4306 0.00 0.56 0.00 0.28 0.02 0.14
#> TCGA.D3.A8GQ.06 5 0.2956 0.7369 0.12 0.00 0.00 0.00 0.84 0.04
#> TCGA.BF.A5EQ.01 2 0.0000 0.6538 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.EB.A5VU.01 5 0.2094 0.7728 0.02 0.00 0.00 0.00 0.90 0.08
#> TCGA.D3.A8GJ.06 4 0.2403 0.7074 0.00 0.04 0.00 0.90 0.02 0.04
#> TCGA.WE.A8ZR.06 3 0.0000 0.9756 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.DA.A95V.06 5 0.4700 0.5395 0.34 0.00 0.00 0.00 0.60 0.06
#> TCGA.EE.A3JB.06 1 0.0000 0.9846 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.WE.A8ZX.06 1 0.0000 0.9846 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D3.A8GS.06 5 0.1092 0.7740 0.00 0.00 0.00 0.02 0.96 0.02
#> TCGA.GN.A4U8.06 1 0.0937 0.9694 0.96 0.00 0.00 0.00 0.00 0.04
#> TCGA.EB.A551.01 4 0.1480 0.7634 0.00 0.02 0.00 0.94 0.04 0.00
#> TCGA.D3.A8GM.06 5 0.4360 0.6250 0.26 0.00 0.00 0.00 0.68 0.06
#> TCGA.YD.A89C.06 1 0.0547 0.9805 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.FR.A726.01 5 0.4962 0.5885 0.28 0.00 0.00 0.02 0.64 0.06
#> TCGA.W3.A825.06 5 0.4078 0.3625 0.00 0.00 0.00 0.02 0.64 0.34
#> TCGA.D3.A5GR.06 4 0.2350 0.7830 0.00 0.02 0.00 0.88 0.10 0.00
#> TCGA.FR.A729.06 5 0.1480 0.7905 0.02 0.00 0.00 0.00 0.94 0.04
#> TCGA.EE.A29P.06 4 0.2474 0.7102 0.00 0.00 0.00 0.88 0.04 0.08
#> TCGA.GN.A26A.06 1 0.0937 0.9694 0.96 0.00 0.00 0.00 0.00 0.04
#> TCGA.EE.A20I.06 1 0.0000 0.9846 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EB.A85J.01 3 0.0547 0.9736 0.00 0.00 0.98 0.00 0.00 0.02
#> TCGA.RP.A6K9.06 2 0.0000 0.6538 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.EE.A17Y.06 1 0.0547 0.9805 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.D9.A149.06 2 0.0547 0.6503 0.00 0.98 0.00 0.00 0.00 0.02
#> TCGA.D3.A1Q9.06 1 0.0000 0.9846 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.ER.A19L.06 3 0.0000 0.9756 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.ER.A19T.06 3 0.0000 0.9756 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.D3.A2JC.06 4 0.4723 0.6475 0.00 0.00 0.00 0.68 0.14 0.18
#> TCGA.BF.A5EO.01 1 0.1267 0.9551 0.94 0.00 0.00 0.00 0.00 0.06
#> TCGA.EE.A2M7.06 5 0.1092 0.7889 0.02 0.00 0.00 0.00 0.96 0.02
#> TCGA.D3.A1Q3.06 3 0.0000 0.9756 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.EB.A85I.01 2 0.4078 0.4038 0.00 0.64 0.00 0.34 0.00 0.02
#> TCGA.DA.A1I2.06 4 0.4803 0.6652 0.00 0.08 0.00 0.72 0.04 0.16
#> TCGA.DA.A1I7.06 4 0.1556 0.7819 0.00 0.00 0.00 0.92 0.08 0.00
#> TCGA.EE.A181.06 1 0.0000 0.9846 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FS.A1ZM.06 4 0.4377 0.6798 0.00 0.00 0.00 0.72 0.12 0.16
#> TCGA.D3.A2JP.06 1 0.0547 0.9805 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.ER.A19C.06 6 0.6023 0.1159 0.00 0.00 0.00 0.26 0.32 0.42
#> TCGA.EB.A82B.01 2 0.0547 0.6532 0.00 0.98 0.00 0.00 0.00 0.02
#> TCGA.FS.A1ZH.06 1 0.0000 0.9846 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D3.A2J6.06 2 0.0547 0.6471 0.00 0.98 0.00 0.00 0.00 0.02
#> TCGA.D3.A2JO.06 5 0.1807 0.7830 0.02 0.00 0.00 0.00 0.92 0.06
#> TCGA.GN.A267.06 3 0.0000 0.9756 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.D3.A3CC.06 2 0.2454 0.5378 0.00 0.84 0.00 0.00 0.00 0.16
#> TCGA.BF.A1PU.01 5 0.4144 0.3371 0.00 0.00 0.00 0.02 0.62 0.36
#> TCGA.D3.A1Q6.06 4 0.4566 0.6668 0.00 0.00 0.00 0.70 0.14 0.16
#> TCGA.EB.A24C.01 3 0.0000 0.9756 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.D3.A2JL.06 5 0.4121 0.6606 0.22 0.00 0.00 0.00 0.72 0.06
#> TCGA.FS.A1ZS.06 2 0.4613 0.4435 0.00 0.66 0.00 0.08 0.00 0.26
#> TCGA.D3.A3C3.06 1 0.0000 0.9846 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D3.A1QA.07 1 0.0000 0.9846 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EE.A29S.06 4 0.4462 0.6038 0.00 0.00 0.00 0.66 0.28 0.06
#> TCGA.GN.A26D.06 6 0.4002 0.2273 0.00 0.32 0.00 0.02 0.00 0.66
#> TCGA.EE.A2M5.06 1 0.1807 0.9342 0.92 0.00 0.00 0.00 0.02 0.06
#> TCGA.GN.A266.06 5 0.1480 0.7905 0.02 0.00 0.00 0.00 0.94 0.04
#> TCGA.D3.A3C1.06 4 0.2350 0.7830 0.00 0.02 0.00 0.88 0.10 0.00
#> TCGA.EE.A20F.06 1 0.0000 0.9846 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.ER.A193.06 2 0.4078 0.4038 0.00 0.64 0.00 0.34 0.00 0.02
#> TCGA.FS.A1ZW.06 1 0.0000 0.9846 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.ER.A19O.06 4 0.4199 0.4824 0.00 0.00 0.00 0.60 0.38 0.02
#> TCGA.EE.A20B.06 1 0.0547 0.9805 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.FS.A1YX.06 4 0.4723 0.6475 0.00 0.00 0.00 0.68 0.14 0.18
#> TCGA.ER.A194.01 5 0.1092 0.7640 0.00 0.00 0.00 0.02 0.96 0.02
#> TCGA.EE.A2MS.06 3 0.0000 0.9756 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.EE.A29X.06 4 0.1814 0.7824 0.00 0.00 0.00 0.90 0.10 0.00
#> TCGA.ER.A2NC.06 6 0.6059 0.0684 0.00 0.00 0.00 0.26 0.36 0.38
#> TCGA.BF.A1Q0.01 2 0.2956 0.6072 0.00 0.84 0.00 0.04 0.00 0.12
#> TCGA.EE.A182.06 3 0.3460 0.6959 0.00 0.22 0.76 0.00 0.00 0.02
#> TCGA.D9.A1JW.06 2 0.0000 0.6538 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.EE.A2GJ.06 3 0.0547 0.9736 0.00 0.00 0.98 0.00 0.00 0.02
#> TCGA.EE.A2GU.06 2 0.5774 0.4306 0.00 0.56 0.00 0.28 0.02 0.14
#> TCGA.FS.A1Z7.06 4 0.1480 0.7244 0.00 0.04 0.00 0.94 0.00 0.02
#> TCGA.ER.A19K.01 4 0.1814 0.7824 0.00 0.00 0.00 0.90 0.10 0.00
#> TCGA.FR.A3YO.06 4 0.1814 0.7824 0.00 0.00 0.00 0.90 0.10 0.00
#> TCGA.RP.A694.06 5 0.2474 0.7019 0.00 0.00 0.00 0.08 0.88 0.04
#> TCGA.EB.A3Y7.01 2 0.0000 0.6538 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.BF.AAP8.01 2 0.3647 0.2755 0.00 0.64 0.00 0.00 0.00 0.36
#> TCGA.DA.A1HW.06 5 0.1480 0.7905 0.02 0.00 0.00 0.00 0.94 0.04
#> TCGA.GF.A6C8.06 5 0.1092 0.7889 0.02 0.00 0.00 0.00 0.96 0.02
#> TCGA.EE.A29V.06 1 0.0937 0.9696 0.96 0.00 0.00 0.00 0.00 0.04
#> TCGA.EE.A3AB.06 1 0.0000 0.9846 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EB.A5SH.06 3 0.0000 0.9756 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.D9.A6E9.06 4 0.2020 0.7561 0.00 0.02 0.00 0.92 0.04 0.02
#> TCGA.BF.AAP4.01 5 0.0547 0.7768 0.00 0.00 0.00 0.02 0.98 0.00
#> TCGA.DA.A1I1.06 5 0.5244 0.4853 0.36 0.00 0.00 0.02 0.56 0.06
#> TCGA.EE.A2MT.06 2 0.4328 0.0712 0.00 0.52 0.00 0.02 0.00 0.46
#> TCGA.ER.A19M.06 5 0.4552 0.5916 0.30 0.00 0.00 0.00 0.64 0.06
#> TCGA.FS.A1ZA.06 5 0.3324 0.7329 0.02 0.00 0.00 0.08 0.84 0.06
#> TCGA.EE.A2MI.06 5 0.2981 0.6468 0.00 0.00 0.00 0.02 0.82 0.16
#> TCGA.D3.A3CE.06 5 0.1092 0.7889 0.02 0.00 0.00 0.00 0.96 0.02
#> TCGA.ER.A2NB.01 2 0.0937 0.6499 0.00 0.96 0.00 0.00 0.00 0.04
#> TCGA.D3.A1Q5.06 6 0.2631 0.3959 0.00 0.18 0.00 0.00 0.00 0.82
#> TCGA.EB.A57M.01 1 0.0000 0.9846 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EE.A2A6.06 2 0.4328 0.1244 0.00 0.52 0.00 0.46 0.00 0.02
#> TCGA.D3.A1Q1.06 6 0.4310 -0.0655 0.00 0.44 0.00 0.02 0.00 0.54
#> TCGA.EB.A3Y6.01 5 0.0547 0.7901 0.02 0.00 0.00 0.00 0.98 0.00
#> TCGA.EB.A3XE.01 3 0.0547 0.9736 0.00 0.00 0.98 0.00 0.00 0.02
#> TCGA.FW.A3R5.06 3 0.0547 0.9736 0.00 0.00 0.98 0.00 0.00 0.02
#> TCGA.EE.A2GI.06 1 0.0000 0.9846 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EB.A3XB.01 5 0.0547 0.7901 0.02 0.00 0.00 0.00 0.98 0.00
#> TCGA.EE.A2MD.06 5 0.0547 0.7901 0.02 0.00 0.00 0.00 0.98 0.00
#> TCGA.W3.AA1V.06 5 0.1480 0.7905 0.02 0.00 0.00 0.00 0.94 0.04
#> TCGA.D3.A2JK.06 5 0.4873 0.3705 0.42 0.00 0.00 0.00 0.52 0.06
#> TCGA.EB.A5UM.01 3 0.0000 0.9756 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.D9.A148.06 1 0.0000 0.9846 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EE.A2ML.06 1 0.0937 0.9694 0.96 0.00 0.00 0.00 0.00 0.04
#> TCGA.EB.A5UL.06 5 0.3660 0.7124 0.16 0.00 0.00 0.00 0.78 0.06
#> TCGA.EE.A29T.06 3 0.0547 0.9736 0.00 0.00 0.98 0.00 0.00 0.02
#> TCGA.ER.A3ES.06 2 0.3706 0.2437 0.00 0.62 0.00 0.00 0.00 0.38
#> TCGA.EB.A44Q.06 4 0.2350 0.7830 0.00 0.02 0.00 0.88 0.10 0.00
#> TCGA.EB.A44R.06 3 0.0547 0.9736 0.00 0.00 0.98 0.00 0.00 0.02
#> TCGA.D3.A51N.06 1 0.0000 0.9846 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.XV.A9W5.01 1 0.0547 0.9805 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.D3.A51J.06 4 0.4328 0.3033 0.00 0.00 0.00 0.52 0.46 0.02
#> TCGA.3N.A9WC.06 2 0.5501 0.4045 0.00 0.58 0.00 0.10 0.02 0.30
#> TCGA.D9.A4Z6.06 5 0.2474 0.7726 0.08 0.00 0.00 0.00 0.88 0.04
#> TCGA.DA.A1I0.06 1 0.1267 0.9551 0.94 0.00 0.00 0.00 0.00 0.06
#> TCGA.EB.A431.01 1 0.0000 0.9846 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BF.AAOX.01 1 0.0000 0.9846 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DA.A3F5.06 4 0.4042 0.5334 0.00 0.04 0.00 0.76 0.02 0.18
#> TCGA.YD.A9TA.06 1 0.0000 0.9846 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EB.A4IQ.01 2 0.1092 0.6382 0.00 0.96 0.02 0.00 0.00 0.02
#> TCGA.ER.A3EV.06 3 0.0547 0.9736 0.00 0.00 0.98 0.00 0.00 0.02
#> TCGA.XV.A9W2.01 2 0.6250 0.0918 0.00 0.40 0.00 0.18 0.02 0.40
#> TCGA.WE.AAA0.06 1 0.0547 0.9805 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.EE.A3J5.06 1 0.0547 0.9805 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.FS.A4FD.06 6 0.3198 0.3610 0.00 0.26 0.00 0.00 0.00 0.74
#> TCGA.WE.AAA3.06 4 0.6487 -0.2829 0.00 0.28 0.00 0.40 0.02 0.30
#> TCGA.ER.A3ET.06 2 0.5626 0.3431 0.00 0.54 0.00 0.10 0.02 0.34
#> TCGA.YG.AA3N.01 4 0.2350 0.7787 0.00 0.00 0.00 0.88 0.10 0.02
cbind(get_classes(res, k = 7), get_membership(res, k = 7))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7
#> TCGA.FS.A4FC.06 2 0.5723 0.1848 0.00 0.48 0.00 0.20 0.00 0.30 0.02
#> TCGA.D3.A8GQ.06 5 0.4070 0.1322 0.02 0.00 0.00 0.00 0.66 0.02 0.30
#> TCGA.BF.A5EQ.01 2 0.0000 0.6897 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EB.A5VU.01 5 0.2081 0.5324 0.00 0.00 0.00 0.00 0.86 0.00 0.14
#> TCGA.D3.A8GJ.06 4 0.2163 0.7342 0.00 0.00 0.00 0.88 0.00 0.10 0.02
#> TCGA.WE.A8ZR.06 3 0.0000 0.9504 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DA.A95V.06 5 0.5437 0.0834 0.20 0.00 0.00 0.00 0.56 0.02 0.22
#> TCGA.EE.A3JB.06 1 0.0000 0.9497 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.WE.A8ZX.06 1 0.0504 0.9487 0.98 0.00 0.00 0.00 0.00 0.02 0.00
#> TCGA.D3.A8GS.06 5 0.0863 0.5513 0.00 0.00 0.00 0.00 0.96 0.00 0.04
#> TCGA.GN.A4U8.06 1 0.2163 0.9055 0.88 0.00 0.00 0.00 0.00 0.02 0.10
#> TCGA.EB.A551.01 4 0.0000 0.7988 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.D3.A8GM.06 5 0.4145 0.3614 0.10 0.00 0.00 0.00 0.74 0.02 0.14
#> TCGA.YD.A89C.06 1 0.2159 0.9203 0.90 0.00 0.00 0.00 0.02 0.02 0.06
#> TCGA.FR.A726.01 7 0.4278 0.5265 0.04 0.00 0.00 0.00 0.46 0.00 0.50
#> TCGA.W3.A825.06 5 0.5452 0.0990 0.00 0.00 0.00 0.00 0.46 0.24 0.30
#> TCGA.D3.A5GR.06 4 0.0504 0.8059 0.00 0.00 0.00 0.98 0.02 0.00 0.00
#> TCGA.FR.A729.06 5 0.0504 0.5679 0.00 0.00 0.00 0.00 0.98 0.00 0.02
#> TCGA.EE.A29P.06 4 0.4681 0.5049 0.00 0.00 0.00 0.58 0.00 0.10 0.32
#> TCGA.GN.A26A.06 1 0.2163 0.9055 0.88 0.00 0.00 0.00 0.00 0.02 0.10
#> TCGA.EE.A20I.06 1 0.0504 0.9487 0.98 0.00 0.00 0.00 0.00 0.02 0.00
#> TCGA.EB.A85J.01 3 0.1363 0.9426 0.00 0.00 0.94 0.00 0.00 0.02 0.04
#> TCGA.RP.A6K9.06 2 0.0504 0.6865 0.00 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.EE.A17Y.06 1 0.1664 0.9293 0.92 0.00 0.00 0.00 0.00 0.02 0.06
#> TCGA.D9.A149.06 2 0.0000 0.6897 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D3.A1Q9.06 1 0.0504 0.9487 0.98 0.00 0.00 0.00 0.00 0.02 0.00
#> TCGA.ER.A19L.06 3 0.0000 0.9504 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.ER.A19T.06 3 0.0000 0.9504 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.D3.A2JC.06 4 0.2857 0.7771 0.00 0.00 0.00 0.86 0.04 0.06 0.04
#> TCGA.BF.A5EO.01 1 0.2654 0.8997 0.86 0.00 0.00 0.00 0.02 0.02 0.10
#> TCGA.EE.A2M7.06 5 0.1363 0.5584 0.00 0.00 0.00 0.00 0.94 0.02 0.04
#> TCGA.D3.A1Q3.06 3 0.0000 0.9504 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.EB.A85I.01 2 0.3139 0.4432 0.00 0.70 0.00 0.30 0.00 0.00 0.00
#> TCGA.DA.A1I2.06 4 0.2159 0.7835 0.00 0.02 0.00 0.90 0.00 0.06 0.02
#> TCGA.DA.A1I7.06 4 0.1363 0.8098 0.00 0.00 0.00 0.94 0.02 0.00 0.04
#> TCGA.EE.A181.06 1 0.0000 0.9497 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FS.A1ZM.06 4 0.4937 0.6864 0.00 0.00 0.00 0.68 0.06 0.14 0.12
#> TCGA.D3.A2JP.06 1 0.1006 0.9436 0.96 0.00 0.00 0.00 0.00 0.02 0.02
#> TCGA.ER.A19C.06 6 0.6972 0.2528 0.00 0.00 0.00 0.16 0.24 0.32 0.28
#> TCGA.EB.A82B.01 2 0.0863 0.6852 0.00 0.96 0.00 0.04 0.00 0.00 0.00
#> TCGA.FS.A1ZH.06 1 0.0000 0.9497 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D3.A2J6.06 2 0.1363 0.6799 0.00 0.94 0.00 0.02 0.00 0.04 0.00
#> TCGA.D3.A2JO.06 5 0.3307 0.2861 0.00 0.00 0.00 0.00 0.74 0.02 0.24
#> TCGA.GN.A267.06 3 0.0000 0.9504 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.D3.A3CC.06 2 0.2906 0.5735 0.00 0.80 0.00 0.02 0.00 0.18 0.00
#> TCGA.BF.A1PU.01 5 0.5875 0.0506 0.00 0.00 0.00 0.02 0.44 0.24 0.30
#> TCGA.D3.A1Q6.06 4 0.3404 0.7729 0.00 0.00 0.00 0.82 0.04 0.06 0.08
#> TCGA.EB.A24C.01 3 0.0000 0.9504 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.D3.A2JL.06 5 0.4377 0.2570 0.06 0.00 0.00 0.00 0.68 0.02 0.24
#> TCGA.FS.A1ZS.06 2 0.3815 0.2377 0.00 0.62 0.00 0.02 0.00 0.36 0.00
#> TCGA.D3.A3C3.06 1 0.0504 0.9487 0.98 0.00 0.00 0.00 0.00 0.02 0.00
#> TCGA.D3.A1QA.07 1 0.0504 0.9487 0.98 0.00 0.00 0.00 0.00 0.02 0.00
#> TCGA.EE.A29S.06 7 0.5123 -0.1559 0.00 0.00 0.00 0.42 0.08 0.02 0.48
#> TCGA.GN.A26D.06 6 0.3867 0.4424 0.00 0.14 0.00 0.00 0.00 0.74 0.12
#> TCGA.EE.A2M5.06 1 0.3765 0.8086 0.78 0.00 0.00 0.00 0.10 0.02 0.10
#> TCGA.GN.A266.06 5 0.2569 0.5289 0.00 0.00 0.00 0.00 0.84 0.02 0.14
#> TCGA.D3.A3C1.06 4 0.0504 0.8059 0.00 0.00 0.00 0.98 0.02 0.00 0.00
#> TCGA.EE.A20F.06 1 0.0504 0.9487 0.98 0.00 0.00 0.00 0.00 0.02 0.00
#> TCGA.ER.A193.06 2 0.3139 0.4432 0.00 0.70 0.00 0.30 0.00 0.00 0.00
#> TCGA.FS.A1ZW.06 1 0.0504 0.9487 0.98 0.00 0.00 0.00 0.00 0.02 0.00
#> TCGA.ER.A19O.06 4 0.3526 0.6714 0.00 0.00 0.00 0.76 0.18 0.00 0.06
#> TCGA.EE.A20B.06 1 0.1363 0.9375 0.94 0.00 0.00 0.00 0.00 0.02 0.04
#> TCGA.FS.A1YX.06 4 0.3656 0.7594 0.00 0.00 0.00 0.80 0.04 0.08 0.08
#> TCGA.ER.A194.01 5 0.3546 -0.4049 0.00 0.00 0.00 0.00 0.54 0.00 0.46
#> TCGA.EE.A2MS.06 3 0.0000 0.9504 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.EE.A29X.06 4 0.2016 0.8052 0.00 0.00 0.00 0.90 0.04 0.00 0.06
#> TCGA.ER.A2NC.06 6 0.6920 0.2370 0.00 0.00 0.00 0.14 0.26 0.32 0.28
#> TCGA.BF.A1Q0.01 2 0.3388 0.4927 0.00 0.76 0.00 0.04 0.00 0.20 0.00
#> TCGA.EE.A182.06 3 0.4388 0.5425 0.00 0.30 0.64 0.00 0.00 0.02 0.04
#> TCGA.D9.A1JW.06 2 0.0000 0.6897 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EE.A2GJ.06 3 0.1363 0.9426 0.00 0.00 0.94 0.00 0.00 0.02 0.04
#> TCGA.EE.A2GU.06 2 0.5723 0.1848 0.00 0.48 0.00 0.20 0.00 0.30 0.02
#> TCGA.FS.A1Z7.06 4 0.0000 0.7988 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.ER.A19K.01 4 0.1718 0.8086 0.00 0.00 0.00 0.92 0.04 0.00 0.04
#> TCGA.FR.A3YO.06 4 0.1718 0.8086 0.00 0.00 0.00 0.92 0.04 0.00 0.04
#> TCGA.RP.A694.06 7 0.4514 0.3843 0.00 0.00 0.00 0.00 0.46 0.06 0.48
#> TCGA.EB.A3Y7.01 2 0.1363 0.6799 0.00 0.94 0.00 0.02 0.00 0.04 0.00
#> TCGA.BF.AAP8.01 2 0.4015 0.4006 0.00 0.68 0.00 0.00 0.00 0.26 0.06
#> TCGA.DA.A1HW.06 5 0.0504 0.5679 0.00 0.00 0.00 0.00 0.98 0.00 0.02
#> TCGA.GF.A6C8.06 5 0.1363 0.5584 0.00 0.00 0.00 0.00 0.94 0.02 0.04
#> TCGA.EE.A29V.06 1 0.2213 0.9237 0.90 0.00 0.00 0.00 0.04 0.02 0.04
#> TCGA.EE.A3AB.06 1 0.0504 0.9487 0.98 0.00 0.00 0.00 0.00 0.02 0.00
#> TCGA.EB.A5SH.06 3 0.0000 0.9504 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.D9.A6E9.06 4 0.0000 0.7988 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.BF.AAP4.01 5 0.2572 0.3882 0.00 0.00 0.00 0.00 0.80 0.00 0.20
#> TCGA.DA.A1I1.06 7 0.4278 0.5265 0.04 0.00 0.00 0.00 0.46 0.00 0.50
#> TCGA.EE.A2MT.06 6 0.3558 -0.1221 0.00 0.48 0.00 0.00 0.00 0.52 0.00
#> TCGA.ER.A19M.06 5 0.4514 0.3058 0.14 0.00 0.00 0.00 0.70 0.02 0.14
#> TCGA.FS.A1ZA.06 7 0.4421 0.5292 0.02 0.00 0.00 0.02 0.46 0.00 0.50
#> TCGA.EE.A2MI.06 5 0.3770 0.4289 0.00 0.00 0.00 0.00 0.74 0.08 0.18
#> TCGA.D3.A3CE.06 5 0.0504 0.5616 0.00 0.00 0.00 0.00 0.98 0.00 0.02
#> TCGA.ER.A2NB.01 2 0.0863 0.6852 0.00 0.96 0.00 0.04 0.00 0.00 0.00
#> TCGA.D3.A1Q5.06 6 0.4121 0.4605 0.00 0.10 0.00 0.00 0.00 0.70 0.20
#> TCGA.EB.A57M.01 1 0.0000 0.9497 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EE.A2A6.06 4 0.3558 -0.0456 0.00 0.48 0.00 0.52 0.00 0.00 0.00
#> TCGA.D3.A1Q1.06 6 0.4175 0.1201 0.00 0.38 0.00 0.00 0.00 0.58 0.04
#> TCGA.EB.A3Y6.01 5 0.2572 0.3882 0.00 0.00 0.00 0.00 0.80 0.00 0.20
#> TCGA.EB.A3XE.01 3 0.2509 0.8924 0.00 0.06 0.88 0.00 0.00 0.02 0.04
#> TCGA.FW.A3R5.06 3 0.1363 0.9426 0.00 0.00 0.94 0.00 0.00 0.02 0.04
#> TCGA.EE.A2GI.06 1 0.0000 0.9497 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EB.A3XB.01 5 0.2572 0.3882 0.00 0.00 0.00 0.00 0.80 0.00 0.20
#> TCGA.EE.A2MD.06 5 0.2572 0.3882 0.00 0.00 0.00 0.00 0.80 0.00 0.20
#> TCGA.W3.AA1V.06 5 0.1664 0.5573 0.00 0.00 0.00 0.00 0.92 0.02 0.06
#> TCGA.D3.A2JK.06 5 0.4813 0.2365 0.24 0.00 0.00 0.00 0.64 0.02 0.10
#> TCGA.EB.A5UM.01 3 0.0000 0.9504 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.D9.A148.06 1 0.0504 0.9487 0.98 0.00 0.00 0.00 0.00 0.02 0.00
#> TCGA.EE.A2ML.06 1 0.1928 0.9145 0.90 0.00 0.00 0.00 0.00 0.02 0.08
#> TCGA.EB.A5UL.06 5 0.3765 0.3996 0.10 0.00 0.00 0.00 0.78 0.02 0.10
#> TCGA.EE.A29T.06 3 0.1363 0.9426 0.00 0.00 0.94 0.00 0.00 0.02 0.04
#> TCGA.ER.A3ES.06 2 0.4015 0.4006 0.00 0.68 0.00 0.00 0.00 0.26 0.06
#> TCGA.EB.A44Q.06 4 0.1363 0.8096 0.00 0.00 0.00 0.94 0.04 0.00 0.02
#> TCGA.EB.A44R.06 3 0.1363 0.9426 0.00 0.00 0.94 0.00 0.00 0.02 0.04
#> TCGA.D3.A51N.06 1 0.0504 0.9487 0.98 0.00 0.00 0.00 0.00 0.02 0.00
#> TCGA.XV.A9W5.01 1 0.2163 0.9055 0.88 0.00 0.00 0.00 0.00 0.02 0.10
#> TCGA.D3.A51J.06 4 0.5241 0.1492 0.00 0.00 0.00 0.50 0.32 0.00 0.18
#> TCGA.3N.A9WC.06 2 0.4278 0.0492 0.00 0.50 0.00 0.04 0.00 0.46 0.00
#> TCGA.D9.A4Z6.06 5 0.2376 0.5379 0.00 0.00 0.00 0.00 0.86 0.02 0.12
#> TCGA.DA.A1I0.06 1 0.2654 0.8997 0.86 0.00 0.00 0.00 0.02 0.02 0.10
#> TCGA.EB.A431.01 1 0.0000 0.9497 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BF.AAOX.01 1 0.0504 0.9487 0.98 0.00 0.00 0.00 0.00 0.02 0.00
#> TCGA.DA.A3F5.06 4 0.4381 0.2518 0.00 0.06 0.00 0.58 0.00 0.36 0.00
#> TCGA.YD.A9TA.06 1 0.0000 0.9497 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EB.A4IQ.01 2 0.2213 0.6531 0.00 0.90 0.02 0.00 0.00 0.04 0.04
#> TCGA.ER.A3EV.06 3 0.1363 0.9426 0.00 0.00 0.94 0.00 0.00 0.02 0.04
#> TCGA.XV.A9W2.01 6 0.4908 0.3403 0.00 0.20 0.00 0.10 0.00 0.66 0.04
#> TCGA.WE.AAA0.06 1 0.1006 0.9436 0.96 0.00 0.00 0.00 0.00 0.02 0.02
#> TCGA.EE.A3J5.06 1 0.1505 0.9401 0.94 0.00 0.00 0.00 0.02 0.02 0.02
#> TCGA.FS.A4FD.06 6 0.5083 0.3764 0.00 0.20 0.00 0.00 0.00 0.56 0.24
#> TCGA.WE.AAA3.06 6 0.5190 0.2115 0.00 0.18 0.00 0.30 0.00 0.52 0.00
#> TCGA.ER.A3ET.06 6 0.4505 -0.0686 0.00 0.44 0.00 0.06 0.00 0.50 0.00
#> TCGA.YG.AA3N.01 4 0.3139 0.6183 0.00 0.00 0.00 0.70 0.00 0.00 0.30
cbind(get_classes(res, k = 8), get_membership(res, k = 8))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7 p8
#> TCGA.FS.A4FC.06 8 0.4938 0.6543 0.00 0.32 0.00 0.06 0.00 0.00 0.06 0.56
#> TCGA.D3.A8GQ.06 5 0.4427 0.6042 0.02 0.00 0.00 0.00 0.68 0.06 0.22 0.02
#> TCGA.BF.A5EQ.01 2 0.0471 0.7298 0.00 0.98 0.00 0.00 0.00 0.00 0.00 0.02
#> TCGA.EB.A5VU.01 5 0.0471 0.7749 0.00 0.00 0.00 0.00 0.98 0.02 0.00 0.00
#> TCGA.D3.A8GJ.06 4 0.3299 0.6617 0.00 0.00 0.00 0.76 0.00 0.00 0.06 0.18
#> TCGA.WE.A8ZR.06 3 0.0000 0.9208 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DA.A95V.06 5 0.6531 0.2148 0.22 0.00 0.00 0.00 0.46 0.04 0.18 0.10
#> TCGA.EE.A3JB.06 1 0.0471 0.9150 0.98 0.00 0.00 0.00 0.00 0.00 0.00 0.02
#> TCGA.WE.A8ZX.06 1 0.1275 0.9078 0.94 0.00 0.00 0.00 0.00 0.00 0.02 0.04
#> TCGA.D3.A8GS.06 5 0.0471 0.7758 0.00 0.00 0.00 0.00 0.98 0.00 0.00 0.02
#> TCGA.GN.A4U8.06 1 0.2265 0.8970 0.88 0.00 0.00 0.00 0.00 0.02 0.02 0.08
#> TCGA.EB.A551.01 4 0.0471 0.8375 0.00 0.00 0.00 0.98 0.00 0.00 0.02 0.00
#> TCGA.D3.A8GM.06 5 0.4134 0.6680 0.06 0.00 0.00 0.00 0.76 0.02 0.08 0.08
#> TCGA.YD.A89C.06 1 0.2265 0.8970 0.88 0.00 0.00 0.00 0.00 0.02 0.02 0.08
#> TCGA.FR.A726.01 7 0.3808 0.4449 0.04 0.00 0.00 0.00 0.34 0.00 0.62 0.00
#> TCGA.W3.A825.06 6 0.3868 0.7130 0.00 0.00 0.00 0.02 0.22 0.72 0.02 0.02
#> TCGA.D3.A5GR.06 4 0.0000 0.8411 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.FR.A729.06 5 0.0000 0.7780 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.EE.A29P.06 7 0.4740 0.2819 0.00 0.00 0.00 0.30 0.00 0.02 0.58 0.10
#> TCGA.GN.A26A.06 1 0.2265 0.8970 0.88 0.00 0.00 0.00 0.00 0.02 0.02 0.08
#> TCGA.EE.A20I.06 1 0.1275 0.9078 0.94 0.00 0.00 0.00 0.00 0.00 0.02 0.04
#> TCGA.EB.A85J.01 3 0.1887 0.9077 0.00 0.00 0.90 0.00 0.00 0.00 0.06 0.04
#> TCGA.RP.A6K9.06 2 0.0471 0.7298 0.00 0.98 0.00 0.00 0.00 0.00 0.00 0.02
#> TCGA.EE.A17Y.06 1 0.2265 0.8970 0.88 0.00 0.00 0.00 0.00 0.02 0.02 0.08
#> TCGA.D9.A149.06 2 0.0471 0.7298 0.00 0.98 0.00 0.00 0.00 0.00 0.00 0.02
#> TCGA.D3.A1Q9.06 1 0.1275 0.9078 0.94 0.00 0.00 0.00 0.00 0.00 0.02 0.04
#> TCGA.ER.A19L.06 3 0.0000 0.9208 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.ER.A19T.06 3 0.0000 0.9208 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D3.A2JC.06 4 0.1557 0.8196 0.00 0.00 0.00 0.92 0.00 0.06 0.00 0.02
#> TCGA.BF.A5EO.01 1 0.2724 0.8853 0.86 0.00 0.00 0.00 0.02 0.02 0.02 0.08
#> TCGA.EE.A2M7.06 5 0.1741 0.7630 0.00 0.00 0.00 0.00 0.92 0.02 0.02 0.04
#> TCGA.D3.A1Q3.06 3 0.0000 0.9208 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EB.A85I.01 2 0.3991 0.3474 0.00 0.62 0.00 0.32 0.00 0.00 0.00 0.06
#> TCGA.DA.A1I2.06 4 0.1091 0.8253 0.00 0.00 0.00 0.94 0.00 0.06 0.00 0.00
#> TCGA.DA.A1I7.06 4 0.1275 0.8320 0.00 0.00 0.00 0.94 0.00 0.02 0.04 0.00
#> TCGA.EE.A181.06 1 0.0808 0.9124 0.96 0.00 0.00 0.00 0.00 0.00 0.00 0.04
#> TCGA.FS.A1ZM.06 4 0.5244 0.3617 0.00 0.00 0.00 0.52 0.00 0.02 0.20 0.26
#> TCGA.D3.A2JP.06 1 0.1804 0.9042 0.90 0.00 0.00 0.00 0.00 0.02 0.00 0.08
#> TCGA.ER.A19C.06 6 0.3002 0.7679 0.00 0.00 0.00 0.02 0.12 0.82 0.00 0.04
#> TCGA.EB.A82B.01 2 0.1341 0.6885 0.00 0.92 0.00 0.00 0.00 0.00 0.00 0.08
#> TCGA.FS.A1ZH.06 1 0.0000 0.9156 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D3.A2J6.06 2 0.0471 0.7281 0.00 0.98 0.00 0.00 0.00 0.02 0.00 0.00
#> TCGA.D3.A2JO.06 5 0.3601 0.6883 0.00 0.00 0.00 0.00 0.76 0.02 0.16 0.06
#> TCGA.GN.A267.06 3 0.0000 0.9208 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D3.A3CC.06 2 0.0471 0.7281 0.00 0.98 0.00 0.00 0.00 0.02 0.00 0.00
#> TCGA.BF.A1PU.01 6 0.2856 0.7462 0.00 0.00 0.00 0.02 0.20 0.78 0.00 0.00
#> TCGA.D3.A1Q6.06 4 0.1741 0.8258 0.00 0.00 0.00 0.92 0.00 0.04 0.02 0.02
#> TCGA.EB.A24C.01 3 0.0000 0.9208 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D3.A2JL.06 5 0.4272 0.6524 0.02 0.00 0.00 0.00 0.72 0.02 0.16 0.08
#> TCGA.FS.A1ZS.06 8 0.3714 0.4723 0.00 0.44 0.00 0.00 0.00 0.00 0.02 0.54
#> TCGA.D3.A3C3.06 1 0.1275 0.9078 0.94 0.00 0.00 0.00 0.00 0.00 0.02 0.04
#> TCGA.D3.A1QA.07 1 0.1275 0.9078 0.94 0.00 0.00 0.00 0.00 0.00 0.02 0.04
#> TCGA.EE.A29S.06 7 0.3095 0.4506 0.00 0.00 0.00 0.24 0.00 0.02 0.74 0.00
#> TCGA.GN.A26D.06 6 0.5126 0.2913 0.00 0.04 0.00 0.00 0.00 0.52 0.10 0.34
#> TCGA.EE.A2M5.06 1 0.3763 0.8007 0.78 0.00 0.00 0.00 0.10 0.02 0.02 0.08
#> TCGA.GN.A266.06 5 0.1275 0.7629 0.00 0.00 0.00 0.00 0.94 0.04 0.02 0.00
#> TCGA.D3.A3C1.06 4 0.0000 0.8411 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.EE.A20F.06 1 0.0808 0.9124 0.96 0.00 0.00 0.00 0.00 0.00 0.00 0.04
#> TCGA.ER.A193.06 2 0.3922 0.3739 0.00 0.64 0.00 0.30 0.00 0.00 0.00 0.06
#> TCGA.FS.A1ZW.06 1 0.1275 0.9078 0.94 0.00 0.00 0.00 0.00 0.00 0.02 0.04
#> TCGA.ER.A19O.06 4 0.2265 0.7811 0.00 0.00 0.00 0.88 0.08 0.00 0.02 0.02
#> TCGA.EE.A20B.06 1 0.1804 0.9042 0.90 0.00 0.00 0.00 0.00 0.02 0.00 0.08
#> TCGA.FS.A1YX.06 4 0.2020 0.8191 0.00 0.00 0.00 0.90 0.00 0.06 0.02 0.02
#> TCGA.ER.A194.01 7 0.3374 0.5132 0.00 0.00 0.00 0.00 0.30 0.00 0.68 0.02
#> TCGA.EE.A2MS.06 3 0.0000 0.9208 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EE.A29X.06 4 0.2025 0.7934 0.00 0.00 0.00 0.88 0.00 0.02 0.10 0.00
#> TCGA.ER.A2NC.06 6 0.3891 0.7599 0.00 0.00 0.00 0.02 0.14 0.76 0.02 0.06
#> TCGA.BF.A1Q0.01 2 0.3272 -0.1793 0.00 0.58 0.00 0.00 0.00 0.00 0.00 0.42
#> TCGA.EE.A182.06 3 0.4886 0.1254 0.00 0.44 0.46 0.00 0.00 0.00 0.06 0.04
#> TCGA.D9.A1JW.06 2 0.0471 0.7298 0.00 0.98 0.00 0.00 0.00 0.00 0.00 0.02
#> TCGA.EE.A2GJ.06 3 0.1887 0.9077 0.00 0.00 0.90 0.00 0.00 0.00 0.06 0.04
#> TCGA.EE.A2GU.06 8 0.4938 0.6543 0.00 0.32 0.00 0.06 0.00 0.00 0.06 0.56
#> TCGA.FS.A1Z7.06 4 0.1557 0.8064 0.00 0.00 0.00 0.92 0.00 0.00 0.02 0.06
#> TCGA.ER.A19K.01 4 0.2025 0.7934 0.00 0.00 0.00 0.88 0.00 0.02 0.10 0.00
#> TCGA.FR.A3YO.06 4 0.0471 0.8397 0.00 0.00 0.00 0.98 0.00 0.00 0.02 0.00
#> TCGA.RP.A694.06 7 0.3657 0.5676 0.00 0.00 0.00 0.00 0.20 0.00 0.72 0.08
#> TCGA.EB.A3Y7.01 2 0.0471 0.7281 0.00 0.98 0.00 0.00 0.00 0.02 0.00 0.00
#> TCGA.BF.AAP8.01 2 0.4503 0.4669 0.00 0.70 0.00 0.00 0.00 0.12 0.08 0.10
#> TCGA.DA.A1HW.06 5 0.0000 0.7780 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.GF.A6C8.06 5 0.2071 0.7556 0.00 0.00 0.00 0.00 0.90 0.04 0.02 0.04
#> TCGA.EE.A29V.06 1 0.2724 0.8853 0.86 0.00 0.00 0.00 0.02 0.02 0.02 0.08
#> TCGA.EE.A3AB.06 1 0.1275 0.9078 0.94 0.00 0.00 0.00 0.00 0.00 0.02 0.04
#> TCGA.EB.A5SH.06 3 0.0000 0.9208 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D9.A6E9.06 4 0.0471 0.8375 0.00 0.00 0.00 0.98 0.00 0.00 0.02 0.00
#> TCGA.BF.AAP4.01 5 0.2406 0.6870 0.00 0.00 0.00 0.00 0.80 0.00 0.20 0.00
#> TCGA.DA.A1I1.06 7 0.3991 0.4549 0.06 0.00 0.00 0.00 0.32 0.00 0.62 0.00
#> TCGA.EE.A2MT.06 2 0.5852 -0.1695 0.00 0.42 0.00 0.00 0.00 0.10 0.12 0.36
#> TCGA.ER.A19M.06 5 0.4521 0.5957 0.12 0.00 0.00 0.00 0.72 0.02 0.06 0.08
#> TCGA.FS.A1ZA.06 7 0.3514 0.4610 0.02 0.00 0.00 0.00 0.34 0.00 0.64 0.00
#> TCGA.EE.A2MI.06 5 0.2724 0.6999 0.00 0.00 0.00 0.02 0.86 0.08 0.02 0.02
#> TCGA.D3.A3CE.06 5 0.0471 0.7758 0.00 0.00 0.00 0.00 0.98 0.00 0.00 0.02
#> TCGA.ER.A2NB.01 2 0.1341 0.6885 0.00 0.92 0.00 0.00 0.00 0.00 0.00 0.08
#> TCGA.D3.A1Q5.06 6 0.2591 0.6972 0.00 0.02 0.00 0.00 0.00 0.86 0.04 0.08
#> TCGA.EB.A57M.01 1 0.0471 0.9152 0.98 0.00 0.00 0.00 0.00 0.00 0.00 0.02
#> TCGA.EE.A2A6.06 4 0.3992 0.0506 0.00 0.44 0.00 0.52 0.00 0.00 0.00 0.04
#> TCGA.D3.A1Q1.06 8 0.5902 0.3721 0.00 0.22 0.00 0.00 0.00 0.16 0.12 0.50
#> TCGA.EB.A3Y6.01 5 0.2406 0.6870 0.00 0.00 0.00 0.00 0.80 0.00 0.20 0.00
#> TCGA.EB.A3XE.01 3 0.2947 0.8609 0.00 0.06 0.84 0.00 0.00 0.00 0.06 0.04
#> TCGA.FW.A3R5.06 3 0.1887 0.9077 0.00 0.00 0.90 0.00 0.00 0.00 0.06 0.04
#> TCGA.EE.A2GI.06 1 0.0000 0.9156 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EB.A3XB.01 5 0.2406 0.6870 0.00 0.00 0.00 0.00 0.80 0.00 0.20 0.00
#> TCGA.EE.A2MD.06 5 0.2406 0.6870 0.00 0.00 0.00 0.00 0.80 0.00 0.20 0.00
#> TCGA.W3.AA1V.06 5 0.2071 0.7536 0.00 0.00 0.00 0.00 0.90 0.04 0.04 0.02
#> TCGA.D3.A2JK.06 5 0.4533 0.4919 0.20 0.00 0.00 0.00 0.68 0.02 0.02 0.08
#> TCGA.EB.A5UM.01 3 0.0000 0.9208 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D9.A148.06 1 0.1275 0.9078 0.94 0.00 0.00 0.00 0.00 0.00 0.02 0.04
#> TCGA.EE.A2ML.06 1 0.2591 0.8869 0.86 0.00 0.00 0.00 0.00 0.02 0.04 0.08
#> TCGA.EB.A5UL.06 5 0.2482 0.7383 0.02 0.00 0.00 0.00 0.88 0.02 0.02 0.06
#> TCGA.EE.A29T.06 3 0.1887 0.9077 0.00 0.00 0.90 0.00 0.00 0.00 0.06 0.04
#> TCGA.ER.A3ES.06 2 0.5028 0.3872 0.00 0.64 0.00 0.00 0.00 0.12 0.10 0.14
#> TCGA.EB.A44Q.06 4 0.0000 0.8411 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.EB.A44R.06 3 0.1887 0.9077 0.00 0.00 0.90 0.00 0.00 0.00 0.06 0.04
#> TCGA.D3.A51N.06 1 0.1275 0.9078 0.94 0.00 0.00 0.00 0.00 0.00 0.02 0.04
#> TCGA.XV.A9W5.01 1 0.2265 0.8970 0.88 0.00 0.00 0.00 0.00 0.02 0.02 0.08
#> TCGA.D3.A51J.06 4 0.4953 0.2414 0.00 0.00 0.00 0.58 0.24 0.02 0.16 0.00
#> TCGA.3N.A9WC.06 8 0.3083 0.6445 0.00 0.34 0.00 0.00 0.00 0.00 0.00 0.66
#> TCGA.D9.A4Z6.06 5 0.0808 0.7709 0.00 0.00 0.00 0.00 0.96 0.04 0.00 0.00
#> TCGA.DA.A1I0.06 1 0.2724 0.8853 0.86 0.00 0.00 0.00 0.02 0.02 0.02 0.08
#> TCGA.EB.A431.01 1 0.0808 0.9124 0.96 0.00 0.00 0.00 0.00 0.00 0.00 0.04
#> TCGA.BF.AAOX.01 1 0.1275 0.9078 0.94 0.00 0.00 0.00 0.00 0.00 0.02 0.04
#> TCGA.DA.A3F5.06 8 0.4826 0.4359 0.00 0.02 0.00 0.30 0.00 0.04 0.04 0.60
#> TCGA.YD.A9TA.06 1 0.0471 0.9128 0.98 0.00 0.00 0.00 0.00 0.02 0.00 0.00
#> TCGA.EB.A4IQ.01 2 0.1741 0.6853 0.00 0.92 0.02 0.00 0.00 0.00 0.02 0.04
#> TCGA.ER.A3EV.06 3 0.1887 0.9077 0.00 0.00 0.90 0.00 0.00 0.00 0.06 0.04
#> TCGA.XV.A9W2.01 8 0.4224 0.6520 0.00 0.14 0.00 0.02 0.00 0.14 0.00 0.70
#> TCGA.WE.AAA0.06 1 0.1804 0.9042 0.90 0.00 0.00 0.00 0.00 0.02 0.00 0.08
#> TCGA.EE.A3J5.06 1 0.1804 0.9042 0.90 0.00 0.00 0.00 0.00 0.02 0.00 0.08
#> TCGA.FS.A4FD.06 6 0.2348 0.6989 0.00 0.04 0.00 0.00 0.00 0.88 0.02 0.06
#> TCGA.WE.AAA3.06 8 0.5046 0.7051 0.00 0.18 0.00 0.04 0.00 0.06 0.06 0.66
#> TCGA.ER.A3ET.06 8 0.3843 0.7076 0.00 0.24 0.00 0.02 0.00 0.04 0.00 0.70
#> TCGA.YG.AA3N.01 7 0.3690 0.0842 0.00 0.00 0.00 0.42 0.00 0.02 0.56 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-leaf , Node0113 , Node0121-leaf , Node0122-leaf , Node0123-leaf , Node0124-leaf , Node0125-leaf , Node0131 , Node0132-leaf , Node0133-leaf , Node0211-leaf , Node0212 , Node0221-leaf , Node0222-leaf , Node0311 , Node0312-leaf , Node0321-leaf , Node0322 , Node0323 , Node0411 , Node0412 , Node0413-leaf , Node0421-leaf , Node0422-leaf , Node0423-leaf , Node0431-leaf , Node0432-leaf , Node0433-leaf , Node0441-leaf , Node0442 , Node0443-leaf , Node0511 , Node0512-leaf , Node0513-leaf , Node0521-leaf , Node0522-leaf , Node0523-leaf , Node0524-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 42 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 0.5022 0.498 0.498
#> 3 3 1.000 0.954 0.981 0.2450 0.833 0.679
#> 4 4 0.696 0.822 0.901 0.1234 0.825 0.589
#> 5 5 0.706 0.653 0.818 0.0594 0.942 0.813
#> 6 6 0.668 0.595 0.807 0.0176 0.970 0.890
#> 7 7 0.669 0.549 0.763 0.0237 0.958 0.854
#> 8 8 0.640 0.500 0.741 0.0218 0.954 0.831
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.D3.A8GQ.06 1 0 1 1 0
#> TCGA.DA.A95V.06 2 0 1 0 1
#> TCGA.EE.A3JB.06 1 0 1 1 0
#> TCGA.WE.A8ZX.06 2 0 1 0 1
#> TCGA.GN.A4U8.06 1 0 1 1 0
#> TCGA.D3.A8GM.06 2 0 1 0 1
#> TCGA.YD.A89C.06 2 0 1 0 1
#> TCGA.FR.A726.01 1 0 1 1 0
#> TCGA.GN.A26A.06 1 0 1 1 0
#> TCGA.EE.A20I.06 2 0 1 0 1
#> TCGA.EE.A17Y.06 2 0 1 0 1
#> TCGA.D3.A1Q9.06 2 0 1 0 1
#> TCGA.BF.A5EO.01 2 0 1 0 1
#> TCGA.EE.A181.06 2 0 1 0 1
#> TCGA.D3.A2JP.06 2 0 1 0 1
#> TCGA.FS.A1ZH.06 1 0 1 1 0
#> TCGA.D3.A2JL.06 2 0 1 0 1
#> TCGA.D3.A3C3.06 1 0 1 1 0
#> TCGA.D3.A1QA.07 1 0 1 1 0
#> TCGA.EE.A2M5.06 2 0 1 0 1
#> TCGA.EE.A20F.06 1 0 1 1 0
#> TCGA.FS.A1ZW.06 1 0 1 1 0
#> TCGA.EE.A20B.06 1 0 1 1 0
#> TCGA.EE.A29V.06 2 0 1 0 1
#> TCGA.EE.A3AB.06 1 0 1 1 0
#> TCGA.DA.A1I1.06 1 0 1 1 0
#> TCGA.ER.A19M.06 1 0 1 1 0
#> TCGA.EB.A57M.01 2 0 1 0 1
#> TCGA.EE.A2GI.06 1 0 1 1 0
#> TCGA.D3.A2JK.06 2 0 1 0 1
#> TCGA.D9.A148.06 2 0 1 0 1
#> TCGA.EE.A2ML.06 1 0 1 1 0
#> TCGA.EB.A5UL.06 2 0 1 0 1
#> TCGA.D3.A51N.06 1 0 1 1 0
#> TCGA.XV.A9W5.01 2 0 1 0 1
#> TCGA.D9.A4Z6.06 2 0 1 0 1
#> TCGA.DA.A1I0.06 2 0 1 0 1
#> TCGA.EB.A431.01 2 0 1 0 1
#> TCGA.BF.AAOX.01 2 0 1 0 1
#> TCGA.YD.A9TA.06 1 0 1 1 0
#> TCGA.WE.AAA0.06 2 0 1 0 1
#> TCGA.EE.A3J5.06 2 0 1 0 1
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.D3.A8GQ.06 1 0.0000 0.969 1.00 0.00 0.00
#> TCGA.DA.A95V.06 2 0.0000 0.980 0.00 1.00 0.00
#> TCGA.EE.A3JB.06 1 0.0000 0.969 1.00 0.00 0.00
#> TCGA.WE.A8ZX.06 2 0.0000 0.980 0.00 1.00 0.00
#> TCGA.GN.A4U8.06 3 0.0892 0.986 0.02 0.00 0.98
#> TCGA.D3.A8GM.06 2 0.0000 0.980 0.00 1.00 0.00
#> TCGA.YD.A89C.06 1 0.2537 0.888 0.92 0.08 0.00
#> TCGA.FR.A726.01 1 0.0000 0.969 1.00 0.00 0.00
#> TCGA.GN.A26A.06 1 0.0000 0.969 1.00 0.00 0.00
#> TCGA.EE.A20I.06 2 0.0000 0.980 0.00 1.00 0.00
#> TCGA.EE.A17Y.06 1 0.4291 0.761 0.82 0.18 0.00
#> TCGA.D3.A1Q9.06 2 0.0000 0.980 0.00 1.00 0.00
#> TCGA.BF.A5EO.01 2 0.0000 0.980 0.00 1.00 0.00
#> TCGA.EE.A181.06 2 0.0000 0.980 0.00 1.00 0.00
#> TCGA.D3.A2JP.06 2 0.0000 0.980 0.00 1.00 0.00
#> TCGA.FS.A1ZH.06 1 0.0000 0.969 1.00 0.00 0.00
#> TCGA.D3.A2JL.06 2 0.6192 0.273 0.00 0.58 0.42
#> TCGA.D3.A3C3.06 3 0.0892 0.986 0.02 0.00 0.98
#> TCGA.D3.A1QA.07 3 0.0000 0.987 0.00 0.00 1.00
#> TCGA.EE.A2M5.06 2 0.0000 0.980 0.00 1.00 0.00
#> TCGA.EE.A20F.06 1 0.0000 0.969 1.00 0.00 0.00
#> TCGA.FS.A1ZW.06 3 0.0000 0.987 0.00 0.00 1.00
#> TCGA.EE.A20B.06 1 0.0000 0.969 1.00 0.00 0.00
#> TCGA.EE.A29V.06 2 0.0000 0.980 0.00 1.00 0.00
#> TCGA.EE.A3AB.06 3 0.1529 0.970 0.04 0.00 0.96
#> TCGA.DA.A1I1.06 3 0.0000 0.987 0.00 0.00 1.00
#> TCGA.ER.A19M.06 1 0.0000 0.969 1.00 0.00 0.00
#> TCGA.EB.A57M.01 2 0.0000 0.980 0.00 1.00 0.00
#> TCGA.EE.A2GI.06 1 0.0000 0.969 1.00 0.00 0.00
#> TCGA.D3.A2JK.06 2 0.0000 0.980 0.00 1.00 0.00
#> TCGA.D9.A148.06 2 0.0000 0.980 0.00 1.00 0.00
#> TCGA.EE.A2ML.06 3 0.0000 0.987 0.00 0.00 1.00
#> TCGA.EB.A5UL.06 2 0.0000 0.980 0.00 1.00 0.00
#> TCGA.D3.A51N.06 3 0.0892 0.986 0.02 0.00 0.98
#> TCGA.XV.A9W5.01 2 0.0000 0.980 0.00 1.00 0.00
#> TCGA.D9.A4Z6.06 2 0.0000 0.980 0.00 1.00 0.00
#> TCGA.DA.A1I0.06 2 0.0000 0.980 0.00 1.00 0.00
#> TCGA.EB.A431.01 2 0.0000 0.980 0.00 1.00 0.00
#> TCGA.BF.AAOX.01 2 0.0000 0.980 0.00 1.00 0.00
#> TCGA.YD.A9TA.06 1 0.0000 0.969 1.00 0.00 0.00
#> TCGA.WE.AAA0.06 2 0.0000 0.980 0.00 1.00 0.00
#> TCGA.EE.A3J5.06 2 0.0000 0.980 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.D3.A8GQ.06 1 0.0000 0.9833 1.00 0.00 0.00 0.00
#> TCGA.DA.A95V.06 2 0.0000 0.8840 0.00 1.00 0.00 0.00
#> TCGA.EE.A3JB.06 1 0.3611 0.8288 0.86 0.00 0.06 0.08
#> TCGA.WE.A8ZX.06 2 0.0000 0.8840 0.00 1.00 0.00 0.00
#> TCGA.GN.A4U8.06 3 0.4088 0.7909 0.14 0.00 0.82 0.04
#> TCGA.D3.A8GM.06 2 0.2345 0.8324 0.00 0.90 0.00 0.10
#> TCGA.YD.A89C.06 2 0.3975 0.5854 0.24 0.76 0.00 0.00
#> TCGA.FR.A726.01 1 0.0000 0.9833 1.00 0.00 0.00 0.00
#> TCGA.GN.A26A.06 1 0.0000 0.9833 1.00 0.00 0.00 0.00
#> TCGA.EE.A20I.06 4 0.2921 0.8885 0.00 0.14 0.00 0.86
#> TCGA.EE.A17Y.06 2 0.3400 0.6772 0.18 0.82 0.00 0.00
#> TCGA.D3.A1Q9.06 4 0.4277 0.7906 0.00 0.28 0.00 0.72
#> TCGA.BF.A5EO.01 2 0.4713 0.3338 0.00 0.64 0.00 0.36
#> TCGA.EE.A181.06 2 0.3606 0.7640 0.00 0.84 0.02 0.14
#> TCGA.D3.A2JP.06 2 0.0000 0.8840 0.00 1.00 0.00 0.00
#> TCGA.FS.A1ZH.06 1 0.0000 0.9833 1.00 0.00 0.00 0.00
#> TCGA.D3.A2JL.06 3 0.7310 -0.0789 0.00 0.16 0.48 0.36
#> TCGA.D3.A3C3.06 3 0.4841 0.7847 0.14 0.00 0.78 0.08
#> TCGA.D3.A1QA.07 3 0.1211 0.7855 0.00 0.00 0.96 0.04
#> TCGA.EE.A2M5.06 2 0.0000 0.8840 0.00 1.00 0.00 0.00
#> TCGA.EE.A20F.06 1 0.0000 0.9833 1.00 0.00 0.00 0.00
#> TCGA.FS.A1ZW.06 3 0.1913 0.7959 0.04 0.00 0.94 0.02
#> TCGA.EE.A20B.06 1 0.0000 0.9833 1.00 0.00 0.00 0.00
#> TCGA.EE.A29V.06 2 0.0000 0.8840 0.00 1.00 0.00 0.00
#> TCGA.EE.A3AB.06 3 0.5486 0.7361 0.20 0.00 0.72 0.08
#> TCGA.DA.A1I1.06 3 0.1211 0.7855 0.00 0.00 0.96 0.04
#> TCGA.ER.A19M.06 1 0.0000 0.9833 1.00 0.00 0.00 0.00
#> TCGA.EB.A57M.01 2 0.0000 0.8840 0.00 1.00 0.00 0.00
#> TCGA.EE.A2GI.06 1 0.0000 0.9833 1.00 0.00 0.00 0.00
#> TCGA.D3.A2JK.06 2 0.0707 0.8772 0.00 0.98 0.00 0.02
#> TCGA.D9.A148.06 4 0.3400 0.9186 0.00 0.18 0.00 0.82
#> TCGA.EE.A2ML.06 3 0.1211 0.7855 0.00 0.00 0.96 0.04
#> TCGA.EB.A5UL.06 2 0.1211 0.8686 0.00 0.96 0.00 0.04
#> TCGA.D3.A51N.06 3 0.5594 0.7567 0.18 0.00 0.72 0.10
#> TCGA.XV.A9W5.01 2 0.0000 0.8840 0.00 1.00 0.00 0.00
#> TCGA.D9.A4Z6.06 2 0.0000 0.8840 0.00 1.00 0.00 0.00
#> TCGA.DA.A1I0.06 2 0.3975 0.6391 0.00 0.76 0.00 0.24
#> TCGA.EB.A431.01 2 0.2647 0.8157 0.00 0.88 0.00 0.12
#> TCGA.BF.AAOX.01 4 0.3400 0.9186 0.00 0.18 0.00 0.82
#> TCGA.YD.A9TA.06 1 0.0000 0.9833 1.00 0.00 0.00 0.00
#> TCGA.WE.AAA0.06 2 0.0000 0.8840 0.00 1.00 0.00 0.00
#> TCGA.EE.A3J5.06 2 0.2345 0.8310 0.00 0.90 0.00 0.10
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> TCGA.D3.A8GQ.06 1 0.0000 0.918 1.00 0.00 0.00 0.00 0.00
#> TCGA.DA.A95V.06 2 0.0609 0.827 0.00 0.98 0.00 0.00 0.02
#> TCGA.EE.A3JB.06 1 0.4227 0.290 0.58 0.00 0.00 0.00 0.42
#> TCGA.WE.A8ZX.06 2 0.0000 0.836 0.00 1.00 0.00 0.00 0.00
#> TCGA.GN.A4U8.06 3 0.5952 -0.522 0.06 0.00 0.50 0.02 0.42
#> TCGA.D3.A8GM.06 2 0.3796 0.574 0.00 0.70 0.00 0.30 0.00
#> TCGA.YD.A89C.06 2 0.2616 0.733 0.10 0.88 0.00 0.00 0.02
#> TCGA.FR.A726.01 1 0.1216 0.909 0.96 0.00 0.02 0.00 0.02
#> TCGA.GN.A26A.06 1 0.2020 0.852 0.90 0.00 0.00 0.00 0.10
#> TCGA.EE.A20I.06 4 0.3291 0.631 0.00 0.04 0.00 0.84 0.12
#> TCGA.EE.A17Y.06 2 0.1648 0.798 0.04 0.94 0.00 0.00 0.02
#> TCGA.D3.A1Q9.06 4 0.6885 0.497 0.00 0.22 0.02 0.50 0.26
#> TCGA.BF.A5EO.01 4 0.4182 0.212 0.00 0.40 0.00 0.60 0.00
#> TCGA.EE.A181.06 2 0.5690 0.445 0.00 0.66 0.02 0.10 0.22
#> TCGA.D3.A2JP.06 2 0.0000 0.836 0.00 1.00 0.00 0.00 0.00
#> TCGA.FS.A1ZH.06 1 0.0000 0.918 1.00 0.00 0.00 0.00 0.00
#> TCGA.D3.A2JL.06 4 0.8440 0.118 0.00 0.16 0.26 0.32 0.26
#> TCGA.D3.A3C3.06 5 0.5351 0.728 0.06 0.00 0.38 0.00 0.56
#> TCGA.D3.A1QA.07 3 0.1732 0.569 0.00 0.00 0.92 0.00 0.08
#> TCGA.EE.A2M5.06 2 0.0000 0.836 0.00 1.00 0.00 0.00 0.00
#> TCGA.EE.A20F.06 1 0.1043 0.908 0.96 0.00 0.00 0.00 0.04
#> TCGA.FS.A1ZW.06 3 0.4726 -0.113 0.00 0.00 0.58 0.02 0.40
#> TCGA.EE.A20B.06 1 0.1043 0.901 0.96 0.00 0.00 0.00 0.04
#> TCGA.EE.A29V.06 2 0.0000 0.836 0.00 1.00 0.00 0.00 0.00
#> TCGA.EE.A3AB.06 5 0.5828 0.619 0.10 0.00 0.38 0.00 0.52
#> TCGA.DA.A1I1.06 3 0.0000 0.590 0.00 0.00 1.00 0.00 0.00
#> TCGA.ER.A19M.06 1 0.0609 0.916 0.98 0.00 0.00 0.00 0.02
#> TCGA.EB.A57M.01 2 0.0000 0.836 0.00 1.00 0.00 0.00 0.00
#> TCGA.EE.A2GI.06 1 0.1216 0.909 0.96 0.00 0.02 0.00 0.02
#> TCGA.D3.A2JK.06 2 0.2280 0.773 0.00 0.88 0.00 0.12 0.00
#> TCGA.D9.A148.06 4 0.2077 0.633 0.00 0.04 0.00 0.92 0.04
#> TCGA.EE.A2ML.06 3 0.0000 0.590 0.00 0.00 1.00 0.00 0.00
#> TCGA.EB.A5UL.06 2 0.2929 0.724 0.00 0.82 0.00 0.18 0.00
#> TCGA.D3.A51N.06 5 0.5232 0.760 0.06 0.00 0.34 0.00 0.60
#> TCGA.XV.A9W5.01 2 0.0000 0.836 0.00 1.00 0.00 0.00 0.00
#> TCGA.D9.A4Z6.06 2 0.0000 0.836 0.00 1.00 0.00 0.00 0.00
#> TCGA.DA.A1I0.06 2 0.4227 0.291 0.00 0.58 0.00 0.42 0.00
#> TCGA.EB.A431.01 2 0.3796 0.580 0.00 0.70 0.00 0.30 0.00
#> TCGA.BF.AAOX.01 4 0.2012 0.644 0.00 0.06 0.00 0.92 0.02
#> TCGA.YD.A9TA.06 1 0.0000 0.918 1.00 0.00 0.00 0.00 0.00
#> TCGA.WE.AAA0.06 2 0.0609 0.827 0.00 0.98 0.00 0.00 0.02
#> TCGA.EE.A3J5.06 2 0.3684 0.613 0.00 0.72 0.00 0.28 0.00
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> TCGA.D3.A8GQ.06 1 0.0937 0.8644 0.96 0.00 0.00 0.00 0.00 0.04
#> TCGA.DA.A95V.06 2 0.0547 0.8077 0.00 0.98 0.00 0.00 0.02 0.00
#> TCGA.EE.A3JB.06 1 0.4873 0.3350 0.60 0.00 0.00 0.00 0.32 0.08
#> TCGA.WE.A8ZX.06 2 0.1267 0.8124 0.00 0.94 0.00 0.06 0.00 0.00
#> TCGA.GN.A4U8.06 5 0.6365 0.4135 0.18 0.00 0.28 0.00 0.50 0.04
#> TCGA.D3.A8GM.06 2 0.3819 0.6052 0.00 0.70 0.00 0.28 0.00 0.02
#> TCGA.YD.A89C.06 2 0.1814 0.7107 0.10 0.90 0.00 0.00 0.00 0.00
#> TCGA.FR.A726.01 1 0.2728 0.8254 0.86 0.00 0.00 0.00 0.04 0.10
#> TCGA.GN.A26A.06 1 0.1865 0.8260 0.92 0.00 0.00 0.00 0.04 0.04
#> TCGA.EE.A20I.06 4 0.5363 -0.0682 0.00 0.08 0.00 0.58 0.02 0.32
#> TCGA.EE.A17Y.06 2 0.0547 0.7980 0.02 0.98 0.00 0.00 0.00 0.00
#> TCGA.D3.A1Q9.06 6 0.6250 0.0000 0.00 0.18 0.00 0.16 0.08 0.58
#> TCGA.BF.A5EO.01 4 0.4646 -0.1690 0.00 0.46 0.00 0.50 0.00 0.04
#> TCGA.EE.A181.06 2 0.6385 0.0713 0.00 0.56 0.00 0.08 0.18 0.18
#> TCGA.D3.A2JP.06 2 0.0547 0.8096 0.00 0.98 0.00 0.02 0.00 0.00
#> TCGA.FS.A1ZH.06 1 0.0547 0.8620 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.D3.A2JL.06 5 0.8419 -0.3713 0.00 0.10 0.10 0.22 0.32 0.26
#> TCGA.D3.A3C3.06 5 0.4838 0.5029 0.10 0.00 0.18 0.00 0.70 0.02
#> TCGA.D3.A1QA.07 3 0.3475 0.7197 0.00 0.00 0.80 0.00 0.14 0.06
#> TCGA.EE.A2M5.06 2 0.0000 0.8086 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.EE.A20F.06 1 0.2728 0.8254 0.86 0.00 0.00 0.00 0.04 0.10
#> TCGA.FS.A1ZW.06 5 0.6674 0.1619 0.06 0.00 0.30 0.00 0.46 0.18
#> TCGA.EE.A20B.06 1 0.1480 0.8505 0.94 0.00 0.00 0.00 0.04 0.02
#> TCGA.EE.A29V.06 2 0.0937 0.8168 0.00 0.96 0.00 0.04 0.00 0.00
#> TCGA.EE.A3AB.06 5 0.6721 0.3461 0.20 0.00 0.28 0.00 0.46 0.06
#> TCGA.DA.A1I1.06 3 0.0000 0.8670 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.ER.A19M.06 1 0.0547 0.8640 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.EB.A57M.01 2 0.0937 0.8168 0.00 0.96 0.00 0.04 0.00 0.00
#> TCGA.EE.A2GI.06 1 0.3483 0.7999 0.82 0.00 0.02 0.00 0.04 0.12
#> TCGA.D3.A2JK.06 2 0.2981 0.7473 0.00 0.82 0.00 0.16 0.00 0.02
#> TCGA.D9.A148.06 4 0.1865 0.3712 0.00 0.04 0.00 0.92 0.00 0.04
#> TCGA.EE.A2ML.06 3 0.0000 0.8670 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.EB.A5UL.06 2 0.3460 0.6920 0.00 0.76 0.00 0.22 0.02 0.00
#> TCGA.D3.A51N.06 5 0.4377 0.5128 0.16 0.00 0.12 0.00 0.72 0.00
#> TCGA.XV.A9W5.01 2 0.0937 0.8168 0.00 0.96 0.00 0.04 0.00 0.00
#> TCGA.D9.A4Z6.06 2 0.0000 0.8086 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DA.A1I0.06 2 0.4637 0.4074 0.00 0.60 0.00 0.36 0.02 0.02
#> TCGA.EB.A431.01 2 0.4574 0.5931 0.00 0.68 0.00 0.26 0.02 0.04
#> TCGA.BF.AAOX.01 4 0.0547 0.3677 0.00 0.02 0.00 0.98 0.00 0.00
#> TCGA.YD.A9TA.06 1 0.1480 0.8538 0.94 0.00 0.00 0.00 0.04 0.02
#> TCGA.WE.AAA0.06 2 0.1092 0.8023 0.00 0.96 0.00 0.00 0.02 0.02
#> TCGA.EE.A3J5.06 2 0.3711 0.6556 0.00 0.72 0.00 0.26 0.02 0.00
cbind(get_classes(res, k = 7), get_membership(res, k = 7))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7
#> TCGA.D3.A8GQ.06 1 0.2654 0.69568 0.86 0.00 0.10 0.00 0.02 0.02 0.00
#> TCGA.DA.A95V.06 2 0.2376 0.74939 0.00 0.86 0.02 0.00 0.00 0.12 0.00
#> TCGA.EE.A3JB.06 1 0.4783 0.12044 0.54 0.00 0.10 0.00 0.36 0.00 0.00
#> TCGA.WE.A8ZX.06 2 0.0504 0.79163 0.00 0.98 0.00 0.00 0.00 0.02 0.00
#> TCGA.GN.A4U8.06 7 0.6799 -0.32357 0.20 0.00 0.08 0.00 0.28 0.02 0.42
#> TCGA.D3.A8GM.06 2 0.2572 0.72988 0.00 0.80 0.00 0.20 0.00 0.00 0.00
#> TCGA.YD.A89C.06 2 0.3208 0.71470 0.04 0.82 0.02 0.00 0.00 0.12 0.00
#> TCGA.FR.A726.01 1 0.3358 0.63824 0.64 0.00 0.36 0.00 0.00 0.00 0.00
#> TCGA.GN.A26A.06 1 0.2512 0.68749 0.86 0.00 0.10 0.00 0.04 0.00 0.00
#> TCGA.EE.A20I.06 4 0.6046 0.07177 0.00 0.00 0.20 0.44 0.04 0.32 0.00
#> TCGA.EE.A17Y.06 2 0.3208 0.71470 0.04 0.82 0.02 0.00 0.00 0.12 0.00
#> TCGA.D3.A1Q9.06 6 0.3199 0.00000 0.00 0.14 0.00 0.06 0.00 0.80 0.00
#> TCGA.BF.A5EO.01 2 0.3525 0.39745 0.00 0.56 0.00 0.44 0.00 0.00 0.00
#> TCGA.EE.A181.06 2 0.6369 0.22220 0.00 0.56 0.04 0.14 0.08 0.18 0.00
#> TCGA.D3.A2JP.06 2 0.0863 0.78820 0.00 0.96 0.00 0.00 0.00 0.04 0.00
#> TCGA.FS.A1ZH.06 1 0.0504 0.73848 0.98 0.00 0.02 0.00 0.00 0.00 0.00
#> TCGA.D3.A2JL.06 4 0.8939 -0.00397 0.00 0.10 0.14 0.26 0.14 0.22 0.14
#> TCGA.D3.A3C3.06 5 0.4308 0.51364 0.10 0.00 0.00 0.00 0.72 0.02 0.16
#> TCGA.D3.A1QA.07 7 0.3863 0.49747 0.00 0.00 0.20 0.00 0.04 0.02 0.74
#> TCGA.EE.A2M5.06 2 0.1671 0.77266 0.00 0.90 0.00 0.00 0.00 0.10 0.00
#> TCGA.EE.A20F.06 1 0.3294 0.65556 0.66 0.00 0.34 0.00 0.00 0.00 0.00
#> TCGA.FS.A1ZW.06 5 0.6993 0.12645 0.08 0.00 0.06 0.00 0.38 0.12 0.36
#> TCGA.EE.A20B.06 1 0.1363 0.71840 0.94 0.00 0.04 0.00 0.02 0.00 0.00
#> TCGA.EE.A29V.06 2 0.0863 0.79081 0.00 0.96 0.00 0.04 0.00 0.00 0.00
#> TCGA.EE.A3AB.06 5 0.6724 0.27989 0.26 0.00 0.10 0.00 0.34 0.00 0.30
#> TCGA.DA.A1I1.06 7 0.0504 0.61971 0.00 0.00 0.00 0.00 0.02 0.00 0.98
#> TCGA.ER.A19M.06 1 0.1886 0.73398 0.88 0.00 0.12 0.00 0.00 0.00 0.00
#> TCGA.EB.A57M.01 2 0.0000 0.79212 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EE.A2GI.06 1 0.3909 0.59678 0.58 0.00 0.40 0.00 0.00 0.02 0.00
#> TCGA.D3.A2JK.06 2 0.1433 0.78150 0.00 0.92 0.00 0.08 0.00 0.00 0.00
#> TCGA.D9.A148.06 4 0.4225 0.33194 0.00 0.08 0.06 0.78 0.04 0.04 0.00
#> TCGA.EE.A2ML.06 7 0.0504 0.61971 0.00 0.00 0.00 0.00 0.02 0.00 0.98
#> TCGA.EB.A5UL.06 2 0.2906 0.72532 0.00 0.80 0.00 0.18 0.00 0.02 0.00
#> TCGA.D3.A51N.06 5 0.3257 0.49335 0.04 0.00 0.02 0.00 0.84 0.02 0.08
#> TCGA.XV.A9W5.01 2 0.0863 0.79081 0.00 0.96 0.00 0.04 0.00 0.00 0.00
#> TCGA.D9.A4Z6.06 2 0.1166 0.78423 0.00 0.94 0.00 0.00 0.00 0.06 0.00
#> TCGA.DA.A1I0.06 2 0.4269 0.52907 0.00 0.60 0.00 0.36 0.02 0.02 0.00
#> TCGA.EB.A431.01 2 0.3984 0.63370 0.00 0.68 0.02 0.28 0.00 0.02 0.00
#> TCGA.BF.AAOX.01 4 0.2654 0.37056 0.00 0.10 0.02 0.86 0.00 0.02 0.00
#> TCGA.YD.A9TA.06 1 0.2654 0.71995 0.86 0.00 0.10 0.00 0.02 0.02 0.00
#> TCGA.WE.AAA0.06 2 0.2163 0.77429 0.00 0.88 0.00 0.02 0.00 0.10 0.00
#> TCGA.EE.A3J5.06 2 0.3307 0.68126 0.00 0.74 0.00 0.24 0.00 0.02 0.00
cbind(get_classes(res, k = 8), get_membership(res, k = 8))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7 p8
#> TCGA.D3.A8GQ.06 1 0.3601 0.2948 0.76 0.00 0.16 0.00 0.06 0.00 0.00 0.02
#> TCGA.DA.A95V.06 2 0.1804 0.7626 0.02 0.90 0.00 0.00 0.00 0.08 0.00 0.00
#> TCGA.EE.A3JB.06 1 0.5089 0.0972 0.52 0.00 0.14 0.00 0.32 0.02 0.00 0.00
#> TCGA.WE.A8ZX.06 2 0.0941 0.8034 0.00 0.96 0.00 0.00 0.00 0.02 0.00 0.02
#> TCGA.GN.A4U8.06 7 0.7062 -0.1242 0.10 0.00 0.10 0.02 0.30 0.08 0.40 0.00
#> TCGA.D3.A8GM.06 2 0.3675 0.7382 0.00 0.76 0.00 0.14 0.00 0.02 0.00 0.08
#> TCGA.YD.A89C.06 2 0.3880 0.4874 0.24 0.68 0.00 0.00 0.00 0.08 0.00 0.00
#> TCGA.FR.A726.01 3 0.3737 0.7760 0.48 0.00 0.50 0.00 0.00 0.00 0.02 0.00
#> TCGA.GN.A26A.06 1 0.1887 0.5244 0.90 0.00 0.06 0.00 0.04 0.00 0.00 0.00
#> TCGA.EE.A20I.06 4 0.4774 -0.3063 0.00 0.00 0.10 0.68 0.02 0.16 0.00 0.04
#> TCGA.EE.A17Y.06 2 0.3154 0.6450 0.16 0.78 0.00 0.00 0.00 0.06 0.00 0.00
#> TCGA.D3.A1Q9.06 6 0.3924 0.0000 0.00 0.00 0.00 0.20 0.04 0.72 0.00 0.04
#> TCGA.BF.A5EO.01 2 0.4650 0.6347 0.00 0.66 0.00 0.20 0.00 0.06 0.00 0.08
#> TCGA.EE.A181.06 4 0.7178 0.1784 0.00 0.28 0.02 0.32 0.16 0.20 0.00 0.02
#> TCGA.D3.A2JP.06 2 0.0471 0.7997 0.00 0.98 0.00 0.00 0.00 0.02 0.00 0.00
#> TCGA.FS.A1ZH.06 1 0.0471 0.5530 0.98 0.00 0.02 0.00 0.00 0.00 0.00 0.00
#> TCGA.D3.A2JL.06 4 0.7110 0.1189 0.00 0.04 0.06 0.54 0.08 0.08 0.14 0.06
#> TCGA.D3.A3C3.06 5 0.3771 0.3785 0.12 0.00 0.00 0.00 0.72 0.00 0.16 0.00
#> TCGA.D3.A1QA.07 7 0.4564 0.4195 0.00 0.00 0.08 0.08 0.02 0.10 0.72 0.00
#> TCGA.EE.A2M5.06 2 0.0808 0.7933 0.00 0.96 0.00 0.00 0.00 0.04 0.00 0.00
#> TCGA.EE.A20F.06 1 0.3198 -0.1397 0.72 0.00 0.26 0.00 0.00 0.02 0.00 0.00
#> TCGA.FS.A1ZW.06 5 0.7749 -0.1404 0.00 0.00 0.20 0.18 0.26 0.08 0.26 0.02
#> TCGA.EE.A20B.06 1 0.0471 0.5576 0.98 0.00 0.02 0.00 0.00 0.00 0.00 0.00
#> TCGA.EE.A29V.06 2 0.0808 0.8051 0.00 0.96 0.00 0.00 0.00 0.00 0.00 0.04
#> TCGA.EE.A3AB.06 5 0.7070 0.2082 0.16 0.00 0.14 0.00 0.40 0.08 0.22 0.00
#> TCGA.DA.A1I1.06 7 0.1557 0.5825 0.00 0.00 0.02 0.00 0.06 0.00 0.92 0.00
#> TCGA.ER.A19M.06 1 0.2224 0.4289 0.86 0.00 0.12 0.00 0.00 0.02 0.00 0.00
#> TCGA.EB.A57M.01 2 0.0471 0.7989 0.00 0.98 0.00 0.00 0.00 0.02 0.00 0.00
#> TCGA.EE.A2GI.06 3 0.4936 0.7895 0.44 0.00 0.48 0.02 0.02 0.02 0.02 0.00
#> TCGA.D3.A2JK.06 2 0.1607 0.8009 0.00 0.92 0.00 0.04 0.00 0.00 0.00 0.04
#> TCGA.D9.A148.06 8 0.0808 0.6476 0.00 0.04 0.00 0.00 0.00 0.00 0.00 0.96
#> TCGA.EE.A2ML.06 7 0.0808 0.5918 0.00 0.00 0.00 0.00 0.04 0.00 0.96 0.00
#> TCGA.EB.A5UL.06 2 0.3154 0.7436 0.00 0.78 0.00 0.16 0.00 0.00 0.00 0.06
#> TCGA.D3.A51N.06 5 0.2724 0.4300 0.08 0.00 0.00 0.02 0.86 0.02 0.02 0.00
#> TCGA.XV.A9W5.01 2 0.1275 0.8044 0.00 0.94 0.00 0.02 0.00 0.00 0.00 0.04
#> TCGA.D9.A4Z6.06 2 0.0808 0.7925 0.00 0.96 0.00 0.00 0.00 0.04 0.00 0.00
#> TCGA.DA.A1I0.06 2 0.4244 0.6123 0.00 0.64 0.00 0.24 0.00 0.00 0.00 0.12
#> TCGA.EB.A431.01 2 0.4345 0.6749 0.00 0.68 0.02 0.18 0.00 0.00 0.00 0.12
#> TCGA.BF.AAOX.01 8 0.4734 0.6508 0.00 0.08 0.04 0.14 0.00 0.04 0.00 0.70
#> TCGA.YD.A9TA.06 1 0.3586 0.3519 0.78 0.00 0.12 0.00 0.06 0.00 0.00 0.04
#> TCGA.WE.AAA0.06 2 0.3627 0.7544 0.02 0.78 0.00 0.14 0.00 0.04 0.00 0.02
#> TCGA.EE.A3J5.06 2 0.4069 0.6812 0.00 0.68 0.00 0.18 0.00 0.00 0.00 0.14
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
consensus_heatmap(res, k = 7)
consensus_heatmap(res, k = 8)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
membership_heatmap(res, k = 7)
membership_heatmap(res, k = 8)
As soon as the classes for columns are determined, the signatures that are significantly different between subgroups can be looked for. Following are the heatmaps for signatures.
get_signatures(res, k = 2)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
get_signatures(res, k = 7)
get_signatures(res, k = 8)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. To get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows (which is done by automatically selecting number of clusters).If there are too many signatures, top_signatures = ... can be set to only show the
signatures with the highest FDRs:
# code only for demonstration
# e.g. to show the top 500 most significant rows
tb = get_signature(res, k = ..., top_signatures = 500)
If the signatures are defined as these which are uniquely high in current group, diff_method argument
can be set to "uniquely_high_in_one_group":
# code only for demonstration
tb = get_signature(res, k = ..., diff_method = "uniquely_high_in_one_group")
UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
dimension_reduction(res, k = 7, method = "UMAP")
dimension_reduction(res, k = 8, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
If matrix rows can be associated to genes, consider to use functional_enrichment(res,
...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.
Parent node: Node041. Child nodes: Node01111-leaf , Node01112-leaf , Node01113-leaf , Node01131-leaf , Node01132-leaf , Node01133-leaf , Node01311-leaf , Node01312-leaf , Node02121-leaf , Node02122-leaf , Node02123-leaf , Node03111-leaf , Node03112-leaf , Node03113-leaf , Node03221-leaf , Node03222-leaf , Node03231-leaf , Node03232-leaf , Node03233-leaf , Node03234-leaf , Node04111-leaf , Node04112-leaf , Node04121-leaf , Node04122-leaf , Node04421-leaf , Node04422-leaf , Node04423-leaf , Node04424-leaf , Node05111-leaf , Node05112-leaf , Node05113-leaf .
The object with results only for a single top-value method and a single partitioning method can be extracted as:
res = res_rh["0411"]
A summary of res and all the functions that can be applied to it:
res
#> A 'ConsensusPartition' object with k = 2, 3, 4, 5, 6, 7, 8.
#> On a matrix with 30000 rows and 12 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 0.833 0.953 0.980 0.3291 0.697 0.697
#> 3 3 0.379 0.708 0.812 0.8891 0.636 0.478
#> 4 4 1.000 0.913 0.998 0.1955 0.894 0.696
#> 5 5 0.848 0.529 0.842 0.0770 0.985 0.941
#> 6 6 0.864 0.779 0.942 0.0621 0.864 0.471
#> 7 7 0.848 0.600 0.910 0.0334 0.985 0.889
#> 8 8 0.818 0.488 0.868 0.0313 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] 4
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.D3.A8GQ.06 2 0.000 1.000 0.00 1.00
#> TCGA.EE.A3JB.06 1 0.000 0.972 1.00 0.00
#> TCGA.YD.A89C.06 1 0.795 0.684 0.76 0.24
#> TCGA.FR.A726.01 1 0.000 0.972 1.00 0.00
#> TCGA.GN.A26A.06 1 0.000 0.972 1.00 0.00
#> TCGA.EE.A17Y.06 1 0.000 0.972 1.00 0.00
#> TCGA.FS.A1ZH.06 1 0.000 0.972 1.00 0.00
#> TCGA.EE.A20F.06 1 0.000 0.972 1.00 0.00
#> TCGA.EE.A20B.06 1 0.000 0.972 1.00 0.00
#> TCGA.ER.A19M.06 1 0.000 0.972 1.00 0.00
#> TCGA.EE.A2GI.06 1 0.000 0.972 1.00 0.00
#> TCGA.YD.A9TA.06 2 0.000 1.000 0.00 1.00
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.D3.A8GQ.06 2 0.814 0.699 0.22 0.64 0.14
#> TCGA.EE.A3JB.06 1 0.480 0.797 0.78 0.00 0.22
#> TCGA.YD.A89C.06 1 0.832 -0.165 0.62 0.24 0.14
#> TCGA.FR.A726.01 3 0.000 0.851 0.00 0.00 1.00
#> TCGA.GN.A26A.06 1 0.480 0.797 0.78 0.00 0.22
#> TCGA.EE.A17Y.06 1 0.480 0.797 0.78 0.00 0.22
#> TCGA.FS.A1ZH.06 1 0.595 0.672 0.64 0.00 0.36
#> TCGA.EE.A20F.06 3 0.369 0.844 0.14 0.00 0.86
#> TCGA.EE.A20B.06 1 0.480 0.797 0.78 0.00 0.22
#> TCGA.ER.A19M.06 3 0.369 0.844 0.14 0.00 0.86
#> TCGA.EE.A2GI.06 3 0.000 0.851 0.00 0.00 1.00
#> TCGA.YD.A9TA.06 2 0.000 0.709 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.D3.A8GQ.06 2 0.0000 1.000 0.00 1.00 0 0
#> TCGA.EE.A3JB.06 1 0.0000 0.995 1.00 0.00 0 0
#> TCGA.YD.A89C.06 2 0.0000 1.000 0.00 1.00 0 0
#> TCGA.FR.A726.01 3 0.0000 1.000 0.00 0.00 1 0
#> TCGA.GN.A26A.06 1 0.0000 0.995 1.00 0.00 0 0
#> TCGA.EE.A17Y.06 1 0.0000 0.995 1.00 0.00 0 0
#> TCGA.FS.A1ZH.06 1 0.0707 0.978 0.98 0.02 0 0
#> TCGA.EE.A20F.06 3 0.0000 1.000 0.00 0.00 1 0
#> TCGA.EE.A20B.06 1 0.0000 0.995 1.00 0.00 0 0
#> TCGA.ER.A19M.06 3 0.0000 1.000 0.00 0.00 1 0
#> TCGA.EE.A2GI.06 3 0.0000 1.000 0.00 0.00 1 0
#> TCGA.YD.A9TA.06 4 0.0000 0.000 0.00 0.00 0 1
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> TCGA.D3.A8GQ.06 2 0.430 0.000 0.00 0.52 0.48 0 0.00
#> TCGA.EE.A3JB.06 1 0.000 0.877 1.00 0.00 0.00 0 0.00
#> TCGA.YD.A89C.06 5 0.430 0.000 0.00 0.00 0.48 0 0.52
#> TCGA.FR.A726.01 3 0.430 0.660 0.00 0.48 0.52 0 0.00
#> TCGA.GN.A26A.06 1 0.000 0.877 1.00 0.00 0.00 0 0.00
#> TCGA.EE.A17Y.06 1 0.000 0.877 1.00 0.00 0.00 0 0.00
#> TCGA.FS.A1ZH.06 1 0.429 0.199 0.54 0.00 0.00 0 0.46
#> TCGA.EE.A20F.06 3 0.430 0.660 0.00 0.00 0.52 0 0.48
#> TCGA.EE.A20B.06 1 0.000 0.877 1.00 0.00 0.00 0 0.00
#> TCGA.ER.A19M.06 3 0.430 0.660 0.00 0.00 0.52 0 0.48
#> TCGA.EE.A2GI.06 3 0.430 0.660 0.00 0.48 0.52 0 0.00
#> TCGA.YD.A9TA.06 4 0.000 0.000 0.00 0.00 0.00 1 0.00
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> TCGA.D3.A8GQ.06 2 0.0000 0.000 0.00 1.00 0.00 0 0.00 0.00
#> TCGA.EE.A3JB.06 1 0.0000 1.000 1.00 0.00 0.00 0 0.00 0.00
#> TCGA.YD.A89C.06 5 0.3156 0.686 0.00 0.02 0.00 0 0.80 0.18
#> TCGA.FR.A726.01 3 0.0547 0.983 0.00 0.00 0.98 0 0.02 0.00
#> TCGA.GN.A26A.06 1 0.0000 1.000 1.00 0.00 0.00 0 0.00 0.00
#> TCGA.EE.A17Y.06 1 0.0000 1.000 1.00 0.00 0.00 0 0.00 0.00
#> TCGA.FS.A1ZH.06 5 0.2048 0.693 0.12 0.00 0.00 0 0.88 0.00
#> TCGA.EE.A20F.06 6 0.2631 1.000 0.00 0.00 0.18 0 0.00 0.82
#> TCGA.EE.A20B.06 1 0.0000 1.000 1.00 0.00 0.00 0 0.00 0.00
#> TCGA.ER.A19M.06 6 0.2631 1.000 0.00 0.00 0.18 0 0.00 0.82
#> TCGA.EE.A2GI.06 3 0.0000 0.983 0.00 0.00 1.00 0 0.00 0.00
#> TCGA.YD.A9TA.06 4 0.0000 0.000 0.00 0.00 0.00 1 0.00 0.00
cbind(get_classes(res, k = 7), get_membership(res, k = 7))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7
#> TCGA.D3.A8GQ.06 2 0.0000 0.000 0.00 1 0.00 0 0.00 0.00 0.00
#> TCGA.EE.A3JB.06 1 0.2569 0.890 0.84 0 0.00 0 0.02 0.14 0.00
#> TCGA.YD.A89C.06 5 0.2572 0.000 0.00 0 0.00 0 0.80 0.00 0.20
#> TCGA.FR.A726.01 3 0.2745 0.840 0.00 0 0.82 0 0.16 0.00 0.02
#> TCGA.GN.A26A.06 1 0.0000 0.893 1.00 0 0.00 0 0.00 0.00 0.00
#> TCGA.EE.A17Y.06 1 0.0000 0.893 1.00 0 0.00 0 0.00 0.00 0.00
#> TCGA.FS.A1ZH.06 7 0.0504 0.000 0.02 0 0.00 0 0.00 0.00 0.98
#> TCGA.EE.A20F.06 6 0.2259 0.982 0.00 0 0.16 0 0.00 0.84 0.00
#> TCGA.EE.A20B.06 1 0.2745 0.882 0.82 0 0.00 0 0.02 0.16 0.00
#> TCGA.ER.A19M.06 6 0.2745 0.982 0.00 0 0.16 0 0.02 0.82 0.00
#> TCGA.EE.A2GI.06 3 0.0000 0.840 0.00 0 1.00 0 0.00 0.00 0.00
#> TCGA.YD.A9TA.06 4 0.0000 0.000 0.00 0 0.00 1 0.00 0.00 0.00
cbind(get_classes(res, k = 8), get_membership(res, k = 8))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7 p8
#> TCGA.D3.A8GQ.06 2 0.0000 0.000 0.00 1 0.00 0 0.00 0.00 0.00 0.00
#> TCGA.EE.A3JB.06 1 0.0000 0.783 1.00 0 0.00 0 0.00 0.00 0.00 0.00
#> TCGA.YD.A89C.06 5 0.0000 0.000 0.00 0 0.00 0 1.00 0.00 0.00 0.00
#> TCGA.FR.A726.01 3 0.0000 0.592 0.00 0 1.00 0 0.00 0.00 0.00 0.00
#> TCGA.GN.A26A.06 1 0.3483 0.783 0.76 0 0.00 0 0.00 0.04 0.02 0.18
#> TCGA.EE.A17Y.06 1 0.3291 0.771 0.70 0 0.00 0 0.00 0.00 0.02 0.28
#> TCGA.FS.A1ZH.06 7 0.0808 0.000 0.00 0 0.00 0 0.04 0.00 0.96 0.00
#> TCGA.EE.A20F.06 6 0.4169 0.814 0.00 0 0.10 0 0.00 0.70 0.02 0.18
#> TCGA.EE.A20B.06 1 0.2623 0.713 0.84 0 0.00 0 0.00 0.06 0.00 0.10
#> TCGA.ER.A19M.06 6 0.1563 0.814 0.00 0 0.10 0 0.00 0.90 0.00 0.00
#> TCGA.EE.A2GI.06 3 0.3299 0.592 0.00 0 0.56 0 0.00 0.00 0.00 0.44
#> TCGA.YD.A9TA.06 4 0.0000 0.000 0.00 0 0.00 1 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: Node041. Child nodes: Node01111-leaf , Node01112-leaf , Node01113-leaf , Node01131-leaf , Node01132-leaf , Node01133-leaf , Node01311-leaf , Node01312-leaf , Node02121-leaf , Node02122-leaf , Node02123-leaf , Node03111-leaf , Node03112-leaf , Node03113-leaf , Node03221-leaf , Node03222-leaf , Node03231-leaf , Node03232-leaf , Node03233-leaf , Node03234-leaf , Node04111-leaf , Node04112-leaf , Node04121-leaf , Node04122-leaf , Node04421-leaf , Node04422-leaf , Node04423-leaf , Node04424-leaf , Node05111-leaf , Node05112-leaf , Node05113-leaf .
The object with results only for a single top-value method and a single partitioning method can be extracted as:
res = res_rh["0412"]
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 22 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 0.3686 0.632 0.632
#> 3 3 0.895 0.946 0.975 0.7358 0.671 0.500
#> 4 4 0.737 0.706 0.854 0.1513 0.892 0.706
#> 5 5 0.889 0.740 0.886 0.0914 0.896 0.642
#> 6 6 0.774 0.651 0.823 0.0318 0.883 0.518
#> 7 7 0.847 0.588 0.768 0.0421 0.944 0.675
#> 8 8 0.879 0.716 0.877 0.0264 0.935 0.571
suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:
suggest_best_k(res)
#> [1] 2
Following 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.DA.A95V.06 2 0 1 0 1
#> TCGA.WE.A8ZX.06 2 0 1 0 1
#> TCGA.D3.A8GM.06 2 0 1 0 1
#> TCGA.EE.A20I.06 1 0 1 1 0
#> TCGA.D3.A1Q9.06 1 0 1 1 0
#> TCGA.BF.A5EO.01 2 0 1 0 1
#> TCGA.EE.A181.06 1 0 1 1 0
#> TCGA.D3.A2JP.06 2 0 1 0 1
#> TCGA.D3.A2JL.06 2 0 1 0 1
#> TCGA.EE.A2M5.06 2 0 1 0 1
#> TCGA.EE.A29V.06 2 0 1 0 1
#> TCGA.EB.A57M.01 2 0 1 0 1
#> TCGA.D3.A2JK.06 2 0 1 0 1
#> TCGA.D9.A148.06 1 0 1 1 0
#> TCGA.EB.A5UL.06 2 0 1 0 1
#> TCGA.XV.A9W5.01 2 0 1 0 1
#> TCGA.D9.A4Z6.06 2 0 1 0 1
#> TCGA.DA.A1I0.06 2 0 1 0 1
#> TCGA.EB.A431.01 2 0 1 0 1
#> TCGA.BF.AAOX.01 1 0 1 1 0
#> TCGA.WE.AAA0.06 2 0 1 0 1
#> TCGA.EE.A3J5.06 2 0 1 0 1
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.DA.A95V.06 2 0.0000 0.985 0.0 1.00 0.00
#> TCGA.WE.A8ZX.06 3 0.4002 0.812 0.0 0.16 0.84
#> TCGA.D3.A8GM.06 2 0.0892 0.974 0.0 0.98 0.02
#> TCGA.EE.A20I.06 1 0.0000 1.000 1.0 0.00 0.00
#> TCGA.D3.A1Q9.06 1 0.0000 1.000 1.0 0.00 0.00
#> TCGA.BF.A5EO.01 3 0.0000 0.910 0.0 0.00 1.00
#> TCGA.EE.A181.06 3 0.2959 0.831 0.1 0.00 0.90
#> TCGA.D3.A2JP.06 3 0.0000 0.910 0.0 0.00 1.00
#> TCGA.D3.A2JL.06 2 0.0892 0.974 0.0 0.98 0.02
#> TCGA.EE.A2M5.06 2 0.0000 0.985 0.0 1.00 0.00
#> TCGA.EE.A29V.06 2 0.0000 0.985 0.0 1.00 0.00
#> TCGA.EB.A57M.01 3 0.0000 0.910 0.0 0.00 1.00
#> TCGA.D3.A2JK.06 2 0.0000 0.985 0.0 1.00 0.00
#> TCGA.D9.A148.06 1 0.0000 1.000 1.0 0.00 0.00
#> TCGA.EB.A5UL.06 2 0.0000 0.985 0.0 1.00 0.00
#> TCGA.XV.A9W5.01 2 0.0000 0.985 0.0 1.00 0.00
#> TCGA.D9.A4Z6.06 2 0.0000 0.985 0.0 1.00 0.00
#> TCGA.DA.A1I0.06 3 0.0000 0.910 0.0 0.00 1.00
#> TCGA.EB.A431.01 2 0.2959 0.891 0.0 0.90 0.10
#> TCGA.BF.AAOX.01 1 0.0000 1.000 1.0 0.00 0.00
#> TCGA.WE.AAA0.06 2 0.0000 0.985 0.0 1.00 0.00
#> TCGA.EE.A3J5.06 3 0.4002 0.812 0.0 0.16 0.84
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> TCGA.DA.A95V.06 2 0.0707 0.731 0.00 0.98 0.00 0.02
#> TCGA.WE.A8ZX.06 4 0.2335 0.671 0.00 0.02 0.06 0.92
#> TCGA.D3.A8GM.06 2 0.6299 0.506 0.00 0.52 0.06 0.42
#> TCGA.EE.A20I.06 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.D3.A1Q9.06 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.BF.A5EO.01 3 0.0000 0.845 0.00 0.00 1.00 0.00
#> TCGA.EE.A181.06 3 0.1637 0.804 0.06 0.00 0.94 0.00
#> TCGA.D3.A2JP.06 4 0.4624 0.156 0.00 0.00 0.34 0.66
#> TCGA.D3.A2JL.06 2 0.6299 0.506 0.00 0.52 0.06 0.42
#> TCGA.EE.A2M5.06 2 0.4713 0.650 0.00 0.64 0.00 0.36
#> TCGA.EE.A29V.06 2 0.0000 0.730 0.00 1.00 0.00 0.00
#> TCGA.EB.A57M.01 3 0.4277 0.481 0.00 0.00 0.72 0.28
#> TCGA.D3.A2JK.06 2 0.0000 0.730 0.00 1.00 0.00 0.00
#> TCGA.D9.A148.06 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.EB.A5UL.06 2 0.4624 0.667 0.00 0.66 0.00 0.34
#> TCGA.XV.A9W5.01 2 0.0000 0.730 0.00 1.00 0.00 0.00
#> TCGA.D9.A4Z6.06 2 0.0000 0.730 0.00 1.00 0.00 0.00
#> TCGA.DA.A1I0.06 3 0.0000 0.845 0.00 0.00 1.00 0.00
#> TCGA.EB.A431.01 4 0.4949 0.412 0.00 0.18 0.06 0.76
#> TCGA.BF.AAOX.01 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.WE.AAA0.06 2 0.4624 0.667 0.00 0.66 0.00 0.34
#> TCGA.EE.A3J5.06 4 0.2647 0.671 0.00 0.00 0.12 0.88
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> TCGA.DA.A95V.06 2 0.0609 0.7376 0 0.98 0.00 0.02 0.00
#> TCGA.WE.A8ZX.06 5 0.1216 0.9352 0 0.00 0.02 0.02 0.96
#> TCGA.D3.A8GM.06 4 0.1043 0.7974 0 0.04 0.00 0.96 0.00
#> TCGA.EE.A20I.06 1 0.0000 1.0000 1 0.00 0.00 0.00 0.00
#> TCGA.D3.A1Q9.06 1 0.0000 1.0000 1 0.00 0.00 0.00 0.00
#> TCGA.BF.A5EO.01 3 0.0000 0.8935 0 0.00 1.00 0.00 0.00
#> TCGA.EE.A181.06 3 0.0609 0.8867 0 0.00 0.98 0.02 0.00
#> TCGA.D3.A2JP.06 5 0.1410 0.9353 0 0.00 0.06 0.00 0.94
#> TCGA.D3.A2JL.06 4 0.1043 0.7974 0 0.04 0.00 0.96 0.00
#> TCGA.EE.A2M5.06 2 0.4818 0.3319 0 0.52 0.00 0.46 0.02
#> TCGA.EE.A29V.06 2 0.0000 0.7439 0 1.00 0.00 0.00 0.00
#> TCGA.EB.A57M.01 3 0.3561 0.6098 0 0.00 0.74 0.00 0.26
#> TCGA.D3.A2JK.06 2 0.0000 0.7439 0 1.00 0.00 0.00 0.00
#> TCGA.D9.A148.06 1 0.0000 1.0000 1 0.00 0.00 0.00 0.00
#> TCGA.EB.A5UL.06 2 0.4818 0.3319 0 0.52 0.00 0.46 0.02
#> TCGA.XV.A9W5.01 2 0.0000 0.7439 0 1.00 0.00 0.00 0.00
#> TCGA.D9.A4Z6.06 2 0.0000 0.7439 0 1.00 0.00 0.00 0.00
#> TCGA.DA.A1I0.06 3 0.0000 0.8935 0 0.00 1.00 0.00 0.00
#> TCGA.EB.A431.01 4 0.2012 0.7806 0 0.02 0.00 0.92 0.06
#> TCGA.BF.AAOX.01 1 0.0000 1.0000 1 0.00 0.00 0.00 0.00
#> TCGA.WE.AAA0.06 2 0.4829 0.2884 0 0.50 0.00 0.48 0.02
#> TCGA.EE.A3J5.06 4 0.4818 0.0956 0 0.00 0.02 0.52 0.46
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> TCGA.DA.A95V.06 2 0.454 0.424 0.00 0.70 0.00 0.12 0.00 0.18
#> TCGA.WE.A8ZX.06 5 0.263 0.752 0.00 0.00 0.00 0.00 0.82 0.18
#> TCGA.D3.A8GM.06 4 0.181 0.359 0.00 0.10 0.00 0.90 0.00 0.00
#> TCGA.EE.A20I.06 1 0.000 0.989 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D3.A1Q9.06 1 0.000 0.989 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BF.A5EO.01 3 0.000 0.817 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.EE.A181.06 3 0.368 0.699 0.00 0.00 0.76 0.04 0.00 0.20
#> TCGA.D3.A2JP.06 5 0.000 0.772 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.D3.A2JL.06 4 0.181 0.359 0.00 0.10 0.00 0.90 0.00 0.00
#> TCGA.EE.A2M5.06 4 0.609 0.497 0.00 0.34 0.00 0.38 0.00 0.28
#> TCGA.EE.A29V.06 2 0.000 0.896 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.EB.A57M.01 3 0.382 0.558 0.00 0.00 0.70 0.00 0.28 0.02
#> TCGA.D3.A2JK.06 2 0.000 0.896 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.D9.A148.06 1 0.000 0.989 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EB.A5UL.06 4 0.605 0.513 0.00 0.34 0.00 0.40 0.00 0.26
#> TCGA.XV.A9W5.01 2 0.000 0.896 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.D9.A4Z6.06 2 0.000 0.896 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.DA.A1I0.06 3 0.000 0.817 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.EB.A431.01 4 0.434 -0.279 0.00 0.02 0.00 0.50 0.00 0.48
#> TCGA.BF.AAOX.01 1 0.109 0.965 0.96 0.00 0.00 0.02 0.00 0.02
#> TCGA.WE.AAA0.06 4 0.605 0.513 0.00 0.34 0.00 0.40 0.00 0.26
#> TCGA.EE.A3J5.06 6 0.517 0.000 0.00 0.00 0.00 0.18 0.20 0.62
cbind(get_classes(res, k = 7), get_membership(res, k = 7))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7
#> TCGA.DA.A95V.06 2 0.7043 -0.467 0.00 0.36 0.30 0.22 0.00 0.10 0.02
#> TCGA.WE.A8ZX.06 5 0.0000 0.529 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.D3.A8GM.06 6 0.0504 1.000 0.00 0.02 0.00 0.00 0.00 0.98 0.00
#> TCGA.EE.A20I.06 1 0.0000 0.994 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D3.A1Q9.06 1 0.0000 0.994 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BF.A5EO.01 3 0.3221 0.458 0.00 0.00 0.68 0.00 0.00 0.00 0.32
#> TCGA.EE.A181.06 7 0.3358 0.000 0.00 0.00 0.36 0.00 0.00 0.00 0.64
#> TCGA.D3.A2JP.06 5 0.4070 0.411 0.00 0.00 0.00 0.04 0.62 0.00 0.34
#> TCGA.D3.A2JL.06 6 0.0504 1.000 0.00 0.02 0.00 0.00 0.00 0.98 0.00
#> TCGA.EE.A2M5.06 4 0.6902 0.664 0.00 0.16 0.30 0.34 0.00 0.20 0.00
#> TCGA.EE.A29V.06 2 0.0000 0.806 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EB.A57M.01 3 0.4514 0.309 0.00 0.00 0.48 0.00 0.06 0.00 0.46
#> TCGA.D3.A2JK.06 2 0.0000 0.806 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D9.A148.06 1 0.0000 0.994 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EB.A5UL.06 4 0.6949 0.672 0.00 0.16 0.30 0.32 0.00 0.22 0.00
#> TCGA.XV.A9W5.01 2 0.0000 0.806 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D9.A4Z6.06 2 0.0000 0.806 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DA.A1I0.06 3 0.3139 0.490 0.00 0.00 0.70 0.00 0.00 0.00 0.30
#> TCGA.EB.A431.01 4 0.2708 -0.203 0.00 0.00 0.00 0.78 0.00 0.22 0.00
#> TCGA.BF.AAOX.01 1 0.0504 0.983 0.98 0.00 0.00 0.00 0.00 0.02 0.00
#> TCGA.WE.AAA0.06 4 0.6949 0.672 0.00 0.16 0.30 0.32 0.00 0.22 0.00
#> TCGA.EE.A3J5.06 5 0.5694 0.219 0.00 0.00 0.12 0.38 0.46 0.04 0.00
cbind(get_classes(res, k = 8), get_membership(res, k = 8))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7 p8
#> TCGA.DA.A95V.06 4 0.4053 0.645 0.0 0.18 0.00 0.72 0.06 0.00 0.00 0.04
#> TCGA.WE.A8ZX.06 5 0.3193 0.311 0.0 0.00 0.00 0.00 0.62 0.00 0.38 0.00
#> TCGA.D3.A8GM.06 6 0.1341 1.000 0.0 0.00 0.00 0.08 0.00 0.92 0.00 0.00
#> TCGA.EE.A20I.06 1 0.0000 0.970 1.0 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D3.A1Q9.06 1 0.0000 0.970 1.0 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BF.A5EO.01 3 0.0000 0.659 0.0 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EE.A181.06 3 0.5211 0.352 0.0 0.00 0.52 0.00 0.06 0.04 0.02 0.36
#> TCGA.D3.A2JP.06 7 0.0471 0.000 0.0 0.00 0.00 0.00 0.02 0.00 0.98 0.00
#> TCGA.D3.A2JL.06 6 0.1341 1.000 0.0 0.00 0.00 0.08 0.00 0.92 0.00 0.00
#> TCGA.EE.A2M5.06 4 0.0808 0.867 0.0 0.04 0.00 0.96 0.00 0.00 0.00 0.00
#> TCGA.EE.A29V.06 2 0.0941 0.964 0.0 0.96 0.00 0.00 0.02 0.00 0.00 0.02
#> TCGA.EB.A57M.01 3 0.4847 0.319 0.0 0.00 0.58 0.04 0.08 0.00 0.30 0.00
#> TCGA.D3.A2JK.06 2 0.0000 0.988 0.0 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D9.A148.06 1 0.0000 0.970 1.0 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EB.A5UL.06 4 0.1275 0.873 0.0 0.04 0.00 0.94 0.00 0.02 0.00 0.00
#> TCGA.XV.A9W5.01 2 0.0000 0.988 0.0 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D9.A4Z6.06 2 0.0000 0.988 0.0 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DA.A1I0.06 3 0.1091 0.658 0.0 0.00 0.94 0.00 0.06 0.00 0.00 0.00
#> TCGA.EB.A431.01 8 0.5398 0.000 0.0 0.00 0.00 0.20 0.12 0.10 0.00 0.58
#> TCGA.BF.AAOX.01 1 0.2071 0.907 0.9 0.00 0.00 0.02 0.04 0.04 0.00 0.00
#> TCGA.WE.AAA0.06 4 0.1275 0.873 0.0 0.04 0.00 0.94 0.00 0.02 0.00 0.00
#> TCGA.EE.A3J5.06 5 0.2569 0.453 0.0 0.00 0.00 0.16 0.82 0.02 0.00 0.00
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
consensus_heatmap(res, k = 7)
consensus_heatmap(res, k = 8)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
membership_heatmap(res, k = 7)
membership_heatmap(res, k = 8)
As soon as the classes for columns are determined, the signatures that are significantly different between subgroups can be looked for. Following are the heatmaps for signatures.
get_signatures(res, k = 2)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
get_signatures(res, k = 7)
get_signatures(res, k = 8)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. To get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows (which is done by automatically selecting number of clusters).If there are too many signatures, top_signatures = ... can be set to only show the
signatures with the highest FDRs:
# code only for demonstration
# e.g. to show the top 500 most significant rows
tb = get_signature(res, k = ..., top_signatures = 500)
If the signatures are defined as these which are uniquely high in current group, diff_method argument
can be set to "uniquely_high_in_one_group":
# code only for demonstration
tb = get_signature(res, k = ..., diff_method = "uniquely_high_in_one_group")
UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
dimension_reduction(res, k = 7, method = "UMAP")
dimension_reduction(res, k = 8, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
If matrix rows can be associated to genes, consider to use functional_enrichment(res,
...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.
Parent node: Node04. Child nodes: Node0111 , Node0112-leaf , Node0113 , Node0121-leaf , Node0122-leaf , Node0123-leaf , Node0124-leaf , Node0125-leaf , Node0131 , Node0132-leaf , Node0133-leaf , Node0211-leaf , Node0212 , Node0221-leaf , Node0222-leaf , Node0311 , Node0312-leaf , Node0321-leaf , Node0322 , Node0323 , Node0411 , Node0412 , Node0413-leaf , Node0421-leaf , Node0422-leaf , Node0423-leaf , Node0431-leaf , Node0432-leaf , Node0433-leaf , Node0441-leaf , Node0442 , Node0443-leaf , Node0511 , Node0512-leaf , Node0513-leaf , Node0521-leaf , Node0522-leaf , Node0523-leaf , Node0524-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 30 columns.
#> Top rows (1000) are extracted by 'ATC' method.
#> Subgroups are detected by 'kmeans' method.
#> Performed in total 350 partitions by row resampling.
#> Best k for subgroups seems to be 3.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_partitions"
#> [7] "compare_signatures" "consensus_heatmap" "dimension_reduction"
#> [10] "functional_enrichment" "get_anno_col" "get_anno"
#> [13] "get_classes" "get_consensus" "get_matrix"
#> [16] "get_membership" "get_param" "get_signatures"
#> [19] "get_stats" "is_best_k" "is_stable_k"
#> [22] "membership_heatmap" "ncol" "nrow"
#> [25] "plot_ecdf" "predict_classes" "rownames"
#> [28] "select_partition_number" "show" "suggest_best_k"
#> [31] "test_to_known_factors" "top_rows_heatmap"
collect_plots() function collects all the plots made from res for all k (number of subgroups)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
The plots are:
k and the heatmap of
predicted classes for each k.k.k.k.All the plots in panels can be made by individual functions and they are plotted later in this section.
select_partition_number() produces several plots showing different
statistics for choosing “optimized” k. There are following statistics:
k;k, the area increased is defined as \(A_k - A_{k-1}\).The detailed explanations of these statistics can be found in the cola vignette.
Generally speaking, higher 1-PAC score, higher mean silhouette score or higher
concordance corresponds to better partition. Rand index and Jaccard index
measure how similar the current partition is compared to partition with k-1.
If they are too similar, we won't accept k is better than k-1.
select_partition_number(res)
The numeric values for all these statistics can be obtained by get_stats().
get_stats(res)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> 2 2 0.814 0.930 0.964 0.4356 0.540 0.540
#> 3 3 1.000 0.972 0.989 0.5469 0.676 0.456
#> 4 4 0.783 0.695 0.864 0.1035 0.929 0.785
#> 5 5 0.780 0.686 0.807 0.0666 0.834 0.459
#> 6 6 0.754 0.645 0.829 0.0382 0.968 0.831
#> 7 7 0.786 0.516 0.757 0.0265 0.959 0.763
#> 8 8 0.817 0.589 0.813 0.0216 0.938 0.625
suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:
suggest_best_k(res)
#> [1] 3
Following is the table of the partitions (You need to click the show/hide
code output link to see it). The membership matrix (columns with name p*)
is inferred by
clue::cl_consensus()
function with the SE method. Basically the value in the membership matrix
represents the probability to belong to a certain group. The finall subgroup
label for an item is determined with the group with highest probability it
belongs to.
In get_classes() function, the entropy is calculated from the membership
matrix and the silhouette score is calculated from the consensus matrix.
cbind(get_classes(res, k = 2), get_membership(res, k = 2))
#> class entropy silhouette p1 p2
#> TCGA.FS.A4FC.06 1 0.000 0.989 1.00 0.00
#> TCGA.BF.A5EQ.01 1 0.000 0.989 1.00 0.00
#> TCGA.RP.A6K9.06 1 0.000 0.989 1.00 0.00
#> TCGA.D9.A149.06 1 0.000 0.989 1.00 0.00
#> TCGA.EB.A85I.01 1 0.000 0.989 1.00 0.00
#> TCGA.EB.A82B.01 1 0.141 0.977 0.98 0.02
#> TCGA.D3.A2J6.06 2 0.881 0.658 0.30 0.70
#> TCGA.D3.A3CC.06 1 0.242 0.962 0.96 0.04
#> TCGA.FS.A1ZS.06 1 0.242 0.962 0.96 0.04
#> TCGA.GN.A26D.06 2 0.000 0.893 0.00 1.00
#> TCGA.ER.A193.06 1 0.000 0.989 1.00 0.00
#> TCGA.BF.A1Q0.01 1 0.000 0.989 1.00 0.00
#> TCGA.D9.A1JW.06 1 0.000 0.989 1.00 0.00
#> TCGA.EE.A2GU.06 1 0.000 0.989 1.00 0.00
#> TCGA.FS.A1Z7.06 2 0.881 0.658 0.30 0.70
#> TCGA.EB.A3Y7.01 1 0.242 0.962 0.96 0.04
#> TCGA.BF.AAP8.01 2 0.000 0.893 0.00 1.00
#> TCGA.EE.A2MT.06 2 0.000 0.893 0.00 1.00
#> TCGA.ER.A2NB.01 1 0.000 0.989 1.00 0.00
#> TCGA.D3.A1Q5.06 2 0.000 0.893 0.00 1.00
#> TCGA.EE.A2A6.06 1 0.000 0.989 1.00 0.00
#> TCGA.D3.A1Q1.06 2 0.000 0.893 0.00 1.00
#> TCGA.ER.A3ES.06 2 0.000 0.893 0.00 1.00
#> TCGA.3N.A9WC.06 1 0.000 0.989 1.00 0.00
#> TCGA.DA.A3F5.06 1 0.000 0.989 1.00 0.00
#> TCGA.EB.A4IQ.01 1 0.000 0.989 1.00 0.00
#> TCGA.XV.A9W2.01 2 0.881 0.658 0.30 0.70
#> TCGA.FS.A4FD.06 2 0.000 0.893 0.00 1.00
#> TCGA.WE.AAA3.06 1 0.242 0.962 0.96 0.04
#> TCGA.ER.A3ET.06 1 0.000 0.989 1.00 0.00
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.FS.A4FC.06 1 0.000 0.968 1.00 0 0.00
#> TCGA.BF.A5EQ.01 1 0.000 0.968 1.00 0 0.00
#> TCGA.RP.A6K9.06 3 0.000 1.000 0.00 0 1.00
#> TCGA.D9.A149.06 1 0.000 0.968 1.00 0 0.00
#> TCGA.EB.A85I.01 1 0.571 0.529 0.68 0 0.32
#> TCGA.EB.A82B.01 3 0.000 1.000 0.00 0 1.00
#> TCGA.D3.A2J6.06 3 0.000 1.000 0.00 0 1.00
#> TCGA.D3.A3CC.06 3 0.000 1.000 0.00 0 1.00
#> TCGA.FS.A1ZS.06 3 0.000 1.000 0.00 0 1.00
#> TCGA.GN.A26D.06 2 0.000 1.000 0.00 1 0.00
#> TCGA.ER.A193.06 1 0.000 0.968 1.00 0 0.00
#> TCGA.BF.A1Q0.01 1 0.000 0.968 1.00 0 0.00
#> TCGA.D9.A1JW.06 1 0.000 0.968 1.00 0 0.00
#> TCGA.EE.A2GU.06 1 0.000 0.968 1.00 0 0.00
#> TCGA.FS.A1Z7.06 3 0.000 1.000 0.00 0 1.00
#> TCGA.EB.A3Y7.01 3 0.000 1.000 0.00 0 1.00
#> TCGA.BF.AAP8.01 2 0.000 1.000 0.00 1 0.00
#> TCGA.EE.A2MT.06 2 0.000 1.000 0.00 1 0.00
#> TCGA.ER.A2NB.01 1 0.000 0.968 1.00 0 0.00
#> TCGA.D3.A1Q5.06 2 0.000 1.000 0.00 1 0.00
#> TCGA.EE.A2A6.06 1 0.000 0.968 1.00 0 0.00
#> TCGA.D3.A1Q1.06 2 0.000 1.000 0.00 1 0.00
#> TCGA.ER.A3ES.06 2 0.000 1.000 0.00 1 0.00
#> TCGA.3N.A9WC.06 1 0.000 0.968 1.00 0 0.00
#> TCGA.DA.A3F5.06 3 0.000 1.000 0.00 0 1.00
#> TCGA.EB.A4IQ.01 1 0.000 0.968 1.00 0 0.00
#> TCGA.XV.A9W2.01 3 0.000 1.000 0.00 0 1.00
#> TCGA.FS.A4FD.06 2 0.000 1.000 0.00 1 0.00
#> TCGA.WE.AAA3.06 3 0.000 1.000 0.00 0 1.00
#> TCGA.ER.A3ET.06 3 0.000 1.000 0.00 0 1.00
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> TCGA.FS.A4FC.06 1 0.0000 0.8818 1.00 0.00 0.00 0.00
#> TCGA.BF.A5EQ.01 1 0.0000 0.8818 1.00 0.00 0.00 0.00
#> TCGA.RP.A6K9.06 3 0.4134 0.3668 0.00 0.00 0.74 0.26
#> TCGA.D9.A149.06 1 0.0707 0.8787 0.98 0.00 0.00 0.02
#> TCGA.EB.A85I.01 4 0.6074 0.0855 0.34 0.00 0.06 0.60
#> TCGA.EB.A82B.01 3 0.4907 0.2856 0.00 0.00 0.58 0.42
#> TCGA.D3.A2J6.06 3 0.4134 0.5738 0.00 0.00 0.74 0.26
#> TCGA.D3.A3CC.06 3 0.0000 0.7330 0.00 0.00 1.00 0.00
#> TCGA.FS.A1ZS.06 4 0.4790 -0.1585 0.00 0.00 0.38 0.62
#> TCGA.GN.A26D.06 2 0.0000 0.9330 0.00 1.00 0.00 0.00
#> TCGA.ER.A193.06 1 0.3975 0.7735 0.76 0.00 0.00 0.24
#> TCGA.BF.A1Q0.01 1 0.0000 0.8818 1.00 0.00 0.00 0.00
#> TCGA.D9.A1JW.06 1 0.3975 0.7735 0.76 0.00 0.00 0.24
#> TCGA.EE.A2GU.06 1 0.0000 0.8818 1.00 0.00 0.00 0.00
#> TCGA.FS.A1Z7.06 3 0.0707 0.7316 0.00 0.00 0.98 0.02
#> TCGA.EB.A3Y7.01 3 0.4977 0.2200 0.00 0.00 0.54 0.46
#> TCGA.BF.AAP8.01 2 0.2921 0.9062 0.00 0.86 0.00 0.14
#> TCGA.EE.A2MT.06 2 0.3801 0.8520 0.00 0.78 0.00 0.22
#> TCGA.ER.A2NB.01 1 0.0000 0.8818 1.00 0.00 0.00 0.00
#> TCGA.D3.A1Q5.06 2 0.0000 0.9330 0.00 1.00 0.00 0.00
#> TCGA.EE.A2A6.06 1 0.0707 0.8787 0.98 0.00 0.00 0.02
#> TCGA.D3.A1Q1.06 2 0.0000 0.9330 0.00 1.00 0.00 0.00
#> TCGA.ER.A3ES.06 2 0.2921 0.9062 0.00 0.86 0.00 0.14
#> TCGA.3N.A9WC.06 1 0.3801 0.7786 0.78 0.00 0.00 0.22
#> TCGA.DA.A3F5.06 4 0.4713 0.1839 0.00 0.00 0.36 0.64
#> TCGA.EB.A4IQ.01 1 0.4642 0.7512 0.74 0.00 0.02 0.24
#> TCGA.XV.A9W2.01 3 0.1637 0.7191 0.00 0.00 0.94 0.06
#> TCGA.FS.A4FD.06 2 0.0000 0.9330 0.00 1.00 0.00 0.00
#> TCGA.WE.AAA3.06 3 0.0000 0.7330 0.00 0.00 1.00 0.00
#> TCGA.ER.A3ET.06 3 0.0000 0.7330 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.FS.A4FC.06 1 0.000 1.000 1.00 0.00 0.00 0.00 0.00
#> TCGA.BF.A5EQ.01 1 0.000 1.000 1.00 0.00 0.00 0.00 0.00
#> TCGA.RP.A6K9.06 4 0.567 -0.131 0.00 0.00 0.42 0.50 0.08
#> TCGA.D9.A149.06 1 0.000 1.000 1.00 0.00 0.00 0.00 0.00
#> TCGA.EB.A85I.01 4 0.311 0.425 0.06 0.00 0.08 0.86 0.00
#> TCGA.EB.A82B.01 3 0.543 0.482 0.00 0.00 0.60 0.32 0.08
#> TCGA.D3.A2J6.06 3 0.000 0.257 0.00 0.00 1.00 0.00 0.00
#> TCGA.D3.A3CC.06 5 0.517 0.973 0.00 0.00 0.46 0.04 0.50
#> TCGA.FS.A1ZS.06 3 0.667 0.385 0.00 0.00 0.44 0.28 0.28
#> TCGA.GN.A26D.06 2 0.000 0.915 0.00 1.00 0.00 0.00 0.00
#> TCGA.ER.A193.06 4 0.430 0.468 0.48 0.00 0.00 0.52 0.00
#> TCGA.BF.A1Q0.01 1 0.000 1.000 1.00 0.00 0.00 0.00 0.00
#> TCGA.D9.A1JW.06 4 0.430 0.468 0.48 0.00 0.00 0.52 0.00
#> TCGA.EE.A2GU.06 1 0.000 1.000 1.00 0.00 0.00 0.00 0.00
#> TCGA.FS.A1Z7.06 5 0.431 0.915 0.00 0.00 0.50 0.00 0.50
#> TCGA.EB.A3Y7.01 3 0.380 0.521 0.00 0.00 0.70 0.30 0.00
#> TCGA.BF.AAP8.01 2 0.228 0.888 0.00 0.88 0.00 0.00 0.12
#> TCGA.EE.A2MT.06 2 0.573 0.659 0.00 0.62 0.16 0.00 0.22
#> TCGA.ER.A2NB.01 1 0.000 1.000 1.00 0.00 0.00 0.00 0.00
#> TCGA.D3.A1Q5.06 2 0.000 0.915 0.00 1.00 0.00 0.00 0.00
#> TCGA.EE.A2A6.06 1 0.000 1.000 1.00 0.00 0.00 0.00 0.00
#> TCGA.D3.A1Q1.06 2 0.000 0.915 0.00 1.00 0.00 0.00 0.00
#> TCGA.ER.A3ES.06 2 0.228 0.888 0.00 0.88 0.00 0.00 0.12
#> TCGA.3N.A9WC.06 4 0.430 0.468 0.48 0.00 0.00 0.52 0.00
#> TCGA.DA.A3F5.06 4 0.173 0.360 0.00 0.00 0.00 0.92 0.08
#> TCGA.EB.A4IQ.01 4 0.389 0.577 0.32 0.00 0.00 0.68 0.00
#> TCGA.XV.A9W2.01 3 0.398 -0.638 0.00 0.00 0.66 0.00 0.34
#> TCGA.FS.A4FD.06 2 0.000 0.915 0.00 1.00 0.00 0.00 0.00
#> TCGA.WE.AAA3.06 5 0.517 0.973 0.00 0.00 0.46 0.04 0.50
#> TCGA.ER.A3ET.06 5 0.517 0.973 0.00 0.00 0.46 0.04 0.50
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> TCGA.FS.A4FC.06 1 0.0000 0.976 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BF.A5EQ.01 1 0.0000 0.976 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.RP.A6K9.06 4 0.5832 0.242 0.00 0.00 0.10 0.56 0.30 0.04
#> TCGA.D9.A149.06 1 0.0547 0.964 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.EB.A85I.01 4 0.3819 0.482 0.00 0.00 0.28 0.70 0.00 0.02
#> TCGA.EB.A82B.01 3 0.3321 0.648 0.00 0.00 0.82 0.08 0.10 0.00
#> TCGA.D3.A2J6.06 3 0.4576 0.206 0.00 0.00 0.56 0.00 0.40 0.04
#> TCGA.D3.A3CC.06 5 0.0000 0.800 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.FS.A1ZS.06 3 0.4938 0.338 0.00 0.00 0.58 0.08 0.00 0.34
#> TCGA.GN.A26D.06 2 0.0000 0.758 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.ER.A193.06 4 0.4348 0.635 0.32 0.00 0.00 0.64 0.00 0.04
#> TCGA.BF.A1Q0.01 1 0.2094 0.867 0.90 0.00 0.00 0.08 0.00 0.02
#> TCGA.D9.A1JW.06 4 0.3499 0.638 0.32 0.00 0.00 0.68 0.00 0.00
#> TCGA.EE.A2GU.06 1 0.0000 0.976 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FS.A1Z7.06 5 0.0547 0.792 0.00 0.00 0.02 0.00 0.98 0.00
#> TCGA.EB.A3Y7.01 3 0.3073 0.651 0.00 0.00 0.84 0.08 0.08 0.00
#> TCGA.BF.AAP8.01 2 0.4613 0.231 0.00 0.66 0.00 0.08 0.00 0.26
#> TCGA.EE.A2MT.06 6 0.4993 0.000 0.00 0.36 0.08 0.00 0.00 0.56
#> TCGA.ER.A2NB.01 1 0.0000 0.976 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D3.A1Q5.06 2 0.0000 0.758 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.EE.A2A6.06 1 0.0000 0.976 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D3.A1Q1.06 2 0.0000 0.758 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.ER.A3ES.06 2 0.4613 0.231 0.00 0.66 0.00 0.08 0.00 0.26
#> TCGA.3N.A9WC.06 4 0.4348 0.635 0.32 0.00 0.00 0.64 0.00 0.04
#> TCGA.DA.A3F5.06 4 0.3324 0.561 0.00 0.00 0.08 0.84 0.02 0.06
#> TCGA.EB.A4IQ.01 4 0.3688 0.670 0.14 0.00 0.04 0.80 0.00 0.02
#> TCGA.XV.A9W2.01 5 0.3578 0.276 0.00 0.00 0.34 0.00 0.66 0.00
#> TCGA.FS.A4FD.06 2 0.0000 0.758 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.WE.AAA3.06 5 0.2474 0.786 0.00 0.00 0.00 0.08 0.88 0.04
#> TCGA.ER.A3ET.06 5 0.2474 0.786 0.00 0.00 0.00 0.08 0.88 0.04
cbind(get_classes(res, k = 7), get_membership(res, k = 7))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7
#> TCGA.FS.A4FC.06 1 0.0863 0.8816 0.96 0.00 0.00 0.00 0.00 0.00 0.04
#> TCGA.BF.A5EQ.01 1 0.0000 0.9029 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.RP.A6K9.06 4 0.4787 0.2436 0.00 0.00 0.12 0.58 0.30 0.00 0.00
#> TCGA.D9.A149.06 1 0.1664 0.8570 0.92 0.00 0.00 0.02 0.00 0.00 0.06
#> TCGA.EB.A85I.01 4 0.4356 0.2869 0.00 0.00 0.40 0.56 0.02 0.00 0.02
#> TCGA.EB.A82B.01 3 0.1433 0.7400 0.00 0.00 0.92 0.00 0.08 0.00 0.00
#> TCGA.D3.A2J6.06 3 0.4778 0.3606 0.00 0.00 0.58 0.02 0.34 0.06 0.00
#> TCGA.D3.A3CC.06 5 0.0504 0.7740 0.00 0.00 0.00 0.02 0.98 0.00 0.00
#> TCGA.FS.A1ZS.06 7 0.7086 -0.3036 0.00 0.00 0.20 0.26 0.00 0.26 0.28
#> TCGA.GN.A26D.06 2 0.0000 0.8348 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.ER.A193.06 7 0.5007 0.1752 0.16 0.00 0.00 0.28 0.00 0.00 0.56
#> TCGA.BF.A1Q0.01 1 0.3413 0.3303 0.62 0.00 0.00 0.00 0.00 0.00 0.38
#> TCGA.D9.A1JW.06 4 0.5247 -0.2296 0.16 0.00 0.00 0.44 0.00 0.00 0.40
#> TCGA.EE.A2GU.06 1 0.0000 0.9029 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FS.A1Z7.06 5 0.0504 0.7676 0.00 0.00 0.02 0.00 0.98 0.00 0.00
#> TCGA.EB.A3Y7.01 3 0.0863 0.7308 0.00 0.00 0.96 0.00 0.04 0.00 0.00
#> TCGA.BF.AAP8.01 2 0.4667 0.5926 0.00 0.70 0.00 0.04 0.00 0.14 0.12
#> TCGA.EE.A2MT.06 6 0.3186 0.0000 0.00 0.22 0.02 0.00 0.00 0.76 0.00
#> TCGA.ER.A2NB.01 1 0.0000 0.9029 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D3.A1Q5.06 2 0.0000 0.8348 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EE.A2A6.06 1 0.0000 0.9029 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D3.A1Q1.06 2 0.0000 0.8348 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.ER.A3ES.06 2 0.4667 0.5926 0.00 0.70 0.00 0.04 0.00 0.14 0.12
#> TCGA.3N.A9WC.06 7 0.5128 0.1511 0.16 0.00 0.00 0.32 0.00 0.00 0.52
#> TCGA.DA.A3F5.06 7 0.3867 -0.0191 0.00 0.00 0.00 0.38 0.02 0.00 0.60
#> TCGA.EB.A4IQ.01 4 0.5026 0.1458 0.06 0.00 0.02 0.62 0.02 0.00 0.28
#> TCGA.XV.A9W2.01 5 0.3496 -0.0820 0.00 0.00 0.42 0.00 0.58 0.00 0.00
#> TCGA.FS.A4FD.06 2 0.0000 0.8348 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.WE.AAA3.06 5 0.1928 0.7731 0.00 0.00 0.00 0.08 0.90 0.00 0.02
#> TCGA.ER.A3ET.06 5 0.1928 0.7731 0.00 0.00 0.00 0.08 0.90 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.FS.A4FC.06 1 0.0000 0.9122 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BF.A5EQ.01 1 0.0000 0.9122 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.RP.A6K9.06 4 0.7120 -0.3146 0.00 0.00 0.08 0.40 0.14 0.02 0.28 0.08
#> TCGA.D9.A149.06 1 0.1408 0.8868 0.94 0.00 0.00 0.02 0.00 0.00 0.02 0.02
#> TCGA.EB.A85I.01 3 0.6199 -0.0334 0.00 0.00 0.40 0.18 0.00 0.02 0.34 0.06
#> TCGA.EB.A82B.01 3 0.2204 0.4156 0.00 0.00 0.90 0.02 0.02 0.00 0.04 0.02
#> TCGA.D3.A2J6.06 3 0.5131 0.1182 0.00 0.00 0.50 0.14 0.34 0.02 0.00 0.00
#> TCGA.D3.A3CC.06 5 0.1408 0.7152 0.00 0.00 0.00 0.02 0.94 0.02 0.00 0.02
#> TCGA.FS.A1ZS.06 8 0.2404 0.0000 0.00 0.00 0.14 0.00 0.00 0.00 0.02 0.84
#> TCGA.GN.A26D.06 2 0.0000 0.9850 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.ER.A193.06 7 0.1765 0.8134 0.12 0.00 0.00 0.00 0.00 0.00 0.88 0.00
#> TCGA.BF.A1Q0.01 1 0.3083 0.4010 0.66 0.00 0.00 0.00 0.00 0.00 0.34 0.00
#> TCGA.D9.A1JW.06 7 0.4763 0.7743 0.10 0.00 0.00 0.10 0.00 0.02 0.70 0.08
#> TCGA.EE.A2GU.06 1 0.0000 0.9122 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FS.A1Z7.06 5 0.0471 0.7222 0.00 0.00 0.00 0.02 0.98 0.00 0.00 0.00
#> TCGA.EB.A3Y7.01 3 0.1557 0.4282 0.00 0.00 0.92 0.06 0.00 0.00 0.02 0.00
#> TCGA.BF.AAP8.01 4 0.4554 0.2145 0.00 0.42 0.00 0.48 0.00 0.10 0.00 0.00
#> TCGA.EE.A2MT.06 6 0.0808 0.0000 0.00 0.00 0.04 0.00 0.00 0.96 0.00 0.00
#> TCGA.ER.A2NB.01 1 0.0000 0.9122 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D3.A1Q5.06 2 0.0941 0.9543 0.00 0.96 0.02 0.00 0.00 0.00 0.00 0.02
#> TCGA.EE.A2A6.06 1 0.0941 0.8973 0.96 0.00 0.00 0.00 0.00 0.00 0.02 0.02
#> TCGA.D3.A1Q1.06 2 0.0000 0.9850 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.ER.A3ES.06 4 0.4554 0.2145 0.00 0.42 0.00 0.48 0.00 0.10 0.00 0.00
#> TCGA.3N.A9WC.06 7 0.2350 0.8100 0.10 0.00 0.00 0.04 0.00 0.00 0.86 0.00
#> TCGA.DA.A3F5.06 7 0.0808 0.7630 0.00 0.00 0.00 0.04 0.00 0.00 0.96 0.00
#> TCGA.EB.A4IQ.01 7 0.4034 0.7383 0.04 0.00 0.00 0.12 0.00 0.02 0.76 0.06
#> TCGA.XV.A9W2.01 5 0.4105 0.1068 0.00 0.00 0.42 0.02 0.54 0.00 0.00 0.02
#> TCGA.FS.A4FD.06 2 0.0000 0.9850 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.WE.AAA3.06 5 0.3178 0.7147 0.00 0.00 0.00 0.14 0.80 0.00 0.04 0.02
#> TCGA.ER.A3ET.06 5 0.3178 0.7147 0.00 0.00 0.00 0.14 0.80 0.00 0.04 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-leaf , Node0113 , Node0121-leaf , Node0122-leaf , Node0123-leaf , Node0124-leaf , Node0125-leaf , Node0131 , Node0132-leaf , Node0133-leaf , Node0211-leaf , Node0212 , Node0221-leaf , Node0222-leaf , Node0311 , Node0312-leaf , Node0321-leaf , Node0322 , Node0323 , Node0411 , Node0412 , Node0413-leaf , Node0421-leaf , Node0422-leaf , Node0423-leaf , Node0431-leaf , Node0432-leaf , Node0433-leaf , Node0441-leaf , Node0442 , Node0443-leaf , Node0511 , Node0512-leaf , Node0513-leaf , Node0521-leaf , Node0522-leaf , Node0523-leaf , Node0524-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 'SD' method.
#> Subgroups are detected by 'kmeans' method.
#> Performed in total 350 partitions by row resampling.
#> Best k for subgroups seems to be 3.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_partitions"
#> [7] "compare_signatures" "consensus_heatmap" "dimension_reduction"
#> [10] "functional_enrichment" "get_anno_col" "get_anno"
#> [13] "get_classes" "get_consensus" "get_matrix"
#> [16] "get_membership" "get_param" "get_signatures"
#> [19] "get_stats" "is_best_k" "is_stable_k"
#> [22] "membership_heatmap" "ncol" "nrow"
#> [25] "plot_ecdf" "predict_classes" "rownames"
#> [28] "select_partition_number" "show" "suggest_best_k"
#> [31] "test_to_known_factors" "top_rows_heatmap"
collect_plots() function collects all the plots made from res for all k (number of subgroups)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
The plots are:
k and the heatmap of
predicted classes for each k.k.k.k.All the plots in panels can be made by individual functions and they are plotted later in this section.
select_partition_number() produces several plots showing different
statistics for choosing “optimized” k. There are following statistics:
k;k, the area increased is defined as \(A_k - A_{k-1}\).The detailed explanations of these statistics can be found in the cola vignette.
Generally speaking, higher 1-PAC score, higher mean silhouette score or higher
concordance corresponds to better partition. Rand index and Jaccard index
measure how similar the current partition is compared to partition with k-1.
If they are too similar, we won't accept k is better than k-1.
select_partition_number(res)
The numeric values for all these statistics can be obtained by get_stats().
get_stats(res)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> 2 2 1.000 1.000 1.000 0.5152 0.485 0.485
#> 3 3 1.000 0.977 0.981 0.2572 0.603 0.357
#> 4 4 0.676 0.455 0.753 0.1789 0.897 0.708
#> 5 5 0.757 0.768 0.896 0.0718 0.904 0.639
#> 6 6 0.809 0.643 0.846 0.0321 0.985 0.920
#> 7 7 0.816 0.585 0.818 0.0313 0.875 0.433
#> 8 8 0.809 0.661 0.875 0.0239 0.956 0.700
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.WE.A8ZR.06 2 0 1 0 1
#> TCGA.EB.A85J.01 2 0 1 0 1
#> TCGA.ER.A19L.06 2 0 1 0 1
#> TCGA.ER.A19T.06 1 0 1 1 0
#> TCGA.D3.A1Q3.06 1 0 1 1 0
#> TCGA.GN.A267.06 2 0 1 0 1
#> TCGA.EB.A24C.01 2 0 1 0 1
#> TCGA.EE.A2MS.06 2 0 1 0 1
#> TCGA.EE.A182.06 2 0 1 0 1
#> TCGA.EE.A2GJ.06 1 0 1 1 0
#> TCGA.EB.A5SH.06 1 0 1 1 0
#> TCGA.EB.A3XE.01 2 0 1 0 1
#> TCGA.FW.A3R5.06 1 0 1 1 0
#> TCGA.EB.A5UM.01 1 0 1 1 0
#> TCGA.EE.A29T.06 1 0 1 1 0
#> TCGA.EB.A44R.06 2 0 1 0 1
#> TCGA.ER.A3EV.06 2 0 1 0 1
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.WE.A8ZR.06 2 0.0892 0.965 0.00 0.98 0.02
#> TCGA.EB.A85J.01 3 0.1529 0.985 0.00 0.04 0.96
#> TCGA.ER.A19L.06 2 0.1529 0.962 0.00 0.96 0.04
#> TCGA.ER.A19T.06 1 0.0000 1.000 1.00 0.00 0.00
#> TCGA.D3.A1Q3.06 1 0.0000 1.000 1.00 0.00 0.00
#> TCGA.GN.A267.06 2 0.0892 0.965 0.00 0.98 0.02
#> TCGA.EB.A24C.01 2 0.0000 0.973 0.00 1.00 0.00
#> TCGA.EE.A2MS.06 3 0.0000 0.955 0.00 0.00 1.00
#> TCGA.EE.A182.06 2 0.0000 0.973 0.00 1.00 0.00
#> TCGA.EE.A2GJ.06 1 0.0000 1.000 1.00 0.00 0.00
#> TCGA.EB.A5SH.06 1 0.0000 1.000 1.00 0.00 0.00
#> TCGA.EB.A3XE.01 2 0.0000 0.973 0.00 1.00 0.00
#> TCGA.FW.A3R5.06 2 0.1529 0.965 0.04 0.96 0.00
#> TCGA.EB.A5UM.01 2 0.1529 0.965 0.04 0.96 0.00
#> TCGA.EE.A29T.06 2 0.1529 0.965 0.04 0.96 0.00
#> TCGA.EB.A44R.06 3 0.1529 0.985 0.00 0.04 0.96
#> TCGA.ER.A3EV.06 3 0.1529 0.985 0.00 0.04 0.96
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> TCGA.WE.A8ZR.06 2 0.7497 0.0629 0.00 0.50 0.26 0.24
#> TCGA.EB.A85J.01 3 0.3037 0.7351 0.00 0.02 0.88 0.10
#> TCGA.ER.A19L.06 4 0.4948 -0.1138 0.00 0.44 0.00 0.56
#> TCGA.ER.A19T.06 1 0.0000 0.9728 1.00 0.00 0.00 0.00
#> TCGA.D3.A1Q3.06 1 0.1211 0.9726 0.96 0.04 0.00 0.00
#> TCGA.GN.A267.06 2 0.7249 0.0482 0.00 0.54 0.26 0.20
#> TCGA.EB.A24C.01 4 0.6554 -0.5913 0.00 0.40 0.08 0.52
#> TCGA.EE.A2MS.06 3 0.4406 0.6061 0.00 0.00 0.70 0.30
#> TCGA.EE.A182.06 2 0.4994 0.3209 0.00 0.52 0.00 0.48
#> TCGA.EE.A2GJ.06 1 0.1211 0.9726 0.96 0.04 0.00 0.00
#> TCGA.EB.A5SH.06 1 0.0000 0.9728 1.00 0.00 0.00 0.00
#> TCGA.EB.A3XE.01 2 0.4948 0.3397 0.00 0.56 0.00 0.44
#> TCGA.FW.A3R5.06 2 0.4948 0.3419 0.00 0.56 0.00 0.44
#> TCGA.EB.A5UM.01 2 0.4936 0.2968 0.02 0.70 0.00 0.28
#> TCGA.EE.A29T.06 2 0.0707 0.1323 0.02 0.98 0.00 0.00
#> TCGA.EB.A44R.06 3 0.0000 0.8332 0.00 0.00 1.00 0.00
#> TCGA.ER.A3EV.06 3 0.0000 0.8332 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.WE.A8ZR.06 5 0.165 0.881 0.00 0.00 0.02 0.04 0.94
#> TCGA.EB.A85J.01 3 0.141 0.848 0.00 0.00 0.94 0.00 0.06
#> TCGA.ER.A19L.06 4 0.173 0.000 0.00 0.00 0.00 0.92 0.08
#> TCGA.ER.A19T.06 1 0.000 0.832 1.00 0.00 0.00 0.00 0.00
#> TCGA.D3.A1Q3.06 1 0.387 0.831 0.80 0.14 0.00 0.06 0.00
#> TCGA.GN.A267.06 5 0.165 0.881 0.00 0.00 0.02 0.04 0.94
#> TCGA.EB.A24C.01 5 0.228 0.766 0.00 0.12 0.00 0.00 0.88
#> TCGA.EE.A2MS.06 3 0.385 0.691 0.00 0.02 0.76 0.22 0.00
#> TCGA.EE.A182.06 2 0.293 0.765 0.00 0.82 0.00 0.00 0.18
#> TCGA.EE.A2GJ.06 1 0.407 0.818 0.78 0.16 0.00 0.06 0.00
#> TCGA.EB.A5SH.06 1 0.000 0.832 1.00 0.00 0.00 0.00 0.00
#> TCGA.EB.A3XE.01 2 0.392 0.779 0.00 0.78 0.00 0.04 0.18
#> TCGA.FW.A3R5.06 2 0.104 0.814 0.00 0.96 0.00 0.00 0.04
#> TCGA.EB.A5UM.01 2 0.262 0.785 0.02 0.88 0.00 0.10 0.00
#> TCGA.EE.A29T.06 2 0.346 0.764 0.02 0.84 0.00 0.12 0.02
#> TCGA.EB.A44R.06 3 0.000 0.886 0.00 0.00 1.00 0.00 0.00
#> TCGA.ER.A3EV.06 3 0.000 0.886 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.WE.A8ZR.06 5 0.0000 1.000 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.EB.A85J.01 3 0.1807 0.842 0.00 0.02 0.92 0.00 0.00 0.06
#> TCGA.ER.A19L.06 4 0.0547 0.000 0.00 0.00 0.00 0.98 0.02 0.00
#> TCGA.ER.A19T.06 1 0.4078 0.677 0.64 0.00 0.00 0.02 0.00 0.34
#> TCGA.D3.A1Q3.06 1 0.0547 0.681 0.98 0.02 0.00 0.00 0.00 0.00
#> TCGA.GN.A267.06 5 0.0000 1.000 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.EB.A24C.01 6 0.5987 0.000 0.00 0.30 0.00 0.00 0.26 0.44
#> TCGA.EE.A2MS.06 3 0.4536 0.618 0.00 0.00 0.70 0.12 0.00 0.18
#> TCGA.EE.A182.06 2 0.2350 0.572 0.00 0.88 0.00 0.00 0.02 0.10
#> TCGA.EE.A2GJ.06 1 0.1807 0.643 0.92 0.06 0.00 0.00 0.00 0.02
#> TCGA.EB.A5SH.06 1 0.3647 0.677 0.64 0.00 0.00 0.00 0.00 0.36
#> TCGA.EB.A3XE.01 2 0.2094 0.588 0.00 0.90 0.00 0.00 0.02 0.08
#> TCGA.FW.A3R5.06 2 0.1480 0.655 0.04 0.94 0.00 0.00 0.00 0.02
#> TCGA.EB.A5UM.01 2 0.3819 0.629 0.28 0.70 0.00 0.00 0.00 0.02
#> TCGA.EE.A29T.06 2 0.3819 0.629 0.28 0.70 0.00 0.00 0.00 0.02
#> TCGA.EB.A44R.06 3 0.0937 0.860 0.00 0.00 0.96 0.00 0.00 0.04
#> TCGA.ER.A3EV.06 3 0.0000 0.857 0.00 0.00 1.00 0.00 0.00 0.00
cbind(get_classes(res, k = 7), get_membership(res, k = 7))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7
#> TCGA.WE.A8ZR.06 5 0.0504 0.8598 0.00 0.00 0.00 0.00 0.98 0.02 0.00
#> TCGA.EB.A85J.01 3 0.1433 0.7817 0.00 0.00 0.92 0.00 0.00 0.08 0.00
#> TCGA.ER.A19L.06 4 0.0000 0.0000 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.ER.A19T.06 1 0.0000 0.9680 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D3.A1Q3.06 2 0.5534 0.2601 0.36 0.40 0.00 0.00 0.00 0.00 0.24
#> TCGA.GN.A267.06 5 0.2569 0.8598 0.00 0.02 0.00 0.00 0.84 0.00 0.14
#> TCGA.EB.A24C.01 6 0.3606 0.0941 0.00 0.00 0.00 0.00 0.02 0.68 0.30
#> TCGA.EE.A2MS.06 3 0.4998 0.3677 0.00 0.00 0.54 0.14 0.00 0.00 0.32
#> TCGA.EE.A182.06 6 0.3294 0.6650 0.00 0.34 0.00 0.00 0.00 0.66 0.00
#> TCGA.EE.A2GJ.06 2 0.5268 0.4247 0.24 0.52 0.00 0.00 0.00 0.00 0.24
#> TCGA.EB.A5SH.06 1 0.1006 0.9680 0.96 0.00 0.00 0.00 0.02 0.02 0.00
#> TCGA.EB.A3XE.01 6 0.3413 0.6522 0.00 0.38 0.00 0.00 0.00 0.62 0.00
#> TCGA.FW.A3R5.06 6 0.3558 0.5583 0.00 0.48 0.00 0.00 0.00 0.52 0.00
#> TCGA.EB.A5UM.01 2 0.0000 0.4341 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EE.A29T.06 2 0.0000 0.4341 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EB.A44R.06 3 0.0504 0.8092 0.00 0.00 0.98 0.00 0.00 0.02 0.00
#> TCGA.ER.A3EV.06 3 0.0000 0.8082 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.WE.A8ZR.06 5 0.0000 0.807 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.EB.A85J.01 3 0.2071 0.853 0.02 0.00 0.90 0.00 0.00 0.00 0.04 0.04
#> TCGA.ER.A19L.06 4 0.0000 0.000 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.ER.A19T.06 1 0.1341 0.950 0.92 0.08 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D3.A1Q3.06 2 0.1341 0.634 0.08 0.92 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.GN.A267.06 5 0.3663 0.807 0.06 0.00 0.00 0.00 0.78 0.00 0.06 0.10
#> TCGA.EB.A24C.01 7 0.2114 0.000 0.00 0.00 0.00 0.00 0.00 0.16 0.84 0.00
#> TCGA.EE.A2MS.06 8 0.3594 0.000 0.00 0.00 0.28 0.04 0.00 0.00 0.00 0.68
#> TCGA.EE.A182.06 6 0.0471 0.857 0.00 0.00 0.00 0.00 0.00 0.98 0.02 0.00
#> TCGA.EE.A2GJ.06 2 0.0808 0.663 0.04 0.96 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EB.A5SH.06 1 0.2407 0.950 0.86 0.08 0.00 0.00 0.00 0.00 0.00 0.06
#> TCGA.EB.A3XE.01 6 0.3080 0.806 0.02 0.02 0.00 0.00 0.00 0.84 0.06 0.06
#> TCGA.FW.A3R5.06 6 0.1741 0.830 0.00 0.02 0.00 0.00 0.00 0.92 0.04 0.02
#> TCGA.EB.A5UM.01 2 0.4333 0.606 0.00 0.62 0.00 0.00 0.00 0.26 0.00 0.12
#> TCGA.EE.A29T.06 2 0.4073 0.640 0.00 0.66 0.00 0.00 0.00 0.24 0.00 0.10
#> TCGA.EB.A44R.06 3 0.0000 0.918 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.ER.A3EV.06 3 0.0471 0.913 0.00 0.00 0.98 0.00 0.00 0.00 0.02 0.00
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
consensus_heatmap(res, k = 7)
consensus_heatmap(res, k = 8)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
membership_heatmap(res, k = 7)
membership_heatmap(res, k = 8)
As soon as the classes for columns are determined, the signatures that are significantly different between subgroups can be looked for. Following are the heatmaps for signatures.
get_signatures(res, k = 2)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
get_signatures(res, k = 7)
get_signatures(res, k = 8)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. To get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows (which is done by automatically selecting number of clusters).If there are too many signatures, top_signatures = ... can be set to only show the
signatures with the highest FDRs:
# code only for demonstration
# e.g. to show the top 500 most significant rows
tb = get_signature(res, k = ..., top_signatures = 500)
If the signatures are defined as these which are uniquely high in current group, diff_method argument
can be set to "uniquely_high_in_one_group":
# code only for demonstration
tb = get_signature(res, k = ..., diff_method = "uniquely_high_in_one_group")
UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
dimension_reduction(res, k = 7, method = "UMAP")
dimension_reduction(res, k = 8, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
If matrix rows can be associated to genes, consider to use functional_enrichment(res,
...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.
Parent node: Node04. Child nodes: Node0111 , Node0112-leaf , Node0113 , Node0121-leaf , Node0122-leaf , Node0123-leaf , Node0124-leaf , Node0125-leaf , Node0131 , Node0132-leaf , Node0133-leaf , Node0211-leaf , Node0212 , Node0221-leaf , Node0222-leaf , Node0311 , Node0312-leaf , Node0321-leaf , Node0322 , Node0323 , Node0411 , Node0412 , Node0413-leaf , Node0421-leaf , Node0422-leaf , Node0423-leaf , Node0431-leaf , Node0432-leaf , Node0433-leaf , Node0441-leaf , Node0442 , Node0443-leaf , Node0511 , Node0512-leaf , Node0513-leaf , Node0521-leaf , Node0522-leaf , Node0523-leaf , Node0524-leaf .
The object with results only for a single top-value method and a single partitioning method can be extracted as:
res = res_rh["044"]
A summary of res and all the functions that can be applied to it:
res
#> A 'ConsensusPartition' object with k = 2, 3, 4, 5, 6, 7, 8.
#> On a matrix with 30000 rows and 42 columns.
#> Top rows (1000) are extracted by 'ATC' method.
#> Subgroups are detected by '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 0.5115 0.489 0.489
#> 3 3 0.958 0.961 0.976 0.2506 0.814 0.640
#> 4 4 0.777 0.874 0.901 0.1564 0.836 0.569
#> 5 5 0.799 0.792 0.895 0.0563 0.987 0.946
#> 6 6 0.756 0.714 0.871 0.0247 0.988 0.948
#> 7 7 0.748 0.657 0.851 0.0269 0.988 0.945
#> 8 8 0.699 0.589 0.804 0.0174 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] 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.EB.A5VU.01 1 0 1 1 0
#> TCGA.D3.A8GJ.06 2 0 1 0 1
#> TCGA.D3.A8GS.06 2 0 1 0 1
#> TCGA.EB.A551.01 2 0 1 0 1
#> TCGA.W3.A825.06 1 0 1 1 0
#> TCGA.D3.A5GR.06 2 0 1 0 1
#> TCGA.FR.A729.06 1 0 1 1 0
#> TCGA.EE.A29P.06 2 0 1 0 1
#> TCGA.D3.A2JC.06 1 0 1 1 0
#> TCGA.EE.A2M7.06 1 0 1 1 0
#> TCGA.DA.A1I2.06 1 0 1 1 0
#> TCGA.DA.A1I7.06 1 0 1 1 0
#> TCGA.FS.A1ZM.06 1 0 1 1 0
#> TCGA.ER.A19C.06 1 0 1 1 0
#> TCGA.D3.A2JO.06 2 0 1 0 1
#> TCGA.BF.A1PU.01 1 0 1 1 0
#> TCGA.D3.A1Q6.06 1 0 1 1 0
#> TCGA.EE.A29S.06 2 0 1 0 1
#> TCGA.GN.A266.06 1 0 1 1 0
#> TCGA.D3.A3C1.06 2 0 1 0 1
#> TCGA.ER.A19O.06 2 0 1 0 1
#> TCGA.FS.A1YX.06 1 0 1 1 0
#> TCGA.ER.A194.01 2 0 1 0 1
#> TCGA.EE.A29X.06 2 0 1 0 1
#> TCGA.ER.A2NC.06 1 0 1 1 0
#> TCGA.ER.A19K.01 2 0 1 0 1
#> TCGA.FR.A3YO.06 2 0 1 0 1
#> TCGA.RP.A694.06 2 0 1 0 1
#> TCGA.DA.A1HW.06 1 0 1 1 0
#> TCGA.GF.A6C8.06 1 0 1 1 0
#> TCGA.D9.A6E9.06 2 0 1 0 1
#> TCGA.BF.AAP4.01 2 0 1 0 1
#> TCGA.FS.A1ZA.06 2 0 1 0 1
#> TCGA.EE.A2MI.06 1 0 1 1 0
#> TCGA.D3.A3CE.06 1 0 1 1 0
#> TCGA.EB.A3Y6.01 1 0 1 1 0
#> TCGA.EB.A3XB.01 2 0 1 0 1
#> TCGA.EE.A2MD.06 2 0 1 0 1
#> TCGA.W3.AA1V.06 1 0 1 1 0
#> TCGA.EB.A44Q.06 2 0 1 0 1
#> TCGA.D3.A51J.06 2 0 1 0 1
#> TCGA.YG.AA3N.01 2 0 1 0 1
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.EB.A5VU.01 3 0.0000 0.991 0.00 0.00 1.00
#> TCGA.D3.A8GJ.06 2 0.0000 0.991 0.00 1.00 0.00
#> TCGA.D3.A8GS.06 1 0.3686 0.801 0.86 0.14 0.00
#> TCGA.EB.A551.01 2 0.0000 0.991 0.00 1.00 0.00
#> TCGA.W3.A825.06 3 0.0000 0.991 0.00 0.00 1.00
#> TCGA.D3.A5GR.06 1 0.4002 0.776 0.84 0.16 0.00
#> TCGA.FR.A729.06 1 0.0892 0.941 0.98 0.00 0.02
#> TCGA.EE.A29P.06 2 0.0000 0.991 0.00 1.00 0.00
#> TCGA.D3.A2JC.06 1 0.1529 0.937 0.96 0.00 0.04
#> TCGA.EE.A2M7.06 1 0.1529 0.937 0.96 0.00 0.04
#> TCGA.DA.A1I2.06 1 0.3340 0.881 0.88 0.00 0.12
#> TCGA.DA.A1I7.06 1 0.0892 0.941 0.98 0.00 0.02
#> TCGA.FS.A1ZM.06 1 0.0000 0.932 1.00 0.00 0.00
#> TCGA.ER.A19C.06 3 0.0000 0.991 0.00 0.00 1.00
#> TCGA.D3.A2JO.06 2 0.0000 0.991 0.00 1.00 0.00
#> TCGA.BF.A1PU.01 3 0.0000 0.991 0.00 0.00 1.00
#> TCGA.D3.A1Q6.06 1 0.0892 0.941 0.98 0.00 0.02
#> TCGA.EE.A29S.06 2 0.0000 0.991 0.00 1.00 0.00
#> TCGA.GN.A266.06 3 0.2066 0.934 0.06 0.00 0.94
#> TCGA.D3.A3C1.06 2 0.0892 0.989 0.02 0.98 0.00
#> TCGA.ER.A19O.06 2 0.0892 0.989 0.02 0.98 0.00
#> TCGA.FS.A1YX.06 1 0.3340 0.881 0.88 0.00 0.12
#> TCGA.ER.A194.01 2 0.0000 0.991 0.00 1.00 0.00
#> TCGA.EE.A29X.06 2 0.0892 0.989 0.02 0.98 0.00
#> TCGA.ER.A2NC.06 3 0.0000 0.991 0.00 0.00 1.00
#> TCGA.ER.A19K.01 2 0.0000 0.991 0.00 1.00 0.00
#> TCGA.FR.A3YO.06 2 0.0000 0.991 0.00 1.00 0.00
#> TCGA.RP.A694.06 2 0.0000 0.991 0.00 1.00 0.00
#> TCGA.DA.A1HW.06 1 0.2066 0.927 0.94 0.00 0.06
#> TCGA.GF.A6C8.06 3 0.0000 0.991 0.00 0.00 1.00
#> TCGA.D9.A6E9.06 2 0.0892 0.989 0.02 0.98 0.00
#> TCGA.BF.AAP4.01 2 0.0892 0.989 0.02 0.98 0.00
#> TCGA.FS.A1ZA.06 2 0.0000 0.991 0.00 1.00 0.00
#> TCGA.EE.A2MI.06 3 0.0000 0.991 0.00 0.00 1.00
#> TCGA.D3.A3CE.06 1 0.0892 0.941 0.98 0.00 0.02
#> TCGA.EB.A3Y6.01 1 0.0000 0.932 1.00 0.00 0.00
#> TCGA.EB.A3XB.01 2 0.0892 0.989 0.02 0.98 0.00
#> TCGA.EE.A2MD.06 2 0.0892 0.989 0.02 0.98 0.00
#> TCGA.W3.AA1V.06 1 0.0892 0.941 0.98 0.00 0.02
#> TCGA.EB.A44Q.06 2 0.0892 0.989 0.02 0.98 0.00
#> TCGA.D3.A51J.06 2 0.0892 0.989 0.02 0.98 0.00
#> TCGA.YG.AA3N.01 2 0.0000 0.991 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.EB.A5VU.01 3 0.0000 0.982 0.00 0.00 1.00 0.00
#> TCGA.D3.A8GJ.06 2 0.0707 0.876 0.00 0.98 0.00 0.02
#> TCGA.D3.A8GS.06 4 0.3972 0.806 0.08 0.08 0.00 0.84
#> TCGA.EB.A551.01 2 0.1637 0.864 0.00 0.94 0.00 0.06
#> TCGA.W3.A825.06 3 0.0000 0.982 0.00 0.00 1.00 0.00
#> TCGA.D3.A5GR.06 4 0.3972 0.806 0.08 0.08 0.00 0.84
#> TCGA.FR.A729.06 1 0.0000 0.955 1.00 0.00 0.00 0.00
#> TCGA.EE.A29P.06 2 0.0000 0.873 0.00 1.00 0.00 0.00
#> TCGA.D3.A2JC.06 1 0.0000 0.955 1.00 0.00 0.00 0.00
#> TCGA.EE.A2M7.06 1 0.0000 0.955 1.00 0.00 0.00 0.00
#> TCGA.DA.A1I2.06 1 0.3037 0.878 0.88 0.00 0.10 0.02
#> TCGA.DA.A1I7.06 1 0.1211 0.948 0.96 0.00 0.00 0.04
#> TCGA.FS.A1ZM.06 1 0.1211 0.948 0.96 0.00 0.00 0.04
#> TCGA.ER.A19C.06 3 0.0000 0.982 0.00 0.00 1.00 0.00
#> TCGA.D3.A2JO.06 2 0.1637 0.864 0.00 0.94 0.00 0.06
#> TCGA.BF.A1PU.01 3 0.0000 0.982 0.00 0.00 1.00 0.00
#> TCGA.D3.A1Q6.06 1 0.0707 0.952 0.98 0.00 0.00 0.02
#> TCGA.EE.A29S.06 2 0.0000 0.873 0.00 1.00 0.00 0.00
#> TCGA.GN.A266.06 3 0.2647 0.860 0.12 0.00 0.88 0.00
#> TCGA.D3.A3C1.06 4 0.3610 0.924 0.00 0.20 0.00 0.80
#> TCGA.ER.A19O.06 4 0.3610 0.924 0.00 0.20 0.00 0.80
#> TCGA.FS.A1YX.06 1 0.2335 0.915 0.92 0.00 0.06 0.02
#> TCGA.ER.A194.01 2 0.1211 0.865 0.00 0.96 0.00 0.04
#> TCGA.EE.A29X.06 4 0.4277 0.854 0.00 0.28 0.00 0.72
#> TCGA.ER.A2NC.06 3 0.0000 0.982 0.00 0.00 1.00 0.00
#> TCGA.ER.A19K.01 2 0.4994 -0.380 0.00 0.52 0.00 0.48
#> TCGA.FR.A3YO.06 2 0.0000 0.873 0.00 1.00 0.00 0.00
#> TCGA.RP.A694.06 2 0.3400 0.740 0.00 0.82 0.00 0.18
#> TCGA.DA.A1HW.06 1 0.0707 0.948 0.98 0.00 0.02 0.00
#> TCGA.GF.A6C8.06 3 0.0000 0.982 0.00 0.00 1.00 0.00
#> TCGA.D9.A6E9.06 4 0.3801 0.908 0.00 0.22 0.00 0.78
#> TCGA.BF.AAP4.01 4 0.3610 0.924 0.00 0.20 0.00 0.80
#> TCGA.FS.A1ZA.06 2 0.2345 0.835 0.00 0.90 0.00 0.10
#> TCGA.EE.A2MI.06 3 0.0000 0.982 0.00 0.00 1.00 0.00
#> TCGA.D3.A3CE.06 1 0.0000 0.955 1.00 0.00 0.00 0.00
#> TCGA.EB.A3Y6.01 1 0.1211 0.946 0.96 0.00 0.00 0.04
#> TCGA.EB.A3XB.01 4 0.3610 0.924 0.00 0.20 0.00 0.80
#> TCGA.EE.A2MD.06 4 0.3610 0.924 0.00 0.20 0.00 0.80
#> TCGA.W3.AA1V.06 1 0.4553 0.825 0.78 0.00 0.04 0.18
#> TCGA.EB.A44Q.06 4 0.3610 0.924 0.00 0.20 0.00 0.80
#> TCGA.D3.A51J.06 4 0.4624 0.731 0.00 0.34 0.00 0.66
#> TCGA.YG.AA3N.01 2 0.0707 0.873 0.00 0.98 0.00 0.02
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> TCGA.EB.A5VU.01 3 0.0000 0.958 0.00 0.00 1.00 0.00 0.00
#> TCGA.D3.A8GJ.06 2 0.1648 0.803 0.00 0.94 0.00 0.02 0.04
#> TCGA.D3.A8GS.06 4 0.2331 0.837 0.02 0.00 0.00 0.90 0.08
#> TCGA.EB.A551.01 2 0.3291 0.766 0.00 0.84 0.00 0.04 0.12
#> TCGA.W3.A825.06 3 0.0000 0.958 0.00 0.00 1.00 0.00 0.00
#> TCGA.D3.A5GR.06 4 0.2873 0.833 0.00 0.02 0.00 0.86 0.12
#> TCGA.FR.A729.06 1 0.0609 0.891 0.98 0.00 0.00 0.00 0.02
#> TCGA.EE.A29P.06 2 0.0609 0.803 0.00 0.98 0.00 0.02 0.00
#> TCGA.D3.A2JC.06 1 0.0000 0.893 1.00 0.00 0.00 0.00 0.00
#> TCGA.EE.A2M7.06 1 0.0000 0.893 1.00 0.00 0.00 0.00 0.00
#> TCGA.DA.A1I2.06 1 0.2438 0.822 0.90 0.00 0.04 0.00 0.06
#> TCGA.DA.A1I7.06 1 0.4252 0.391 0.70 0.00 0.00 0.02 0.28
#> TCGA.FS.A1ZM.06 1 0.2616 0.767 0.88 0.00 0.00 0.02 0.10
#> TCGA.ER.A19C.06 3 0.1732 0.929 0.00 0.00 0.92 0.00 0.08
#> TCGA.D3.A2JO.06 2 0.3291 0.766 0.00 0.84 0.00 0.04 0.12
#> TCGA.BF.A1PU.01 3 0.0000 0.958 0.00 0.00 1.00 0.00 0.00
#> TCGA.D3.A1Q6.06 1 0.1410 0.873 0.94 0.00 0.00 0.00 0.06
#> TCGA.EE.A29S.06 2 0.0609 0.803 0.00 0.98 0.00 0.02 0.00
#> TCGA.GN.A266.06 3 0.3110 0.868 0.06 0.00 0.86 0.00 0.08
#> TCGA.D3.A3C1.06 4 0.2616 0.875 0.00 0.02 0.00 0.88 0.10
#> TCGA.ER.A19O.06 4 0.0609 0.894 0.00 0.02 0.00 0.98 0.00
#> TCGA.FS.A1YX.06 1 0.1648 0.854 0.94 0.00 0.02 0.00 0.04
#> TCGA.ER.A194.01 2 0.2516 0.763 0.00 0.86 0.00 0.14 0.00
#> TCGA.EE.A29X.06 4 0.2516 0.810 0.00 0.14 0.00 0.86 0.00
#> TCGA.ER.A2NC.06 3 0.0000 0.958 0.00 0.00 1.00 0.00 0.00
#> TCGA.ER.A19K.01 2 0.4262 0.209 0.00 0.56 0.00 0.44 0.00
#> TCGA.FR.A3YO.06 2 0.0609 0.803 0.00 0.98 0.00 0.02 0.00
#> TCGA.RP.A694.06 2 0.5558 0.465 0.00 0.56 0.00 0.36 0.08
#> TCGA.DA.A1HW.06 1 0.0609 0.891 0.98 0.00 0.00 0.00 0.02
#> TCGA.GF.A6C8.06 3 0.0000 0.958 0.00 0.00 1.00 0.00 0.00
#> TCGA.D9.A6E9.06 4 0.1648 0.889 0.00 0.02 0.00 0.94 0.04
#> TCGA.BF.AAP4.01 4 0.0609 0.894 0.00 0.02 0.00 0.98 0.00
#> TCGA.FS.A1ZA.06 2 0.5444 0.631 0.00 0.66 0.00 0.16 0.18
#> TCGA.EE.A2MI.06 3 0.1732 0.929 0.00 0.00 0.92 0.00 0.08
#> TCGA.D3.A3CE.06 1 0.0000 0.893 1.00 0.00 0.00 0.00 0.00
#> TCGA.EB.A3Y6.01 1 0.1216 0.878 0.96 0.00 0.00 0.02 0.02
#> TCGA.EB.A3XB.01 4 0.0609 0.894 0.00 0.02 0.00 0.98 0.00
#> TCGA.EE.A2MD.06 4 0.2077 0.874 0.00 0.04 0.00 0.92 0.04
#> TCGA.W3.AA1V.06 5 0.4540 0.000 0.34 0.00 0.00 0.02 0.64
#> TCGA.EB.A44Q.06 4 0.1648 0.887 0.00 0.04 0.00 0.94 0.02
#> TCGA.D3.A51J.06 4 0.5788 0.423 0.00 0.30 0.00 0.58 0.12
#> TCGA.YG.AA3N.01 2 0.1410 0.798 0.00 0.94 0.00 0.06 0.00
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> TCGA.EB.A5VU.01 3 0.0000 0.899 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.D3.A8GJ.06 2 0.1556 0.681 0.00 0.92 0.00 0.00 0.00 0.08
#> TCGA.D3.A8GS.06 4 0.2725 0.776 0.02 0.00 0.00 0.88 0.06 0.04
#> TCGA.EB.A551.01 2 0.3198 0.426 0.00 0.74 0.00 0.00 0.00 0.26
#> TCGA.W3.A825.06 3 0.0000 0.899 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.D3.A5GR.06 4 0.4265 0.700 0.02 0.00 0.00 0.76 0.08 0.14
#> TCGA.FR.A729.06 1 0.0547 0.879 0.98 0.00 0.00 0.00 0.02 0.00
#> TCGA.EE.A29P.06 2 0.0000 0.722 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.D3.A2JC.06 1 0.0547 0.878 0.98 0.00 0.00 0.00 0.02 0.00
#> TCGA.EE.A2M7.06 1 0.1092 0.875 0.96 0.00 0.00 0.02 0.02 0.00
#> TCGA.DA.A1I2.06 1 0.2629 0.810 0.88 0.00 0.08 0.00 0.02 0.02
#> TCGA.DA.A1I7.06 1 0.5027 0.550 0.64 0.00 0.00 0.00 0.16 0.20
#> TCGA.FS.A1ZM.06 1 0.4042 0.746 0.76 0.00 0.00 0.02 0.18 0.04
#> TCGA.ER.A19C.06 3 0.3575 0.831 0.06 0.00 0.84 0.02 0.06 0.02
#> TCGA.D3.A2JO.06 2 0.3076 0.469 0.00 0.76 0.00 0.00 0.00 0.24
#> TCGA.BF.A1PU.01 3 0.0000 0.899 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.D3.A1Q6.06 1 0.2956 0.834 0.84 0.00 0.00 0.00 0.12 0.04
#> TCGA.EE.A29S.06 2 0.0000 0.722 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.GN.A266.06 3 0.5073 0.650 0.14 0.00 0.68 0.02 0.16 0.00
#> TCGA.D3.A3C1.06 4 0.2190 0.844 0.00 0.04 0.00 0.90 0.00 0.06
#> TCGA.ER.A19O.06 4 0.0937 0.852 0.00 0.04 0.00 0.96 0.00 0.00
#> TCGA.FS.A1YX.06 1 0.1480 0.862 0.94 0.00 0.02 0.00 0.04 0.00
#> TCGA.ER.A194.01 2 0.2512 0.672 0.00 0.88 0.00 0.06 0.00 0.06
#> TCGA.EE.A29X.06 4 0.3163 0.782 0.00 0.14 0.00 0.82 0.00 0.04
#> TCGA.ER.A2NC.06 3 0.0000 0.899 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.ER.A19K.01 2 0.4380 0.394 0.00 0.70 0.00 0.22 0.00 0.08
#> TCGA.FR.A3YO.06 2 0.0000 0.722 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.RP.A694.06 2 0.5029 0.216 0.00 0.62 0.00 0.26 0.00 0.12
#> TCGA.DA.A1HW.06 1 0.0547 0.878 0.98 0.00 0.00 0.00 0.02 0.00
#> TCGA.GF.A6C8.06 3 0.0000 0.899 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.D9.A6E9.06 4 0.1865 0.849 0.00 0.04 0.00 0.92 0.00 0.04
#> TCGA.BF.AAP4.01 4 0.2190 0.843 0.00 0.04 0.00 0.90 0.00 0.06
#> TCGA.FS.A1ZA.06 6 0.5267 0.000 0.00 0.32 0.00 0.12 0.00 0.56
#> TCGA.EE.A2MI.06 3 0.3851 0.816 0.08 0.00 0.82 0.02 0.06 0.02
#> TCGA.D3.A3CE.06 1 0.0547 0.877 0.98 0.00 0.00 0.00 0.02 0.00
#> TCGA.EB.A3Y6.01 1 0.3045 0.830 0.84 0.00 0.00 0.00 0.10 0.06
#> TCGA.EB.A3XB.01 4 0.0937 0.852 0.00 0.04 0.00 0.96 0.00 0.00
#> TCGA.EE.A2MD.06 4 0.2956 0.815 0.00 0.04 0.00 0.84 0.00 0.12
#> TCGA.W3.AA1V.06 5 0.0547 0.000 0.02 0.00 0.00 0.00 0.98 0.00
#> TCGA.EB.A44Q.06 4 0.2474 0.829 0.00 0.08 0.00 0.88 0.00 0.04
#> TCGA.D3.A51J.06 4 0.5267 0.333 0.00 0.32 0.00 0.56 0.00 0.12
#> TCGA.YG.AA3N.01 2 0.1865 0.697 0.00 0.92 0.00 0.04 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.EB.A5VU.01 3 0.0504 0.92455 0.00 0.00 0.98 0.00 0.00 0.02 0.00
#> TCGA.D3.A8GJ.06 2 0.1433 0.68669 0.00 0.92 0.00 0.00 0.00 0.08 0.00
#> TCGA.D3.A8GS.06 4 0.2509 0.75921 0.00 0.00 0.00 0.88 0.02 0.06 0.04
#> TCGA.EB.A551.01 2 0.3795 0.45336 0.00 0.72 0.00 0.06 0.00 0.22 0.00
#> TCGA.W3.A825.06 3 0.0000 0.92741 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.D3.A5GR.06 4 0.3848 0.69669 0.00 0.00 0.00 0.76 0.02 0.06 0.16
#> TCGA.FR.A729.06 1 0.2016 0.79740 0.90 0.00 0.00 0.00 0.00 0.06 0.04
#> TCGA.EE.A29P.06 2 0.0000 0.71636 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D3.A2JC.06 1 0.0504 0.80522 0.98 0.00 0.00 0.00 0.00 0.00 0.02
#> TCGA.EE.A2M7.06 1 0.1363 0.80570 0.94 0.00 0.00 0.00 0.02 0.04 0.00
#> TCGA.DA.A1I2.06 1 0.3744 0.66155 0.78 0.00 0.02 0.00 0.00 0.12 0.08
#> TCGA.DA.A1I7.06 7 0.3745 0.00000 0.26 0.00 0.00 0.00 0.04 0.00 0.70
#> TCGA.FS.A1ZM.06 1 0.5094 0.58651 0.70 0.00 0.00 0.06 0.06 0.04 0.14
#> TCGA.ER.A19C.06 3 0.2857 0.86804 0.06 0.00 0.86 0.00 0.04 0.04 0.00
#> TCGA.D3.A2JO.06 2 0.3911 0.41371 0.00 0.70 0.00 0.06 0.00 0.24 0.00
#> TCGA.BF.A1PU.01 3 0.0504 0.92455 0.00 0.00 0.98 0.00 0.00 0.02 0.00
#> TCGA.D3.A1Q6.06 1 0.2512 0.76606 0.86 0.00 0.00 0.00 0.00 0.04 0.10
#> TCGA.EE.A29S.06 2 0.0000 0.71636 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.GN.A266.06 3 0.3722 0.70868 0.18 0.00 0.76 0.00 0.04 0.00 0.02
#> TCGA.D3.A3C1.06 4 0.2512 0.75182 0.00 0.00 0.00 0.86 0.00 0.04 0.10
#> TCGA.ER.A19O.06 4 0.0504 0.78148 0.00 0.00 0.00 0.98 0.00 0.02 0.00
#> TCGA.FS.A1YX.06 1 0.1664 0.78884 0.92 0.00 0.00 0.00 0.00 0.06 0.02
#> TCGA.ER.A194.01 2 0.3635 0.66761 0.00 0.82 0.00 0.04 0.02 0.06 0.06
#> TCGA.EE.A29X.06 4 0.4260 0.63696 0.00 0.14 0.00 0.74 0.00 0.04 0.08
#> TCGA.ER.A2NC.06 3 0.0000 0.92741 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.ER.A19K.01 2 0.5166 0.41399 0.00 0.66 0.00 0.20 0.02 0.04 0.08
#> TCGA.FR.A3YO.06 2 0.0504 0.71200 0.00 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.RP.A694.06 2 0.5695 -0.00567 0.00 0.50 0.00 0.26 0.00 0.22 0.02
#> TCGA.DA.A1HW.06 1 0.1006 0.80359 0.96 0.00 0.00 0.00 0.00 0.02 0.02
#> TCGA.GF.A6C8.06 3 0.0000 0.92741 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.D9.A6E9.06 4 0.2081 0.73621 0.00 0.00 0.00 0.86 0.00 0.14 0.00
#> TCGA.BF.AAP4.01 4 0.2569 0.73289 0.00 0.00 0.00 0.84 0.00 0.14 0.02
#> TCGA.FS.A1ZA.06 6 0.4033 0.00000 0.00 0.22 0.00 0.08 0.00 0.70 0.00
#> TCGA.EE.A2MI.06 3 0.1363 0.90530 0.04 0.00 0.94 0.00 0.02 0.00 0.00
#> TCGA.D3.A3CE.06 1 0.3630 0.70961 0.80 0.00 0.00 0.00 0.06 0.04 0.10
#> TCGA.EB.A3Y6.01 1 0.4311 0.66783 0.76 0.00 0.00 0.02 0.04 0.06 0.12
#> TCGA.EB.A3XB.01 4 0.0863 0.77974 0.00 0.00 0.00 0.96 0.00 0.04 0.00
#> TCGA.EE.A2MD.06 4 0.3519 0.63482 0.00 0.00 0.00 0.74 0.00 0.22 0.04
#> TCGA.W3.AA1V.06 5 0.0504 0.00000 0.02 0.00 0.00 0.00 0.98 0.00 0.00
#> TCGA.EB.A44Q.06 4 0.2857 0.76238 0.00 0.04 0.00 0.86 0.00 0.06 0.04
#> TCGA.D3.A51J.06 4 0.5618 0.36057 0.00 0.28 0.00 0.54 0.00 0.04 0.14
#> TCGA.YG.AA3N.01 2 0.2003 0.69974 0.00 0.92 0.00 0.02 0.02 0.02 0.02
cbind(get_classes(res, k = 8), get_membership(res, k = 8))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7 p8
#> TCGA.EB.A5VU.01 8 0.0471 0.8377 0.00 0.00 0.00 0.00 0.00 0.00 0.02 0.98
#> TCGA.D3.A8GJ.06 2 0.2348 0.6583 0.00 0.88 0.02 0.04 0.00 0.06 0.00 0.00
#> TCGA.D3.A8GS.06 4 0.3913 0.6289 0.04 0.00 0.16 0.74 0.00 0.00 0.06 0.00
#> TCGA.EB.A551.01 2 0.4650 0.4747 0.00 0.66 0.06 0.08 0.00 0.20 0.00 0.00
#> TCGA.W3.A825.06 8 0.0000 0.8437 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.D3.A5GR.06 4 0.5880 0.5182 0.06 0.00 0.26 0.54 0.00 0.08 0.06 0.00
#> TCGA.FR.A729.06 1 0.0471 0.7590 0.98 0.00 0.02 0.00 0.00 0.00 0.00 0.00
#> TCGA.EE.A29P.06 2 0.0000 0.6846 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D3.A2JC.06 1 0.2265 0.7462 0.88 0.00 0.08 0.00 0.02 0.00 0.02 0.00
#> TCGA.EE.A2M7.06 1 0.1408 0.7452 0.94 0.00 0.00 0.00 0.02 0.02 0.02 0.00
#> TCGA.DA.A1I2.06 1 0.4604 0.5966 0.72 0.00 0.12 0.00 0.00 0.06 0.06 0.04
#> TCGA.DA.A1I7.06 7 0.1563 0.0000 0.10 0.00 0.00 0.00 0.00 0.00 0.90 0.00
#> TCGA.FS.A1ZM.06 1 0.5531 0.4940 0.62 0.00 0.16 0.02 0.04 0.02 0.14 0.00
#> TCGA.ER.A19C.06 8 0.4662 0.7175 0.04 0.00 0.06 0.00 0.02 0.08 0.06 0.74
#> TCGA.D3.A2JO.06 2 0.4865 0.4503 0.00 0.64 0.08 0.08 0.00 0.20 0.00 0.00
#> TCGA.BF.A1PU.01 8 0.1275 0.8168 0.00 0.00 0.04 0.00 0.00 0.00 0.02 0.94
#> TCGA.D3.A1Q6.06 1 0.4764 0.6051 0.66 0.00 0.16 0.00 0.06 0.00 0.12 0.00
#> TCGA.EE.A29S.06 2 0.0000 0.6846 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.GN.A266.06 8 0.5999 0.3413 0.30 0.00 0.04 0.00 0.12 0.02 0.02 0.50
#> TCGA.D3.A3C1.06 4 0.3337 0.7109 0.00 0.04 0.16 0.78 0.00 0.02 0.00 0.00
#> TCGA.ER.A19O.06 4 0.1275 0.7352 0.00 0.02 0.04 0.94 0.00 0.00 0.00 0.00
#> TCGA.FS.A1YX.06 1 0.3688 0.6761 0.80 0.00 0.08 0.00 0.00 0.04 0.04 0.04
#> TCGA.ER.A194.01 2 0.3913 0.5749 0.00 0.74 0.16 0.06 0.00 0.04 0.00 0.00
#> TCGA.EE.A29X.06 4 0.3771 0.6640 0.00 0.12 0.16 0.72 0.00 0.00 0.00 0.00
#> TCGA.ER.A2NC.06 8 0.0000 0.8437 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.ER.A19K.01 2 0.4693 0.0085 0.00 0.46 0.12 0.42 0.00 0.00 0.00 0.00
#> TCGA.FR.A3YO.06 2 0.0471 0.6873 0.00 0.98 0.00 0.02 0.00 0.00 0.00 0.00
#> TCGA.RP.A694.06 2 0.6192 0.2754 0.00 0.44 0.18 0.24 0.00 0.14 0.00 0.00
#> TCGA.DA.A1HW.06 1 0.2532 0.7518 0.88 0.00 0.04 0.00 0.02 0.00 0.04 0.02
#> TCGA.GF.A6C8.06 8 0.0000 0.8437 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.D9.A6E9.06 4 0.1091 0.7221 0.00 0.00 0.00 0.94 0.00 0.06 0.00 0.00
#> TCGA.BF.AAP4.01 4 0.1804 0.7091 0.00 0.00 0.08 0.90 0.00 0.02 0.00 0.00
#> TCGA.FS.A1ZA.06 6 0.2350 0.0000 0.00 0.10 0.00 0.04 0.00 0.86 0.00 0.00
#> TCGA.EE.A2MI.06 8 0.3821 0.7543 0.08 0.00 0.04 0.00 0.04 0.02 0.02 0.80
#> TCGA.D3.A3CE.06 1 0.2482 0.7197 0.88 0.00 0.02 0.00 0.02 0.02 0.06 0.00
#> TCGA.EB.A3Y6.01 1 0.5261 0.5749 0.64 0.00 0.18 0.04 0.06 0.00 0.08 0.00
#> TCGA.EB.A3XB.01 4 0.1804 0.7092 0.00 0.00 0.08 0.90 0.00 0.02 0.00 0.00
#> TCGA.EE.A2MD.06 4 0.3729 0.5901 0.00 0.00 0.18 0.72 0.00 0.10 0.00 0.00
#> TCGA.W3.AA1V.06 5 0.0000 0.0000 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.EB.A44Q.06 4 0.4169 0.6793 0.00 0.10 0.18 0.70 0.00 0.02 0.00 0.00
#> TCGA.D3.A51J.06 4 0.5755 0.2472 0.00 0.30 0.24 0.42 0.00 0.04 0.00 0.00
#> TCGA.YG.AA3N.01 2 0.1607 0.6759 0.00 0.92 0.04 0.04 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: Node044. Child nodes: Node01111-leaf , Node01112-leaf , Node01113-leaf , Node01131-leaf , Node01132-leaf , Node01133-leaf , Node01311-leaf , Node01312-leaf , Node02121-leaf , Node02122-leaf , Node02123-leaf , Node03111-leaf , Node03112-leaf , Node03113-leaf , Node03221-leaf , Node03222-leaf , Node03231-leaf , Node03232-leaf , Node03233-leaf , Node03234-leaf , Node04111-leaf , Node04112-leaf , Node04121-leaf , Node04122-leaf , Node04421-leaf , Node04422-leaf , Node04423-leaf , Node04424-leaf , Node05111-leaf , Node05112-leaf , Node05113-leaf .
The object with results only for a single top-value method and a single partitioning method can be extracted as:
res = res_rh["0442"]
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 20 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 0.3953 0.605 0.605
#> 3 3 1.000 1.000 1.000 0.4788 0.811 0.687
#> 4 4 1.000 0.995 0.995 0.0533 0.968 0.924
#> 5 5 0.989 0.918 0.975 0.0333 0.989 0.973
#> 6 6 0.805 0.805 0.905 0.0674 1.000 1.000
#> 7 7 0.758 0.663 0.852 0.0794 0.847 0.592
#> 8 8 0.726 0.610 0.883 0.0561 0.995 0.976
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.D3.A8GJ.06 1 0 1 1 0
#> TCGA.EB.A551.01 2 0 1 0 1
#> TCGA.EE.A29P.06 2 0 1 0 1
#> TCGA.D3.A2JO.06 2 0 1 0 1
#> TCGA.EE.A29S.06 2 0 1 0 1
#> TCGA.D3.A3C1.06 1 0 1 1 0
#> TCGA.ER.A19O.06 1 0 1 1 0
#> TCGA.ER.A194.01 1 0 1 1 0
#> TCGA.EE.A29X.06 1 0 1 1 0
#> TCGA.ER.A19K.01 1 0 1 1 0
#> TCGA.FR.A3YO.06 1 0 1 1 0
#> TCGA.RP.A694.06 1 0 1 1 0
#> TCGA.D9.A6E9.06 1 0 1 1 0
#> TCGA.BF.AAP4.01 1 0 1 1 0
#> TCGA.FS.A1ZA.06 2 0 1 0 1
#> TCGA.EB.A3XB.01 1 0 1 1 0
#> TCGA.EE.A2MD.06 1 0 1 1 0
#> TCGA.EB.A44Q.06 1 0 1 1 0
#> TCGA.D3.A51J.06 1 0 1 1 0
#> TCGA.YG.AA3N.01 1 0 1 1 0
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.D3.A8GJ.06 3 0 1 0 0 1
#> TCGA.EB.A551.01 2 0 1 0 1 0
#> TCGA.EE.A29P.06 2 0 1 0 1 0
#> TCGA.D3.A2JO.06 2 0 1 0 1 0
#> TCGA.EE.A29S.06 2 0 1 0 1 0
#> TCGA.D3.A3C1.06 1 0 1 1 0 0
#> TCGA.ER.A19O.06 1 0 1 1 0 0
#> TCGA.ER.A194.01 3 0 1 0 0 1
#> TCGA.EE.A29X.06 1 0 1 1 0 0
#> TCGA.ER.A19K.01 1 0 1 1 0 0
#> TCGA.FR.A3YO.06 1 0 1 1 0 0
#> TCGA.RP.A694.06 3 0 1 0 0 1
#> TCGA.D9.A6E9.06 1 0 1 1 0 0
#> TCGA.BF.AAP4.01 1 0 1 1 0 0
#> TCGA.FS.A1ZA.06 2 0 1 0 1 0
#> TCGA.EB.A3XB.01 1 0 1 1 0 0
#> TCGA.EE.A2MD.06 1 0 1 1 0 0
#> TCGA.EB.A44Q.06 1 0 1 1 0 0
#> TCGA.D3.A51J.06 1 0 1 1 0 0
#> TCGA.YG.AA3N.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.D3.A8GJ.06 3 0.0000 1.000 0 0.00 1 0.00
#> TCGA.EB.A551.01 2 0.1211 0.975 0 0.96 0 0.04
#> TCGA.EE.A29P.06 4 0.0000 1.000 0 0.00 0 1.00
#> TCGA.D3.A2JO.06 2 0.1211 0.975 0 0.96 0 0.04
#> TCGA.EE.A29S.06 4 0.0000 1.000 0 0.00 0 1.00
#> TCGA.D3.A3C1.06 1 0.0000 1.000 1 0.00 0 0.00
#> TCGA.ER.A19O.06 1 0.0000 1.000 1 0.00 0 0.00
#> TCGA.ER.A194.01 3 0.0000 1.000 0 0.00 1 0.00
#> TCGA.EE.A29X.06 1 0.0000 1.000 1 0.00 0 0.00
#> TCGA.ER.A19K.01 1 0.0000 1.000 1 0.00 0 0.00
#> TCGA.FR.A3YO.06 1 0.0000 1.000 1 0.00 0 0.00
#> TCGA.RP.A694.06 3 0.0000 1.000 0 0.00 1 0.00
#> TCGA.D9.A6E9.06 1 0.0000 1.000 1 0.00 0 0.00
#> TCGA.BF.AAP4.01 1 0.0000 1.000 1 0.00 0 0.00
#> TCGA.FS.A1ZA.06 2 0.0707 0.949 0 0.98 0 0.02
#> TCGA.EB.A3XB.01 1 0.0000 1.000 1 0.00 0 0.00
#> TCGA.EE.A2MD.06 1 0.0000 1.000 1 0.00 0 0.00
#> TCGA.EB.A44Q.06 1 0.0000 1.000 1 0.00 0 0.00
#> TCGA.D3.A51J.06 1 0.0000 1.000 1 0.00 0 0.00
#> TCGA.YG.AA3N.01 1 0.0000 1.000 1 0.00 0 0.00
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> TCGA.D3.A8GJ.06 3 0.0000 0.991 0.00 0.00 1.00 0.00 0.00
#> TCGA.EB.A551.01 2 0.2616 0.859 0.00 0.88 0.00 0.02 0.10
#> TCGA.EE.A29P.06 4 0.0000 1.000 0.00 0.00 0.00 1.00 0.00
#> TCGA.D3.A2JO.06 2 0.0000 0.865 0.00 1.00 0.00 0.00 0.00
#> TCGA.EE.A29S.06 4 0.0000 1.000 0.00 0.00 0.00 1.00 0.00
#> TCGA.D3.A3C1.06 1 0.0609 0.975 0.98 0.00 0.00 0.00 0.02
#> TCGA.ER.A19O.06 1 0.0609 0.975 0.98 0.00 0.00 0.00 0.02
#> TCGA.ER.A194.01 3 0.0609 0.983 0.00 0.00 0.98 0.00 0.02
#> TCGA.EE.A29X.06 1 0.0000 0.977 1.00 0.00 0.00 0.00 0.00
#> TCGA.ER.A19K.01 1 0.0000 0.977 1.00 0.00 0.00 0.00 0.00
#> TCGA.FR.A3YO.06 1 0.0000 0.977 1.00 0.00 0.00 0.00 0.00
#> TCGA.RP.A694.06 3 0.0000 0.991 0.00 0.00 1.00 0.00 0.00
#> TCGA.D9.A6E9.06 1 0.1410 0.963 0.94 0.00 0.00 0.00 0.06
#> TCGA.BF.AAP4.01 1 0.1410 0.963 0.94 0.00 0.00 0.00 0.06
#> TCGA.FS.A1ZA.06 5 0.1732 0.000 0.00 0.08 0.00 0.00 0.92
#> TCGA.EB.A3XB.01 1 0.1410 0.963 0.94 0.00 0.00 0.00 0.06
#> TCGA.EE.A2MD.06 1 0.1410 0.963 0.94 0.00 0.00 0.00 0.06
#> TCGA.EB.A44Q.06 1 0.0000 0.977 1.00 0.00 0.00 0.00 0.00
#> TCGA.D3.A51J.06 1 0.0000 0.977 1.00 0.00 0.00 0.00 0.00
#> TCGA.YG.AA3N.01 1 0.0000 0.977 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.D3.A8GJ.06 6 0.0000 0.707 0.00 0.00 0.00 0 0.00 1.00
#> TCGA.EB.A551.01 2 0.3409 0.720 0.00 0.70 0.30 0 0.00 0.00
#> TCGA.EE.A29P.06 4 0.0000 1.000 0.00 0.00 0.00 1 0.00 0.00
#> TCGA.D3.A2JO.06 2 0.0000 0.723 0.00 1.00 0.00 0 0.00 0.00
#> TCGA.EE.A29S.06 4 0.0000 1.000 0.00 0.00 0.00 1 0.00 0.00
#> TCGA.D3.A3C1.06 1 0.0937 0.899 0.96 0.00 0.04 0 0.00 0.00
#> TCGA.ER.A19O.06 1 0.0000 0.902 1.00 0.00 0.00 0 0.00 0.00
#> TCGA.ER.A194.01 6 0.3828 0.706 0.00 0.00 0.00 0 0.44 0.56
#> TCGA.EE.A29X.06 1 0.0547 0.901 0.98 0.00 0.02 0 0.00 0.00
#> TCGA.ER.A19K.01 1 0.0547 0.901 0.98 0.00 0.02 0 0.00 0.00
#> TCGA.FR.A3YO.06 1 0.0547 0.901 0.98 0.00 0.02 0 0.00 0.00
#> TCGA.RP.A694.06 6 0.2941 0.787 0.00 0.00 0.00 0 0.22 0.78
#> TCGA.D9.A6E9.06 1 0.2631 0.846 0.82 0.00 0.18 0 0.00 0.00
#> TCGA.BF.AAP4.01 1 0.3076 0.812 0.76 0.00 0.24 0 0.00 0.00
#> TCGA.FS.A1ZA.06 5 0.4310 0.000 0.00 0.02 0.44 0 0.54 0.00
#> TCGA.EB.A3XB.01 1 0.3076 0.812 0.76 0.00 0.24 0 0.00 0.00
#> TCGA.EE.A2MD.06 1 0.3592 0.795 0.74 0.00 0.24 0 0.00 0.02
#> TCGA.EB.A44Q.06 1 0.0547 0.901 0.98 0.00 0.02 0 0.00 0.00
#> TCGA.D3.A51J.06 1 0.0937 0.897 0.96 0.00 0.04 0 0.00 0.00
#> TCGA.YG.AA3N.01 1 0.1480 0.896 0.94 0.00 0.04 0 0.02 0.00
cbind(get_classes(res, k = 7), get_membership(res, k = 7))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7
#> TCGA.D3.A8GJ.06 3 0.5401 0.000 0.00 0.0 0.44 0 0.00 0.20 0.36
#> TCGA.EB.A551.01 2 0.4278 0.510 0.00 0.5 0.46 0 0.04 0.00 0.00
#> TCGA.EE.A29P.06 4 0.0000 1.000 0.00 0.0 0.00 1 0.00 0.00 0.00
#> TCGA.D3.A2JO.06 2 0.0000 0.524 0.00 1.0 0.00 0 0.00 0.00 0.00
#> TCGA.EE.A29S.06 4 0.0000 1.000 0.00 0.0 0.00 1 0.00 0.00 0.00
#> TCGA.D3.A3C1.06 1 0.0863 0.841 0.96 0.0 0.00 0 0.00 0.00 0.04
#> TCGA.ER.A19O.06 1 0.0000 0.869 1.00 0.0 0.00 0 0.00 0.00 0.00
#> TCGA.ER.A194.01 6 0.0000 0.547 0.00 0.0 0.00 0 0.00 1.00 0.00
#> TCGA.EE.A29X.06 1 0.0000 0.869 1.00 0.0 0.00 0 0.00 0.00 0.00
#> TCGA.ER.A19K.01 1 0.0000 0.869 1.00 0.0 0.00 0 0.00 0.00 0.00
#> TCGA.FR.A3YO.06 1 0.0504 0.854 0.98 0.0 0.00 0 0.00 0.00 0.02
#> TCGA.RP.A694.06 6 0.4243 0.421 0.00 0.0 0.22 0 0.00 0.68 0.10
#> TCGA.D9.A6E9.06 1 0.3294 -0.324 0.66 0.0 0.00 0 0.00 0.00 0.34
#> TCGA.BF.AAP4.01 7 0.3546 0.955 0.46 0.0 0.00 0 0.00 0.00 0.54
#> TCGA.FS.A1ZA.06 5 0.0000 0.000 0.00 0.0 0.00 0 1.00 0.00 0.00
#> TCGA.EB.A3XB.01 7 0.3546 0.955 0.46 0.0 0.00 0 0.00 0.00 0.54
#> TCGA.EE.A2MD.06 7 0.3496 0.915 0.42 0.0 0.00 0 0.00 0.00 0.58
#> TCGA.EB.A44Q.06 1 0.0000 0.869 1.00 0.0 0.00 0 0.00 0.00 0.00
#> TCGA.D3.A51J.06 1 0.2163 0.769 0.88 0.0 0.02 0 0.00 0.00 0.10
#> TCGA.YG.AA3N.01 1 0.1664 0.810 0.92 0.0 0.02 0 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.D3.A8GJ.06 3 0.2938 0.0000 0.00 0.00 0.70 0 0 0.30 0.00 0.00
#> TCGA.EB.A551.01 2 0.2534 0.0000 0.00 0.78 0.00 0 0 0.00 0.00 0.22
#> TCGA.EE.A29P.06 4 0.0000 1.0000 0.00 0.00 0.00 1 0 0.00 0.00 0.00
#> TCGA.D3.A2JO.06 8 0.0000 0.0000 0.00 0.00 0.00 0 0 0.00 0.00 1.00
#> TCGA.EE.A29S.06 4 0.0000 1.0000 0.00 0.00 0.00 1 0 0.00 0.00 0.00
#> TCGA.D3.A3C1.06 1 0.1341 0.8042 0.92 0.00 0.00 0 0 0.00 0.08 0.00
#> TCGA.ER.A19O.06 1 0.0000 0.8638 1.00 0.00 0.00 0 0 0.00 0.00 0.00
#> TCGA.ER.A194.01 6 0.5485 0.4567 0.00 0.14 0.28 0 0 0.52 0.06 0.00
#> TCGA.EE.A29X.06 1 0.0000 0.8638 1.00 0.00 0.00 0 0 0.00 0.00 0.00
#> TCGA.ER.A19K.01 1 0.0000 0.8638 1.00 0.00 0.00 0 0 0.00 0.00 0.00
#> TCGA.FR.A3YO.06 1 0.0471 0.8544 0.98 0.00 0.00 0 0 0.00 0.02 0.00
#> TCGA.RP.A694.06 6 0.0471 0.3086 0.00 0.00 0.00 0 0 0.98 0.02 0.00
#> TCGA.D9.A6E9.06 1 0.3193 0.0279 0.62 0.00 0.00 0 0 0.00 0.38 0.00
#> TCGA.BF.AAP4.01 7 0.2852 0.9515 0.28 0.00 0.00 0 0 0.00 0.72 0.00
#> TCGA.FS.A1ZA.06 5 0.0000 0.0000 0.00 0.00 0.00 0 1 0.00 0.00 0.00
#> TCGA.EB.A3XB.01 7 0.2852 0.9515 0.28 0.00 0.00 0 0 0.00 0.72 0.00
#> TCGA.EE.A2MD.06 7 0.2534 0.9056 0.22 0.00 0.00 0 0 0.00 0.78 0.00
#> TCGA.EB.A44Q.06 1 0.0000 0.8638 1.00 0.00 0.00 0 0 0.00 0.00 0.00
#> TCGA.D3.A51J.06 1 0.3178 0.7067 0.80 0.04 0.02 0 0 0.00 0.14 0.00
#> TCGA.YG.AA3N.01 1 0.2350 0.7690 0.86 0.04 0.00 0 0 0.00 0.10 0.00
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
consensus_heatmap(res, k = 7)
consensus_heatmap(res, k = 8)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
membership_heatmap(res, k = 7)
membership_heatmap(res, k = 8)
As soon as the classes for columns are determined, the signatures that are significantly different between subgroups can be looked for. Following are the heatmaps for signatures.
get_signatures(res, k = 2)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
get_signatures(res, k = 7)
get_signatures(res, k = 8)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. To get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows (which is done by automatically selecting number of clusters).If there are too many signatures, top_signatures = ... can be set to only show the
signatures with the highest FDRs:
# code only for demonstration
# e.g. to show the top 500 most significant rows
tb = get_signature(res, k = ..., top_signatures = 500)
If the signatures are defined as these which are uniquely high in current group, diff_method argument
can be set to "uniquely_high_in_one_group":
# code only for demonstration
tb = get_signature(res, k = ..., diff_method = "uniquely_high_in_one_group")
UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
dimension_reduction(res, k = 7, method = "UMAP")
dimension_reduction(res, k = 8, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
If matrix rows can be associated to genes, consider to use functional_enrichment(res,
...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.
Parent node: Node0. Child nodes: Node011 , Node012 , Node013 , Node014-leaf , Node021 , Node022 , Node023-leaf , Node031 , Node032 , Node041 , Node042 , Node043 , Node044 , Node051 , Node052 .
The object with results only for a single top-value method and a single partitioning method can be extracted as:
res = res_rh["05"]
A summary of res and all the functions that can be applied to it:
res
#> A 'ConsensusPartition' object with k = 2, 3, 4, 5, 6, 7, 8.
#> On a matrix with 30000 rows and 68 columns.
#> Top rows (1000) are extracted by 'SD' method.
#> Subgroups are detected by 'kmeans' method.
#> Performed in total 350 partitions by row resampling.
#> Best k for subgroups seems to be 2.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_partitions"
#> [7] "compare_signatures" "consensus_heatmap" "dimension_reduction"
#> [10] "functional_enrichment" "get_anno_col" "get_anno"
#> [13] "get_classes" "get_consensus" "get_matrix"
#> [16] "get_membership" "get_param" "get_signatures"
#> [19] "get_stats" "is_best_k" "is_stable_k"
#> [22] "membership_heatmap" "ncol" "nrow"
#> [25] "plot_ecdf" "predict_classes" "rownames"
#> [28] "select_partition_number" "show" "suggest_best_k"
#> [31] "test_to_known_factors" "top_rows_heatmap"
collect_plots() function collects all the plots made from res for all k (number of subgroups)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
The plots are:
k and the heatmap of
predicted classes for each k.k.k.k.All the plots in panels can be made by individual functions and they are plotted later in this section.
select_partition_number() produces several plots showing different
statistics for choosing “optimized” k. There are following statistics:
k;k, the area increased is defined as \(A_k - A_{k-1}\).The detailed explanations of these statistics can be found in the cola vignette.
Generally speaking, higher 1-PAC score, higher mean silhouette score or higher
concordance corresponds to better partition. Rand index and Jaccard index
measure how similar the current partition is compared to partition with k-1.
If they are too similar, we won't accept k is better than k-1.
select_partition_number(res)
The numeric values for all these statistics can be obtained by get_stats().
get_stats(res)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> 2 2 1.000 0.984 0.994 0.5028 0.496 0.496
#> 3 3 0.638 0.628 0.829 0.2947 0.813 0.638
#> 4 4 0.625 0.585 0.779 0.1273 0.863 0.637
#> 5 5 0.688 0.720 0.821 0.0719 0.873 0.574
#> 6 6 0.743 0.657 0.782 0.0449 1.000 1.000
#> 7 7 0.757 0.597 0.739 0.0285 0.939 0.710
#> 8 8 0.737 0.555 0.706 0.0187 0.962 0.786
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.D3.A8GK.06 2 0.000 1.000 0.0 1.0
#> TCGA.WE.A8ZO.06 1 0.000 0.987 1.0 0.0
#> TCGA.D3.A8GI.06 1 0.000 0.987 1.0 0.0
#> TCGA.WE.A8ZM.06 2 0.000 1.000 0.0 1.0
#> TCGA.EB.A3HV.01 2 0.000 1.000 0.0 1.0
#> TCGA.HR.A5NC.01 2 0.000 1.000 0.0 1.0
#> TCGA.GN.A8LK.06 2 0.000 1.000 0.0 1.0
#> TCGA.BF.A5ER.01 1 0.000 0.987 1.0 0.0
#> TCGA.FR.A8YD.06 1 0.000 0.987 1.0 0.0
#> TCGA.FS.A4F9.06 1 0.000 0.987 1.0 0.0
#> TCGA.BF.A9VF.01 2 0.000 1.000 0.0 1.0
#> TCGA.D3.A8GC.06 1 0.000 0.987 1.0 0.0
#> TCGA.D3.A3MO.06 2 0.000 1.000 0.0 1.0
#> TCGA.ER.A42H.01 1 0.000 0.987 1.0 0.0
#> TCGA.WE.A8ZQ.06 2 0.000 1.000 0.0 1.0
#> TCGA.D3.A5GU.06 1 0.000 0.987 1.0 0.0
#> TCGA.D3.A3ML.06 1 0.000 0.987 1.0 0.0
#> TCGA.FR.A2OS.01 2 0.000 1.000 0.0 1.0
#> TCGA.D3.A2JE.06 2 0.000 1.000 0.0 1.0
#> TCGA.D3.A8GR.06 1 0.000 0.987 1.0 0.0
#> TCGA.GN.A4U9.06 2 0.000 1.000 0.0 1.0
#> TCGA.FS.A1ZR.06 2 0.000 1.000 0.0 1.0
#> TCGA.EB.A553.01 1 0.000 0.987 1.0 0.0
#> TCGA.EE.A2GP.06 2 0.000 1.000 0.0 1.0
#> TCGA.GF.A2C7.01 1 0.000 0.987 1.0 0.0
#> TCGA.BF.A5ES.01 1 0.000 0.987 1.0 0.0
#> TCGA.EE.A2A5.06 2 0.000 1.000 0.0 1.0
#> TCGA.EE.A2GC.06 2 0.000 1.000 0.0 1.0
#> TCGA.ER.A19E.06 2 0.000 1.000 0.0 1.0
#> TCGA.FS.A1ZK.06 2 0.000 1.000 0.0 1.0
#> TCGA.FS.A1ZU.06 2 0.000 1.000 0.0 1.0
#> TCGA.EB.A24D.01 1 0.000 0.987 1.0 0.0
#> TCGA.EE.A2MQ.06 1 0.000 0.987 1.0 0.0
#> TCGA.W3.A824.06 1 0.000 0.987 1.0 0.0
#> TCGA.EE.A17Z.06 2 0.000 1.000 0.0 1.0
#> TCGA.EE.A2MN.06 1 0.000 0.987 1.0 0.0
#> TCGA.ER.A19T.01 2 0.000 1.000 0.0 1.0
#> TCGA.EE.A2GN.06 2 0.000 1.000 0.0 1.0
#> TCGA.EE.A29B.06 1 0.000 0.987 1.0 0.0
#> TCGA.EE.A20H.06 2 0.000 1.000 0.0 1.0
#> TCGA.BF.A1PV.01 1 0.000 0.987 1.0 0.0
#> TCGA.ER.A198.06 1 0.971 0.333 0.6 0.4
#> TCGA.FS.A1ZJ.06 2 0.000 1.000 0.0 1.0
#> TCGA.EE.A3AC.06 2 0.000 1.000 0.0 1.0
#> TCGA.EE.A2GR.06 2 0.000 1.000 0.0 1.0
#> TCGA.FS.A1ZD.06 2 0.000 1.000 0.0 1.0
#> TCGA.FS.A1ZP.06 2 0.000 1.000 0.0 1.0
#> TCGA.RP.A695.06 1 0.000 0.987 1.0 0.0
#> TCGA.FW.A3TU.06 1 0.000 0.987 1.0 0.0
#> TCGA.EE.A2MM.06 1 0.000 0.987 1.0 0.0
#> TCGA.DA.A1IC.06 2 0.000 1.000 0.0 1.0
#> TCGA.ER.A3PL.06 2 0.000 1.000 0.0 1.0
#> TCGA.D3.A5GT.01 1 0.000 0.987 1.0 0.0
#> TCGA.DA.A1IA.06 1 0.000 0.987 1.0 0.0
#> TCGA.D9.A3Z4.01 2 0.000 1.000 0.0 1.0
#> TCGA.YD.A9TB.06 2 0.000 1.000 0.0 1.0
#> TCGA.ER.A2ND.06 2 0.000 1.000 0.0 1.0
#> TCGA.D9.A4Z3.01 2 0.000 1.000 0.0 1.0
#> TCGA.EE.A3J4.06 1 0.000 0.987 1.0 0.0
#> TCGA.IH.A3EA.01 1 0.000 0.987 1.0 0.0
#> TCGA.EB.A44O.01 2 0.000 1.000 0.0 1.0
#> TCGA.YG.AA3O.06 1 0.000 0.987 1.0 0.0
#> TCGA.W3.AA1Q.06 1 0.000 0.987 1.0 0.0
#> TCGA.YG.AA3P.06 2 0.000 1.000 0.0 1.0
#> TCGA.W3.AA1O.06 1 0.000 0.987 1.0 0.0
#> TCGA.EE.A3J7.06 1 0.000 0.987 1.0 0.0
#> TCGA.D3.A51K.06 2 0.000 1.000 0.0 1.0
#> TCGA.EB.A44P.01 2 0.000 1.000 0.0 1.0
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.D3.A8GK.06 2 0.5016 0.62535 0.00 0.76 0.24
#> TCGA.WE.A8ZO.06 3 0.5706 0.33236 0.32 0.00 0.68
#> TCGA.D3.A8GI.06 3 0.6280 0.12924 0.46 0.00 0.54
#> TCGA.WE.A8ZM.06 2 0.0000 0.78102 0.00 1.00 0.00
#> TCGA.EB.A3HV.01 2 0.6309 0.10715 0.00 0.50 0.50
#> TCGA.HR.A5NC.01 2 0.0000 0.78102 0.00 1.00 0.00
#> TCGA.GN.A8LK.06 3 0.4796 0.47307 0.00 0.22 0.78
#> TCGA.BF.A5ER.01 1 0.1529 0.90339 0.96 0.00 0.04
#> TCGA.FR.A8YD.06 1 0.0000 0.90241 1.00 0.00 0.00
#> TCGA.FS.A4F9.06 1 0.1529 0.90339 0.96 0.00 0.04
#> TCGA.BF.A9VF.01 3 0.4555 0.49750 0.00 0.20 0.80
#> TCGA.D3.A8GC.06 1 0.1529 0.90339 0.96 0.00 0.04
#> TCGA.D3.A3MO.06 2 0.0000 0.78102 0.00 1.00 0.00
#> TCGA.ER.A42H.01 1 0.0000 0.90241 1.00 0.00 0.00
#> TCGA.WE.A8ZQ.06 2 0.0892 0.77788 0.00 0.98 0.02
#> TCGA.D3.A5GU.06 1 0.0000 0.90241 1.00 0.00 0.00
#> TCGA.D3.A3ML.06 1 0.1529 0.90339 0.96 0.00 0.04
#> TCGA.FR.A2OS.01 2 0.0000 0.78102 0.00 1.00 0.00
#> TCGA.D3.A2JE.06 2 0.4555 0.71807 0.00 0.80 0.20
#> TCGA.D3.A8GR.06 1 0.6309 -0.20071 0.50 0.00 0.50
#> TCGA.GN.A4U9.06 2 0.4555 0.71807 0.00 0.80 0.20
#> TCGA.FS.A1ZR.06 2 0.5706 0.53435 0.00 0.68 0.32
#> TCGA.EB.A553.01 1 0.0892 0.89615 0.98 0.00 0.02
#> TCGA.EE.A2GP.06 2 0.5216 0.61153 0.00 0.74 0.26
#> TCGA.GF.A2C7.01 1 0.0000 0.90241 1.00 0.00 0.00
#> TCGA.BF.A5ES.01 3 0.6302 0.11999 0.48 0.00 0.52
#> TCGA.EE.A2A5.06 2 0.4555 0.71807 0.00 0.80 0.20
#> TCGA.EE.A2GC.06 3 0.4555 0.49750 0.00 0.20 0.80
#> TCGA.ER.A19E.06 2 0.0000 0.78102 0.00 1.00 0.00
#> TCGA.FS.A1ZK.06 2 0.5216 0.61153 0.00 0.74 0.26
#> TCGA.FS.A1ZU.06 2 0.4555 0.71807 0.00 0.80 0.20
#> TCGA.EB.A24D.01 1 0.0000 0.90241 1.00 0.00 0.00
#> TCGA.EE.A2MQ.06 1 0.5835 0.45506 0.66 0.00 0.34
#> TCGA.W3.A824.06 1 0.1529 0.90339 0.96 0.00 0.04
#> TCGA.EE.A17Z.06 2 0.3686 0.73188 0.00 0.86 0.14
#> TCGA.EE.A2MN.06 1 0.0000 0.90241 1.00 0.00 0.00
#> TCGA.ER.A19T.01 2 0.2537 0.76522 0.00 0.92 0.08
#> TCGA.EE.A2GN.06 2 0.0000 0.78102 0.00 1.00 0.00
#> TCGA.EE.A29B.06 1 0.1529 0.90339 0.96 0.00 0.04
#> TCGA.EE.A20H.06 2 0.0892 0.77788 0.00 0.98 0.02
#> TCGA.BF.A1PV.01 3 0.6280 0.12924 0.46 0.00 0.54
#> TCGA.ER.A198.06 3 0.6109 0.54440 0.08 0.14 0.78
#> TCGA.FS.A1ZJ.06 2 0.5406 0.70183 0.02 0.78 0.20
#> TCGA.EE.A3AC.06 3 0.4002 0.35007 0.00 0.16 0.84
#> TCGA.EE.A2GR.06 2 0.6280 0.22134 0.00 0.54 0.46
#> TCGA.FS.A1ZD.06 2 0.0892 0.77788 0.00 0.98 0.02
#> TCGA.FS.A1ZP.06 2 0.4555 0.71807 0.00 0.80 0.20
#> TCGA.RP.A695.06 3 0.6244 0.17515 0.44 0.00 0.56
#> TCGA.FW.A3TU.06 1 0.1529 0.88251 0.96 0.00 0.04
#> TCGA.EE.A2MM.06 1 0.1529 0.90339 0.96 0.00 0.04
#> TCGA.DA.A1IC.06 3 0.6126 0.05195 0.00 0.40 0.60
#> TCGA.ER.A3PL.06 2 0.6302 0.16612 0.00 0.52 0.48
#> TCGA.D3.A5GT.01 1 0.0000 0.90241 1.00 0.00 0.00
#> TCGA.DA.A1IA.06 1 0.0892 0.89615 0.98 0.00 0.02
#> TCGA.D9.A3Z4.01 2 0.0892 0.77788 0.00 0.98 0.02
#> TCGA.YD.A9TB.06 2 0.5706 0.53435 0.00 0.68 0.32
#> TCGA.ER.A2ND.06 3 0.4555 0.49750 0.00 0.20 0.80
#> TCGA.D9.A4Z3.01 2 0.4555 0.71807 0.00 0.80 0.20
#> TCGA.EE.A3J4.06 1 0.1529 0.90339 0.96 0.00 0.04
#> TCGA.IH.A3EA.01 1 0.6302 0.00399 0.52 0.00 0.48
#> TCGA.EB.A44O.01 3 0.6244 -0.09489 0.00 0.44 0.56
#> TCGA.YG.AA3O.06 3 0.6280 0.12924 0.46 0.00 0.54
#> TCGA.W3.AA1Q.06 1 0.1529 0.90339 0.96 0.00 0.04
#> TCGA.YG.AA3P.06 2 0.6495 0.66182 0.06 0.74 0.20
#> TCGA.W3.AA1O.06 1 0.2066 0.89410 0.94 0.00 0.06
#> TCGA.EE.A3J7.06 1 0.0000 0.90241 1.00 0.00 0.00
#> TCGA.D3.A51K.06 2 0.0000 0.78102 0.00 1.00 0.00
#> TCGA.EB.A44P.01 2 0.5706 0.53435 0.00 0.68 0.32
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> TCGA.D3.A8GK.06 2 0.4277 0.531 0.00 0.72 0.00 0.28
#> TCGA.WE.A8ZO.06 3 0.6453 0.428 0.08 0.00 0.56 0.36
#> TCGA.D3.A8GI.06 3 0.3853 0.696 0.16 0.00 0.82 0.02
#> TCGA.WE.A8ZM.06 2 0.0000 0.595 0.00 1.00 0.00 0.00
#> TCGA.EB.A3HV.01 2 0.7816 0.315 0.00 0.40 0.26 0.34
#> TCGA.HR.A5NC.01 2 0.0707 0.590 0.00 0.98 0.00 0.02
#> TCGA.GN.A8LK.06 3 0.6831 0.232 0.00 0.10 0.48 0.42
#> TCGA.BF.A5ER.01 1 0.0707 0.913 0.98 0.00 0.02 0.00
#> TCGA.FR.A8YD.06 1 0.1637 0.894 0.94 0.00 0.00 0.06
#> TCGA.FS.A4F9.06 1 0.0707 0.913 0.98 0.00 0.02 0.00
#> TCGA.BF.A9VF.01 3 0.6649 0.320 0.00 0.10 0.56 0.34
#> TCGA.D3.A8GC.06 1 0.0707 0.913 0.98 0.00 0.02 0.00
#> TCGA.D3.A3MO.06 2 0.0000 0.595 0.00 1.00 0.00 0.00
#> TCGA.ER.A42H.01 1 0.1637 0.894 0.94 0.00 0.00 0.06
#> TCGA.WE.A8ZQ.06 2 0.3525 0.587 0.00 0.86 0.04 0.10
#> TCGA.D3.A5GU.06 1 0.1637 0.894 0.94 0.00 0.00 0.06
#> TCGA.D3.A3ML.06 1 0.0707 0.913 0.98 0.00 0.02 0.00
#> TCGA.FR.A2OS.01 2 0.0000 0.595 0.00 1.00 0.00 0.00
#> TCGA.D3.A2JE.06 4 0.4977 0.554 0.00 0.46 0.00 0.54
#> TCGA.D3.A8GR.06 3 0.3335 0.695 0.12 0.00 0.86 0.02
#> TCGA.GN.A4U9.06 4 0.4977 0.554 0.00 0.46 0.00 0.54
#> TCGA.FS.A1ZR.06 2 0.6881 0.451 0.00 0.54 0.12 0.34
#> TCGA.EB.A553.01 1 0.4949 0.759 0.76 0.00 0.18 0.06
#> TCGA.EE.A2GP.06 2 0.4277 0.531 0.00 0.72 0.00 0.28
#> TCGA.GF.A2C7.01 1 0.1637 0.894 0.94 0.00 0.00 0.06
#> TCGA.BF.A5ES.01 3 0.2647 0.700 0.12 0.00 0.88 0.00
#> TCGA.EE.A2A5.06 2 0.3400 0.266 0.00 0.82 0.00 0.18
#> TCGA.EE.A2GC.06 3 0.7016 0.300 0.00 0.14 0.54 0.32
#> TCGA.ER.A19E.06 2 0.0000 0.595 0.00 1.00 0.00 0.00
#> TCGA.FS.A1ZK.06 2 0.6074 0.492 0.00 0.60 0.06 0.34
#> TCGA.FS.A1ZU.06 4 0.4977 0.554 0.00 0.46 0.00 0.54
#> TCGA.EB.A24D.01 1 0.1637 0.894 0.94 0.00 0.00 0.06
#> TCGA.EE.A2MQ.06 3 0.4406 0.517 0.30 0.00 0.70 0.00
#> TCGA.W3.A824.06 1 0.0707 0.913 0.98 0.00 0.02 0.00
#> TCGA.EE.A17Z.06 2 0.3172 0.295 0.00 0.84 0.00 0.16
#> TCGA.EE.A2MN.06 1 0.0707 0.913 0.98 0.00 0.02 0.00
#> TCGA.ER.A19T.01 2 0.4553 0.523 0.00 0.78 0.04 0.18
#> TCGA.EE.A2GN.06 2 0.0000 0.595 0.00 1.00 0.00 0.00
#> TCGA.EE.A29B.06 1 0.0707 0.913 0.98 0.00 0.02 0.00
#> TCGA.EE.A20H.06 2 0.2345 0.599 0.00 0.90 0.00 0.10
#> TCGA.BF.A1PV.01 3 0.3606 0.703 0.14 0.00 0.84 0.02
#> TCGA.ER.A198.06 3 0.0000 0.632 0.00 0.00 1.00 0.00
#> TCGA.FS.A1ZJ.06 4 0.5793 0.524 0.00 0.36 0.04 0.60
#> TCGA.EE.A3AC.06 4 0.5355 -0.186 0.00 0.02 0.36 0.62
#> TCGA.EE.A2GR.06 2 0.7654 0.331 0.00 0.44 0.22 0.34
#> TCGA.FS.A1ZD.06 2 0.3525 0.587 0.00 0.86 0.04 0.10
#> TCGA.FS.A1ZP.06 4 0.4994 0.538 0.00 0.48 0.00 0.52
#> TCGA.RP.A695.06 3 0.3037 0.696 0.10 0.00 0.88 0.02
#> TCGA.FW.A3TU.06 1 0.6212 0.395 0.56 0.00 0.38 0.06
#> TCGA.EE.A2MM.06 1 0.0707 0.913 0.98 0.00 0.02 0.00
#> TCGA.DA.A1IC.06 4 0.7738 -0.215 0.00 0.30 0.26 0.44
#> TCGA.ER.A3PL.06 2 0.7816 0.315 0.00 0.40 0.26 0.34
#> TCGA.D3.A5GT.01 1 0.1637 0.894 0.94 0.00 0.00 0.06
#> TCGA.DA.A1IA.06 1 0.3611 0.844 0.86 0.00 0.08 0.06
#> TCGA.D9.A3Z4.01 2 0.3037 0.592 0.00 0.88 0.02 0.10
#> TCGA.YD.A9TB.06 2 0.6649 0.467 0.00 0.56 0.10 0.34
#> TCGA.ER.A2ND.06 3 0.6570 0.302 0.00 0.10 0.58 0.32
#> TCGA.D9.A4Z3.01 4 0.4977 0.554 0.00 0.46 0.00 0.54
#> TCGA.EE.A3J4.06 1 0.0707 0.913 0.98 0.00 0.02 0.00
#> TCGA.IH.A3EA.01 3 0.4642 0.606 0.24 0.00 0.74 0.02
#> TCGA.EB.A44O.01 4 0.7684 -0.320 0.00 0.36 0.22 0.42
#> TCGA.YG.AA3O.06 3 0.3606 0.703 0.14 0.00 0.84 0.02
#> TCGA.W3.AA1Q.06 1 0.0707 0.913 0.98 0.00 0.02 0.00
#> TCGA.YG.AA3P.06 4 0.6362 0.477 0.04 0.26 0.04 0.66
#> TCGA.W3.AA1O.06 1 0.4855 0.343 0.60 0.00 0.40 0.00
#> TCGA.EE.A3J7.06 1 0.0707 0.913 0.98 0.00 0.02 0.00
#> TCGA.D3.A51K.06 2 0.0000 0.595 0.00 1.00 0.00 0.00
#> TCGA.EB.A44P.01 2 0.6881 0.451 0.00 0.54 0.12 0.34
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> TCGA.D3.A8GK.06 2 0.4798 -0.0239 0.00 0.54 0.00 0.02 0.44
#> TCGA.WE.A8ZO.06 4 0.6000 0.3861 0.06 0.00 0.24 0.64 0.06
#> TCGA.D3.A8GI.06 3 0.2438 0.8730 0.06 0.00 0.90 0.00 0.04
#> TCGA.WE.A8ZM.06 2 0.0000 0.7910 0.00 1.00 0.00 0.00 0.00
#> TCGA.EB.A3HV.01 5 0.5588 0.4790 0.00 0.38 0.02 0.04 0.56
#> TCGA.HR.A5NC.01 2 0.0609 0.7890 0.00 0.98 0.00 0.02 0.00
#> TCGA.GN.A8LK.06 5 0.3455 0.7180 0.00 0.04 0.06 0.04 0.86
#> TCGA.BF.A5ER.01 1 0.0609 0.8810 0.98 0.00 0.02 0.00 0.00
#> TCGA.FR.A8YD.06 1 0.4974 0.8310 0.76 0.00 0.06 0.12 0.06
#> TCGA.FS.A4F9.06 1 0.0609 0.8810 0.98 0.00 0.02 0.00 0.00
#> TCGA.BF.A9VF.01 5 0.3521 0.6995 0.00 0.04 0.14 0.00 0.82
#> TCGA.D3.A8GC.06 1 0.0609 0.8810 0.98 0.00 0.02 0.00 0.00
#> TCGA.D3.A3MO.06 2 0.0000 0.7910 0.00 1.00 0.00 0.00 0.00
#> TCGA.ER.A42H.01 1 0.4389 0.8524 0.80 0.00 0.04 0.10 0.06
#> TCGA.WE.A8ZQ.06 2 0.3700 0.7373 0.00 0.84 0.02 0.06 0.08
#> TCGA.D3.A5GU.06 1 0.4389 0.8504 0.80 0.00 0.04 0.10 0.06
#> TCGA.D3.A3ML.06 1 0.0609 0.8810 0.98 0.00 0.02 0.00 0.00
#> TCGA.FR.A2OS.01 2 0.0609 0.7838 0.00 0.98 0.00 0.02 0.00
#> TCGA.D3.A2JE.06 4 0.3684 0.8337 0.00 0.28 0.00 0.72 0.00
#> TCGA.D3.A8GR.06 3 0.3455 0.8161 0.04 0.00 0.86 0.06 0.04
#> TCGA.GN.A4U9.06 4 0.3684 0.8337 0.00 0.28 0.00 0.72 0.00
#> TCGA.FS.A1ZR.06 5 0.4798 0.4091 0.00 0.44 0.00 0.02 0.54
#> TCGA.EB.A553.01 1 0.6254 0.6876 0.64 0.00 0.20 0.10 0.06
#> TCGA.EE.A2GP.06 2 0.3319 0.6102 0.00 0.82 0.00 0.02 0.16
#> TCGA.GF.A2C7.01 1 0.4389 0.8524 0.80 0.00 0.04 0.10 0.06
#> TCGA.BF.A5ES.01 3 0.2331 0.8556 0.02 0.00 0.90 0.00 0.08
#> TCGA.EE.A2A5.06 2 0.3274 0.4814 0.00 0.78 0.00 0.22 0.00
#> TCGA.EE.A2GC.06 5 0.3878 0.7130 0.00 0.04 0.12 0.02 0.82
#> TCGA.ER.A19E.06 2 0.0000 0.7910 0.00 1.00 0.00 0.00 0.00
#> TCGA.FS.A1ZK.06 5 0.4227 0.2882 0.00 0.42 0.00 0.00 0.58
#> TCGA.FS.A1ZU.06 4 0.3684 0.8337 0.00 0.28 0.00 0.72 0.00
#> TCGA.EB.A24D.01 1 0.5389 0.8041 0.72 0.00 0.06 0.16 0.06
#> TCGA.EE.A2MQ.06 3 0.2280 0.8441 0.12 0.00 0.88 0.00 0.00
#> TCGA.W3.A824.06 1 0.0609 0.8810 0.98 0.00 0.02 0.00 0.00
#> TCGA.EE.A17Z.06 2 0.3424 0.4308 0.00 0.76 0.00 0.24 0.00
#> TCGA.EE.A2MN.06 1 0.3034 0.8644 0.88 0.00 0.02 0.06 0.04
#> TCGA.ER.A19T.01 2 0.6094 0.2635 0.00 0.54 0.02 0.08 0.36
#> TCGA.EE.A2GN.06 2 0.0000 0.7910 0.00 1.00 0.00 0.00 0.00
#> TCGA.EE.A29B.06 1 0.1216 0.8782 0.96 0.00 0.02 0.02 0.00
#> TCGA.EE.A20H.06 2 0.2438 0.7683 0.00 0.90 0.00 0.04 0.06
#> TCGA.BF.A1PV.01 3 0.2438 0.8751 0.04 0.00 0.90 0.00 0.06
#> TCGA.ER.A198.06 3 0.2280 0.8259 0.00 0.00 0.88 0.00 0.12
#> TCGA.FS.A1ZJ.06 4 0.4449 0.7648 0.00 0.14 0.02 0.78 0.06
#> TCGA.EE.A3AC.06 5 0.4106 0.6710 0.00 0.02 0.04 0.14 0.80
#> TCGA.EE.A2GR.06 5 0.3106 0.7247 0.00 0.14 0.00 0.02 0.84
#> TCGA.FS.A1ZD.06 2 0.2797 0.7574 0.00 0.88 0.00 0.06 0.06
#> TCGA.FS.A1ZP.06 4 0.3684 0.8337 0.00 0.28 0.00 0.72 0.00
#> TCGA.RP.A695.06 3 0.2754 0.8672 0.04 0.00 0.88 0.00 0.08
#> TCGA.FW.A3TU.06 3 0.6254 0.5553 0.20 0.00 0.64 0.10 0.06
#> TCGA.EE.A2MM.06 1 0.1216 0.8782 0.96 0.00 0.02 0.02 0.00
#> TCGA.DA.A1IC.06 5 0.3106 0.7296 0.00 0.14 0.00 0.02 0.84
#> TCGA.ER.A3PL.06 5 0.5534 0.5119 0.00 0.36 0.02 0.04 0.58
#> TCGA.D3.A5GT.01 1 0.4389 0.8524 0.80 0.00 0.04 0.10 0.06
#> TCGA.DA.A1IA.06 1 0.5677 0.7983 0.70 0.00 0.06 0.16 0.08
#> TCGA.D9.A3Z4.01 2 0.2438 0.7683 0.00 0.90 0.00 0.04 0.06
#> TCGA.YD.A9TB.06 2 0.5173 -0.2998 0.00 0.50 0.00 0.04 0.46
#> TCGA.ER.A2ND.06 5 0.4042 0.7165 0.00 0.04 0.10 0.04 0.82
#> TCGA.D9.A4Z3.01 4 0.3684 0.8337 0.00 0.28 0.00 0.72 0.00
#> TCGA.EE.A3J4.06 1 0.0609 0.8810 0.98 0.00 0.02 0.00 0.00
#> TCGA.IH.A3EA.01 3 0.2331 0.8660 0.08 0.00 0.90 0.00 0.02
#> TCGA.EB.A44O.01 5 0.2873 0.7289 0.00 0.12 0.00 0.02 0.86
#> TCGA.YG.AA3O.06 3 0.2438 0.8751 0.04 0.00 0.90 0.00 0.06
#> TCGA.W3.AA1Q.06 1 0.0609 0.8810 0.98 0.00 0.02 0.00 0.00
#> TCGA.YG.AA3P.06 4 0.3099 0.6928 0.00 0.04 0.04 0.88 0.04
#> TCGA.W3.AA1O.06 3 0.3684 0.6852 0.28 0.00 0.72 0.00 0.00
#> TCGA.EE.A3J7.06 1 0.1648 0.8785 0.94 0.00 0.00 0.04 0.02
#> TCGA.D3.A51K.06 2 0.0000 0.7910 0.00 1.00 0.00 0.00 0.00
#> TCGA.EB.A44P.01 5 0.4798 0.4091 0.00 0.44 0.00 0.02 0.54
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> TCGA.D3.A8GK.06 2 0.3828 0.12677 0.00 0.56 0.00 0.00 0.44 0.00
#> TCGA.WE.A8ZO.06 4 0.7201 0.23482 0.22 0.00 0.24 0.46 0.04 0.04
#> TCGA.D3.A8GI.06 3 0.0000 0.83940 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.WE.A8ZM.06 2 0.1556 0.73460 0.00 0.92 0.00 0.08 0.00 0.00
#> TCGA.EB.A3HV.01 5 0.5523 0.32343 0.14 0.36 0.00 0.00 0.50 0.00
#> TCGA.HR.A5NC.01 2 0.0547 0.72778 0.00 0.98 0.00 0.00 0.02 0.00
#> TCGA.GN.A8LK.06 5 0.4864 0.65563 0.26 0.00 0.02 0.06 0.66 0.00
#> TCGA.BF.A5ER.01 6 0.3409 0.80505 0.30 0.00 0.00 0.00 0.00 0.70
#> TCGA.FR.A8YD.06 6 0.3321 0.66679 0.08 0.00 0.00 0.10 0.00 0.82
#> TCGA.FS.A4F9.06 6 0.3409 0.80505 0.30 0.00 0.00 0.00 0.00 0.70
#> TCGA.BF.A9VF.01 5 0.2474 0.70406 0.00 0.00 0.08 0.04 0.88 0.00
#> TCGA.D3.A8GC.06 6 0.3409 0.80505 0.30 0.00 0.00 0.00 0.00 0.70
#> TCGA.D3.A3MO.06 2 0.1556 0.73460 0.00 0.92 0.00 0.08 0.00 0.00
#> TCGA.ER.A42H.01 6 0.1092 0.72730 0.02 0.00 0.00 0.02 0.00 0.96
#> TCGA.WE.A8ZQ.06 2 0.4008 0.65714 0.06 0.80 0.00 0.08 0.06 0.00
#> TCGA.D3.A5GU.06 6 0.1092 0.72818 0.02 0.00 0.00 0.02 0.00 0.96
#> TCGA.D3.A3ML.06 6 0.3409 0.80505 0.30 0.00 0.00 0.00 0.00 0.70
#> TCGA.FR.A2OS.01 2 0.1807 0.73438 0.00 0.92 0.00 0.06 0.02 0.00
#> TCGA.D3.A2JE.06 4 0.3076 0.77127 0.00 0.24 0.00 0.76 0.00 0.00
#> TCGA.D3.A8GR.06 3 0.3499 0.74178 0.32 0.00 0.68 0.00 0.00 0.00
#> TCGA.GN.A4U9.06 4 0.2941 0.76762 0.00 0.22 0.00 0.78 0.00 0.00
#> TCGA.FS.A1ZR.06 5 0.4067 0.52911 0.04 0.26 0.00 0.00 0.70 0.00
#> TCGA.EB.A553.01 6 0.6251 0.00277 0.28 0.00 0.22 0.02 0.00 0.48
#> TCGA.EE.A2GP.06 2 0.3950 0.55987 0.00 0.72 0.00 0.04 0.24 0.00
#> TCGA.GF.A2C7.01 6 0.1092 0.72730 0.02 0.00 0.00 0.02 0.00 0.96
#> TCGA.BF.A5ES.01 3 0.3309 0.76514 0.28 0.00 0.72 0.00 0.00 0.00
#> TCGA.EE.A2A5.06 2 0.3076 0.55844 0.00 0.76 0.00 0.24 0.00 0.00
#> TCGA.EE.A2GC.06 5 0.3697 0.70024 0.06 0.00 0.08 0.04 0.82 0.00
#> TCGA.ER.A19E.06 2 0.1556 0.73460 0.00 0.92 0.00 0.08 0.00 0.00
#> TCGA.FS.A1ZK.06 5 0.4360 0.50471 0.00 0.26 0.00 0.06 0.68 0.00
#> TCGA.FS.A1ZU.06 4 0.3076 0.77127 0.00 0.24 0.00 0.76 0.00 0.00
#> TCGA.EB.A24D.01 6 0.3321 0.66072 0.08 0.00 0.00 0.10 0.00 0.82
#> TCGA.EE.A2MQ.06 3 0.0937 0.82459 0.00 0.00 0.96 0.00 0.00 0.04
#> TCGA.W3.A824.06 6 0.3409 0.80505 0.30 0.00 0.00 0.00 0.00 0.70
#> TCGA.EE.A17Z.06 2 0.3076 0.55187 0.00 0.76 0.00 0.24 0.00 0.00
#> TCGA.EE.A2MN.06 6 0.4265 0.77325 0.30 0.00 0.00 0.04 0.00 0.66
#> TCGA.ER.A19T.01 2 0.7197 0.04528 0.24 0.40 0.00 0.10 0.26 0.00
#> TCGA.EE.A2GN.06 2 0.1556 0.73460 0.00 0.92 0.00 0.08 0.00 0.00
#> TCGA.EE.A29B.06 6 0.3309 0.79866 0.28 0.00 0.00 0.00 0.00 0.72
#> TCGA.EE.A20H.06 2 0.3420 0.68483 0.06 0.84 0.00 0.06 0.04 0.00
#> TCGA.BF.A1PV.01 3 0.0000 0.83940 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.ER.A198.06 3 0.3309 0.76514 0.28 0.00 0.72 0.00 0.00 0.00
#> TCGA.FS.A1ZJ.06 4 0.3156 0.67713 0.00 0.18 0.00 0.80 0.00 0.02
#> TCGA.EE.A3AC.06 5 0.4851 0.67571 0.20 0.00 0.04 0.06 0.70 0.00
#> TCGA.EE.A2GR.06 5 0.1480 0.70576 0.02 0.04 0.00 0.00 0.94 0.00
#> TCGA.FS.A1ZD.06 2 0.3420 0.68395 0.06 0.84 0.00 0.06 0.04 0.00
#> TCGA.FS.A1ZP.06 4 0.3076 0.77127 0.00 0.24 0.00 0.76 0.00 0.00
#> TCGA.RP.A695.06 3 0.0000 0.83940 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.FW.A3TU.06 3 0.6047 0.45770 0.34 0.00 0.40 0.00 0.00 0.26
#> TCGA.EE.A2MM.06 6 0.3409 0.80505 0.30 0.00 0.00 0.00 0.00 0.70
#> TCGA.DA.A1IC.06 5 0.3679 0.69923 0.20 0.00 0.04 0.00 0.76 0.00
#> TCGA.ER.A3PL.06 5 0.5102 0.53184 0.14 0.24 0.00 0.00 0.62 0.00
#> TCGA.D3.A5GT.01 6 0.1092 0.72730 0.02 0.00 0.00 0.02 0.00 0.96
#> TCGA.DA.A1IA.06 6 0.4482 0.35975 0.36 0.00 0.00 0.04 0.00 0.60
#> TCGA.D9.A3Z4.01 2 0.3103 0.69318 0.06 0.86 0.00 0.04 0.04 0.00
#> TCGA.YD.A9TB.06 2 0.4632 -0.09254 0.04 0.52 0.00 0.00 0.44 0.00
#> TCGA.ER.A2ND.06 5 0.4962 0.61125 0.18 0.08 0.00 0.04 0.70 0.00
#> TCGA.D9.A4Z3.01 4 0.3076 0.77127 0.00 0.24 0.00 0.76 0.00 0.00
#> TCGA.EE.A3J4.06 6 0.3409 0.80505 0.30 0.00 0.00 0.00 0.00 0.70
#> TCGA.IH.A3EA.01 3 0.0000 0.83940 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.EB.A44O.01 5 0.3679 0.69300 0.20 0.00 0.00 0.04 0.76 0.00
#> TCGA.YG.AA3O.06 3 0.0000 0.83940 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.W3.AA1Q.06 6 0.3409 0.80505 0.30 0.00 0.00 0.00 0.00 0.70
#> TCGA.YG.AA3P.06 4 0.4165 0.53174 0.16 0.00 0.00 0.74 0.00 0.10
#> TCGA.W3.AA1O.06 3 0.3045 0.76069 0.06 0.00 0.84 0.00 0.00 0.10
#> TCGA.EE.A3J7.06 6 0.3409 0.80143 0.30 0.00 0.00 0.00 0.00 0.70
#> TCGA.D3.A51K.06 2 0.1556 0.73460 0.00 0.92 0.00 0.08 0.00 0.00
#> TCGA.EB.A44P.01 5 0.4067 0.52911 0.04 0.26 0.00 0.00 0.70 0.00
cbind(get_classes(res, k = 7), get_membership(res, k = 7))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7
#> TCGA.D3.A8GK.06 2 0.4146 0.3798 0.00 0.68 0.00 0.00 0.24 0.00 0.08
#> TCGA.WE.A8ZO.06 4 0.7554 0.0857 0.28 0.00 0.18 0.38 0.10 0.02 0.04
#> TCGA.D3.A8GI.06 3 0.0000 0.9092 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.WE.A8ZM.06 2 0.0000 0.7192 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EB.A3HV.01 7 0.5055 0.4895 0.00 0.18 0.00 0.00 0.26 0.00 0.56
#> TCGA.HR.A5NC.01 2 0.2945 0.4362 0.00 0.74 0.00 0.00 0.00 0.00 0.26
#> TCGA.GN.A8LK.06 5 0.5588 0.5177 0.14 0.00 0.02 0.04 0.62 0.00 0.18
#> TCGA.BF.A5ER.01 6 0.0000 0.8390 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.FR.A8YD.06 6 0.5617 0.5974 0.30 0.00 0.00 0.06 0.00 0.54 0.10
#> TCGA.FS.A4F9.06 6 0.0000 0.8390 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.BF.A9VF.01 5 0.2769 0.5364 0.02 0.00 0.08 0.00 0.86 0.00 0.04
#> TCGA.D3.A8GC.06 6 0.0000 0.8390 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.D3.A3MO.06 2 0.0000 0.7192 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.ER.A42H.01 6 0.4429 0.7149 0.22 0.00 0.00 0.00 0.00 0.66 0.12
#> TCGA.WE.A8ZQ.06 7 0.3562 -0.1811 0.00 0.50 0.00 0.00 0.00 0.00 0.50
#> TCGA.D3.A5GU.06 6 0.4146 0.7202 0.24 0.00 0.00 0.00 0.00 0.68 0.08
#> TCGA.D3.A3ML.06 6 0.0000 0.8390 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.FR.A2OS.01 2 0.0000 0.7192 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D3.A2JE.06 4 0.1886 0.8160 0.00 0.12 0.00 0.88 0.00 0.00 0.00
#> TCGA.D3.A8GR.06 1 0.4954 0.6124 0.52 0.00 0.40 0.00 0.04 0.00 0.04
#> TCGA.GN.A4U9.06 4 0.1886 0.8160 0.00 0.12 0.00 0.88 0.00 0.00 0.00
#> TCGA.FS.A1ZR.06 5 0.5830 -0.0097 0.02 0.28 0.00 0.00 0.46 0.00 0.24
#> TCGA.EB.A553.01 1 0.4353 0.5956 0.66 0.00 0.24 0.00 0.00 0.10 0.00
#> TCGA.EE.A2GP.06 2 0.2572 0.5923 0.00 0.86 0.00 0.00 0.06 0.00 0.08
#> TCGA.GF.A2C7.01 6 0.4429 0.7149 0.22 0.00 0.00 0.00 0.00 0.66 0.12
#> TCGA.BF.A5ES.01 1 0.4995 0.5531 0.46 0.00 0.46 0.00 0.04 0.00 0.04
#> TCGA.EE.A2A5.06 2 0.3186 0.5265 0.00 0.76 0.00 0.22 0.02 0.00 0.00
#> TCGA.EE.A2GC.06 5 0.1363 0.5580 0.02 0.00 0.04 0.00 0.94 0.00 0.00
#> TCGA.ER.A19E.06 2 0.0000 0.7192 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FS.A1ZK.06 5 0.4813 0.3289 0.02 0.24 0.00 0.00 0.64 0.00 0.10
#> TCGA.FS.A1ZU.06 4 0.1886 0.8160 0.00 0.12 0.00 0.88 0.00 0.00 0.00
#> TCGA.EB.A24D.01 6 0.5743 0.5314 0.34 0.00 0.00 0.08 0.00 0.50 0.08
#> TCGA.EE.A2MQ.06 3 0.0863 0.8689 0.00 0.00 0.96 0.00 0.00 0.04 0.00
#> TCGA.W3.A824.06 6 0.0000 0.8390 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.EE.A17Z.06 2 0.2422 0.5786 0.00 0.82 0.00 0.18 0.00 0.00 0.00
#> TCGA.EE.A2MN.06 6 0.3680 0.7331 0.14 0.00 0.00 0.06 0.00 0.78 0.02
#> TCGA.ER.A19T.01 7 0.6026 0.1144 0.06 0.14 0.00 0.04 0.16 0.00 0.60
#> TCGA.EE.A2GN.06 2 0.0000 0.7192 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EE.A29B.06 6 0.1006 0.8312 0.02 0.00 0.00 0.00 0.00 0.96 0.02
#> TCGA.EE.A20H.06 2 0.3496 0.1149 0.00 0.58 0.00 0.00 0.00 0.00 0.42
#> TCGA.BF.A1PV.01 3 0.0000 0.9092 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.ER.A198.06 1 0.4995 0.5531 0.46 0.00 0.46 0.00 0.04 0.00 0.04
#> TCGA.FS.A1ZJ.06 4 0.4193 0.6656 0.04 0.04 0.00 0.72 0.00 0.00 0.20
#> TCGA.EE.A3AC.06 5 0.5566 0.5569 0.14 0.00 0.02 0.06 0.64 0.00 0.14
#> TCGA.EE.A2GR.06 5 0.3526 0.4579 0.00 0.06 0.00 0.00 0.76 0.00 0.18
#> TCGA.FS.A1ZD.06 2 0.3546 0.0374 0.00 0.54 0.00 0.00 0.00 0.00 0.46
#> TCGA.FS.A1ZP.06 4 0.1886 0.8160 0.00 0.12 0.00 0.88 0.00 0.00 0.00
#> TCGA.RP.A695.06 3 0.1006 0.8678 0.02 0.00 0.96 0.00 0.02 0.00 0.00
#> TCGA.FW.A3TU.06 1 0.5157 0.6535 0.60 0.00 0.30 0.00 0.04 0.04 0.02
#> TCGA.EE.A2MM.06 6 0.0504 0.8333 0.00 0.00 0.00 0.00 0.00 0.98 0.02
#> TCGA.DA.A1IC.06 5 0.5763 0.5690 0.14 0.02 0.02 0.04 0.64 0.00 0.14
#> TCGA.ER.A3PL.06 7 0.5007 0.4691 0.00 0.16 0.00 0.00 0.28 0.00 0.56
#> TCGA.D3.A5GT.01 6 0.4429 0.7149 0.22 0.00 0.00 0.00 0.00 0.66 0.12
#> TCGA.DA.A1IA.06 1 0.2912 0.4659 0.82 0.00 0.04 0.00 0.00 0.14 0.00
#> TCGA.D9.A3Z4.01 2 0.3358 0.2585 0.00 0.64 0.00 0.00 0.00 0.00 0.36
#> TCGA.YD.A9TB.06 7 0.5467 0.4315 0.00 0.28 0.00 0.00 0.26 0.00 0.46
#> TCGA.ER.A2ND.06 5 0.5007 0.1114 0.16 0.00 0.00 0.00 0.56 0.00 0.28
#> TCGA.D9.A4Z3.01 4 0.1886 0.8160 0.00 0.12 0.00 0.88 0.00 0.00 0.00
#> TCGA.EE.A3J4.06 6 0.0000 0.8390 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.IH.A3EA.01 3 0.0000 0.9092 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.EB.A44O.01 5 0.5763 0.5690 0.14 0.02 0.02 0.04 0.64 0.00 0.14
#> TCGA.YG.AA3O.06 3 0.0000 0.9092 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.W3.AA1Q.06 6 0.0000 0.8390 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.YG.AA3P.06 4 0.4478 0.5604 0.20 0.00 0.00 0.66 0.00 0.00 0.14
#> TCGA.W3.AA1O.06 3 0.3052 0.5726 0.02 0.00 0.78 0.00 0.00 0.20 0.00
#> TCGA.EE.A3J7.06 6 0.1363 0.8272 0.04 0.00 0.00 0.00 0.00 0.94 0.02
#> TCGA.D3.A51K.06 2 0.0000 0.7192 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EB.A44P.01 5 0.5830 -0.0097 0.02 0.28 0.00 0.00 0.46 0.00 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.D3.A8GK.06 2 0.4534 0.3698 0.04 0.62 0.00 0.02 0.30 0.00 0.00 0.02
#> TCGA.WE.A8ZO.06 7 0.7063 0.2629 0.10 0.00 0.12 0.24 0.02 0.00 0.44 0.08
#> TCGA.D3.A8GI.06 3 0.0000 0.8981 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.WE.A8ZM.06 2 0.3135 0.7157 0.02 0.82 0.00 0.12 0.02 0.00 0.00 0.02
#> TCGA.EB.A3HV.01 5 0.5145 0.3733 0.26 0.18 0.00 0.00 0.54 0.00 0.02 0.00
#> TCGA.HR.A5NC.01 2 0.3847 0.6854 0.06 0.78 0.00 0.10 0.00 0.00 0.02 0.04
#> TCGA.GN.A8LK.06 5 0.6598 0.1686 0.28 0.06 0.00 0.00 0.36 0.00 0.26 0.04
#> TCGA.BF.A5ER.01 6 0.0000 0.7383 0.00 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.FR.A8YD.06 6 0.5211 0.2690 0.00 0.00 0.00 0.00 0.00 0.40 0.34 0.26
#> TCGA.FS.A4F9.06 6 0.0000 0.7383 0.00 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.BF.A9VF.01 5 0.4727 0.4921 0.20 0.00 0.10 0.00 0.66 0.00 0.02 0.02
#> TCGA.D3.A8GC.06 6 0.0000 0.7383 0.00 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.D3.A3MO.06 2 0.2224 0.7165 0.00 0.86 0.00 0.12 0.00 0.00 0.00 0.02
#> TCGA.ER.A42H.01 6 0.3329 0.4500 0.00 0.00 0.00 0.00 0.00 0.52 0.00 0.48
#> TCGA.WE.A8ZQ.06 2 0.6661 0.1879 0.12 0.48 0.00 0.00 0.08 0.00 0.20 0.12
#> TCGA.D3.A5GU.06 6 0.3618 0.5121 0.00 0.00 0.00 0.00 0.00 0.60 0.02 0.38
#> TCGA.D3.A3ML.06 6 0.0000 0.7383 0.00 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.FR.A2OS.01 2 0.2547 0.7115 0.00 0.84 0.00 0.12 0.04 0.00 0.00 0.00
#> TCGA.D3.A2JE.06 4 0.0941 0.8622 0.00 0.00 0.00 0.96 0.00 0.00 0.02 0.02
#> TCGA.D3.A8GR.06 1 0.5386 0.4844 0.48 0.00 0.28 0.00 0.00 0.00 0.02 0.22
#> TCGA.GN.A4U9.06 4 0.0808 0.8544 0.00 0.00 0.00 0.96 0.00 0.00 0.00 0.04
#> TCGA.FS.A1ZR.06 5 0.1765 0.5507 0.00 0.12 0.00 0.00 0.88 0.00 0.00 0.00
#> TCGA.EB.A553.01 8 0.6523 0.6639 0.30 0.00 0.14 0.00 0.00 0.14 0.02 0.40
#> TCGA.EE.A2GP.06 2 0.2406 0.6068 0.00 0.80 0.00 0.00 0.20 0.00 0.00 0.00
#> TCGA.GF.A2C7.01 6 0.3329 0.4500 0.00 0.00 0.00 0.00 0.00 0.52 0.00 0.48
#> TCGA.BF.A5ES.01 1 0.4996 0.4926 0.48 0.00 0.32 0.00 0.00 0.00 0.00 0.20
#> TCGA.EE.A2A5.06 2 0.4556 0.3875 0.00 0.54 0.00 0.38 0.02 0.00 0.00 0.06
#> TCGA.EE.A2GC.06 5 0.5158 0.5109 0.26 0.02 0.06 0.00 0.60 0.00 0.06 0.00
#> TCGA.ER.A19E.06 2 0.2680 0.7163 0.02 0.84 0.00 0.12 0.00 0.00 0.00 0.02
#> TCGA.FS.A1ZK.06 5 0.6108 0.2670 0.18 0.32 0.00 0.00 0.40 0.00 0.10 0.00
#> TCGA.FS.A1ZU.06 4 0.0471 0.8643 0.00 0.00 0.00 0.98 0.00 0.00 0.02 0.00
#> TCGA.EB.A24D.01 6 0.5252 0.1983 0.00 0.00 0.00 0.00 0.00 0.36 0.36 0.28
#> TCGA.EE.A2MQ.06 3 0.0471 0.8864 0.00 0.00 0.98 0.00 0.00 0.02 0.00 0.00
#> TCGA.W3.A824.06 6 0.0000 0.7383 0.00 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.EE.A17Z.06 2 0.4028 0.5538 0.00 0.66 0.00 0.28 0.02 0.00 0.00 0.04
#> TCGA.EE.A2MN.06 6 0.3991 0.4832 0.00 0.00 0.00 0.00 0.00 0.62 0.32 0.06
#> TCGA.ER.A19T.01 7 0.6350 0.1450 0.08 0.20 0.00 0.00 0.12 0.00 0.52 0.08
#> TCGA.EE.A2GN.06 2 0.2224 0.7134 0.00 0.86 0.00 0.12 0.00 0.00 0.00 0.02
#> TCGA.EE.A29B.06 6 0.2114 0.6747 0.00 0.00 0.00 0.00 0.00 0.84 0.00 0.16
#> TCGA.EE.A20H.06 2 0.4744 0.4825 0.08 0.70 0.00 0.00 0.02 0.00 0.12 0.08
#> TCGA.BF.A1PV.01 3 0.0000 0.8981 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.ER.A198.06 1 0.5355 0.5021 0.48 0.00 0.30 0.00 0.00 0.00 0.02 0.20
#> TCGA.FS.A1ZJ.06 4 0.5072 0.3548 0.00 0.06 0.00 0.62 0.02 0.00 0.24 0.06
#> TCGA.EE.A3AC.06 5 0.6724 0.3691 0.26 0.00 0.00 0.10 0.44 0.00 0.12 0.08
#> TCGA.EE.A2GR.06 5 0.3299 0.5620 0.18 0.06 0.00 0.00 0.76 0.00 0.00 0.00
#> TCGA.FS.A1ZD.06 2 0.6045 0.3528 0.10 0.58 0.00 0.00 0.08 0.00 0.12 0.12
#> TCGA.FS.A1ZP.06 4 0.0808 0.8544 0.00 0.00 0.00 0.96 0.00 0.00 0.00 0.04
#> TCGA.RP.A695.06 3 0.1741 0.8693 0.02 0.00 0.92 0.00 0.00 0.00 0.04 0.02
#> TCGA.FW.A3TU.06 1 0.5575 -0.0187 0.46 0.00 0.18 0.00 0.00 0.04 0.00 0.32
#> TCGA.EE.A2MM.06 6 0.0000 0.7383 0.00 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.DA.A1IC.06 5 0.6050 0.5011 0.26 0.06 0.00 0.00 0.52 0.00 0.10 0.06
#> TCGA.ER.A3PL.06 5 0.5145 0.3733 0.26 0.18 0.00 0.00 0.54 0.00 0.02 0.00
#> TCGA.D3.A5GT.01 6 0.3329 0.4500 0.00 0.00 0.00 0.00 0.00 0.52 0.00 0.48
#> TCGA.DA.A1IA.06 8 0.6162 0.7123 0.32 0.00 0.02 0.00 0.00 0.14 0.08 0.44
#> TCGA.D9.A3Z4.01 2 0.5298 0.4453 0.08 0.66 0.00 0.00 0.06 0.00 0.12 0.08
#> TCGA.YD.A9TB.06 5 0.4898 0.3052 0.12 0.30 0.00 0.00 0.56 0.00 0.02 0.00
#> TCGA.ER.A2ND.06 1 0.4276 -0.1694 0.64 0.06 0.00 0.00 0.28 0.00 0.02 0.00
#> TCGA.D9.A4Z3.01 4 0.0471 0.8659 0.00 0.00 0.00 0.98 0.00 0.00 0.00 0.02
#> TCGA.EE.A3J4.06 6 0.0000 0.7383 0.00 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.IH.A3EA.01 3 0.0941 0.8960 0.00 0.00 0.96 0.00 0.00 0.00 0.02 0.02
#> TCGA.EB.A44O.01 5 0.5823 0.4895 0.26 0.04 0.00 0.00 0.54 0.00 0.10 0.06
#> TCGA.YG.AA3O.06 3 0.0941 0.8960 0.00 0.00 0.96 0.00 0.00 0.00 0.02 0.02
#> TCGA.W3.AA1Q.06 6 0.0000 0.7383 0.00 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.YG.AA3P.06 7 0.3015 0.1682 0.00 0.00 0.00 0.32 0.00 0.00 0.68 0.00
#> TCGA.W3.AA1O.06 3 0.3735 0.5240 0.02 0.00 0.72 0.00 0.00 0.22 0.00 0.04
#> TCGA.EE.A3J7.06 6 0.1557 0.7125 0.00 0.00 0.00 0.00 0.00 0.92 0.02 0.06
#> TCGA.D3.A51K.06 2 0.3320 0.7003 0.00 0.80 0.00 0.12 0.04 0.00 0.00 0.04
#> TCGA.EB.A44P.01 5 0.1765 0.5507 0.00 0.12 0.00 0.00 0.88 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: Node05. Child nodes: Node0111 , Node0112-leaf , Node0113 , Node0121-leaf , Node0122-leaf , Node0123-leaf , Node0124-leaf , Node0125-leaf , Node0131 , Node0132-leaf , Node0133-leaf , Node0211-leaf , Node0212 , Node0221-leaf , Node0222-leaf , Node0311 , Node0312-leaf , Node0321-leaf , Node0322 , Node0323 , Node0411 , Node0412 , Node0413-leaf , Node0421-leaf , Node0422-leaf , Node0423-leaf , Node0431-leaf , Node0432-leaf , Node0433-leaf , Node0441-leaf , Node0442 , Node0443-leaf , Node0511 , Node0512-leaf , Node0513-leaf , Node0521-leaf , Node0522-leaf , Node0523-leaf , Node0524-leaf .
The object with results only for a single top-value method and a single partitioning method can be extracted as:
res = res_rh["051"]
A summary of res and all the functions that can be applied to it:
res
#> A 'ConsensusPartition' object with k = 2, 3, 4, 5, 6, 7, 8.
#> On a matrix with 30000 rows and 31 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 0.989 0.995 0.4702 0.527 0.527
#> 3 3 1.000 1.000 1.000 0.2951 0.839 0.701
#> 4 4 0.810 0.805 0.848 0.1419 1.000 1.000
#> 5 5 0.701 0.837 0.853 0.0898 0.832 0.571
#> 6 6 0.786 0.799 0.863 0.0483 0.970 0.865
#> 7 7 0.815 0.731 0.815 0.0312 0.940 0.702
#> 8 8 0.865 0.653 0.845 0.0309 0.976 0.851
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.WE.A8ZO.06 1 0.000 1.000 1.00 0.00
#> TCGA.D3.A8GI.06 2 0.000 0.984 0.00 1.00
#> TCGA.BF.A5ER.01 2 0.000 0.984 0.00 1.00
#> TCGA.FR.A8YD.06 1 0.000 1.000 1.00 0.00
#> TCGA.FS.A4F9.06 1 0.000 1.000 1.00 0.00
#> TCGA.D3.A8GC.06 1 0.000 1.000 1.00 0.00
#> TCGA.ER.A42H.01 1 0.000 1.000 1.00 0.00
#> TCGA.D3.A5GU.06 1 0.000 1.000 1.00 0.00
#> TCGA.D3.A3ML.06 1 0.000 1.000 1.00 0.00
#> TCGA.D3.A8GR.06 1 0.000 1.000 1.00 0.00
#> TCGA.EB.A553.01 1 0.000 1.000 1.00 0.00
#> TCGA.GF.A2C7.01 1 0.000 1.000 1.00 0.00
#> TCGA.BF.A5ES.01 1 0.000 1.000 1.00 0.00
#> TCGA.EB.A24D.01 1 0.000 1.000 1.00 0.00
#> TCGA.EE.A2MQ.06 2 0.000 0.984 0.00 1.00
#> TCGA.W3.A824.06 1 0.000 1.000 1.00 0.00
#> TCGA.EE.A2MN.06 1 0.000 1.000 1.00 0.00
#> TCGA.EE.A29B.06 1 0.000 1.000 1.00 0.00
#> TCGA.BF.A1PV.01 2 0.000 0.984 0.00 1.00
#> TCGA.ER.A198.06 2 0.000 0.984 0.00 1.00
#> TCGA.RP.A695.06 2 0.000 0.984 0.00 1.00
#> TCGA.FW.A3TU.06 1 0.000 1.000 1.00 0.00
#> TCGA.EE.A2MM.06 2 0.634 0.810 0.16 0.84
#> TCGA.D3.A5GT.01 1 0.000 1.000 1.00 0.00
#> TCGA.DA.A1IA.06 1 0.000 1.000 1.00 0.00
#> TCGA.EE.A3J4.06 1 0.000 1.000 1.00 0.00
#> TCGA.IH.A3EA.01 2 0.000 0.984 0.00 1.00
#> TCGA.YG.AA3O.06 2 0.000 0.984 0.00 1.00
#> TCGA.W3.AA1Q.06 2 0.000 0.984 0.00 1.00
#> TCGA.W3.AA1O.06 2 0.000 0.984 0.00 1.00
#> TCGA.EE.A3J7.06 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.WE.A8ZO.06 1 0 1 1 0 0
#> TCGA.D3.A8GI.06 2 0 1 0 1 0
#> TCGA.BF.A5ER.01 2 0 1 0 1 0
#> TCGA.FR.A8YD.06 1 0 1 1 0 0
#> TCGA.FS.A4F9.06 1 0 1 1 0 0
#> TCGA.D3.A8GC.06 3 0 1 0 0 1
#> TCGA.ER.A42H.01 1 0 1 1 0 0
#> TCGA.D3.A5GU.06 1 0 1 1 0 0
#> TCGA.D3.A3ML.06 1 0 1 1 0 0
#> TCGA.D3.A8GR.06 1 0 1 1 0 0
#> TCGA.EB.A553.01 3 0 1 0 0 1
#> TCGA.GF.A2C7.01 1 0 1 1 0 0
#> TCGA.BF.A5ES.01 1 0 1 1 0 0
#> TCGA.EB.A24D.01 1 0 1 1 0 0
#> TCGA.EE.A2MQ.06 2 0 1 0 1 0
#> TCGA.W3.A824.06 1 0 1 1 0 0
#> TCGA.EE.A2MN.06 3 0 1 0 0 1
#> TCGA.EE.A29B.06 1 0 1 1 0 0
#> TCGA.BF.A1PV.01 2 0 1 0 1 0
#> TCGA.ER.A198.06 2 0 1 0 1 0
#> TCGA.RP.A695.06 2 0 1 0 1 0
#> TCGA.FW.A3TU.06 1 0 1 1 0 0
#> TCGA.EE.A2MM.06 3 0 1 0 0 1
#> TCGA.D3.A5GT.01 1 0 1 1 0 0
#> TCGA.DA.A1IA.06 1 0 1 1 0 0
#> TCGA.EE.A3J4.06 1 0 1 1 0 0
#> TCGA.IH.A3EA.01 2 0 1 0 1 0
#> TCGA.YG.AA3O.06 2 0 1 0 1 0
#> TCGA.W3.AA1Q.06 2 0 1 0 1 0
#> TCGA.W3.AA1O.06 3 0 1 0 0 1
#> TCGA.EE.A3J7.06 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.WE.A8ZO.06 1 0.3801 0.567 0.78 0.22 0.00 0.00
#> TCGA.D3.A8GI.06 4 0.0000 0.949 0.00 0.00 0.00 1.00
#> TCGA.BF.A5ER.01 4 0.0000 0.949 0.00 0.00 0.00 1.00
#> TCGA.FR.A8YD.06 1 0.4790 0.749 0.62 0.38 0.00 0.00
#> TCGA.FS.A4F9.06 1 0.4522 0.755 0.68 0.32 0.00 0.00
#> TCGA.D3.A8GC.06 3 0.4277 0.837 0.00 0.28 0.72 0.00
#> TCGA.ER.A42H.01 1 0.4790 0.749 0.62 0.38 0.00 0.00
#> TCGA.D3.A5GU.06 1 0.4790 0.749 0.62 0.38 0.00 0.00
#> TCGA.D3.A3ML.06 1 0.4790 0.749 0.62 0.38 0.00 0.00
#> TCGA.D3.A8GR.06 1 0.1637 0.732 0.94 0.06 0.00 0.00
#> TCGA.EB.A553.01 3 0.1637 0.863 0.00 0.06 0.94 0.00
#> TCGA.GF.A2C7.01 1 0.0000 0.759 1.00 0.00 0.00 0.00
#> TCGA.BF.A5ES.01 1 0.1637 0.732 0.94 0.06 0.00 0.00
#> TCGA.EB.A24D.01 1 0.4790 0.749 0.62 0.38 0.00 0.00
#> TCGA.EE.A2MQ.06 4 0.0000 0.949 0.00 0.00 0.00 1.00
#> TCGA.W3.A824.06 1 0.3801 0.567 0.78 0.22 0.00 0.00
#> TCGA.EE.A2MN.06 3 0.4277 0.837 0.00 0.28 0.72 0.00
#> TCGA.EE.A29B.06 1 0.0000 0.759 1.00 0.00 0.00 0.00
#> TCGA.BF.A1PV.01 4 0.3801 0.826 0.00 0.22 0.00 0.78
#> TCGA.ER.A198.06 4 0.0000 0.949 0.00 0.00 0.00 1.00
#> TCGA.RP.A695.06 4 0.1211 0.933 0.00 0.04 0.00 0.96
#> TCGA.FW.A3TU.06 1 0.4790 0.749 0.62 0.38 0.00 0.00
#> TCGA.EE.A2MM.06 3 0.1637 0.866 0.00 0.06 0.94 0.00
#> TCGA.D3.A5GT.01 1 0.0707 0.752 0.98 0.02 0.00 0.00
#> TCGA.DA.A1IA.06 1 0.4790 0.749 0.62 0.38 0.00 0.00
#> TCGA.EE.A3J4.06 1 0.0000 0.759 1.00 0.00 0.00 0.00
#> TCGA.IH.A3EA.01 4 0.0000 0.949 0.00 0.00 0.00 1.00
#> TCGA.YG.AA3O.06 4 0.0000 0.949 0.00 0.00 0.00 1.00
#> TCGA.W3.AA1Q.06 4 0.3801 0.826 0.00 0.22 0.00 0.78
#> TCGA.W3.AA1O.06 3 0.0000 0.875 0.00 0.00 1.00 0.00
#> TCGA.EE.A3J7.06 1 0.0000 0.759 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.WE.A8ZO.06 1 0.311 0.681 0.84 0.02 0.00 0.00 0.14
#> TCGA.D3.A8GI.06 4 0.000 0.944 0.00 0.00 0.00 1.00 0.00
#> TCGA.BF.A5ER.01 4 0.000 0.944 0.00 0.00 0.00 1.00 0.00
#> TCGA.FR.A8YD.06 5 0.000 0.978 0.00 0.00 0.00 0.00 1.00
#> TCGA.FS.A4F9.06 5 0.202 0.823 0.10 0.00 0.00 0.00 0.90
#> TCGA.D3.A8GC.06 2 0.633 1.000 0.20 0.52 0.28 0.00 0.00
#> TCGA.ER.A42H.01 5 0.000 0.978 0.00 0.00 0.00 0.00 1.00
#> TCGA.D3.A5GU.06 5 0.000 0.978 0.00 0.00 0.00 0.00 1.00
#> TCGA.D3.A3ML.06 5 0.000 0.978 0.00 0.00 0.00 0.00 1.00
#> TCGA.D3.A8GR.06 1 0.627 0.614 0.52 0.30 0.00 0.00 0.18
#> TCGA.EB.A553.01 3 0.561 0.451 0.08 0.38 0.54 0.00 0.00
#> TCGA.GF.A2C7.01 1 0.406 0.751 0.64 0.00 0.00 0.00 0.36
#> TCGA.BF.A5ES.01 1 0.627 0.614 0.52 0.30 0.00 0.00 0.18
#> TCGA.EB.A24D.01 5 0.000 0.978 0.00 0.00 0.00 0.00 1.00
#> TCGA.EE.A2MQ.06 4 0.000 0.944 0.00 0.00 0.00 1.00 0.00
#> TCGA.W3.A824.06 1 0.311 0.681 0.84 0.02 0.00 0.00 0.14
#> TCGA.EE.A2MN.06 2 0.633 1.000 0.20 0.52 0.28 0.00 0.00
#> TCGA.EE.A29B.06 1 0.398 0.762 0.66 0.00 0.00 0.00 0.34
#> TCGA.BF.A1PV.01 4 0.407 0.819 0.06 0.16 0.00 0.78 0.00
#> TCGA.ER.A198.06 4 0.000 0.944 0.00 0.00 0.00 1.00 0.00
#> TCGA.RP.A695.06 4 0.141 0.919 0.00 0.06 0.00 0.94 0.00
#> TCGA.FW.A3TU.06 5 0.000 0.978 0.00 0.00 0.00 0.00 1.00
#> TCGA.EE.A2MM.06 3 0.000 0.618 0.00 0.00 1.00 0.00 0.00
#> TCGA.D3.A5GT.01 1 0.513 0.762 0.68 0.10 0.00 0.00 0.22
#> TCGA.DA.A1IA.06 5 0.000 0.978 0.00 0.00 0.00 0.00 1.00
#> TCGA.EE.A3J4.06 1 0.398 0.762 0.66 0.00 0.00 0.00 0.34
#> TCGA.IH.A3EA.01 4 0.000 0.944 0.00 0.00 0.00 1.00 0.00
#> TCGA.YG.AA3O.06 4 0.000 0.944 0.00 0.00 0.00 1.00 0.00
#> TCGA.W3.AA1Q.06 4 0.407 0.819 0.06 0.16 0.00 0.78 0.00
#> TCGA.W3.AA1O.06 3 0.202 0.615 0.00 0.10 0.90 0.00 0.00
#> TCGA.EE.A3J7.06 1 0.406 0.751 0.64 0.00 0.00 0.00 0.36
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> TCGA.WE.A8ZO.06 1 0.3270 0.630 0.82 0.12 0.00 0.00 0.06 0.00
#> TCGA.D3.A8GI.06 4 0.0000 0.873 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.BF.A5ER.01 4 0.0000 0.873 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.FR.A8YD.06 5 0.0000 0.988 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.FS.A4F9.06 5 0.1267 0.911 0.06 0.00 0.00 0.00 0.94 0.00
#> TCGA.D3.A8GC.06 2 0.0000 1.000 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.ER.A42H.01 5 0.0000 0.988 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.D3.A5GU.06 5 0.0000 0.988 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.D3.A3ML.06 5 0.0000 0.988 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.D3.A8GR.06 6 0.5406 1.000 0.38 0.00 0.00 0.00 0.12 0.50
#> TCGA.EB.A553.01 3 0.4420 0.611 0.02 0.02 0.66 0.00 0.00 0.30
#> TCGA.GF.A2C7.01 1 0.5173 0.276 0.62 0.00 0.00 0.00 0.18 0.20
#> TCGA.BF.A5ES.01 6 0.5406 1.000 0.38 0.00 0.00 0.00 0.12 0.50
#> TCGA.EB.A24D.01 5 0.0000 0.988 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.EE.A2MQ.06 4 0.0000 0.873 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.W3.A824.06 1 0.3270 0.630 0.82 0.12 0.00 0.00 0.06 0.00
#> TCGA.EE.A2MN.06 2 0.0000 1.000 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.EE.A29B.06 1 0.2454 0.693 0.84 0.00 0.00 0.00 0.16 0.00
#> TCGA.BF.A1PV.01 4 0.4310 0.557 0.00 0.00 0.02 0.54 0.00 0.44
#> TCGA.ER.A198.06 4 0.0000 0.873 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.RP.A695.06 4 0.3572 0.785 0.06 0.00 0.02 0.82 0.00 0.10
#> TCGA.FW.A3TU.06 5 0.0000 0.988 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.EE.A2MM.06 3 0.3045 0.725 0.06 0.02 0.86 0.00 0.00 0.06
#> TCGA.D3.A5GT.01 1 0.4926 0.119 0.64 0.00 0.00 0.00 0.12 0.24
#> TCGA.DA.A1IA.06 5 0.0000 0.988 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.EE.A3J4.06 1 0.2260 0.694 0.86 0.00 0.00 0.00 0.14 0.00
#> TCGA.IH.A3EA.01 4 0.0000 0.873 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.YG.AA3O.06 4 0.0000 0.873 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.W3.AA1Q.06 4 0.5288 0.563 0.06 0.00 0.02 0.54 0.00 0.38
#> TCGA.W3.AA1O.06 3 0.0547 0.756 0.00 0.02 0.98 0.00 0.00 0.00
#> TCGA.EE.A3J7.06 1 0.2793 0.656 0.80 0.00 0.00 0.00 0.20 0.00
cbind(get_classes(res, k = 7), get_membership(res, k = 7))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7
#> TCGA.WE.A8ZO.06 1 0.6134 0.570 0.50 0.08 0.00 0.00 0.02 0.32 0.08
#> TCGA.D3.A8GI.06 4 0.0000 0.925 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.BF.A5ER.01 4 0.0000 0.925 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.FR.A8YD.06 5 0.0000 0.985 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.FS.A4F9.06 5 0.1433 0.888 0.00 0.00 0.00 0.00 0.92 0.08 0.00
#> TCGA.D3.A8GC.06 2 0.0000 0.880 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.ER.A42H.01 5 0.0000 0.985 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.D3.A5GU.06 5 0.0000 0.985 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.D3.A3ML.06 5 0.0000 0.985 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.D3.A8GR.06 6 0.0504 0.526 0.00 0.00 0.00 0.00 0.02 0.98 0.00
#> TCGA.EB.A553.01 3 0.3558 0.321 0.00 0.00 0.52 0.00 0.00 0.48 0.00
#> TCGA.GF.A2C7.01 6 0.6578 0.101 0.26 0.00 0.00 0.00 0.14 0.44 0.16
#> TCGA.BF.A5ES.01 6 0.0504 0.526 0.00 0.00 0.00 0.00 0.02 0.98 0.00
#> TCGA.EB.A24D.01 5 0.0000 0.985 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.EE.A2MQ.06 4 0.0000 0.925 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.W3.A824.06 1 0.5686 0.595 0.54 0.08 0.00 0.00 0.02 0.32 0.04
#> TCGA.EE.A2MN.06 2 0.2278 0.881 0.04 0.88 0.00 0.00 0.00 0.00 0.08
#> TCGA.EE.A29B.06 1 0.4535 0.625 0.64 0.00 0.00 0.00 0.12 0.24 0.00
#> TCGA.BF.A1PV.01 7 0.5342 0.803 0.18 0.00 0.00 0.40 0.00 0.00 0.42
#> TCGA.ER.A198.06 4 0.0000 0.925 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.RP.A695.06 4 0.2945 0.309 0.00 0.00 0.00 0.74 0.00 0.00 0.26
#> TCGA.FW.A3TU.06 5 0.0000 0.985 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.EE.A2MM.06 3 0.4514 0.492 0.14 0.00 0.70 0.00 0.00 0.02 0.14
#> TCGA.D3.A5GT.01 6 0.5922 0.279 0.26 0.00 0.00 0.00 0.06 0.52 0.16
#> TCGA.DA.A1IA.06 5 0.0000 0.985 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.EE.A3J4.06 1 0.4908 0.602 0.62 0.00 0.00 0.00 0.10 0.26 0.02
#> TCGA.IH.A3EA.01 4 0.0000 0.925 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.YG.AA3O.06 4 0.0000 0.925 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.W3.AA1Q.06 7 0.3459 0.799 0.00 0.00 0.00 0.40 0.00 0.00 0.60
#> TCGA.W3.AA1O.06 3 0.0504 0.572 0.00 0.00 0.98 0.00 0.00 0.00 0.02
#> TCGA.EE.A3J7.06 1 0.5560 0.427 0.42 0.00 0.00 0.00 0.30 0.28 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.WE.A8ZO.06 1 0.3675 0.60409 0.66 0.00 0.00 0.00 0.00 0.04 0.30 0.00
#> TCGA.D3.A8GI.06 4 0.0000 0.89171 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.BF.A5ER.01 4 0.0808 0.86041 0.00 0.00 0.00 0.96 0.00 0.04 0.00 0.00
#> TCGA.FR.A8YD.06 5 0.0000 0.98853 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.FS.A4F9.06 5 0.1874 0.91471 0.02 0.00 0.00 0.00 0.92 0.02 0.02 0.02
#> TCGA.D3.A8GC.06 2 0.0000 0.71062 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.ER.A42H.01 5 0.0000 0.98853 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.D3.A5GU.06 5 0.0000 0.98853 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.D3.A3ML.06 5 0.0000 0.98853 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.D3.A8GR.06 6 0.2404 0.66506 0.14 0.00 0.00 0.00 0.02 0.84 0.00 0.00
#> TCGA.EB.A553.01 6 0.4125 0.10680 0.00 0.02 0.44 0.00 0.00 0.52 0.00 0.02
#> TCGA.GF.A2C7.01 8 0.5748 0.28419 0.34 0.00 0.00 0.00 0.04 0.22 0.00 0.40
#> TCGA.BF.A5ES.01 6 0.2404 0.66506 0.14 0.00 0.00 0.00 0.02 0.84 0.00 0.00
#> TCGA.EB.A24D.01 5 0.0000 0.98853 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.EE.A2MQ.06 4 0.0000 0.89171 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.W3.A824.06 1 0.2719 0.66600 0.80 0.00 0.00 0.00 0.00 0.02 0.18 0.00
#> TCGA.EE.A2MN.06 2 0.2852 0.71533 0.00 0.72 0.00 0.00 0.00 0.00 0.28 0.00
#> TCGA.EE.A29B.06 1 0.0941 0.63718 0.96 0.00 0.00 0.00 0.00 0.02 0.02 0.00
#> TCGA.BF.A1PV.01 7 0.4757 0.00000 0.00 0.00 0.00 0.24 0.00 0.00 0.56 0.20
#> TCGA.ER.A198.06 4 0.0000 0.89171 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.RP.A695.06 4 0.4141 -0.00546 0.00 0.00 0.00 0.56 0.00 0.00 0.06 0.38
#> TCGA.FW.A3TU.06 5 0.0000 0.98853 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.EE.A2MM.06 3 0.3710 0.75124 0.00 0.00 0.76 0.00 0.00 0.10 0.12 0.02
#> TCGA.D3.A5GT.01 8 0.5550 0.27705 0.34 0.00 0.00 0.00 0.02 0.24 0.00 0.40
#> TCGA.DA.A1IA.06 5 0.0000 0.98853 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.EE.A3J4.06 1 0.0000 0.65814 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.IH.A3EA.01 4 0.0000 0.89171 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.YG.AA3O.06 4 0.0000 0.89171 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.W3.AA1Q.06 8 0.4849 -0.73356 0.00 0.00 0.00 0.24 0.00 0.00 0.22 0.54
#> TCGA.W3.AA1O.06 3 0.0471 0.74265 0.00 0.02 0.98 0.00 0.00 0.00 0.00 0.00
#> TCGA.EE.A3J7.06 1 0.3995 0.34659 0.60 0.00 0.00 0.00 0.36 0.02 0.02 0.00
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
consensus_heatmap(res, k = 7)
consensus_heatmap(res, k = 8)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
membership_heatmap(res, k = 7)
membership_heatmap(res, k = 8)
As soon as the classes for columns are determined, the signatures that are significantly different between subgroups can be looked for. Following are the heatmaps for signatures.
get_signatures(res, k = 2)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
get_signatures(res, k = 7)
get_signatures(res, k = 8)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. To get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows (which is done by automatically selecting number of clusters).If there are too many signatures, top_signatures = ... can be set to only show the
signatures with the highest FDRs:
# code only for demonstration
# e.g. to show the top 500 most significant rows
tb = get_signature(res, k = ..., top_signatures = 500)
If the signatures are defined as these which are uniquely high in current group, diff_method argument
can be set to "uniquely_high_in_one_group":
# code only for demonstration
tb = get_signature(res, k = ..., diff_method = "uniquely_high_in_one_group")
UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
dimension_reduction(res, k = 7, method = "UMAP")
dimension_reduction(res, k = 8, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
If matrix rows can be associated to genes, consider to use functional_enrichment(res,
...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.
Parent node: Node051. Child nodes: Node01111-leaf , Node01112-leaf , Node01113-leaf , Node01131-leaf , Node01132-leaf , Node01133-leaf , Node01311-leaf , Node01312-leaf , Node02121-leaf , Node02122-leaf , Node02123-leaf , Node03111-leaf , Node03112-leaf , Node03113-leaf , Node03221-leaf , Node03222-leaf , Node03231-leaf , Node03232-leaf , Node03233-leaf , Node03234-leaf , Node04111-leaf , Node04112-leaf , Node04121-leaf , Node04122-leaf , Node04421-leaf , Node04422-leaf , Node04423-leaf , Node04424-leaf , Node05111-leaf , Node05112-leaf , Node05113-leaf .
The object with results only for a single top-value method and a single partitioning method can be extracted as:
res = res_rh["0511"]
A summary of res and all the functions that can be applied to it:
res
#> A 'ConsensusPartition' object with k = 2, 3, 4, 5, 6, 7, 8.
#> On a matrix with 30000 rows and 17 columns.
#> Top rows (1000) are extracted by 'ATC' method.
#> Subgroups are detected by 'skmeans' method.
#> Performed in total 350 partitions by row resampling.
#> Best k for subgroups seems to be 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 0.5152 0.485 0.485
#> 3 3 0.743 0.955 0.976 0.3422 0.691 0.440
#> 4 4 0.868 0.933 0.967 0.1237 0.868 0.600
#> 5 5 0.816 0.737 0.891 0.0379 0.978 0.900
#> 6 6 0.809 0.759 0.906 0.0579 0.853 0.394
#> 7 7 0.882 0.711 0.914 0.0343 0.978 0.842
#> 8 8 0.897 0.593 0.892 0.0222 0.985 0.875
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.WE.A8ZO.06 1 0 1 1 0
#> TCGA.FR.A8YD.06 2 0 1 0 1
#> TCGA.FS.A4F9.06 2 0 1 0 1
#> TCGA.ER.A42H.01 2 0 1 0 1
#> TCGA.D3.A5GU.06 1 0 1 1 0
#> TCGA.D3.A3ML.06 2 0 1 0 1
#> TCGA.D3.A8GR.06 1 0 1 1 0
#> TCGA.GF.A2C7.01 2 0 1 0 1
#> TCGA.BF.A5ES.01 1 0 1 1 0
#> TCGA.EB.A24D.01 1 0 1 1 0
#> TCGA.W3.A824.06 2 0 1 0 1
#> TCGA.EE.A29B.06 2 0 1 0 1
#> TCGA.FW.A3TU.06 1 0 1 1 0
#> TCGA.D3.A5GT.01 2 0 1 0 1
#> TCGA.DA.A1IA.06 1 0 1 1 0
#> TCGA.EE.A3J4.06 2 0 1 0 1
#> TCGA.EE.A3J7.06 2 0 1 0 1
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.WE.A8ZO.06 3 0.296 0.893 0.1 0.0 0.9
#> TCGA.FR.A8YD.06 3 0.000 0.932 0.0 0.0 1.0
#> TCGA.FS.A4F9.06 2 0.296 0.894 0.0 0.9 0.1
#> TCGA.ER.A42H.01 2 0.000 0.983 0.0 1.0 0.0
#> TCGA.D3.A5GU.06 3 0.000 0.932 0.0 0.0 1.0
#> TCGA.D3.A3ML.06 3 0.296 0.856 0.0 0.1 0.9
#> TCGA.D3.A8GR.06 1 0.000 1.000 1.0 0.0 0.0
#> TCGA.GF.A2C7.01 2 0.000 0.983 0.0 1.0 0.0
#> TCGA.BF.A5ES.01 1 0.000 1.000 1.0 0.0 0.0
#> TCGA.EB.A24D.01 3 0.296 0.893 0.1 0.0 0.9
#> TCGA.W3.A824.06 2 0.000 0.983 0.0 1.0 0.0
#> TCGA.EE.A29B.06 2 0.000 0.983 0.0 1.0 0.0
#> TCGA.FW.A3TU.06 1 0.000 1.000 1.0 0.0 0.0
#> TCGA.D3.A5GT.01 2 0.000 0.983 0.0 1.0 0.0
#> TCGA.DA.A1IA.06 1 0.000 1.000 1.0 0.0 0.0
#> TCGA.EE.A3J4.06 2 0.000 0.983 0.0 1.0 0.0
#> TCGA.EE.A3J7.06 3 0.000 0.932 0.0 0.0 1.0
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> TCGA.WE.A8ZO.06 3 0.000 0.867 0 0.0 1.00 0.00
#> TCGA.FR.A8YD.06 4 0.164 0.945 0 0.0 0.06 0.94
#> TCGA.FS.A4F9.06 4 0.000 0.947 0 0.0 0.00 1.00
#> TCGA.ER.A42H.01 2 0.000 0.960 0 1.0 0.00 0.00
#> TCGA.D3.A5GU.06 3 0.398 0.664 0 0.0 0.76 0.24
#> TCGA.D3.A3ML.06 4 0.000 0.947 0 0.0 0.00 1.00
#> TCGA.D3.A8GR.06 1 0.000 1.000 1 0.0 0.00 0.00
#> TCGA.GF.A2C7.01 2 0.000 0.960 0 1.0 0.00 0.00
#> TCGA.BF.A5ES.01 1 0.000 1.000 1 0.0 0.00 0.00
#> TCGA.EB.A24D.01 3 0.000 0.867 0 0.0 1.00 0.00
#> TCGA.W3.A824.06 2 0.234 0.917 0 0.9 0.00 0.10
#> TCGA.EE.A29B.06 2 0.000 0.960 0 1.0 0.00 0.00
#> TCGA.FW.A3TU.06 1 0.000 1.000 1 0.0 0.00 0.00
#> TCGA.D3.A5GT.01 2 0.000 0.960 0 1.0 0.00 0.00
#> TCGA.DA.A1IA.06 1 0.000 1.000 1 0.0 0.00 0.00
#> TCGA.EE.A3J4.06 2 0.234 0.917 0 0.9 0.00 0.10
#> TCGA.EE.A3J7.06 4 0.164 0.945 0 0.0 0.06 0.94
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> TCGA.WE.A8ZO.06 3 0.000 0.726 0.00 0.00 1.00 0.00 0.00
#> TCGA.FR.A8YD.06 4 0.141 0.774 0.00 0.00 0.06 0.94 0.00
#> TCGA.FS.A4F9.06 4 0.369 0.746 0.00 0.02 0.00 0.78 0.20
#> TCGA.ER.A42H.01 2 0.000 0.844 0.00 1.00 0.00 0.00 0.00
#> TCGA.D3.A5GU.06 3 0.509 0.318 0.00 0.00 0.56 0.40 0.04
#> TCGA.D3.A3ML.06 4 0.293 0.778 0.00 0.00 0.00 0.82 0.18
#> TCGA.D3.A8GR.06 1 0.000 1.000 1.00 0.00 0.00 0.00 0.00
#> TCGA.GF.A2C7.01 2 0.000 0.844 0.00 1.00 0.00 0.00 0.00
#> TCGA.BF.A5ES.01 5 0.327 0.000 0.22 0.00 0.00 0.00 0.78
#> TCGA.EB.A24D.01 3 0.000 0.726 0.00 0.00 1.00 0.00 0.00
#> TCGA.W3.A824.06 2 0.541 0.658 0.00 0.66 0.00 0.14 0.20
#> TCGA.EE.A29B.06 2 0.000 0.844 0.00 1.00 0.00 0.00 0.00
#> TCGA.FW.A3TU.06 1 0.000 1.000 1.00 0.00 0.00 0.00 0.00
#> TCGA.D3.A5GT.01 2 0.000 0.844 0.00 1.00 0.00 0.00 0.00
#> TCGA.DA.A1IA.06 1 0.000 1.000 1.00 0.00 0.00 0.00 0.00
#> TCGA.EE.A3J4.06 2 0.541 0.658 0.00 0.66 0.00 0.14 0.20
#> TCGA.EE.A3J7.06 4 0.141 0.774 0.00 0.00 0.06 0.94 0.00
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> TCGA.WE.A8ZO.06 3 0.000 1.000 0 0.00 1.00 0.00 0 0.00
#> TCGA.FR.A8YD.06 4 0.127 0.691 0 0.00 0.00 0.94 0 0.06
#> TCGA.FS.A4F9.06 6 0.294 0.553 0 0.00 0.00 0.22 0 0.78
#> TCGA.ER.A42H.01 2 0.000 0.961 0 1.00 0.00 0.00 0 0.00
#> TCGA.D3.A5GU.06 4 0.350 0.526 0 0.00 0.32 0.68 0 0.00
#> TCGA.D3.A3ML.06 6 0.350 0.323 0 0.00 0.00 0.32 0 0.68
#> TCGA.D3.A8GR.06 1 0.000 1.000 1 0.00 0.00 0.00 0 0.00
#> TCGA.GF.A2C7.01 2 0.000 0.961 0 1.00 0.00 0.00 0 0.00
#> TCGA.BF.A5ES.01 5 0.000 0.000 0 0.00 0.00 0.00 1 0.00
#> TCGA.EB.A24D.01 3 0.000 1.000 0 0.00 1.00 0.00 0 0.00
#> TCGA.W3.A824.06 6 0.308 0.656 0 0.24 0.00 0.00 0 0.76
#> TCGA.EE.A29B.06 2 0.181 0.874 0 0.90 0.00 0.00 0 0.10
#> TCGA.FW.A3TU.06 1 0.000 1.000 1 0.00 0.00 0.00 0 0.00
#> TCGA.D3.A5GT.01 2 0.000 0.961 0 1.00 0.00 0.00 0 0.00
#> TCGA.DA.A1IA.06 1 0.000 1.000 1 0.00 0.00 0.00 0 0.00
#> TCGA.EE.A3J4.06 6 0.308 0.656 0 0.24 0.00 0.00 0 0.76
#> TCGA.EE.A3J7.06 4 0.219 0.733 0 0.00 0.04 0.90 0 0.06
cbind(get_classes(res, k = 7), get_membership(res, k = 7))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7
#> TCGA.WE.A8ZO.06 3 0.000 1.000 0 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.FR.A8YD.06 4 0.319 0.588 0 0.00 0.00 0.76 0.00 0.02 0.22
#> TCGA.FS.A4F9.06 6 0.445 0.414 0 0.00 0.00 0.26 0.00 0.64 0.10
#> TCGA.ER.A42H.01 2 0.000 0.900 0 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D3.A5GU.06 4 0.399 0.598 0 0.00 0.22 0.72 0.04 0.00 0.02
#> TCGA.D3.A3ML.06 7 0.172 0.000 0 0.00 0.00 0.04 0.00 0.04 0.92
#> TCGA.D3.A8GR.06 1 0.000 1.000 1 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.GF.A2C7.01 2 0.000 0.900 0 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BF.A5ES.01 5 0.000 0.000 0 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.EB.A24D.01 3 0.000 1.000 0 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.W3.A824.06 6 0.143 0.753 0 0.08 0.00 0.00 0.00 0.92 0.00
#> TCGA.EE.A29B.06 2 0.294 0.639 0 0.74 0.00 0.00 0.00 0.26 0.00
#> TCGA.FW.A3TU.06 1 0.000 1.000 1 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D3.A5GT.01 2 0.000 0.900 0 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.DA.A1IA.06 1 0.000 1.000 1 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EE.A3J4.06 6 0.143 0.753 0 0.08 0.00 0.00 0.00 0.92 0.00
#> TCGA.EE.A3J7.06 4 0.166 0.632 0 0.00 0.00 0.92 0.00 0.06 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.WE.A8ZO.06 3 0.0000 0.977 0.00 0.00 1.00 0.00 0 0.00 0.00 0.00
#> TCGA.FR.A8YD.06 8 0.3971 0.000 0.00 0.00 0.00 0.42 0 0.00 0.04 0.54
#> TCGA.FS.A4F9.06 6 0.5162 0.418 0.00 0.00 0.00 0.10 0 0.50 0.04 0.36
#> TCGA.ER.A42H.01 2 0.1341 0.739 0.00 0.92 0.00 0.00 0 0.00 0.00 0.08
#> TCGA.D3.A5GU.06 4 0.1804 0.423 0.00 0.00 0.08 0.90 0 0.00 0.02 0.00
#> TCGA.D3.A3ML.06 7 0.0000 0.000 0.00 0.00 0.00 0.00 0 0.00 1.00 0.00
#> TCGA.D3.A8GR.06 1 0.0000 0.991 1.00 0.00 0.00 0.00 0 0.00 0.00 0.00
#> TCGA.GF.A2C7.01 2 0.0471 0.771 0.00 0.98 0.00 0.00 0 0.00 0.00 0.02
#> TCGA.BF.A5ES.01 5 0.0000 0.000 0.00 0.00 0.00 0.00 1 0.00 0.00 0.00
#> TCGA.EB.A24D.01 3 0.0471 0.977 0.00 0.00 0.98 0.02 0 0.00 0.00 0.00
#> TCGA.W3.A824.06 6 0.0808 0.728 0.00 0.00 0.00 0.00 0 0.96 0.00 0.04
#> TCGA.EE.A29B.06 2 0.3737 0.157 0.00 0.50 0.00 0.00 0 0.48 0.00 0.02
#> TCGA.FW.A3TU.06 1 0.0471 0.983 0.98 0.00 0.00 0.00 0 0.00 0.00 0.02
#> TCGA.D3.A5GT.01 2 0.0000 0.773 0.00 1.00 0.00 0.00 0 0.00 0.00 0.00
#> TCGA.DA.A1IA.06 1 0.0000 0.991 1.00 0.00 0.00 0.00 0 0.00 0.00 0.00
#> TCGA.EE.A3J4.06 6 0.0471 0.727 0.00 0.00 0.00 0.00 0 0.98 0.00 0.02
#> TCGA.EE.A3J7.06 4 0.2856 0.423 0.00 0.00 0.00 0.78 0 0.02 0.00 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: Node05. Child nodes: Node0111 , Node0112-leaf , Node0113 , Node0121-leaf , Node0122-leaf , Node0123-leaf , Node0124-leaf , Node0125-leaf , Node0131 , Node0132-leaf , Node0133-leaf , Node0211-leaf , Node0212 , Node0221-leaf , Node0222-leaf , Node0311 , Node0312-leaf , Node0321-leaf , Node0322 , Node0323 , Node0411 , Node0412 , Node0413-leaf , Node0421-leaf , Node0422-leaf , Node0423-leaf , Node0431-leaf , Node0432-leaf , Node0433-leaf , Node0441-leaf , Node0442 , Node0443-leaf , Node0511 , Node0512-leaf , Node0513-leaf , Node0521-leaf , Node0522-leaf , Node0523-leaf , Node0524-leaf .
The object with results only for a single top-value method and a single partitioning method can be extracted as:
res = res_rh["052"]
A summary of res and all the functions that can be applied to it:
res
#> A 'ConsensusPartition' object with k = 2, 3, 4, 5, 6, 7, 8.
#> On a matrix with 30000 rows and 37 columns.
#> Top rows (1000) are extracted by 'ATC' method.
#> Subgroups are detected by 'kmeans' method.
#> Performed in total 350 partitions by row resampling.
#> Best k for subgroups seems to be 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 0.991 0.996 0.5100 0.489 0.489
#> 3 3 0.833 0.861 0.946 0.3256 0.757 0.537
#> 4 4 1.000 0.990 0.995 0.0861 0.901 0.711
#> 5 5 0.850 0.851 0.912 0.0579 0.944 0.798
#> 6 6 0.803 0.714 0.855 0.0356 0.973 0.882
#> 7 7 0.782 0.576 0.786 0.0340 0.953 0.782
#> 8 8 0.820 0.577 0.735 0.0209 0.970 0.833
suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:
suggest_best_k(res)
#> [1] 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.D3.A8GK.06 1 0.000 0.990 1.00 0.00
#> TCGA.WE.A8ZM.06 2 0.000 1.000 0.00 1.00
#> TCGA.EB.A3HV.01 1 0.000 0.990 1.00 0.00
#> TCGA.HR.A5NC.01 2 0.000 1.000 0.00 1.00
#> TCGA.GN.A8LK.06 1 0.000 0.990 1.00 0.00
#> TCGA.BF.A9VF.01 1 0.000 0.990 1.00 0.00
#> TCGA.D3.A3MO.06 2 0.000 1.000 0.00 1.00
#> TCGA.WE.A8ZQ.06 2 0.000 1.000 0.00 1.00
#> TCGA.FR.A2OS.01 1 0.584 0.840 0.86 0.14
#> TCGA.D3.A2JE.06 2 0.000 1.000 0.00 1.00
#> TCGA.GN.A4U9.06 2 0.000 1.000 0.00 1.00
#> TCGA.FS.A1ZR.06 1 0.000 0.990 1.00 0.00
#> TCGA.EE.A2GP.06 1 0.141 0.973 0.98 0.02
#> TCGA.EE.A2A5.06 2 0.000 1.000 0.00 1.00
#> TCGA.EE.A2GC.06 1 0.000 0.990 1.00 0.00
#> TCGA.ER.A19E.06 2 0.000 1.000 0.00 1.00
#> TCGA.FS.A1ZK.06 2 0.000 1.000 0.00 1.00
#> TCGA.FS.A1ZU.06 2 0.000 1.000 0.00 1.00
#> TCGA.EE.A17Z.06 2 0.000 1.000 0.00 1.00
#> TCGA.ER.A19T.01 1 0.000 0.990 1.00 0.00
#> TCGA.EE.A2GN.06 2 0.000 1.000 0.00 1.00
#> TCGA.EE.A20H.06 2 0.000 1.000 0.00 1.00
#> TCGA.FS.A1ZJ.06 2 0.000 1.000 0.00 1.00
#> TCGA.EE.A3AC.06 1 0.000 0.990 1.00 0.00
#> TCGA.EE.A2GR.06 1 0.000 0.990 1.00 0.00
#> TCGA.FS.A1ZD.06 2 0.000 1.000 0.00 1.00
#> TCGA.FS.A1ZP.06 2 0.000 1.000 0.00 1.00
#> TCGA.DA.A1IC.06 1 0.000 0.990 1.00 0.00
#> TCGA.ER.A3PL.06 1 0.000 0.990 1.00 0.00
#> TCGA.D9.A3Z4.01 2 0.000 1.000 0.00 1.00
#> TCGA.YD.A9TB.06 1 0.000 0.990 1.00 0.00
#> TCGA.ER.A2ND.06 1 0.000 0.990 1.00 0.00
#> TCGA.D9.A4Z3.01 2 0.000 1.000 0.00 1.00
#> TCGA.EB.A44O.01 1 0.000 0.990 1.00 0.00
#> TCGA.YG.AA3P.06 2 0.000 1.000 0.00 1.00
#> TCGA.D3.A51K.06 2 0.000 1.000 0.00 1.00
#> TCGA.EB.A44P.01 1 0.000 0.990 1.00 0.00
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.D3.A8GK.06 1 0.604 0.363 0.62 0.00 0.38
#> TCGA.WE.A8ZM.06 3 0.595 0.484 0.00 0.36 0.64
#> TCGA.EB.A3HV.01 1 0.000 0.933 1.00 0.00 0.00
#> TCGA.HR.A5NC.01 3 0.000 0.878 0.00 0.00 1.00
#> TCGA.GN.A8LK.06 1 0.000 0.933 1.00 0.00 0.00
#> TCGA.BF.A9VF.01 1 0.000 0.933 1.00 0.00 0.00
#> TCGA.D3.A3MO.06 2 0.000 0.987 0.00 1.00 0.00
#> TCGA.WE.A8ZQ.06 3 0.000 0.878 0.00 0.00 1.00
#> TCGA.FR.A2OS.01 3 0.000 0.878 0.00 0.00 1.00
#> TCGA.D3.A2JE.06 2 0.000 0.987 0.00 1.00 0.00
#> TCGA.GN.A4U9.06 2 0.000 0.987 0.00 1.00 0.00
#> TCGA.FS.A1ZR.06 1 0.000 0.933 1.00 0.00 0.00
#> TCGA.EE.A2GP.06 3 0.613 0.260 0.40 0.00 0.60
#> TCGA.EE.A2A5.06 2 0.334 0.838 0.00 0.88 0.12
#> TCGA.EE.A2GC.06 1 0.604 0.363 0.62 0.00 0.38
#> TCGA.ER.A19E.06 2 0.000 0.987 0.00 1.00 0.00
#> TCGA.FS.A1ZK.06 3 0.595 0.484 0.00 0.36 0.64
#> TCGA.FS.A1ZU.06 2 0.000 0.987 0.00 1.00 0.00
#> TCGA.EE.A17Z.06 2 0.000 0.987 0.00 1.00 0.00
#> TCGA.ER.A19T.01 3 0.000 0.878 0.00 0.00 1.00
#> TCGA.EE.A2GN.06 2 0.000 0.987 0.00 1.00 0.00
#> TCGA.EE.A20H.06 2 0.000 0.987 0.00 1.00 0.00
#> TCGA.FS.A1ZJ.06 3 0.000 0.878 0.00 0.00 1.00
#> TCGA.EE.A3AC.06 1 0.000 0.933 1.00 0.00 0.00
#> TCGA.EE.A2GR.06 1 0.000 0.933 1.00 0.00 0.00
#> TCGA.FS.A1ZD.06 3 0.000 0.878 0.00 0.00 1.00
#> TCGA.FS.A1ZP.06 2 0.000 0.987 0.00 1.00 0.00
#> TCGA.DA.A1IC.06 1 0.000 0.933 1.00 0.00 0.00
#> TCGA.ER.A3PL.06 1 0.000 0.933 1.00 0.00 0.00
#> TCGA.D9.A3Z4.01 3 0.000 0.878 0.00 0.00 1.00
#> TCGA.YD.A9TB.06 1 0.000 0.933 1.00 0.00 0.00
#> TCGA.ER.A2ND.06 1 0.000 0.933 1.00 0.00 0.00
#> TCGA.D9.A4Z3.01 2 0.000 0.987 0.00 1.00 0.00
#> TCGA.EB.A44O.01 1 0.000 0.933 1.00 0.00 0.00
#> TCGA.YG.AA3P.06 3 0.000 0.878 0.00 0.00 1.00
#> TCGA.D3.A51K.06 2 0.000 0.987 0.00 1.00 0.00
#> TCGA.EB.A44P.01 1 0.000 0.933 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.D3.A8GK.06 4 0.0000 0.993 0 0.00 0.00 1.00
#> TCGA.WE.A8ZM.06 2 0.2830 0.898 0 0.90 0.04 0.06
#> TCGA.EB.A3HV.01 1 0.0000 1.000 1 0.00 0.00 0.00
#> TCGA.HR.A5NC.01 3 0.0000 0.991 0 0.00 1.00 0.00
#> TCGA.GN.A8LK.06 1 0.0000 1.000 1 0.00 0.00 0.00
#> TCGA.BF.A9VF.01 1 0.0000 1.000 1 0.00 0.00 0.00
#> TCGA.D3.A3MO.06 2 0.0000 0.990 0 1.00 0.00 0.00
#> TCGA.WE.A8ZQ.06 3 0.0000 0.991 0 0.00 1.00 0.00
#> TCGA.FR.A2OS.01 3 0.0000 0.991 0 0.00 1.00 0.00
#> TCGA.D3.A2JE.06 2 0.0000 0.990 0 1.00 0.00 0.00
#> TCGA.GN.A4U9.06 2 0.0000 0.990 0 1.00 0.00 0.00
#> TCGA.FS.A1ZR.06 1 0.0000 1.000 1 0.00 0.00 0.00
#> TCGA.EE.A2GP.06 4 0.0707 0.978 0 0.00 0.02 0.98
#> TCGA.EE.A2A5.06 2 0.0707 0.974 0 0.98 0.02 0.00
#> TCGA.EE.A2GC.06 4 0.0000 0.993 0 0.00 0.00 1.00
#> TCGA.ER.A19E.06 2 0.0000 0.990 0 1.00 0.00 0.00
#> TCGA.FS.A1ZK.06 4 0.0000 0.993 0 0.00 0.00 1.00
#> TCGA.FS.A1ZU.06 2 0.0000 0.990 0 1.00 0.00 0.00
#> TCGA.EE.A17Z.06 2 0.0000 0.990 0 1.00 0.00 0.00
#> TCGA.ER.A19T.01 3 0.0707 0.984 0 0.00 0.98 0.02
#> TCGA.EE.A2GN.06 2 0.0000 0.990 0 1.00 0.00 0.00
#> TCGA.EE.A20H.06 2 0.0000 0.990 0 1.00 0.00 0.00
#> TCGA.FS.A1ZJ.06 3 0.0000 0.991 0 0.00 1.00 0.00
#> TCGA.EE.A3AC.06 1 0.0000 1.000 1 0.00 0.00 0.00
#> TCGA.EE.A2GR.06 1 0.0000 1.000 1 0.00 0.00 0.00
#> TCGA.FS.A1ZD.06 3 0.0000 0.991 0 0.00 1.00 0.00
#> TCGA.FS.A1ZP.06 2 0.0000 0.990 0 1.00 0.00 0.00
#> TCGA.DA.A1IC.06 1 0.0000 1.000 1 0.00 0.00 0.00
#> TCGA.ER.A3PL.06 1 0.0000 1.000 1 0.00 0.00 0.00
#> TCGA.D9.A3Z4.01 3 0.0707 0.984 0 0.00 0.98 0.02
#> TCGA.YD.A9TB.06 1 0.0000 1.000 1 0.00 0.00 0.00
#> TCGA.ER.A2ND.06 1 0.0000 1.000 1 0.00 0.00 0.00
#> TCGA.D9.A4Z3.01 2 0.0000 0.990 0 1.00 0.00 0.00
#> TCGA.EB.A44O.01 1 0.0000 1.000 1 0.00 0.00 0.00
#> TCGA.YG.AA3P.06 3 0.0707 0.984 0 0.00 0.98 0.02
#> TCGA.D3.A51K.06 2 0.0000 0.990 0 1.00 0.00 0.00
#> TCGA.EB.A44P.01 1 0.0000 1.000 1 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.D3.A8GK.06 4 0.0000 0.9798 0.00 0.00 0.00 1.00 0.00
#> TCGA.WE.A8ZM.06 5 0.4373 0.6408 0.00 0.16 0.08 0.00 0.76
#> TCGA.EB.A3HV.01 1 0.1043 0.9421 0.96 0.00 0.00 0.00 0.04
#> TCGA.HR.A5NC.01 5 0.4060 0.2214 0.00 0.00 0.36 0.00 0.64
#> TCGA.GN.A8LK.06 1 0.0000 0.9468 1.00 0.00 0.00 0.00 0.00
#> TCGA.BF.A9VF.01 1 0.0000 0.9468 1.00 0.00 0.00 0.00 0.00
#> TCGA.D3.A3MO.06 2 0.0000 0.9710 0.00 1.00 0.00 0.00 0.00
#> TCGA.WE.A8ZQ.06 3 0.3109 0.7703 0.00 0.00 0.80 0.00 0.20
#> TCGA.FR.A2OS.01 3 0.3684 0.7203 0.00 0.00 0.72 0.00 0.28
#> TCGA.D3.A2JE.06 2 0.0000 0.9710 0.00 1.00 0.00 0.00 0.00
#> TCGA.GN.A4U9.06 2 0.0000 0.9710 0.00 1.00 0.00 0.00 0.00
#> TCGA.FS.A1ZR.06 1 0.2732 0.8798 0.84 0.00 0.00 0.00 0.16
#> TCGA.EE.A2GP.06 5 0.4227 0.0733 0.00 0.00 0.00 0.42 0.58
#> TCGA.EE.A2A5.06 5 0.4254 0.6184 0.00 0.22 0.04 0.00 0.74
#> TCGA.EE.A2GC.06 4 0.0609 0.9899 0.00 0.00 0.00 0.98 0.02
#> TCGA.ER.A19E.06 2 0.0000 0.9710 0.00 1.00 0.00 0.00 0.00
#> TCGA.FS.A1ZK.06 4 0.0609 0.9899 0.00 0.00 0.00 0.98 0.02
#> TCGA.FS.A1ZU.06 2 0.1043 0.9491 0.00 0.96 0.00 0.00 0.04
#> TCGA.EE.A17Z.06 2 0.0000 0.9710 0.00 1.00 0.00 0.00 0.00
#> TCGA.ER.A19T.01 3 0.3109 0.6719 0.00 0.00 0.80 0.00 0.20
#> TCGA.EE.A2GN.06 2 0.0000 0.9710 0.00 1.00 0.00 0.00 0.00
#> TCGA.EE.A20H.06 2 0.2280 0.8605 0.00 0.88 0.00 0.00 0.12
#> TCGA.FS.A1ZJ.06 3 0.2516 0.8144 0.00 0.00 0.86 0.00 0.14
#> TCGA.EE.A3AC.06 1 0.2732 0.8798 0.84 0.00 0.00 0.00 0.16
#> TCGA.EE.A2GR.06 1 0.0000 0.9468 1.00 0.00 0.00 0.00 0.00
#> TCGA.FS.A1ZD.06 3 0.2732 0.8064 0.00 0.00 0.84 0.00 0.16
#> TCGA.FS.A1ZP.06 2 0.1043 0.9491 0.00 0.96 0.00 0.00 0.04
#> TCGA.DA.A1IC.06 1 0.0000 0.9468 1.00 0.00 0.00 0.00 0.00
#> TCGA.ER.A3PL.06 1 0.1043 0.9421 0.96 0.00 0.00 0.00 0.04
#> TCGA.D9.A3Z4.01 3 0.0000 0.8156 0.00 0.00 1.00 0.00 0.00
#> TCGA.YD.A9TB.06 1 0.1043 0.9421 0.96 0.00 0.00 0.00 0.04
#> TCGA.ER.A2ND.06 1 0.3424 0.8093 0.76 0.00 0.00 0.00 0.24
#> TCGA.D9.A4Z3.01 2 0.1410 0.9281 0.00 0.94 0.00 0.00 0.06
#> TCGA.EB.A44O.01 1 0.0000 0.9468 1.00 0.00 0.00 0.00 0.00
#> TCGA.YG.AA3P.06 3 0.0000 0.8156 0.00 0.00 1.00 0.00 0.00
#> TCGA.D3.A51K.06 2 0.0000 0.9710 0.00 1.00 0.00 0.00 0.00
#> TCGA.EB.A44P.01 1 0.0000 0.9468 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.D3.A8GK.06 4 0.2793 0.8274 0.00 0.00 0.00 0.80 0.00 0.20
#> TCGA.WE.A8ZM.06 5 0.4690 0.7642 0.00 0.04 0.22 0.00 0.70 0.04
#> TCGA.EB.A3HV.01 1 0.2048 0.8272 0.88 0.00 0.00 0.00 0.00 0.12
#> TCGA.HR.A5NC.01 5 0.4199 0.6025 0.00 0.00 0.38 0.00 0.60 0.02
#> TCGA.GN.A8LK.06 1 0.0547 0.8571 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.BF.A9VF.01 1 0.0547 0.8571 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.D3.A3MO.06 2 0.0000 0.9280 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.WE.A8ZQ.06 3 0.0937 0.7157 0.00 0.00 0.96 0.00 0.00 0.04
#> TCGA.FR.A2OS.01 3 0.6047 0.0288 0.00 0.00 0.40 0.00 0.26 0.34
#> TCGA.D3.A2JE.06 2 0.2190 0.8995 0.00 0.90 0.00 0.00 0.06 0.04
#> TCGA.GN.A4U9.06 2 0.0000 0.9280 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.FS.A1ZR.06 1 0.3499 0.5715 0.68 0.00 0.00 0.00 0.00 0.32
#> TCGA.EE.A2GP.06 5 0.3578 0.4220 0.00 0.00 0.00 0.34 0.66 0.00
#> TCGA.EE.A2A5.06 5 0.3982 0.7513 0.00 0.06 0.20 0.00 0.74 0.00
#> TCGA.EE.A2GC.06 4 0.0000 0.8999 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.ER.A19E.06 2 0.0000 0.9280 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.FS.A1ZK.06 4 0.1092 0.8947 0.00 0.00 0.00 0.96 0.02 0.02
#> TCGA.FS.A1ZU.06 2 0.2474 0.8918 0.00 0.88 0.00 0.00 0.08 0.04
#> TCGA.EE.A17Z.06 2 0.0000 0.9280 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.ER.A19T.01 6 0.6010 -0.4982 0.00 0.00 0.36 0.00 0.24 0.40
#> TCGA.EE.A2GN.06 2 0.0000 0.9280 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.EE.A20H.06 2 0.4213 0.7524 0.00 0.78 0.04 0.00 0.08 0.10
#> TCGA.FS.A1ZJ.06 3 0.0000 0.7381 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.EE.A3AC.06 1 0.3499 0.5715 0.68 0.00 0.00 0.00 0.00 0.32
#> TCGA.EE.A2GR.06 1 0.0547 0.8571 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.FS.A1ZD.06 3 0.0547 0.7359 0.00 0.00 0.98 0.00 0.00 0.02
#> TCGA.FS.A1ZP.06 2 0.2474 0.8918 0.00 0.88 0.00 0.00 0.08 0.04
#> TCGA.DA.A1IC.06 1 0.0000 0.8597 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.ER.A3PL.06 1 0.2454 0.8133 0.84 0.00 0.00 0.00 0.00 0.16
#> TCGA.D9.A3Z4.01 3 0.3315 0.6889 0.00 0.00 0.78 0.00 0.20 0.02
#> TCGA.YD.A9TB.06 1 0.2048 0.8272 0.88 0.00 0.00 0.00 0.00 0.12
#> TCGA.ER.A2ND.06 6 0.3851 -0.4273 0.46 0.00 0.00 0.00 0.00 0.54
#> TCGA.D9.A4Z3.01 2 0.3787 0.8253 0.00 0.78 0.00 0.00 0.12 0.10
#> TCGA.EB.A44O.01 1 0.0000 0.8597 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.YG.AA3P.06 3 0.3315 0.6889 0.00 0.00 0.78 0.00 0.20 0.02
#> TCGA.D3.A51K.06 2 0.0000 0.9280 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.EB.A44P.01 1 0.0000 0.8597 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.D3.A8GK.06 4 0.3526 0.8007 0.00 0.00 0.00 0.76 0.00 0.06 0.18
#> TCGA.WE.A8ZM.06 5 0.2512 0.6351 0.00 0.00 0.00 0.00 0.86 0.04 0.10
#> TCGA.EB.A3HV.01 1 0.2422 0.6406 0.82 0.00 0.00 0.00 0.00 0.18 0.00
#> TCGA.HR.A5NC.01 5 0.5128 -0.2043 0.00 0.00 0.16 0.00 0.52 0.00 0.32
#> TCGA.GN.A8LK.06 1 0.0000 0.8602 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BF.A9VF.01 1 0.0000 0.8602 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D3.A3MO.06 2 0.0000 0.8111 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.WE.A8ZQ.06 7 0.5694 0.0000 0.00 0.00 0.38 0.00 0.12 0.04 0.46
#> TCGA.FR.A2OS.01 3 0.6301 0.0137 0.00 0.00 0.38 0.00 0.06 0.20 0.36
#> TCGA.D3.A2JE.06 2 0.4187 0.7486 0.00 0.76 0.00 0.00 0.08 0.08 0.08
#> TCGA.GN.A4U9.06 2 0.0504 0.8084 0.00 0.98 0.00 0.00 0.00 0.02 0.00
#> TCGA.FS.A1ZR.06 6 0.3558 0.7943 0.48 0.00 0.00 0.00 0.00 0.52 0.00
#> TCGA.EE.A2GP.06 5 0.3530 0.5611 0.00 0.00 0.00 0.20 0.76 0.02 0.02
#> TCGA.EE.A2A5.06 5 0.0863 0.6449 0.00 0.00 0.00 0.00 0.96 0.04 0.00
#> TCGA.EE.A2GC.06 4 0.0000 0.8873 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.ER.A19E.06 2 0.0000 0.8111 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FS.A1ZK.06 4 0.1006 0.8856 0.00 0.00 0.00 0.96 0.00 0.02 0.02
#> TCGA.FS.A1ZU.06 2 0.5022 0.7123 0.00 0.68 0.00 0.00 0.10 0.12 0.10
#> TCGA.EE.A17Z.06 2 0.2278 0.7863 0.00 0.88 0.00 0.00 0.00 0.04 0.08
#> TCGA.ER.A19T.01 3 0.4714 0.2592 0.00 0.00 0.60 0.00 0.00 0.28 0.12
#> TCGA.EE.A2GN.06 2 0.0504 0.8084 0.00 0.98 0.00 0.00 0.00 0.02 0.00
#> TCGA.EE.A20H.06 2 0.5830 0.2236 0.00 0.50 0.00 0.00 0.32 0.06 0.12
#> TCGA.FS.A1ZJ.06 3 0.4649 -0.3900 0.00 0.00 0.62 0.00 0.06 0.02 0.30
#> TCGA.EE.A3AC.06 6 0.3558 0.7943 0.48 0.00 0.00 0.00 0.00 0.52 0.00
#> TCGA.EE.A2GR.06 1 0.0000 0.8602 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FS.A1ZD.06 3 0.4461 -0.4646 0.00 0.00 0.54 0.00 0.06 0.00 0.40
#> TCGA.FS.A1ZP.06 2 0.4833 0.7144 0.00 0.70 0.00 0.00 0.10 0.10 0.10
#> TCGA.DA.A1IC.06 1 0.0000 0.8602 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.ER.A3PL.06 1 0.2572 0.5892 0.80 0.00 0.00 0.00 0.00 0.20 0.00
#> TCGA.D9.A3Z4.01 3 0.0000 0.3426 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.YD.A9TB.06 1 0.2422 0.6406 0.82 0.00 0.00 0.00 0.00 0.18 0.00
#> TCGA.ER.A2ND.06 6 0.3221 0.6795 0.32 0.00 0.00 0.00 0.00 0.68 0.00
#> TCGA.D9.A4Z3.01 2 0.4381 0.4511 0.00 0.58 0.00 0.00 0.36 0.06 0.00
#> TCGA.EB.A44O.01 1 0.0000 0.8602 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.YG.AA3P.06 3 0.0000 0.3426 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.D3.A51K.06 2 0.0000 0.8111 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EB.A44P.01 1 0.0000 0.8602 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.D3.A8GK.06 4 0.4642 0.631 0.00 0.00 0.04 0.60 0.00 0.06 0.00 0.30
#> TCGA.WE.A8ZM.06 5 0.2165 0.727 0.00 0.00 0.06 0.00 0.88 0.06 0.00 0.00
#> TCGA.EB.A3HV.01 1 0.3170 0.589 0.76 0.00 0.00 0.00 0.00 0.20 0.00 0.04
#> TCGA.HR.A5NC.01 5 0.3880 0.494 0.00 0.00 0.02 0.00 0.64 0.02 0.32 0.00
#> TCGA.GN.A8LK.06 1 0.0941 0.817 0.96 0.00 0.00 0.00 0.00 0.02 0.00 0.02
#> TCGA.BF.A9VF.01 1 0.0941 0.817 0.96 0.00 0.00 0.00 0.00 0.02 0.00 0.02
#> TCGA.D3.A3MO.06 2 0.0000 0.648 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.WE.A8ZQ.06 7 0.0471 0.888 0.00 0.00 0.00 0.00 0.00 0.02 0.98 0.00
#> TCGA.FR.A2OS.01 3 0.6091 0.232 0.00 0.00 0.46 0.00 0.12 0.20 0.22 0.00
#> TCGA.D3.A2JE.06 2 0.4276 0.355 0.00 0.64 0.06 0.00 0.02 0.00 0.00 0.28
#> TCGA.GN.A4U9.06 2 0.0471 0.642 0.00 0.98 0.00 0.00 0.00 0.00 0.00 0.02
#> TCGA.FS.A1ZR.06 6 0.3237 0.764 0.40 0.00 0.00 0.00 0.00 0.60 0.00 0.00
#> TCGA.EE.A2GP.06 5 0.2114 0.707 0.00 0.00 0.00 0.16 0.84 0.00 0.00 0.00
#> TCGA.EE.A2A5.06 5 0.1091 0.729 0.00 0.00 0.00 0.00 0.94 0.00 0.00 0.06
#> TCGA.EE.A2GC.06 4 0.0000 0.789 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.ER.A19E.06 2 0.0000 0.648 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FS.A1ZK.06 4 0.1887 0.768 0.00 0.00 0.00 0.90 0.00 0.04 0.00 0.06
#> TCGA.FS.A1ZU.06 2 0.4812 0.323 0.00 0.60 0.06 0.00 0.06 0.00 0.00 0.28
#> TCGA.EE.A17Z.06 2 0.1563 0.607 0.00 0.90 0.00 0.00 0.00 0.00 0.00 0.10
#> TCGA.ER.A19T.01 3 0.3757 0.371 0.00 0.00 0.68 0.00 0.00 0.26 0.06 0.00
#> TCGA.EE.A2GN.06 2 0.0471 0.642 0.00 0.98 0.00 0.00 0.00 0.00 0.00 0.02
#> TCGA.EE.A20H.06 2 0.5618 -0.621 0.00 0.50 0.02 0.00 0.18 0.02 0.00 0.28
#> TCGA.FS.A1ZJ.06 7 0.1091 0.850 0.00 0.00 0.06 0.00 0.00 0.00 0.94 0.00
#> TCGA.EE.A3AC.06 6 0.3618 0.782 0.38 0.00 0.00 0.02 0.00 0.60 0.00 0.00
#> TCGA.EE.A2GR.06 1 0.0941 0.817 0.96 0.00 0.00 0.00 0.00 0.02 0.00 0.02
#> TCGA.FS.A1ZD.06 7 0.1275 0.847 0.00 0.00 0.04 0.00 0.00 0.02 0.94 0.00
#> TCGA.FS.A1ZP.06 2 0.4733 0.331 0.00 0.62 0.06 0.00 0.06 0.00 0.00 0.26
#> TCGA.DA.A1IC.06 1 0.0000 0.823 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.ER.A3PL.06 1 0.3095 0.570 0.74 0.00 0.00 0.00 0.00 0.24 0.00 0.02
#> TCGA.D9.A3Z4.01 3 0.3737 0.110 0.00 0.00 0.50 0.00 0.00 0.00 0.48 0.02
#> TCGA.YD.A9TB.06 1 0.3170 0.589 0.76 0.00 0.00 0.00 0.00 0.20 0.00 0.04
#> TCGA.ER.A2ND.06 6 0.2406 0.677 0.20 0.00 0.00 0.00 0.00 0.80 0.00 0.00
#> TCGA.D9.A4Z3.01 8 0.4999 0.000 0.00 0.40 0.00 0.00 0.18 0.00 0.00 0.42
#> TCGA.EB.A44O.01 1 0.0000 0.823 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.YG.AA3P.06 3 0.3737 0.110 0.00 0.00 0.50 0.00 0.00 0.00 0.48 0.02
#> TCGA.D3.A51K.06 2 0.0000 0.648 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EB.A44P.01 1 0.0471 0.817 0.98 0.00 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.
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