Date: 2021-07-22 18:09:17 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 375933 rows and 398 columns.
#> Performed in total 103600 partitions.
#> There are 50 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, 398 cols
#> |-- 01, 176 cols, 19830 signatures
#> | |-- 011, 67 cols, 7619 signatures
#> | | |-- 0111, 17 cols, 17153 signatures
#> | | | |-- 01111, 4 cols (b)
#> | | | |-- 01112, 5 cols (b)
#> | | | |-- 01113, 2 cols (b)
#> | | | |-- 01114, 2 cols (b)
#> | | | |-- 01115, 2 cols (b)
#> | | | `-- 01116, 2 cols (b)
#> | | |-- 0112, 23 cols, 4126 signatures
#> | | | |-- 01121, 14 cols, 27 signatures (c)
#> | | | |-- 01122, 7 cols (b)
#> | | | `-- 01123, 2 cols (b)
#> | | |-- 0113, 18 cols, 10459 signatures
#> | | | |-- 01131, 6 cols (b)
#> | | | |-- 01132, 3 cols (b)
#> | | | |-- 01133, 6 cols (b)
#> | | | `-- 01134, 3 cols (b)
#> | | `-- 0114, 9 cols (b)
#> | |-- 012, 59 cols, 6799 signatures
#> | | |-- 0121, 19 cols, 1613 signatures
#> | | | |-- 01211, 9 cols (b)
#> | | | `-- 01212, 10 cols (b)
#> | | |-- 0122, 21 cols, 2372 signatures
#> | | | |-- 01221, 3 cols (b)
#> | | | `-- 01222, 18 cols, 644 signatures (c)
#> | | `-- 0123, 19 cols, 2422 signatures
#> | | |-- 01231, 9 cols (b)
#> | | |-- 01232, 6 cols (b)
#> | | `-- 01233, 4 cols (b)
#> | `-- 013, 50 cols, 1377 signatures
#> | |-- 0131, 34 cols, 2448 signatures
#> | | |-- 01311, 10 cols (b)
#> | | `-- 01312, 24 cols, 2012 signatures
#> | | |-- 013121, 10 cols (b)
#> | | |-- 013122, 5 cols (b)
#> | | `-- 013123, 9 cols (b)
#> | `-- 0132, 16 cols, 948 signatures (c)
#> |-- 02, 105 cols, 29355 signatures
#> | |-- 021, 28 cols, 3226 signatures
#> | | |-- 0211, 21 cols, 732 signatures (c)
#> | | `-- 0212, 7 cols (b)
#> | |-- 022, 48 cols, 1033 signatures
#> | | |-- 0221, 24 cols, 411 signatures (c)
#> | | `-- 0222, 24 cols, 2903 signatures
#> | | |-- 02221, 7 cols (b)
#> | | |-- 02222, 9 cols (b)
#> | | |-- 02223, 5 cols (b)
#> | | `-- 02224, 3 cols (b)
#> | `-- 023, 29 cols, 3913 signatures
#> | |-- 0231, 12 cols, 34 signatures (c)
#> | |-- 0232, 11 cols (b)
#> | `-- 0233, 6 cols (b)
#> `-- 03, 117 cols, 16188 signatures
#> |-- 031, 50 cols, 11163 signatures
#> | |-- 0311, 23 cols, 2546 signatures
#> | | |-- 03111, 11 cols (b)
#> | | |-- 03112, 7 cols (b)
#> | | `-- 03113, 5 cols (b)
#> | |-- 0312, 6 cols (b)
#> | |-- 0313, 10 cols (b)
#> | `-- 0314, 11 cols (b)
#> |-- 032, 31 cols, 584 signatures (c)
#> |-- 033, 15 cols, 7939 signatures
#> | |-- 0331, 7 cols (b)
#> | |-- 0332, 5 cols (b)
#> | `-- 0333, 3 cols (b)
#> `-- 034, 21 cols, 6100 signatures
#> |-- 0341, 16 cols, 2116 signatures
#> | |-- 03411, 4 cols (b)
#> | |-- 03412, 7 cols (b)
#> | `-- 03413, 5 cols (b)
#> `-- 0342, 5 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] 375933 398
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" "01114" "01115" "01116"
#> [11] "0112" "01121" "01122" "01123" "0113" "01131" "01132" "01133" "01134" "0114"
#> [21] "012" "0121" "01211" "01212" "0122" "01221" "01222" "0123" "01231" "01232"
#> [31] "01233" "013" "0131" "01311" "01312" "013121" "013122" "013123" "0132" "02"
#> [41] "021" "0211" "0212" "022" "0221" "0222" "02221" "02222" "02223" "02224"
#> [51] "023" "0231" "0232" "0233" "03" "031" "0311" "03111" "03112" "03113"
#> [61] "0312" "0313" "0314" "032" "033" "0331" "0332" "0333" "034" "0341"
#> [71] "03411" "03412" "03413" "0342"
all_leaves(res_rh)
#> [1] "01111" "01112" "01113" "01114" "01115" "01116" "01121" "01122" "01123" "01131"
#> [11] "01132" "01133" "01134" "0114" "01211" "01212" "01221" "01222" "01231" "01232"
#> [21] "01233" "01311" "013121" "013122" "013123" "0132" "0211" "0212" "0221" "02221"
#> [31] "02222" "02223" "02224" "0231" "0232" "0233" "03111" "03112" "03113" "0312"
#> [41] "0313" "0314" "032" "0331" "0332" "0333" "03411" "03412" "03413" "0342"
node_info(res_rh)
#> id best_method depth best_k n_columns n_signatures p_signatures is_leaf
#> 1 0 SD:kmeans 1 3 398 26007 6.92e-02 FALSE
#> 2 01 ATC:kmeans 2 3 176 19830 5.27e-02 FALSE
#> 3 011 SD:skmeans 3 4 67 7619 2.03e-02 FALSE
#> 4 0111 ATC:skmeans 4 6 17 17153 4.56e-02 FALSE
#> 5 01111 not applied 5 NA 4 NA NA TRUE
#> 6 01112 not applied 5 NA 5 NA NA TRUE
#> 7 01113 not applied 5 NA 2 NA NA TRUE
#> 8 01114 not applied 5 NA 2 NA NA TRUE
#> 9 01115 not applied 5 NA 2 NA NA TRUE
#> 10 01116 not applied 5 NA 2 NA NA TRUE
#> 11 0112 ATC:kmeans 4 3 23 4126 1.10e-02 FALSE
#> 12 01121 ATC:skmeans 5 2 14 27 7.18e-05 TRUE
#> 13 01122 not applied 5 NA 7 NA NA TRUE
#> 14 01123 not applied 5 NA 2 NA NA TRUE
#> 15 0113 ATC:kmeans 4 4 18 10459 2.78e-02 FALSE
#> 16 01131 not applied 5 NA 6 NA NA TRUE
#> 17 01132 not applied 5 NA 3 NA NA TRUE
#> 18 01133 not applied 5 NA 6 NA NA TRUE
#> 19 01134 not applied 5 NA 3 NA NA TRUE
#> 20 0114 not applied 4 NA 9 NA NA TRUE
#> 21 012 ATC:kmeans 3 3 59 6799 1.81e-02 FALSE
#> 22 0121 ATC:kmeans 4 2 19 1613 4.29e-03 FALSE
#> 23 01211 not applied 5 NA 9 NA NA TRUE
#> 24 01212 not applied 5 NA 10 NA NA TRUE
#> 25 0122 ATC:kmeans 4 2 21 2372 6.31e-03 FALSE
#> 26 01221 not applied 5 NA 3 NA NA TRUE
#> 27 01222 ATC:kmeans 5 3 18 644 1.71e-03 TRUE
#> 28 0123 ATC:kmeans 4 3 19 2422 6.44e-03 FALSE
#> 29 01231 not applied 5 NA 9 NA NA TRUE
#> 30 01232 not applied 5 NA 6 NA NA TRUE
#> 31 01233 not applied 5 NA 4 NA NA TRUE
#> 32 013 ATC:kmeans 3 2 50 1377 3.66e-03 FALSE
#> 33 0131 SD:kmeans 4 2 34 2448 6.51e-03 FALSE
#> 34 01311 not applied 5 NA 10 NA NA TRUE
#> 35 01312 ATC:kmeans 5 3 24 2012 5.35e-03 FALSE
#> 36 013121 not applied 6 NA 10 NA NA TRUE
#> 37 013122 not applied 6 NA 5 NA NA TRUE
#> 38 013123 not applied 6 NA 9 NA NA TRUE
#> 39 0132 ATC:skmeans 4 4 16 948 2.52e-03 TRUE
#> 40 02 ATC:kmeans 2 3 105 29355 7.81e-02 FALSE
#> 41 021 ATC:kmeans 3 2 28 3226 8.58e-03 FALSE
#> 42 0211 ATC:skmeans 4 2 21 732 1.95e-03 TRUE
#> 43 0212 not applied 4 NA 7 NA NA TRUE
#> 44 022 ATC:kmeans 3 2 48 1033 2.75e-03 FALSE
#> 45 0221 SD:kmeans 4 2 24 411 1.09e-03 TRUE
#> 46 0222 ATC:kmeans 4 4 24 2903 7.72e-03 FALSE
#> 47 02221 not applied 5 NA 7 NA NA TRUE
#> 48 02222 not applied 5 NA 9 NA NA TRUE
#> 49 02223 not applied 5 NA 5 NA NA TRUE
#> 50 02224 not applied 5 NA 3 NA NA TRUE
#> 51 023 SD:kmeans 3 3 29 3913 1.04e-02 FALSE
#> 52 0231 SD:skmeans 4 2 12 34 9.04e-05 TRUE
#> 53 0232 not applied 4 NA 11 NA NA TRUE
#> 54 0233 not applied 4 NA 6 NA NA TRUE
#> 55 03 ATC:skmeans 2 4 117 16188 4.31e-02 FALSE
#> 56 031 ATC:skmeans 3 4 50 11163 2.97e-02 FALSE
#> 57 0311 SD:kmeans 4 3 23 2546 6.77e-03 FALSE
#> 58 03111 not applied 5 NA 11 NA NA TRUE
#> 59 03112 not applied 5 NA 7 NA NA TRUE
#> 60 03113 not applied 5 NA 5 NA NA TRUE
#> 61 0312 not applied 4 NA 6 NA NA TRUE
#> 62 0313 not applied 4 NA 10 NA NA TRUE
#> 63 0314 not applied 4 NA 11 NA NA TRUE
#> 64 032 ATC:kmeans 3 2 31 584 1.55e-03 TRUE
#> 65 033 ATC:kmeans 3 3 15 7939 2.11e-02 FALSE
#> 66 0331 not applied 4 NA 7 NA NA TRUE
#> 67 0332 not applied 4 NA 5 NA NA TRUE
#> 68 0333 not applied 4 NA 3 NA NA TRUE
#> 69 034 ATC:skmeans 3 2 21 6100 1.62e-02 FALSE
#> 70 0341 ATC:kmeans 4 3 16 2116 5.63e-03 FALSE
#> 71 03411 not applied 5 NA 4 NA NA TRUE
#> 72 03412 not applied 5 NA 7 NA NA TRUE
#> 73 03413 not applied 5 NA 5 NA NA TRUE
#> 74 0342 not applied 4 NA 5 NA NA TRUE
In the output from node_info(), there are the following columns:
id: The node id.best_method: The best method selected.depth: Depth of the node in the hierarchy.best_k: Best number of groups of the partition on that node.n_columns: Number of columns in the submatrix.n_signatures: Number of signatures with the best_k.p_signatures: Proportion of hte signatures in total number of rows in the matrix.is_leaf: Whether the node is a leaf.Labels of nodes are encoded in a special way. The number of digits correspond to the depth of the node in the hierarchy and the value of the digits correspond to the index of the subgroup in the current node, E.g. a label of “012” means the node is the second subgroup of the partition which is the first subgroup of the root node.
Following table shows the best k (number of partitions) for each node in the
partition hierarchy. Clicking on the node name in the table goes to the
corresponding section for the partitioning on that node.
The cola vignette explains the definition of the metrics used for determining the best number of partitions.
suggest_best_k(res_rh)
| Node | Best method | Is leaf | Best k | 1-PAC | Mean silhouette | Concordance | #samples | |
|---|---|---|---|---|---|---|---|---|
| Node0 | SD:kmeans | 3 | 0.99 | 0.95 | 0.98 | 398 | ** | |
| Node01 | ATC:kmeans | 3 | 1.00 | 0.98 | 0.99 | 176 | ** | |
| Node011 | SD:skmeans | 4 | 0.99 | 0.96 | 0.98 | 67 | ** | |
| Node0111 | ATC:skmeans | 8 | 0.91 | 0.71 | 0.91 | 17 | * | |
| Node01111-leaf | not applied | ✓ (b) | 4 | |||||
| Node01112-leaf | not applied | ✓ (b) | 5 | |||||
| Node01113-leaf | not applied | ✓ (b) | 2 | |||||
| Node01114-leaf | not applied | ✓ (b) | 2 | |||||
| Node01115-leaf | not applied | ✓ (b) | 2 | |||||
| Node01116-leaf | not applied | ✓ (b) | 2 | |||||
| Node0112 | ATC:kmeans | 2 | 0.53 | 0.95 | 0.92 | 23 | ||
| Node01121-leaf | ATC:skmeans | ✓ (c) | 2 | 1.00 | 1.00 | 1.00 | 14 | ** |
| Node01122-leaf | not applied | ✓ (b) | 7 | |||||
| Node01123-leaf | not applied | ✓ (b) | 2 | |||||
| Node0113 | ATC:kmeans | 2 | 1.00 | 1.00 | 1.00 | 18 | ** | |
| Node01131-leaf | not applied | ✓ (b) | 6 | |||||
| Node01132-leaf | not applied | ✓ (b) | 3 | |||||
| Node01133-leaf | not applied | ✓ (b) | 6 | |||||
| Node01134-leaf | not applied | ✓ (b) | 3 | |||||
| Node0114-leaf | not applied | ✓ (b) | 9 | |||||
| Node012 | ATC:kmeans | 3 | 1.00 | 0.99 | 0.99 | 59 | ** | |
| Node0121 | ATC:kmeans | 2 | 1.00 | 1.00 | 1.00 | 19 | ** | |
| Node01211-leaf | not applied | ✓ (b) | 9 | |||||
| Node01212-leaf | not applied | ✓ (b) | 10 | |||||
| Node0122 | ATC:kmeans | 2 | 1.00 | 1.00 | 1.00 | 21 | ** | |
| Node01221-leaf | not applied | ✓ (b) | 3 | |||||
| Node01222-leaf | ATC:kmeans | ✓ (c) | 3 | 1.00 | 1.00 | 1.00 | 18 | ** |
| Node0123 | ATC:kmeans | 3 | 0.98 | 0.99 | 0.97 | 19 | ** | |
| Node01231-leaf | not applied | ✓ (b) | 9 | |||||
| Node01232-leaf | not applied | ✓ (b) | 6 | |||||
| Node01233-leaf | not applied | ✓ (b) | 4 | |||||
| Node013 | ATC:kmeans | 2 | 1.00 | 1.00 | 1.00 | 50 | ** | |
| Node0131 | SD:kmeans | 2 | 1.00 | 1.00 | 1.00 | 34 | ** | |
| Node01311-leaf | not applied | ✓ (b) | 10 | |||||
| Node01312 | ATC:kmeans | 3 | 1.00 | 0.97 | 0.99 | 24 | ** | |
| Node013121-leaf | not applied | ✓ (b) | 10 | |||||
| Node013122-leaf | not applied | ✓ (b) | 5 | |||||
| Node013123-leaf | not applied | ✓ (b) | 9 | |||||
| Node0132-leaf | ATC:skmeans | ✓ (c) | 3 | 1.00 | 1.00 | 1.00 | 16 | ** |
| Node02 | ATC:kmeans | 3 | 0.98 | 0.99 | 0.97 | 105 | ** | |
| Node021 | ATC:kmeans | 2 | 1.00 | 1.00 | 1.00 | 28 | ** | |
| Node0211-leaf | ATC:skmeans | ✓ (c) | 2 | 1.00 | 1.00 | 1.00 | 21 | ** |
| Node0212-leaf | not applied | ✓ (b) | 7 | |||||
| Node022 | ATC:kmeans | 2 | 1.00 | 1.00 | 1.00 | 48 | ** | |
| Node0221-leaf | SD:kmeans | ✓ (c) | 2 | 1.00 | 0.97 | 0.98 | 24 | ** |
| Node0222 | ATC:kmeans | 4 | 0.83 | 0.95 | 0.96 | 24 | ||
| Node02221-leaf | not applied | ✓ (b) | 7 | |||||
| Node02222-leaf | not applied | ✓ (b) | 9 | |||||
| Node02223-leaf | not applied | ✓ (b) | 5 | |||||
| Node02224-leaf | not applied | ✓ (b) | 3 | |||||
| Node023 | SD:kmeans | 2 | 1.00 | 1.00 | 1.00 | 29 | ** | |
| Node0231-leaf | SD:skmeans | ✓ (c) | 2 | 1.00 | 0.97 | 0.98 | 12 | ** |
| Node0232-leaf | not applied | ✓ (b) | 11 | |||||
| Node0233-leaf | not applied | ✓ (b) | 6 | |||||
| Node03 | ATC:skmeans | 5 | 0.94 | 0.91 | 0.97 | 117 | * | |
| Node031 | ATC:skmeans | 4 | 1.00 | 1.00 | 1.00 | 50 | ** | |
| Node0311 | SD:kmeans | 3 | 0.97 | 0.97 | 0.97 | 23 | ** | |
| Node03111-leaf | not applied | ✓ (b) | 11 | |||||
| Node03112-leaf | not applied | ✓ (b) | 7 | |||||
| Node03113-leaf | not applied | ✓ (b) | 5 | |||||
| Node0312-leaf | not applied | ✓ (b) | 6 | |||||
| Node0313-leaf | not applied | ✓ (b) | 10 | |||||
| Node0314-leaf | not applied | ✓ (b) | 11 | |||||
| Node032-leaf | ATC:kmeans | ✓ (c) | 3 | 0.90 | 0.91 | 0.97 | 31 | * |
| Node033 | ATC:kmeans | 3 | 1.00 | 1.00 | 1.00 | 15 | ** | |
| Node0331-leaf | not applied | ✓ (b) | 7 | |||||
| Node0332-leaf | not applied | ✓ (b) | 5 | |||||
| Node0333-leaf | not applied | ✓ (b) | 3 | |||||
| Node034 | ATC:skmeans | 2 | 1.00 | 0.97 | 0.99 | 21 | ** | |
| Node0341 | ATC:kmeans | 3 | 0.93 | 0.95 | 0.98 | 16 | * | |
| Node03411-leaf | not applied | ✓ (b) | 4 | |||||
| Node03412-leaf | not applied | ✓ (b) | 7 | |||||
| Node03413-leaf | not applied | ✓ (b) | 5 | |||||
| Node0342-leaf | not applied | ✓ (b) | 5 |
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 = 1033))
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 1377))
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 1613))
#> Error in lt[[hierarchy[i, 1]]]$AddChildNode({: attempt to apply non-function
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 2012))
#> Error in lt[[hierarchy[i, 1]]]$AddChildNode({: attempt to apply non-function
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 2116))
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 2372))
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 2422))
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 2448))
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 2546))
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 2903))
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 3226))
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 3913))
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 4126))
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 6100))
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 6799))
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 7619))
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 7939))
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 10459))
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 11163))
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 16188))
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 17153))
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 19830))
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 26007))
collect_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 29355))
#> Error in max(children_height): invalid 'type' (list) of argument
Following shows the table of the partitions (You need to click the show/hide code output link to see it).
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 1033))
#> TCGA.VQ.A94P.01 TCGA.D7.6521.01 TCGA.VQ.A8PE.01 TCGA.D7.6519.01 TCGA.BR.6452.01 TCGA.BR.8485.01
#> "01133" "01121" "01233" "0132" "0231" "01232"
#> TCGA.VQ.A8PO.01 TCGA.VQ.AA69.01 TCGA.BR.8683.01 TCGA.BR.8486.01 TCGA.D7.6522.01 TCGA.CG.5716.01
#> "02221" "0212" "032" "01232" "01131" "0314"
#> TCGA.BR.8589.01 TCGA.BR.8382.01 TCGA.VQ.AA68.01 TCGA.VQ.A8PJ.01 TCGA.VQ.A8PH.01 TCGA.HU.8604.01
#> "0211" "0231" "03412" "01222" "01233" "0231"
#> TCGA.BR.8676.01 TCGA.CG.4441.01 TCGA.D7.6520.01 TCGA.VQ.AA64.01 TCGA.D7.6527.01 TCGA.VQ.A8PM.01
#> "0212" "0342" "01211" "01122" "01231" "013123"
#> TCGA.VQ.A923.01 TCGA.BR.8384.01 TCGA.BR.6453.01 TCGA.VQ.A928.01 TCGA.VQ.A8E0.01 TCGA.BR.8679.01
#> "0212" "03111" "03112" "01122" "01122" "02222"
#> TCGA.VQ.A91S.01 TCGA.BR.8678.01 TCGA.D7.6528.01 TCGA.VQ.A8E7.01 TCGA.BR.8680.01 TCGA.BR.8483.01
#> "032" "01221" "0332" "03411" "03411" "0331"
#> TCGA.BR.6566.01 TCGA.VQ.A91X.01 TCGA.VQ.A91Q.01 TCGA.VQ.A92D.01 TCGA.VQ.A91Z.01 TCGA.BR.6455.01
#> "032" "0332" "01122" "0221" "01221" "0212"
#> TCGA.BR.8591.01 TCGA.HU.8608.01 TCGA.VQ.A94U.01 TCGA.VQ.A94T.01 TCGA.VQ.A91A.01 TCGA.VQ.A91D.01
#> "0233" "0211" "0333" "01123" "032" "0233"
#> TCGA.D7.6518.01 TCGA.BR.8484.01 TCGA.VQ.A91N.01 TCGA.VQ.A91E.01 TCGA.VQ.A8PY.01 TCGA.HU.8602.01
#> "03111" "0132" "01222" "032" "032" "0231"
#> TCGA.BR.8381.01 TCGA.BR.6452.11 TCGA.IN.8663.01 TCGA.VQ.A8PS.01 TCGA.VQ.A91W.01 TCGA.BR.6454.01
#> "0211" "0314" "0221" "01122" "0212" "01121"
#> TCGA.BR.8682.01 TCGA.VQ.A91V.01 TCGA.VQ.A8PZ.01 TCGA.BR.8590.01 TCGA.F1.6177.01 TCGA.VQ.A8PQ.01
#> "032" "0333" "0314" "01133" "0221" "01112"
#> TCGA.VQ.A91U.01 TCGA.VQ.AA6I.01 TCGA.CG.4437.01 TCGA.VQ.A8PP.01 TCGA.BR.6565.01 TCGA.VQ.A91Y.01
#> "01222" "02222" "0232" "0232" "01212" "013123"
#> TCGA.VQ.A8PF.01 TCGA.BR.6456.01 TCGA.BR.6458.01 TCGA.VQ.A925.01 TCGA.VQ.A927.01 TCGA.BR.8592.01
#> "0211" "01311" "032" "0132" "01132" "0313"
#> TCGA.BR.6566.11 TCGA.IN.AB1V.01 TCGA.VQ.AA6F.01 TCGA.VQ.AA6J.01 TCGA.BR.8487.01 TCGA.D7.6525.01
#> "01114" "013121" "01121" "01121" "02223" "032"
#> TCGA.VQ.A94O.01 TCGA.BR.8588.01 TCGA.HU.8610.01 TCGA.D7.6526.01 TCGA.VQ.A8PD.01 TCGA.D7.6524.01
#> "01211" "0313" "03111" "01231" "03112" "0314"
#> TCGA.3M.AB46.01 TCGA.3M.AB47.01 TCGA.BR.8677.01 TCGA.BR.6457.01 TCGA.BR.8687.01 TCGA.VQ.A91K.01
#> "01222" "03112" "0114" "03111" "0132" "0221"
#> TCGA.BR.8690.01 TCGA.BR.8686.01 TCGA.FP.8631.01 TCGA.VQ.A922.01 TCGA.BR.A452.01 TCGA.IN.A6RO.01
#> "01311" "0211" "01212" "01212" "01121" "0221"
#> TCGA.BR.A4QI.01 TCGA.D7.A6EV.01 TCGA.HU.A4G2.01 TCGA.BR.A4IY.01 TCGA.VQ.A8PU.01 TCGA.BR.A4J4.01
#> "0231" "03413" "0211" "0211" "01123" "0211"
#> TCGA.VQ.A94R.01 TCGA.HU.A4H4.01 TCGA.BR.7707.01 TCGA.FP.7829.01 TCGA.BR.A4J5.01 TCGA.HU.A4H0.01
#> "02222" "032" "0221" "02224" "03113" "0211"
#> TCGA.HU.A4HD.01 TCGA.KB.A6F5.01 TCGA.VQ.AA6K.01 TCGA.HF.7133.01 TCGA.F1.6875.01 TCGA.MX.A666.01
#> "01211" "013123" "01121" "0132" "01221" "01211"
#> TCGA.BR.7717.01 TCGA.BR.A4PF.01 TCGA.BR.A4IU.01 TCGA.VQ.A8PX.01 TCGA.BR.A4IV.01 TCGA.D7.A6EX.01
#> "03412" "0232" "0313" "01121" "01133" "0132"
#> TCGA.BR.A4IZ.01 TCGA.BR.A4J9.01 TCGA.CD.A4MJ.01 TCGA.B7.A5TN.01 TCGA.BR.7715.01 TCGA.BR.7704.01
#> "01115" "01133" "0233" "01222" "0332" "01232"
#> TCGA.BR.A4J1.01 TCGA.HU.A4GP.01 TCGA.D7.A4YY.01 TCGA.VQ.AA6G.01 TCGA.HU.A4GJ.01 TCGA.CD.A4MI.01
#> "01211" "02222" "0221" "0221" "0314" "0232"
#> TCGA.BR.7196.01 TCGA.BR.6563.01 TCGA.VQ.A924.01 TCGA.BR.7716.01 TCGA.FP.7735.01 TCGA.BR.7723.01
#> "0312" "03111" "0233" "01311" "0132" "013122"
#> TCGA.HU.A4H8.01 TCGA.IN.A6RJ.01 TCGA.HU.A4H3.01 TCGA.EQ.A4SO.01 TCGA.CD.A4MH.01 TCGA.BR.A4J7.01
#> "02223" "03113" "02223" "01122" "01232" "01121"
#> TCGA.HF.7131.01 TCGA.D7.A74B.01 TCGA.BR.A4PE.01 TCGA.BR.A4J8.01 TCGA.HU.A4GX.01 TCGA.HU.A4G8.01
#> "01231" "01116" "0221" "0231" "032" "03413"
#> TCGA.HU.A4GT.01 TCGA.HU.A4GC.01 TCGA.BR.A4CQ.01 TCGA.D7.A6F2.01 TCGA.RD.A7BT.01 TCGA.BR.A4J6.01
#> "0221" "03413" "0221" "01222" "01222" "0114"
#> TCGA.HU.A4GQ.01 TCGA.HF.7136.01 TCGA.BR.A4QM.01 TCGA.BR.A4PD.01 TCGA.VQ.A8PK.01 TCGA.B7.A5TK.01
#> "0232" "0132" "0232" "01222" "01212" "0312"
#> TCGA.D7.A4YX.01 TCGA.D7.A4Z0.01 TCGA.VQ.A8PT.01 TCGA.IN.A6RN.01 TCGA.CD.A4MG.01 TCGA.D7.A747.01
#> "0211" "0313" "0221" "01212" "02223" "01133"
#> TCGA.R5.A7O7.01 TCGA.F1.A72C.01 TCGA.BR.A4J2.01 TCGA.MX.A663.01 TCGA.D7.A4YV.01 TCGA.HU.A4GD.01
#> "03113" "01121" "03113" "013122" "0231" "0331"
#> TCGA.BR.A4QL.01 TCGA.BR.7703.01 TCGA.VQ.AA6B.01 TCGA.VQ.AA6D.01 TCGA.D7.A6EZ.01 TCGA.D7.A4YU.01
#> "0221" "0221" "0332" "01232" "0211" "0232"
#> TCGA.VQ.AA6A.01 TCGA.IN.7806.01 TCGA.HU.A4HB.01 TCGA.HU.A4H2.01 TCGA.IN.A6RP.01 TCGA.HU.A4H5.01
#> "01231" "01222" "03113" "0342" "0221" "01231"
#> TCGA.HU.A4GU.01 TCGA.MX.A5UJ.01 TCGA.HU.A4GN.01 TCGA.CD.5804.01 TCGA.HU.A4H6.01 TCGA.HF.7132.01
#> "0221" "02221" "0232" "013123" "0231" "0232"
#> TCGA.D7.A4YT.01 TCGA.HF.7134.01 TCGA.BR.6852.01 TCGA.BR.8370.01 TCGA.EQ.5647.01 TCGA.IN.A7NT.01
#> "0132" "02222" "0314" "0233" "0132" "032"
#> TCGA.RD.A8N9.01 TCGA.D7.5577.01 TCGA.CG.5717.01 TCGA.D7.6818.01 TCGA.CG.5734.01 TCGA.VQ.A8P8.01
#> "0114" "0211" "01134" "013121" "03111" "0314"
#> TCGA.BR.6707.01 TCGA.B7.5818.01 TCGA.CD.8525.01 TCGA.BR.6705.01 TCGA.BR.4288.01 TCGA.CD.5813.01
#> "0211" "0211" "01311" "0313" "013122" "01121"
#> TCGA.CG.5723.01 TCGA.CD.5800.01 TCGA.CG.5718.01 TCGA.BR.8080.01 TCGA.CG.5733.01 TCGA.D7.6817.01
#> "01121" "01311" "01232" "0114" "02221" "01231"
#> TCGA.KB.A93G.01 TCGA.CD.5799.01 TCGA.BR.7851.01 TCGA.BR.7722.01 TCGA.MX.A5UG.01 TCGA.CD.8533.01
#> "01133" "013121" "0232" "01121" "03111" "0331"
#> TCGA.BR.7957.01 TCGA.CG.5722.01 TCGA.F1.6874.01 TCGA.CG.5730.01 TCGA.CG.5726.01 TCGA.IP.7968.01
#> "0313" "0312" "032" "0331" "02222" "0331"
#> TCGA.BR.8363.01 TCGA.BR.7901.01 TCGA.D7.6822.01 TCGA.BR.6710.01 TCGA.CG.5720.01 TCGA.D7.8570.01
#> "0231" "01212" "03411" "01132" "0221" "0211"
#> TCGA.B7.A5TI.01 TCGA.D7.6815.01 TCGA.BR.8284.01 TCGA.BR.8295.01 TCGA.BR.7197.01 TCGA.B7.A5TJ.01
#> "0132" "01222" "0231" "01211" "01222" "0221"
#> TCGA.D7.A6EY.01 TCGA.BR.8366.01 TCGA.IN.A7NR.01 TCGA.BR.6706.01 TCGA.IN.7808.01 TCGA.BR.6564.01
#> "0313" "0211" "01114" "0312" "03112" "01111"
#> TCGA.KB.A93H.01 TCGA.KB.A93J.01 TCGA.CD.5798.01 TCGA.CD.8530.01 TCGA.BR.6802.01 TCGA.CG.5719.01
#> "0332" "01222" "01134" "013121" "03112" "0114"
#> TCGA.VQ.A8E3.01 TCGA.CD.5801.01 TCGA.FP.A9TM.01 TCGA.BR.7958.01 TCGA.FP.7998.01 TCGA.IN.A6RS.01
#> "02221" "0211" "032" "0211" "0312" "032"
#> TCGA.BR.6709.01 TCGA.FP.7916.01 TCGA.R5.A7ZR.01 TCGA.B7.5816.01 TCGA.CG.5721.01 TCGA.SW.A7EA.01
#> "01112" "0211" "01222" "0314" "03111" "0221"
#> TCGA.RD.A8NB.01 TCGA.BR.6801.01 TCGA.IN.AB1X.01 TCGA.D7.5579.01 TCGA.CG.5728.01 TCGA.R5.A7ZI.01
#> "0313" "0132" "0314" "013121" "0313" "01311"
#> TCGA.IN.A7NU.01 TCGA.CG.5732.01 TCGA.ZQ.A9CR.01 TCGA.D7.5578.01 TCGA.BR.6803.01 TCGA.BR.8368.01
#> "032" "013123" "01311" "032" "01111" "02221"
#> TCGA.SW.A7EB.01 TCGA.BR.8081.01 TCGA.VQ.A8P5.01 TCGA.CD.8535.01 TCGA.CG.5724.01 TCGA.D7.8574.01
#> "01132" "0231" "032" "02224" "03412" "01131"
#> TCGA.HJ.7597.01 TCGA.HF.A5NB.01 TCGA.VQ.A8PB.01 TCGA.R5.A7ZE.01 TCGA.CD.5803.01 TCGA.CG.5725.01
#> "0114" "02223" "03412" "01222" "01112" "01212"
#> TCGA.D7.6820.01 TCGA.CD.5802.01 TCGA.R5.A7ZF.01 TCGA.D7.A6F0.01 TCGA.CG.5727.01 TCGA.VQ.A8PC.01
#> "01231" "013123" "01311" "01211" "032" "03111"
#> TCGA.CD.A486.01 TCGA.RD.A8N2.01 TCGA.IN.A6RI.01 TCGA.HU.8243.01 TCGA.CD.A48C.01 TCGA.RD.A8N5.01
#> "01211" "01113" "01212" "0342" "02222" "01131"
#> TCGA.RD.A8N1.01 TCGA.HU.A4GF.01 TCGA.BR.8362.01 TCGA.BR.8285.01 TCGA.CD.8532.01 TCGA.VQ.A8E2.01
#> "013121" "01222" "032" "0211" "01121" "013122"
#> TCGA.BR.8373.01 TCGA.BR.8361.01 TCGA.BR.8058.01 TCGA.IN.8462.01 TCGA.HU.A4G9.01 TCGA.CD.8524.01
#> "01222" "02221" "0114" "03412" "0221" "032"
#> TCGA.D7.A748.01 TCGA.CD.8527.01 TCGA.VQ.A8DV.01 TCGA.CD.8528.01 TCGA.BR.A453.01 TCGA.RD.A8N6.01
#> "01115" "0132" "01233" "02221" "03111" "0132"
#> TCGA.HU.8245.01 TCGA.ZA.A8F6.01 TCGA.BR.8367.01 TCGA.BR.8380.01 TCGA.FP.A4BE.01 TCGA.HU.8238.01
#> "01231" "013121" "032" "03112" "0233" "03413"
#> TCGA.BR.8078.01 TCGA.HU.8249.01 TCGA.RD.A8N0.01 TCGA.BR.8365.01 TCGA.FP.8211.01 TCGA.RD.A8N4.01
#> "0231" "0331" "01112" "01111" "01122" "01113"
#> TCGA.VQ.A8DU.01 TCGA.VQ.A8DL.01 TCGA.VQ.A8DZ.01 TCGA.D7.8572.01 TCGA.RD.A7BW.01 TCGA.R5.A804.01
#> "01233" "01311" "01231" "013122" "01116" "0314"
#> TCGA.BR.A4CS.01 TCGA.CD.8531.01 TCGA.CD.A487.01 TCGA.BR.8371.01 TCGA.BR.8059.01 TCGA.D7.A6ET.01
#> "032" "0212" "0132" "01131" "013121" "0312"
#> TCGA.FP.8099.01 TCGA.D7.8579.01 TCGA.BR.8297.01 TCGA.D7.8576.01 TCGA.VQ.A8DT.01 TCGA.FP.A8CX.01
#> "0333" "0313" "032" "0114" "02222" "013121"
#> TCGA.HU.A4GH.01 TCGA.CD.8526.01 TCGA.HU.A4G6.01 TCGA.D7.8578.01 TCGA.HU.A4G3.01 TCGA.D7.A74A.01
#> "01212" "01311" "0211" "013123" "0221" "0221"
#> TCGA.RD.A7C1.01 TCGA.F1.A448.01 TCGA.D7.8575.01 TCGA.BR.8372.01 TCGA.VQ.A8P3.01 TCGA.RD.A8MW.01
#> "032" "03112" "03411" "0221" "03412" "013123"
#> TCGA.BR.8286.01 TCGA.BR.8369.01 TCGA.BR.8364.01 TCGA.HU.8244.01 TCGA.KB.A6F7.01 TCGA.FP.A4BF.01
#> "03412" "032" "01111" "02222" "01211" "032"
#> TCGA.R5.A805.01 TCGA.IN.A6RL.01 TCGA.IN.A6RR.01 TCGA.BR.A4CR.01 TCGA.CD.A489.01 TCGA.HU.A4GY.01
#> "032" "0342" "02224" "0132" "01121" "0114"
#> TCGA.BR.8289.01 TCGA.FP.8209.01 TCGA.BR.8296.01 TCGA.CD.A48A.01 TCGA.BR.8060.01 TCGA.BR.8077.01
#> "0342" "01131" "0314" "0331" "01212" "01222"
#> TCGA.CD.8534.01 TCGA.BR.7959.01 TCGA.VQ.A8P2.01 TCGA.EQ.8122.01 TCGA.D7.8573.01 TCGA.BR.A44T.01
#> "032" "032" "0221" "01222" "0212" "01112"
#> TCGA.RD.A8MV.01 TCGA.CD.8536.01 TCGA.BR.8360.01 TCGA.BR.8291.01 TCGA.FP.8210.01 TCGA.RD.A7BS.01
#> "03111" "032" "0232" "013123" "01131" "01134"
#> TCGA.BR.A44U.01 TCGA.CD.8529.01
#> "03413" "013121"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 1377))
#> TCGA.VQ.A94P.01 TCGA.D7.6521.01 TCGA.VQ.A8PE.01 TCGA.D7.6519.01 TCGA.BR.6452.01 TCGA.BR.8485.01
#> "01133" "01121" "01233" "0132" "0231" "01232"
#> TCGA.VQ.A8PO.01 TCGA.VQ.AA69.01 TCGA.BR.8683.01 TCGA.BR.8486.01 TCGA.D7.6522.01 TCGA.CG.5716.01
#> "022" "0212" "032" "01232" "01131" "0314"
#> TCGA.BR.8589.01 TCGA.BR.8382.01 TCGA.VQ.AA68.01 TCGA.VQ.A8PJ.01 TCGA.VQ.A8PH.01 TCGA.HU.8604.01
#> "0211" "0231" "03412" "01222" "01233" "0231"
#> TCGA.BR.8676.01 TCGA.CG.4441.01 TCGA.D7.6520.01 TCGA.VQ.AA64.01 TCGA.D7.6527.01 TCGA.VQ.A8PM.01
#> "0212" "0342" "01211" "01122" "01231" "013123"
#> TCGA.VQ.A923.01 TCGA.BR.8384.01 TCGA.BR.6453.01 TCGA.VQ.A928.01 TCGA.VQ.A8E0.01 TCGA.BR.8679.01
#> "0212" "03111" "03112" "01122" "01122" "022"
#> TCGA.VQ.A91S.01 TCGA.BR.8678.01 TCGA.D7.6528.01 TCGA.VQ.A8E7.01 TCGA.BR.8680.01 TCGA.BR.8483.01
#> "032" "01221" "0332" "03411" "03411" "0331"
#> TCGA.BR.6566.01 TCGA.VQ.A91X.01 TCGA.VQ.A91Q.01 TCGA.VQ.A92D.01 TCGA.VQ.A91Z.01 TCGA.BR.6455.01
#> "032" "0332" "01122" "022" "01221" "0212"
#> TCGA.BR.8591.01 TCGA.HU.8608.01 TCGA.VQ.A94U.01 TCGA.VQ.A94T.01 TCGA.VQ.A91A.01 TCGA.VQ.A91D.01
#> "0233" "0211" "0333" "01123" "032" "0233"
#> TCGA.D7.6518.01 TCGA.BR.8484.01 TCGA.VQ.A91N.01 TCGA.VQ.A91E.01 TCGA.VQ.A8PY.01 TCGA.HU.8602.01
#> "03111" "0132" "01222" "032" "032" "0231"
#> TCGA.BR.8381.01 TCGA.BR.6452.11 TCGA.IN.8663.01 TCGA.VQ.A8PS.01 TCGA.VQ.A91W.01 TCGA.BR.6454.01
#> "0211" "0314" "022" "01122" "0212" "01121"
#> TCGA.BR.8682.01 TCGA.VQ.A91V.01 TCGA.VQ.A8PZ.01 TCGA.BR.8590.01 TCGA.F1.6177.01 TCGA.VQ.A8PQ.01
#> "032" "0333" "0314" "01133" "022" "01112"
#> TCGA.VQ.A91U.01 TCGA.VQ.AA6I.01 TCGA.CG.4437.01 TCGA.VQ.A8PP.01 TCGA.BR.6565.01 TCGA.VQ.A91Y.01
#> "01222" "022" "0232" "0232" "01212" "013123"
#> TCGA.VQ.A8PF.01 TCGA.BR.6456.01 TCGA.BR.6458.01 TCGA.VQ.A925.01 TCGA.VQ.A927.01 TCGA.BR.8592.01
#> "0211" "01311" "032" "0132" "01132" "0313"
#> TCGA.BR.6566.11 TCGA.IN.AB1V.01 TCGA.VQ.AA6F.01 TCGA.VQ.AA6J.01 TCGA.BR.8487.01 TCGA.D7.6525.01
#> "01114" "013121" "01121" "01121" "022" "032"
#> TCGA.VQ.A94O.01 TCGA.BR.8588.01 TCGA.HU.8610.01 TCGA.D7.6526.01 TCGA.VQ.A8PD.01 TCGA.D7.6524.01
#> "01211" "0313" "03111" "01231" "03112" "0314"
#> TCGA.3M.AB46.01 TCGA.3M.AB47.01 TCGA.BR.8677.01 TCGA.BR.6457.01 TCGA.BR.8687.01 TCGA.VQ.A91K.01
#> "01222" "03112" "0114" "03111" "0132" "022"
#> TCGA.BR.8690.01 TCGA.BR.8686.01 TCGA.FP.8631.01 TCGA.VQ.A922.01 TCGA.BR.A452.01 TCGA.IN.A6RO.01
#> "01311" "0211" "01212" "01212" "01121" "022"
#> TCGA.BR.A4QI.01 TCGA.D7.A6EV.01 TCGA.HU.A4G2.01 TCGA.BR.A4IY.01 TCGA.VQ.A8PU.01 TCGA.BR.A4J4.01
#> "0231" "03413" "0211" "0211" "01123" "0211"
#> TCGA.VQ.A94R.01 TCGA.HU.A4H4.01 TCGA.BR.7707.01 TCGA.FP.7829.01 TCGA.BR.A4J5.01 TCGA.HU.A4H0.01
#> "022" "032" "022" "022" "03113" "0211"
#> TCGA.HU.A4HD.01 TCGA.KB.A6F5.01 TCGA.VQ.AA6K.01 TCGA.HF.7133.01 TCGA.F1.6875.01 TCGA.MX.A666.01
#> "01211" "013123" "01121" "0132" "01221" "01211"
#> TCGA.BR.7717.01 TCGA.BR.A4PF.01 TCGA.BR.A4IU.01 TCGA.VQ.A8PX.01 TCGA.BR.A4IV.01 TCGA.D7.A6EX.01
#> "03412" "0232" "0313" "01121" "01133" "0132"
#> TCGA.BR.A4IZ.01 TCGA.BR.A4J9.01 TCGA.CD.A4MJ.01 TCGA.B7.A5TN.01 TCGA.BR.7715.01 TCGA.BR.7704.01
#> "01115" "01133" "0233" "01222" "0332" "01232"
#> TCGA.BR.A4J1.01 TCGA.HU.A4GP.01 TCGA.D7.A4YY.01 TCGA.VQ.AA6G.01 TCGA.HU.A4GJ.01 TCGA.CD.A4MI.01
#> "01211" "022" "022" "022" "0314" "0232"
#> TCGA.BR.7196.01 TCGA.BR.6563.01 TCGA.VQ.A924.01 TCGA.BR.7716.01 TCGA.FP.7735.01 TCGA.BR.7723.01
#> "0312" "03111" "0233" "01311" "0132" "013122"
#> TCGA.HU.A4H8.01 TCGA.IN.A6RJ.01 TCGA.HU.A4H3.01 TCGA.EQ.A4SO.01 TCGA.CD.A4MH.01 TCGA.BR.A4J7.01
#> "022" "03113" "022" "01122" "01232" "01121"
#> TCGA.HF.7131.01 TCGA.D7.A74B.01 TCGA.BR.A4PE.01 TCGA.BR.A4J8.01 TCGA.HU.A4GX.01 TCGA.HU.A4G8.01
#> "01231" "01116" "022" "0231" "032" "03413"
#> TCGA.HU.A4GT.01 TCGA.HU.A4GC.01 TCGA.BR.A4CQ.01 TCGA.D7.A6F2.01 TCGA.RD.A7BT.01 TCGA.BR.A4J6.01
#> "022" "03413" "022" "01222" "01222" "0114"
#> TCGA.HU.A4GQ.01 TCGA.HF.7136.01 TCGA.BR.A4QM.01 TCGA.BR.A4PD.01 TCGA.VQ.A8PK.01 TCGA.B7.A5TK.01
#> "0232" "0132" "0232" "01222" "01212" "0312"
#> TCGA.D7.A4YX.01 TCGA.D7.A4Z0.01 TCGA.VQ.A8PT.01 TCGA.IN.A6RN.01 TCGA.CD.A4MG.01 TCGA.D7.A747.01
#> "0211" "0313" "022" "01212" "022" "01133"
#> TCGA.R5.A7O7.01 TCGA.F1.A72C.01 TCGA.BR.A4J2.01 TCGA.MX.A663.01 TCGA.D7.A4YV.01 TCGA.HU.A4GD.01
#> "03113" "01121" "03113" "013122" "0231" "0331"
#> TCGA.BR.A4QL.01 TCGA.BR.7703.01 TCGA.VQ.AA6B.01 TCGA.VQ.AA6D.01 TCGA.D7.A6EZ.01 TCGA.D7.A4YU.01
#> "022" "022" "0332" "01232" "0211" "0232"
#> TCGA.VQ.AA6A.01 TCGA.IN.7806.01 TCGA.HU.A4HB.01 TCGA.HU.A4H2.01 TCGA.IN.A6RP.01 TCGA.HU.A4H5.01
#> "01231" "01222" "03113" "0342" "022" "01231"
#> TCGA.HU.A4GU.01 TCGA.MX.A5UJ.01 TCGA.HU.A4GN.01 TCGA.CD.5804.01 TCGA.HU.A4H6.01 TCGA.HF.7132.01
#> "022" "022" "0232" "013123" "0231" "0232"
#> TCGA.D7.A4YT.01 TCGA.HF.7134.01 TCGA.BR.6852.01 TCGA.BR.8370.01 TCGA.EQ.5647.01 TCGA.IN.A7NT.01
#> "0132" "022" "0314" "0233" "0132" "032"
#> TCGA.RD.A8N9.01 TCGA.D7.5577.01 TCGA.CG.5717.01 TCGA.D7.6818.01 TCGA.CG.5734.01 TCGA.VQ.A8P8.01
#> "0114" "0211" "01134" "013121" "03111" "0314"
#> TCGA.BR.6707.01 TCGA.B7.5818.01 TCGA.CD.8525.01 TCGA.BR.6705.01 TCGA.BR.4288.01 TCGA.CD.5813.01
#> "0211" "0211" "01311" "0313" "013122" "01121"
#> TCGA.CG.5723.01 TCGA.CD.5800.01 TCGA.CG.5718.01 TCGA.BR.8080.01 TCGA.CG.5733.01 TCGA.D7.6817.01
#> "01121" "01311" "01232" "0114" "022" "01231"
#> TCGA.KB.A93G.01 TCGA.CD.5799.01 TCGA.BR.7851.01 TCGA.BR.7722.01 TCGA.MX.A5UG.01 TCGA.CD.8533.01
#> "01133" "013121" "0232" "01121" "03111" "0331"
#> TCGA.BR.7957.01 TCGA.CG.5722.01 TCGA.F1.6874.01 TCGA.CG.5730.01 TCGA.CG.5726.01 TCGA.IP.7968.01
#> "0313" "0312" "032" "0331" "022" "0331"
#> TCGA.BR.8363.01 TCGA.BR.7901.01 TCGA.D7.6822.01 TCGA.BR.6710.01 TCGA.CG.5720.01 TCGA.D7.8570.01
#> "0231" "01212" "03411" "01132" "022" "0211"
#> TCGA.B7.A5TI.01 TCGA.D7.6815.01 TCGA.BR.8284.01 TCGA.BR.8295.01 TCGA.BR.7197.01 TCGA.B7.A5TJ.01
#> "0132" "01222" "0231" "01211" "01222" "022"
#> TCGA.D7.A6EY.01 TCGA.BR.8366.01 TCGA.IN.A7NR.01 TCGA.BR.6706.01 TCGA.IN.7808.01 TCGA.BR.6564.01
#> "0313" "0211" "01114" "0312" "03112" "01111"
#> TCGA.KB.A93H.01 TCGA.KB.A93J.01 TCGA.CD.5798.01 TCGA.CD.8530.01 TCGA.BR.6802.01 TCGA.CG.5719.01
#> "0332" "01222" "01134" "013121" "03112" "0114"
#> TCGA.VQ.A8E3.01 TCGA.CD.5801.01 TCGA.FP.A9TM.01 TCGA.BR.7958.01 TCGA.FP.7998.01 TCGA.IN.A6RS.01
#> "022" "0211" "032" "0211" "0312" "032"
#> TCGA.BR.6709.01 TCGA.FP.7916.01 TCGA.R5.A7ZR.01 TCGA.B7.5816.01 TCGA.CG.5721.01 TCGA.SW.A7EA.01
#> "01112" "0211" "01222" "0314" "03111" "022"
#> TCGA.RD.A8NB.01 TCGA.BR.6801.01 TCGA.IN.AB1X.01 TCGA.D7.5579.01 TCGA.CG.5728.01 TCGA.R5.A7ZI.01
#> "0313" "0132" "0314" "013121" "0313" "01311"
#> TCGA.IN.A7NU.01 TCGA.CG.5732.01 TCGA.ZQ.A9CR.01 TCGA.D7.5578.01 TCGA.BR.6803.01 TCGA.BR.8368.01
#> "032" "013123" "01311" "032" "01111" "022"
#> TCGA.SW.A7EB.01 TCGA.BR.8081.01 TCGA.VQ.A8P5.01 TCGA.CD.8535.01 TCGA.CG.5724.01 TCGA.D7.8574.01
#> "01132" "0231" "032" "022" "03412" "01131"
#> TCGA.HJ.7597.01 TCGA.HF.A5NB.01 TCGA.VQ.A8PB.01 TCGA.R5.A7ZE.01 TCGA.CD.5803.01 TCGA.CG.5725.01
#> "0114" "022" "03412" "01222" "01112" "01212"
#> TCGA.D7.6820.01 TCGA.CD.5802.01 TCGA.R5.A7ZF.01 TCGA.D7.A6F0.01 TCGA.CG.5727.01 TCGA.VQ.A8PC.01
#> "01231" "013123" "01311" "01211" "032" "03111"
#> TCGA.CD.A486.01 TCGA.RD.A8N2.01 TCGA.IN.A6RI.01 TCGA.HU.8243.01 TCGA.CD.A48C.01 TCGA.RD.A8N5.01
#> "01211" "01113" "01212" "0342" "022" "01131"
#> TCGA.RD.A8N1.01 TCGA.HU.A4GF.01 TCGA.BR.8362.01 TCGA.BR.8285.01 TCGA.CD.8532.01 TCGA.VQ.A8E2.01
#> "013121" "01222" "032" "0211" "01121" "013122"
#> TCGA.BR.8373.01 TCGA.BR.8361.01 TCGA.BR.8058.01 TCGA.IN.8462.01 TCGA.HU.A4G9.01 TCGA.CD.8524.01
#> "01222" "022" "0114" "03412" "022" "032"
#> TCGA.D7.A748.01 TCGA.CD.8527.01 TCGA.VQ.A8DV.01 TCGA.CD.8528.01 TCGA.BR.A453.01 TCGA.RD.A8N6.01
#> "01115" "0132" "01233" "022" "03111" "0132"
#> TCGA.HU.8245.01 TCGA.ZA.A8F6.01 TCGA.BR.8367.01 TCGA.BR.8380.01 TCGA.FP.A4BE.01 TCGA.HU.8238.01
#> "01231" "013121" "032" "03112" "0233" "03413"
#> TCGA.BR.8078.01 TCGA.HU.8249.01 TCGA.RD.A8N0.01 TCGA.BR.8365.01 TCGA.FP.8211.01 TCGA.RD.A8N4.01
#> "0231" "0331" "01112" "01111" "01122" "01113"
#> TCGA.VQ.A8DU.01 TCGA.VQ.A8DL.01 TCGA.VQ.A8DZ.01 TCGA.D7.8572.01 TCGA.RD.A7BW.01 TCGA.R5.A804.01
#> "01233" "01311" "01231" "013122" "01116" "0314"
#> TCGA.BR.A4CS.01 TCGA.CD.8531.01 TCGA.CD.A487.01 TCGA.BR.8371.01 TCGA.BR.8059.01 TCGA.D7.A6ET.01
#> "032" "0212" "0132" "01131" "013121" "0312"
#> TCGA.FP.8099.01 TCGA.D7.8579.01 TCGA.BR.8297.01 TCGA.D7.8576.01 TCGA.VQ.A8DT.01 TCGA.FP.A8CX.01
#> "0333" "0313" "032" "0114" "022" "013121"
#> TCGA.HU.A4GH.01 TCGA.CD.8526.01 TCGA.HU.A4G6.01 TCGA.D7.8578.01 TCGA.HU.A4G3.01 TCGA.D7.A74A.01
#> "01212" "01311" "0211" "013123" "022" "022"
#> TCGA.RD.A7C1.01 TCGA.F1.A448.01 TCGA.D7.8575.01 TCGA.BR.8372.01 TCGA.VQ.A8P3.01 TCGA.RD.A8MW.01
#> "032" "03112" "03411" "022" "03412" "013123"
#> TCGA.BR.8286.01 TCGA.BR.8369.01 TCGA.BR.8364.01 TCGA.HU.8244.01 TCGA.KB.A6F7.01 TCGA.FP.A4BF.01
#> "03412" "032" "01111" "022" "01211" "032"
#> TCGA.R5.A805.01 TCGA.IN.A6RL.01 TCGA.IN.A6RR.01 TCGA.BR.A4CR.01 TCGA.CD.A489.01 TCGA.HU.A4GY.01
#> "032" "0342" "022" "0132" "01121" "0114"
#> TCGA.BR.8289.01 TCGA.FP.8209.01 TCGA.BR.8296.01 TCGA.CD.A48A.01 TCGA.BR.8060.01 TCGA.BR.8077.01
#> "0342" "01131" "0314" "0331" "01212" "01222"
#> TCGA.CD.8534.01 TCGA.BR.7959.01 TCGA.VQ.A8P2.01 TCGA.EQ.8122.01 TCGA.D7.8573.01 TCGA.BR.A44T.01
#> "032" "032" "022" "01222" "0212" "01112"
#> TCGA.RD.A8MV.01 TCGA.CD.8536.01 TCGA.BR.8360.01 TCGA.BR.8291.01 TCGA.FP.8210.01 TCGA.RD.A7BS.01
#> "03111" "032" "0232" "013123" "01131" "01134"
#> TCGA.BR.A44U.01 TCGA.CD.8529.01
#> "03413" "013121"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 1613))
#> TCGA.VQ.A94P.01 TCGA.D7.6521.01 TCGA.VQ.A8PE.01 TCGA.D7.6519.01 TCGA.BR.6452.01 TCGA.BR.8485.01
#> "01133" "01121" "01233" "013" "0231" "01232"
#> TCGA.VQ.A8PO.01 TCGA.VQ.AA69.01 TCGA.BR.8683.01 TCGA.BR.8486.01 TCGA.D7.6522.01 TCGA.CG.5716.01
#> "022" "0212" "032" "01232" "01131" "0314"
#> TCGA.BR.8589.01 TCGA.BR.8382.01 TCGA.VQ.AA68.01 TCGA.VQ.A8PJ.01 TCGA.VQ.A8PH.01 TCGA.HU.8604.01
#> "0211" "0231" "03412" "01222" "01233" "0231"
#> TCGA.BR.8676.01 TCGA.CG.4441.01 TCGA.D7.6520.01 TCGA.VQ.AA64.01 TCGA.D7.6527.01 TCGA.VQ.A8PM.01
#> "0212" "0342" "01211" "01122" "01231" "013123"
#> TCGA.VQ.A923.01 TCGA.BR.8384.01 TCGA.BR.6453.01 TCGA.VQ.A928.01 TCGA.VQ.A8E0.01 TCGA.BR.8679.01
#> "0212" "03111" "03112" "01122" "01122" "022"
#> TCGA.VQ.A91S.01 TCGA.BR.8678.01 TCGA.D7.6528.01 TCGA.VQ.A8E7.01 TCGA.BR.8680.01 TCGA.BR.8483.01
#> "032" "01221" "0332" "03411" "03411" "0331"
#> TCGA.BR.6566.01 TCGA.VQ.A91X.01 TCGA.VQ.A91Q.01 TCGA.VQ.A92D.01 TCGA.VQ.A91Z.01 TCGA.BR.6455.01
#> "032" "0332" "01122" "022" "01221" "0212"
#> TCGA.BR.8591.01 TCGA.HU.8608.01 TCGA.VQ.A94U.01 TCGA.VQ.A94T.01 TCGA.VQ.A91A.01 TCGA.VQ.A91D.01
#> "0233" "0211" "0333" "01123" "032" "0233"
#> TCGA.D7.6518.01 TCGA.BR.8484.01 TCGA.VQ.A91N.01 TCGA.VQ.A91E.01 TCGA.VQ.A8PY.01 TCGA.HU.8602.01
#> "03111" "013" "01222" "032" "032" "0231"
#> TCGA.BR.8381.01 TCGA.BR.6452.11 TCGA.IN.8663.01 TCGA.VQ.A8PS.01 TCGA.VQ.A91W.01 TCGA.BR.6454.01
#> "0211" "0314" "022" "01122" "0212" "01121"
#> TCGA.BR.8682.01 TCGA.VQ.A91V.01 TCGA.VQ.A8PZ.01 TCGA.BR.8590.01 TCGA.F1.6177.01 TCGA.VQ.A8PQ.01
#> "032" "0333" "0314" "01133" "022" "01112"
#> TCGA.VQ.A91U.01 TCGA.VQ.AA6I.01 TCGA.CG.4437.01 TCGA.VQ.A8PP.01 TCGA.BR.6565.01 TCGA.VQ.A91Y.01
#> "01222" "022" "0232" "0232" "01212" "013123"
#> TCGA.VQ.A8PF.01 TCGA.BR.6456.01 TCGA.BR.6458.01 TCGA.VQ.A925.01 TCGA.VQ.A927.01 TCGA.BR.8592.01
#> "0211" "013" "032" "013" "01132" "0313"
#> TCGA.BR.6566.11 TCGA.IN.AB1V.01 TCGA.VQ.AA6F.01 TCGA.VQ.AA6J.01 TCGA.BR.8487.01 TCGA.D7.6525.01
#> "01114" "013121" "01121" "01121" "022" "032"
#> TCGA.VQ.A94O.01 TCGA.BR.8588.01 TCGA.HU.8610.01 TCGA.D7.6526.01 TCGA.VQ.A8PD.01 TCGA.D7.6524.01
#> "01211" "0313" "03111" "01231" "03112" "0314"
#> TCGA.3M.AB46.01 TCGA.3M.AB47.01 TCGA.BR.8677.01 TCGA.BR.6457.01 TCGA.BR.8687.01 TCGA.VQ.A91K.01
#> "01222" "03112" "0114" "03111" "013" "022"
#> TCGA.BR.8690.01 TCGA.BR.8686.01 TCGA.FP.8631.01 TCGA.VQ.A922.01 TCGA.BR.A452.01 TCGA.IN.A6RO.01
#> "013" "0211" "01212" "01212" "01121" "022"
#> TCGA.BR.A4QI.01 TCGA.D7.A6EV.01 TCGA.HU.A4G2.01 TCGA.BR.A4IY.01 TCGA.VQ.A8PU.01 TCGA.BR.A4J4.01
#> "0231" "03413" "0211" "0211" "01123" "0211"
#> TCGA.VQ.A94R.01 TCGA.HU.A4H4.01 TCGA.BR.7707.01 TCGA.FP.7829.01 TCGA.BR.A4J5.01 TCGA.HU.A4H0.01
#> "022" "032" "022" "022" "03113" "0211"
#> TCGA.HU.A4HD.01 TCGA.KB.A6F5.01 TCGA.VQ.AA6K.01 TCGA.HF.7133.01 TCGA.F1.6875.01 TCGA.MX.A666.01
#> "01211" "013123" "01121" "013" "01221" "01211"
#> TCGA.BR.7717.01 TCGA.BR.A4PF.01 TCGA.BR.A4IU.01 TCGA.VQ.A8PX.01 TCGA.BR.A4IV.01 TCGA.D7.A6EX.01
#> "03412" "0232" "0313" "01121" "01133" "013"
#> TCGA.BR.A4IZ.01 TCGA.BR.A4J9.01 TCGA.CD.A4MJ.01 TCGA.B7.A5TN.01 TCGA.BR.7715.01 TCGA.BR.7704.01
#> "01115" "01133" "0233" "01222" "0332" "01232"
#> TCGA.BR.A4J1.01 TCGA.HU.A4GP.01 TCGA.D7.A4YY.01 TCGA.VQ.AA6G.01 TCGA.HU.A4GJ.01 TCGA.CD.A4MI.01
#> "01211" "022" "022" "022" "0314" "0232"
#> TCGA.BR.7196.01 TCGA.BR.6563.01 TCGA.VQ.A924.01 TCGA.BR.7716.01 TCGA.FP.7735.01 TCGA.BR.7723.01
#> "0312" "03111" "0233" "013" "013" "013122"
#> TCGA.HU.A4H8.01 TCGA.IN.A6RJ.01 TCGA.HU.A4H3.01 TCGA.EQ.A4SO.01 TCGA.CD.A4MH.01 TCGA.BR.A4J7.01
#> "022" "03113" "022" "01122" "01232" "01121"
#> TCGA.HF.7131.01 TCGA.D7.A74B.01 TCGA.BR.A4PE.01 TCGA.BR.A4J8.01 TCGA.HU.A4GX.01 TCGA.HU.A4G8.01
#> "01231" "01116" "022" "0231" "032" "03413"
#> TCGA.HU.A4GT.01 TCGA.HU.A4GC.01 TCGA.BR.A4CQ.01 TCGA.D7.A6F2.01 TCGA.RD.A7BT.01 TCGA.BR.A4J6.01
#> "022" "03413" "022" "01222" "01222" "0114"
#> TCGA.HU.A4GQ.01 TCGA.HF.7136.01 TCGA.BR.A4QM.01 TCGA.BR.A4PD.01 TCGA.VQ.A8PK.01 TCGA.B7.A5TK.01
#> "0232" "013" "0232" "01222" "01212" "0312"
#> TCGA.D7.A4YX.01 TCGA.D7.A4Z0.01 TCGA.VQ.A8PT.01 TCGA.IN.A6RN.01 TCGA.CD.A4MG.01 TCGA.D7.A747.01
#> "0211" "0313" "022" "01212" "022" "01133"
#> TCGA.R5.A7O7.01 TCGA.F1.A72C.01 TCGA.BR.A4J2.01 TCGA.MX.A663.01 TCGA.D7.A4YV.01 TCGA.HU.A4GD.01
#> "03113" "01121" "03113" "013122" "0231" "0331"
#> TCGA.BR.A4QL.01 TCGA.BR.7703.01 TCGA.VQ.AA6B.01 TCGA.VQ.AA6D.01 TCGA.D7.A6EZ.01 TCGA.D7.A4YU.01
#> "022" "022" "0332" "01232" "0211" "0232"
#> TCGA.VQ.AA6A.01 TCGA.IN.7806.01 TCGA.HU.A4HB.01 TCGA.HU.A4H2.01 TCGA.IN.A6RP.01 TCGA.HU.A4H5.01
#> "01231" "01222" "03113" "0342" "022" "01231"
#> TCGA.HU.A4GU.01 TCGA.MX.A5UJ.01 TCGA.HU.A4GN.01 TCGA.CD.5804.01 TCGA.HU.A4H6.01 TCGA.HF.7132.01
#> "022" "022" "0232" "013123" "0231" "0232"
#> TCGA.D7.A4YT.01 TCGA.HF.7134.01 TCGA.BR.6852.01 TCGA.BR.8370.01 TCGA.EQ.5647.01 TCGA.IN.A7NT.01
#> "013" "022" "0314" "0233" "013" "032"
#> TCGA.RD.A8N9.01 TCGA.D7.5577.01 TCGA.CG.5717.01 TCGA.D7.6818.01 TCGA.CG.5734.01 TCGA.VQ.A8P8.01
#> "0114" "0211" "01134" "013121" "03111" "0314"
#> TCGA.BR.6707.01 TCGA.B7.5818.01 TCGA.CD.8525.01 TCGA.BR.6705.01 TCGA.BR.4288.01 TCGA.CD.5813.01
#> "0211" "0211" "013" "0313" "013122" "01121"
#> TCGA.CG.5723.01 TCGA.CD.5800.01 TCGA.CG.5718.01 TCGA.BR.8080.01 TCGA.CG.5733.01 TCGA.D7.6817.01
#> "01121" "013" "01232" "0114" "022" "01231"
#> TCGA.KB.A93G.01 TCGA.CD.5799.01 TCGA.BR.7851.01 TCGA.BR.7722.01 TCGA.MX.A5UG.01 TCGA.CD.8533.01
#> "01133" "013121" "0232" "01121" "03111" "0331"
#> TCGA.BR.7957.01 TCGA.CG.5722.01 TCGA.F1.6874.01 TCGA.CG.5730.01 TCGA.CG.5726.01 TCGA.IP.7968.01
#> "0313" "0312" "032" "0331" "022" "0331"
#> TCGA.BR.8363.01 TCGA.BR.7901.01 TCGA.D7.6822.01 TCGA.BR.6710.01 TCGA.CG.5720.01 TCGA.D7.8570.01
#> "0231" "01212" "03411" "01132" "022" "0211"
#> TCGA.B7.A5TI.01 TCGA.D7.6815.01 TCGA.BR.8284.01 TCGA.BR.8295.01 TCGA.BR.7197.01 TCGA.B7.A5TJ.01
#> "013" "01222" "0231" "01211" "01222" "022"
#> TCGA.D7.A6EY.01 TCGA.BR.8366.01 TCGA.IN.A7NR.01 TCGA.BR.6706.01 TCGA.IN.7808.01 TCGA.BR.6564.01
#> "0313" "0211" "01114" "0312" "03112" "01111"
#> TCGA.KB.A93H.01 TCGA.KB.A93J.01 TCGA.CD.5798.01 TCGA.CD.8530.01 TCGA.BR.6802.01 TCGA.CG.5719.01
#> "0332" "01222" "01134" "013121" "03112" "0114"
#> TCGA.VQ.A8E3.01 TCGA.CD.5801.01 TCGA.FP.A9TM.01 TCGA.BR.7958.01 TCGA.FP.7998.01 TCGA.IN.A6RS.01
#> "022" "0211" "032" "0211" "0312" "032"
#> TCGA.BR.6709.01 TCGA.FP.7916.01 TCGA.R5.A7ZR.01 TCGA.B7.5816.01 TCGA.CG.5721.01 TCGA.SW.A7EA.01
#> "01112" "0211" "01222" "0314" "03111" "022"
#> TCGA.RD.A8NB.01 TCGA.BR.6801.01 TCGA.IN.AB1X.01 TCGA.D7.5579.01 TCGA.CG.5728.01 TCGA.R5.A7ZI.01
#> "0313" "013" "0314" "013121" "0313" "013"
#> TCGA.IN.A7NU.01 TCGA.CG.5732.01 TCGA.ZQ.A9CR.01 TCGA.D7.5578.01 TCGA.BR.6803.01 TCGA.BR.8368.01
#> "032" "013123" "013" "032" "01111" "022"
#> TCGA.SW.A7EB.01 TCGA.BR.8081.01 TCGA.VQ.A8P5.01 TCGA.CD.8535.01 TCGA.CG.5724.01 TCGA.D7.8574.01
#> "01132" "0231" "032" "022" "03412" "01131"
#> TCGA.HJ.7597.01 TCGA.HF.A5NB.01 TCGA.VQ.A8PB.01 TCGA.R5.A7ZE.01 TCGA.CD.5803.01 TCGA.CG.5725.01
#> "0114" "022" "03412" "01222" "01112" "01212"
#> TCGA.D7.6820.01 TCGA.CD.5802.01 TCGA.R5.A7ZF.01 TCGA.D7.A6F0.01 TCGA.CG.5727.01 TCGA.VQ.A8PC.01
#> "01231" "013123" "013" "01211" "032" "03111"
#> TCGA.CD.A486.01 TCGA.RD.A8N2.01 TCGA.IN.A6RI.01 TCGA.HU.8243.01 TCGA.CD.A48C.01 TCGA.RD.A8N5.01
#> "01211" "01113" "01212" "0342" "022" "01131"
#> TCGA.RD.A8N1.01 TCGA.HU.A4GF.01 TCGA.BR.8362.01 TCGA.BR.8285.01 TCGA.CD.8532.01 TCGA.VQ.A8E2.01
#> "013121" "01222" "032" "0211" "01121" "013122"
#> TCGA.BR.8373.01 TCGA.BR.8361.01 TCGA.BR.8058.01 TCGA.IN.8462.01 TCGA.HU.A4G9.01 TCGA.CD.8524.01
#> "01222" "022" "0114" "03412" "022" "032"
#> TCGA.D7.A748.01 TCGA.CD.8527.01 TCGA.VQ.A8DV.01 TCGA.CD.8528.01 TCGA.BR.A453.01 TCGA.RD.A8N6.01
#> "01115" "013" "01233" "022" "03111" "013"
#> TCGA.HU.8245.01 TCGA.ZA.A8F6.01 TCGA.BR.8367.01 TCGA.BR.8380.01 TCGA.FP.A4BE.01 TCGA.HU.8238.01
#> "01231" "013121" "032" "03112" "0233" "03413"
#> TCGA.BR.8078.01 TCGA.HU.8249.01 TCGA.RD.A8N0.01 TCGA.BR.8365.01 TCGA.FP.8211.01 TCGA.RD.A8N4.01
#> "0231" "0331" "01112" "01111" "01122" "01113"
#> TCGA.VQ.A8DU.01 TCGA.VQ.A8DL.01 TCGA.VQ.A8DZ.01 TCGA.D7.8572.01 TCGA.RD.A7BW.01 TCGA.R5.A804.01
#> "01233" "013" "01231" "013122" "01116" "0314"
#> TCGA.BR.A4CS.01 TCGA.CD.8531.01 TCGA.CD.A487.01 TCGA.BR.8371.01 TCGA.BR.8059.01 TCGA.D7.A6ET.01
#> "032" "0212" "013" "01131" "013121" "0312"
#> TCGA.FP.8099.01 TCGA.D7.8579.01 TCGA.BR.8297.01 TCGA.D7.8576.01 TCGA.VQ.A8DT.01 TCGA.FP.A8CX.01
#> "0333" "0313" "032" "0114" "022" "013121"
#> TCGA.HU.A4GH.01 TCGA.CD.8526.01 TCGA.HU.A4G6.01 TCGA.D7.8578.01 TCGA.HU.A4G3.01 TCGA.D7.A74A.01
#> "01212" "013" "0211" "013123" "022" "022"
#> TCGA.RD.A7C1.01 TCGA.F1.A448.01 TCGA.D7.8575.01 TCGA.BR.8372.01 TCGA.VQ.A8P3.01 TCGA.RD.A8MW.01
#> "032" "03112" "03411" "022" "03412" "013123"
#> TCGA.BR.8286.01 TCGA.BR.8369.01 TCGA.BR.8364.01 TCGA.HU.8244.01 TCGA.KB.A6F7.01 TCGA.FP.A4BF.01
#> "03412" "032" "01111" "022" "01211" "032"
#> TCGA.R5.A805.01 TCGA.IN.A6RL.01 TCGA.IN.A6RR.01 TCGA.BR.A4CR.01 TCGA.CD.A489.01 TCGA.HU.A4GY.01
#> "032" "0342" "022" "013" "01121" "0114"
#> TCGA.BR.8289.01 TCGA.FP.8209.01 TCGA.BR.8296.01 TCGA.CD.A48A.01 TCGA.BR.8060.01 TCGA.BR.8077.01
#> "0342" "01131" "0314" "0331" "01212" "01222"
#> TCGA.CD.8534.01 TCGA.BR.7959.01 TCGA.VQ.A8P2.01 TCGA.EQ.8122.01 TCGA.D7.8573.01 TCGA.BR.A44T.01
#> "032" "032" "022" "01222" "0212" "01112"
#> TCGA.RD.A8MV.01 TCGA.CD.8536.01 TCGA.BR.8360.01 TCGA.BR.8291.01 TCGA.FP.8210.01 TCGA.RD.A7BS.01
#> "03111" "032" "0232" "013123" "01131" "01134"
#> TCGA.BR.A44U.01 TCGA.CD.8529.01
#> "03413" "013121"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 2012))
#> TCGA.VQ.A94P.01 TCGA.D7.6521.01 TCGA.VQ.A8PE.01 TCGA.D7.6519.01 TCGA.BR.6452.01 TCGA.BR.8485.01
#> "01133" "01121" "01233" "013" "0231" "01232"
#> TCGA.VQ.A8PO.01 TCGA.VQ.AA69.01 TCGA.BR.8683.01 TCGA.BR.8486.01 TCGA.D7.6522.01 TCGA.CG.5716.01
#> "022" "0212" "032" "01232" "01131" "0314"
#> TCGA.BR.8589.01 TCGA.BR.8382.01 TCGA.VQ.AA68.01 TCGA.VQ.A8PJ.01 TCGA.VQ.A8PH.01 TCGA.HU.8604.01
#> "0211" "0231" "03412" "01222" "01233" "0231"
#> TCGA.BR.8676.01 TCGA.CG.4441.01 TCGA.D7.6520.01 TCGA.VQ.AA64.01 TCGA.D7.6527.01 TCGA.VQ.A8PM.01
#> "0212" "0342" "0121" "01122" "01231" "013123"
#> TCGA.VQ.A923.01 TCGA.BR.8384.01 TCGA.BR.6453.01 TCGA.VQ.A928.01 TCGA.VQ.A8E0.01 TCGA.BR.8679.01
#> "0212" "03111" "03112" "01122" "01122" "022"
#> TCGA.VQ.A91S.01 TCGA.BR.8678.01 TCGA.D7.6528.01 TCGA.VQ.A8E7.01 TCGA.BR.8680.01 TCGA.BR.8483.01
#> "032" "01221" "0332" "03411" "03411" "0331"
#> TCGA.BR.6566.01 TCGA.VQ.A91X.01 TCGA.VQ.A91Q.01 TCGA.VQ.A92D.01 TCGA.VQ.A91Z.01 TCGA.BR.6455.01
#> "032" "0332" "01122" "022" "01221" "0212"
#> TCGA.BR.8591.01 TCGA.HU.8608.01 TCGA.VQ.A94U.01 TCGA.VQ.A94T.01 TCGA.VQ.A91A.01 TCGA.VQ.A91D.01
#> "0233" "0211" "0333" "01123" "032" "0233"
#> TCGA.D7.6518.01 TCGA.BR.8484.01 TCGA.VQ.A91N.01 TCGA.VQ.A91E.01 TCGA.VQ.A8PY.01 TCGA.HU.8602.01
#> "03111" "013" "01222" "032" "032" "0231"
#> TCGA.BR.8381.01 TCGA.BR.6452.11 TCGA.IN.8663.01 TCGA.VQ.A8PS.01 TCGA.VQ.A91W.01 TCGA.BR.6454.01
#> "0211" "0314" "022" "01122" "0212" "01121"
#> TCGA.BR.8682.01 TCGA.VQ.A91V.01 TCGA.VQ.A8PZ.01 TCGA.BR.8590.01 TCGA.F1.6177.01 TCGA.VQ.A8PQ.01
#> "032" "0333" "0314" "01133" "022" "01112"
#> TCGA.VQ.A91U.01 TCGA.VQ.AA6I.01 TCGA.CG.4437.01 TCGA.VQ.A8PP.01 TCGA.BR.6565.01 TCGA.VQ.A91Y.01
#> "01222" "022" "0232" "0232" "0121" "013123"
#> TCGA.VQ.A8PF.01 TCGA.BR.6456.01 TCGA.BR.6458.01 TCGA.VQ.A925.01 TCGA.VQ.A927.01 TCGA.BR.8592.01
#> "0211" "013" "032" "013" "01132" "0313"
#> TCGA.BR.6566.11 TCGA.IN.AB1V.01 TCGA.VQ.AA6F.01 TCGA.VQ.AA6J.01 TCGA.BR.8487.01 TCGA.D7.6525.01
#> "01114" "013121" "01121" "01121" "022" "032"
#> TCGA.VQ.A94O.01 TCGA.BR.8588.01 TCGA.HU.8610.01 TCGA.D7.6526.01 TCGA.VQ.A8PD.01 TCGA.D7.6524.01
#> "0121" "0313" "03111" "01231" "03112" "0314"
#> TCGA.3M.AB46.01 TCGA.3M.AB47.01 TCGA.BR.8677.01 TCGA.BR.6457.01 TCGA.BR.8687.01 TCGA.VQ.A91K.01
#> "01222" "03112" "0114" "03111" "013" "022"
#> TCGA.BR.8690.01 TCGA.BR.8686.01 TCGA.FP.8631.01 TCGA.VQ.A922.01 TCGA.BR.A452.01 TCGA.IN.A6RO.01
#> "013" "0211" "0121" "0121" "01121" "022"
#> TCGA.BR.A4QI.01 TCGA.D7.A6EV.01 TCGA.HU.A4G2.01 TCGA.BR.A4IY.01 TCGA.VQ.A8PU.01 TCGA.BR.A4J4.01
#> "0231" "03413" "0211" "0211" "01123" "0211"
#> TCGA.VQ.A94R.01 TCGA.HU.A4H4.01 TCGA.BR.7707.01 TCGA.FP.7829.01 TCGA.BR.A4J5.01 TCGA.HU.A4H0.01
#> "022" "032" "022" "022" "03113" "0211"
#> TCGA.HU.A4HD.01 TCGA.KB.A6F5.01 TCGA.VQ.AA6K.01 TCGA.HF.7133.01 TCGA.F1.6875.01 TCGA.MX.A666.01
#> "0121" "013123" "01121" "013" "01221" "0121"
#> TCGA.BR.7717.01 TCGA.BR.A4PF.01 TCGA.BR.A4IU.01 TCGA.VQ.A8PX.01 TCGA.BR.A4IV.01 TCGA.D7.A6EX.01
#> "03412" "0232" "0313" "01121" "01133" "013"
#> TCGA.BR.A4IZ.01 TCGA.BR.A4J9.01 TCGA.CD.A4MJ.01 TCGA.B7.A5TN.01 TCGA.BR.7715.01 TCGA.BR.7704.01
#> "01115" "01133" "0233" "01222" "0332" "01232"
#> TCGA.BR.A4J1.01 TCGA.HU.A4GP.01 TCGA.D7.A4YY.01 TCGA.VQ.AA6G.01 TCGA.HU.A4GJ.01 TCGA.CD.A4MI.01
#> "0121" "022" "022" "022" "0314" "0232"
#> TCGA.BR.7196.01 TCGA.BR.6563.01 TCGA.VQ.A924.01 TCGA.BR.7716.01 TCGA.FP.7735.01 TCGA.BR.7723.01
#> "0312" "03111" "0233" "013" "013" "013122"
#> TCGA.HU.A4H8.01 TCGA.IN.A6RJ.01 TCGA.HU.A4H3.01 TCGA.EQ.A4SO.01 TCGA.CD.A4MH.01 TCGA.BR.A4J7.01
#> "022" "03113" "022" "01122" "01232" "01121"
#> TCGA.HF.7131.01 TCGA.D7.A74B.01 TCGA.BR.A4PE.01 TCGA.BR.A4J8.01 TCGA.HU.A4GX.01 TCGA.HU.A4G8.01
#> "01231" "01116" "022" "0231" "032" "03413"
#> TCGA.HU.A4GT.01 TCGA.HU.A4GC.01 TCGA.BR.A4CQ.01 TCGA.D7.A6F2.01 TCGA.RD.A7BT.01 TCGA.BR.A4J6.01
#> "022" "03413" "022" "01222" "01222" "0114"
#> TCGA.HU.A4GQ.01 TCGA.HF.7136.01 TCGA.BR.A4QM.01 TCGA.BR.A4PD.01 TCGA.VQ.A8PK.01 TCGA.B7.A5TK.01
#> "0232" "013" "0232" "01222" "0121" "0312"
#> TCGA.D7.A4YX.01 TCGA.D7.A4Z0.01 TCGA.VQ.A8PT.01 TCGA.IN.A6RN.01 TCGA.CD.A4MG.01 TCGA.D7.A747.01
#> "0211" "0313" "022" "0121" "022" "01133"
#> TCGA.R5.A7O7.01 TCGA.F1.A72C.01 TCGA.BR.A4J2.01 TCGA.MX.A663.01 TCGA.D7.A4YV.01 TCGA.HU.A4GD.01
#> "03113" "01121" "03113" "013122" "0231" "0331"
#> TCGA.BR.A4QL.01 TCGA.BR.7703.01 TCGA.VQ.AA6B.01 TCGA.VQ.AA6D.01 TCGA.D7.A6EZ.01 TCGA.D7.A4YU.01
#> "022" "022" "0332" "01232" "0211" "0232"
#> TCGA.VQ.AA6A.01 TCGA.IN.7806.01 TCGA.HU.A4HB.01 TCGA.HU.A4H2.01 TCGA.IN.A6RP.01 TCGA.HU.A4H5.01
#> "01231" "01222" "03113" "0342" "022" "01231"
#> TCGA.HU.A4GU.01 TCGA.MX.A5UJ.01 TCGA.HU.A4GN.01 TCGA.CD.5804.01 TCGA.HU.A4H6.01 TCGA.HF.7132.01
#> "022" "022" "0232" "013123" "0231" "0232"
#> TCGA.D7.A4YT.01 TCGA.HF.7134.01 TCGA.BR.6852.01 TCGA.BR.8370.01 TCGA.EQ.5647.01 TCGA.IN.A7NT.01
#> "013" "022" "0314" "0233" "013" "032"
#> TCGA.RD.A8N9.01 TCGA.D7.5577.01 TCGA.CG.5717.01 TCGA.D7.6818.01 TCGA.CG.5734.01 TCGA.VQ.A8P8.01
#> "0114" "0211" "01134" "013121" "03111" "0314"
#> TCGA.BR.6707.01 TCGA.B7.5818.01 TCGA.CD.8525.01 TCGA.BR.6705.01 TCGA.BR.4288.01 TCGA.CD.5813.01
#> "0211" "0211" "013" "0313" "013122" "01121"
#> TCGA.CG.5723.01 TCGA.CD.5800.01 TCGA.CG.5718.01 TCGA.BR.8080.01 TCGA.CG.5733.01 TCGA.D7.6817.01
#> "01121" "013" "01232" "0114" "022" "01231"
#> TCGA.KB.A93G.01 TCGA.CD.5799.01 TCGA.BR.7851.01 TCGA.BR.7722.01 TCGA.MX.A5UG.01 TCGA.CD.8533.01
#> "01133" "013121" "0232" "01121" "03111" "0331"
#> TCGA.BR.7957.01 TCGA.CG.5722.01 TCGA.F1.6874.01 TCGA.CG.5730.01 TCGA.CG.5726.01 TCGA.IP.7968.01
#> "0313" "0312" "032" "0331" "022" "0331"
#> TCGA.BR.8363.01 TCGA.BR.7901.01 TCGA.D7.6822.01 TCGA.BR.6710.01 TCGA.CG.5720.01 TCGA.D7.8570.01
#> "0231" "0121" "03411" "01132" "022" "0211"
#> TCGA.B7.A5TI.01 TCGA.D7.6815.01 TCGA.BR.8284.01 TCGA.BR.8295.01 TCGA.BR.7197.01 TCGA.B7.A5TJ.01
#> "013" "01222" "0231" "0121" "01222" "022"
#> TCGA.D7.A6EY.01 TCGA.BR.8366.01 TCGA.IN.A7NR.01 TCGA.BR.6706.01 TCGA.IN.7808.01 TCGA.BR.6564.01
#> "0313" "0211" "01114" "0312" "03112" "01111"
#> TCGA.KB.A93H.01 TCGA.KB.A93J.01 TCGA.CD.5798.01 TCGA.CD.8530.01 TCGA.BR.6802.01 TCGA.CG.5719.01
#> "0332" "01222" "01134" "013121" "03112" "0114"
#> TCGA.VQ.A8E3.01 TCGA.CD.5801.01 TCGA.FP.A9TM.01 TCGA.BR.7958.01 TCGA.FP.7998.01 TCGA.IN.A6RS.01
#> "022" "0211" "032" "0211" "0312" "032"
#> TCGA.BR.6709.01 TCGA.FP.7916.01 TCGA.R5.A7ZR.01 TCGA.B7.5816.01 TCGA.CG.5721.01 TCGA.SW.A7EA.01
#> "01112" "0211" "01222" "0314" "03111" "022"
#> TCGA.RD.A8NB.01 TCGA.BR.6801.01 TCGA.IN.AB1X.01 TCGA.D7.5579.01 TCGA.CG.5728.01 TCGA.R5.A7ZI.01
#> "0313" "013" "0314" "013121" "0313" "013"
#> TCGA.IN.A7NU.01 TCGA.CG.5732.01 TCGA.ZQ.A9CR.01 TCGA.D7.5578.01 TCGA.BR.6803.01 TCGA.BR.8368.01
#> "032" "013123" "013" "032" "01111" "022"
#> TCGA.SW.A7EB.01 TCGA.BR.8081.01 TCGA.VQ.A8P5.01 TCGA.CD.8535.01 TCGA.CG.5724.01 TCGA.D7.8574.01
#> "01132" "0231" "032" "022" "03412" "01131"
#> TCGA.HJ.7597.01 TCGA.HF.A5NB.01 TCGA.VQ.A8PB.01 TCGA.R5.A7ZE.01 TCGA.CD.5803.01 TCGA.CG.5725.01
#> "0114" "022" "03412" "01222" "01112" "0121"
#> TCGA.D7.6820.01 TCGA.CD.5802.01 TCGA.R5.A7ZF.01 TCGA.D7.A6F0.01 TCGA.CG.5727.01 TCGA.VQ.A8PC.01
#> "01231" "013123" "013" "0121" "032" "03111"
#> TCGA.CD.A486.01 TCGA.RD.A8N2.01 TCGA.IN.A6RI.01 TCGA.HU.8243.01 TCGA.CD.A48C.01 TCGA.RD.A8N5.01
#> "0121" "01113" "0121" "0342" "022" "01131"
#> TCGA.RD.A8N1.01 TCGA.HU.A4GF.01 TCGA.BR.8362.01 TCGA.BR.8285.01 TCGA.CD.8532.01 TCGA.VQ.A8E2.01
#> "013121" "01222" "032" "0211" "01121" "013122"
#> TCGA.BR.8373.01 TCGA.BR.8361.01 TCGA.BR.8058.01 TCGA.IN.8462.01 TCGA.HU.A4G9.01 TCGA.CD.8524.01
#> "01222" "022" "0114" "03412" "022" "032"
#> TCGA.D7.A748.01 TCGA.CD.8527.01 TCGA.VQ.A8DV.01 TCGA.CD.8528.01 TCGA.BR.A453.01 TCGA.RD.A8N6.01
#> "01115" "013" "01233" "022" "03111" "013"
#> TCGA.HU.8245.01 TCGA.ZA.A8F6.01 TCGA.BR.8367.01 TCGA.BR.8380.01 TCGA.FP.A4BE.01 TCGA.HU.8238.01
#> "01231" "013121" "032" "03112" "0233" "03413"
#> TCGA.BR.8078.01 TCGA.HU.8249.01 TCGA.RD.A8N0.01 TCGA.BR.8365.01 TCGA.FP.8211.01 TCGA.RD.A8N4.01
#> "0231" "0331" "01112" "01111" "01122" "01113"
#> TCGA.VQ.A8DU.01 TCGA.VQ.A8DL.01 TCGA.VQ.A8DZ.01 TCGA.D7.8572.01 TCGA.RD.A7BW.01 TCGA.R5.A804.01
#> "01233" "013" "01231" "013122" "01116" "0314"
#> TCGA.BR.A4CS.01 TCGA.CD.8531.01 TCGA.CD.A487.01 TCGA.BR.8371.01 TCGA.BR.8059.01 TCGA.D7.A6ET.01
#> "032" "0212" "013" "01131" "013121" "0312"
#> TCGA.FP.8099.01 TCGA.D7.8579.01 TCGA.BR.8297.01 TCGA.D7.8576.01 TCGA.VQ.A8DT.01 TCGA.FP.A8CX.01
#> "0333" "0313" "032" "0114" "022" "013121"
#> TCGA.HU.A4GH.01 TCGA.CD.8526.01 TCGA.HU.A4G6.01 TCGA.D7.8578.01 TCGA.HU.A4G3.01 TCGA.D7.A74A.01
#> "0121" "013" "0211" "013123" "022" "022"
#> TCGA.RD.A7C1.01 TCGA.F1.A448.01 TCGA.D7.8575.01 TCGA.BR.8372.01 TCGA.VQ.A8P3.01 TCGA.RD.A8MW.01
#> "032" "03112" "03411" "022" "03412" "013123"
#> TCGA.BR.8286.01 TCGA.BR.8369.01 TCGA.BR.8364.01 TCGA.HU.8244.01 TCGA.KB.A6F7.01 TCGA.FP.A4BF.01
#> "03412" "032" "01111" "022" "0121" "032"
#> TCGA.R5.A805.01 TCGA.IN.A6RL.01 TCGA.IN.A6RR.01 TCGA.BR.A4CR.01 TCGA.CD.A489.01 TCGA.HU.A4GY.01
#> "032" "0342" "022" "013" "01121" "0114"
#> TCGA.BR.8289.01 TCGA.FP.8209.01 TCGA.BR.8296.01 TCGA.CD.A48A.01 TCGA.BR.8060.01 TCGA.BR.8077.01
#> "0342" "01131" "0314" "0331" "0121" "01222"
#> TCGA.CD.8534.01 TCGA.BR.7959.01 TCGA.VQ.A8P2.01 TCGA.EQ.8122.01 TCGA.D7.8573.01 TCGA.BR.A44T.01
#> "032" "032" "022" "01222" "0212" "01112"
#> TCGA.RD.A8MV.01 TCGA.CD.8536.01 TCGA.BR.8360.01 TCGA.BR.8291.01 TCGA.FP.8210.01 TCGA.RD.A7BS.01
#> "03111" "032" "0232" "013123" "01131" "01134"
#> TCGA.BR.A44U.01 TCGA.CD.8529.01
#> "03413" "013121"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 2116))
#> TCGA.VQ.A94P.01 TCGA.D7.6521.01 TCGA.VQ.A8PE.01 TCGA.D7.6519.01 TCGA.BR.6452.01 TCGA.BR.8485.01
#> "01133" "01121" "01233" "013" "0231" "01232"
#> TCGA.VQ.A8PO.01 TCGA.VQ.AA69.01 TCGA.BR.8683.01 TCGA.BR.8486.01 TCGA.D7.6522.01 TCGA.CG.5716.01
#> "022" "0212" "032" "01232" "01131" "0314"
#> TCGA.BR.8589.01 TCGA.BR.8382.01 TCGA.VQ.AA68.01 TCGA.VQ.A8PJ.01 TCGA.VQ.A8PH.01 TCGA.HU.8604.01
#> "0211" "0231" "03412" "01222" "01233" "0231"
#> TCGA.BR.8676.01 TCGA.CG.4441.01 TCGA.D7.6520.01 TCGA.VQ.AA64.01 TCGA.D7.6527.01 TCGA.VQ.A8PM.01
#> "0212" "0342" "0121" "01122" "01231" "013"
#> TCGA.VQ.A923.01 TCGA.BR.8384.01 TCGA.BR.6453.01 TCGA.VQ.A928.01 TCGA.VQ.A8E0.01 TCGA.BR.8679.01
#> "0212" "03111" "03112" "01122" "01122" "022"
#> TCGA.VQ.A91S.01 TCGA.BR.8678.01 TCGA.D7.6528.01 TCGA.VQ.A8E7.01 TCGA.BR.8680.01 TCGA.BR.8483.01
#> "032" "01221" "0332" "03411" "03411" "0331"
#> TCGA.BR.6566.01 TCGA.VQ.A91X.01 TCGA.VQ.A91Q.01 TCGA.VQ.A92D.01 TCGA.VQ.A91Z.01 TCGA.BR.6455.01
#> "032" "0332" "01122" "022" "01221" "0212"
#> TCGA.BR.8591.01 TCGA.HU.8608.01 TCGA.VQ.A94U.01 TCGA.VQ.A94T.01 TCGA.VQ.A91A.01 TCGA.VQ.A91D.01
#> "0233" "0211" "0333" "01123" "032" "0233"
#> TCGA.D7.6518.01 TCGA.BR.8484.01 TCGA.VQ.A91N.01 TCGA.VQ.A91E.01 TCGA.VQ.A8PY.01 TCGA.HU.8602.01
#> "03111" "013" "01222" "032" "032" "0231"
#> TCGA.BR.8381.01 TCGA.BR.6452.11 TCGA.IN.8663.01 TCGA.VQ.A8PS.01 TCGA.VQ.A91W.01 TCGA.BR.6454.01
#> "0211" "0314" "022" "01122" "0212" "01121"
#> TCGA.BR.8682.01 TCGA.VQ.A91V.01 TCGA.VQ.A8PZ.01 TCGA.BR.8590.01 TCGA.F1.6177.01 TCGA.VQ.A8PQ.01
#> "032" "0333" "0314" "01133" "022" "01112"
#> TCGA.VQ.A91U.01 TCGA.VQ.AA6I.01 TCGA.CG.4437.01 TCGA.VQ.A8PP.01 TCGA.BR.6565.01 TCGA.VQ.A91Y.01
#> "01222" "022" "0232" "0232" "0121" "013"
#> TCGA.VQ.A8PF.01 TCGA.BR.6456.01 TCGA.BR.6458.01 TCGA.VQ.A925.01 TCGA.VQ.A927.01 TCGA.BR.8592.01
#> "0211" "013" "032" "013" "01132" "0313"
#> TCGA.BR.6566.11 TCGA.IN.AB1V.01 TCGA.VQ.AA6F.01 TCGA.VQ.AA6J.01 TCGA.BR.8487.01 TCGA.D7.6525.01
#> "01114" "013" "01121" "01121" "022" "032"
#> TCGA.VQ.A94O.01 TCGA.BR.8588.01 TCGA.HU.8610.01 TCGA.D7.6526.01 TCGA.VQ.A8PD.01 TCGA.D7.6524.01
#> "0121" "0313" "03111" "01231" "03112" "0314"
#> TCGA.3M.AB46.01 TCGA.3M.AB47.01 TCGA.BR.8677.01 TCGA.BR.6457.01 TCGA.BR.8687.01 TCGA.VQ.A91K.01
#> "01222" "03112" "0114" "03111" "013" "022"
#> TCGA.BR.8690.01 TCGA.BR.8686.01 TCGA.FP.8631.01 TCGA.VQ.A922.01 TCGA.BR.A452.01 TCGA.IN.A6RO.01
#> "013" "0211" "0121" "0121" "01121" "022"
#> TCGA.BR.A4QI.01 TCGA.D7.A6EV.01 TCGA.HU.A4G2.01 TCGA.BR.A4IY.01 TCGA.VQ.A8PU.01 TCGA.BR.A4J4.01
#> "0231" "03413" "0211" "0211" "01123" "0211"
#> TCGA.VQ.A94R.01 TCGA.HU.A4H4.01 TCGA.BR.7707.01 TCGA.FP.7829.01 TCGA.BR.A4J5.01 TCGA.HU.A4H0.01
#> "022" "032" "022" "022" "03113" "0211"
#> TCGA.HU.A4HD.01 TCGA.KB.A6F5.01 TCGA.VQ.AA6K.01 TCGA.HF.7133.01 TCGA.F1.6875.01 TCGA.MX.A666.01
#> "0121" "013" "01121" "013" "01221" "0121"
#> TCGA.BR.7717.01 TCGA.BR.A4PF.01 TCGA.BR.A4IU.01 TCGA.VQ.A8PX.01 TCGA.BR.A4IV.01 TCGA.D7.A6EX.01
#> "03412" "0232" "0313" "01121" "01133" "013"
#> TCGA.BR.A4IZ.01 TCGA.BR.A4J9.01 TCGA.CD.A4MJ.01 TCGA.B7.A5TN.01 TCGA.BR.7715.01 TCGA.BR.7704.01
#> "01115" "01133" "0233" "01222" "0332" "01232"
#> TCGA.BR.A4J1.01 TCGA.HU.A4GP.01 TCGA.D7.A4YY.01 TCGA.VQ.AA6G.01 TCGA.HU.A4GJ.01 TCGA.CD.A4MI.01
#> "0121" "022" "022" "022" "0314" "0232"
#> TCGA.BR.7196.01 TCGA.BR.6563.01 TCGA.VQ.A924.01 TCGA.BR.7716.01 TCGA.FP.7735.01 TCGA.BR.7723.01
#> "0312" "03111" "0233" "013" "013" "013"
#> TCGA.HU.A4H8.01 TCGA.IN.A6RJ.01 TCGA.HU.A4H3.01 TCGA.EQ.A4SO.01 TCGA.CD.A4MH.01 TCGA.BR.A4J7.01
#> "022" "03113" "022" "01122" "01232" "01121"
#> TCGA.HF.7131.01 TCGA.D7.A74B.01 TCGA.BR.A4PE.01 TCGA.BR.A4J8.01 TCGA.HU.A4GX.01 TCGA.HU.A4G8.01
#> "01231" "01116" "022" "0231" "032" "03413"
#> TCGA.HU.A4GT.01 TCGA.HU.A4GC.01 TCGA.BR.A4CQ.01 TCGA.D7.A6F2.01 TCGA.RD.A7BT.01 TCGA.BR.A4J6.01
#> "022" "03413" "022" "01222" "01222" "0114"
#> TCGA.HU.A4GQ.01 TCGA.HF.7136.01 TCGA.BR.A4QM.01 TCGA.BR.A4PD.01 TCGA.VQ.A8PK.01 TCGA.B7.A5TK.01
#> "0232" "013" "0232" "01222" "0121" "0312"
#> TCGA.D7.A4YX.01 TCGA.D7.A4Z0.01 TCGA.VQ.A8PT.01 TCGA.IN.A6RN.01 TCGA.CD.A4MG.01 TCGA.D7.A747.01
#> "0211" "0313" "022" "0121" "022" "01133"
#> TCGA.R5.A7O7.01 TCGA.F1.A72C.01 TCGA.BR.A4J2.01 TCGA.MX.A663.01 TCGA.D7.A4YV.01 TCGA.HU.A4GD.01
#> "03113" "01121" "03113" "013" "0231" "0331"
#> TCGA.BR.A4QL.01 TCGA.BR.7703.01 TCGA.VQ.AA6B.01 TCGA.VQ.AA6D.01 TCGA.D7.A6EZ.01 TCGA.D7.A4YU.01
#> "022" "022" "0332" "01232" "0211" "0232"
#> TCGA.VQ.AA6A.01 TCGA.IN.7806.01 TCGA.HU.A4HB.01 TCGA.HU.A4H2.01 TCGA.IN.A6RP.01 TCGA.HU.A4H5.01
#> "01231" "01222" "03113" "0342" "022" "01231"
#> TCGA.HU.A4GU.01 TCGA.MX.A5UJ.01 TCGA.HU.A4GN.01 TCGA.CD.5804.01 TCGA.HU.A4H6.01 TCGA.HF.7132.01
#> "022" "022" "0232" "013" "0231" "0232"
#> TCGA.D7.A4YT.01 TCGA.HF.7134.01 TCGA.BR.6852.01 TCGA.BR.8370.01 TCGA.EQ.5647.01 TCGA.IN.A7NT.01
#> "013" "022" "0314" "0233" "013" "032"
#> TCGA.RD.A8N9.01 TCGA.D7.5577.01 TCGA.CG.5717.01 TCGA.D7.6818.01 TCGA.CG.5734.01 TCGA.VQ.A8P8.01
#> "0114" "0211" "01134" "013" "03111" "0314"
#> TCGA.BR.6707.01 TCGA.B7.5818.01 TCGA.CD.8525.01 TCGA.BR.6705.01 TCGA.BR.4288.01 TCGA.CD.5813.01
#> "0211" "0211" "013" "0313" "013" "01121"
#> TCGA.CG.5723.01 TCGA.CD.5800.01 TCGA.CG.5718.01 TCGA.BR.8080.01 TCGA.CG.5733.01 TCGA.D7.6817.01
#> "01121" "013" "01232" "0114" "022" "01231"
#> TCGA.KB.A93G.01 TCGA.CD.5799.01 TCGA.BR.7851.01 TCGA.BR.7722.01 TCGA.MX.A5UG.01 TCGA.CD.8533.01
#> "01133" "013" "0232" "01121" "03111" "0331"
#> TCGA.BR.7957.01 TCGA.CG.5722.01 TCGA.F1.6874.01 TCGA.CG.5730.01 TCGA.CG.5726.01 TCGA.IP.7968.01
#> "0313" "0312" "032" "0331" "022" "0331"
#> TCGA.BR.8363.01 TCGA.BR.7901.01 TCGA.D7.6822.01 TCGA.BR.6710.01 TCGA.CG.5720.01 TCGA.D7.8570.01
#> "0231" "0121" "03411" "01132" "022" "0211"
#> TCGA.B7.A5TI.01 TCGA.D7.6815.01 TCGA.BR.8284.01 TCGA.BR.8295.01 TCGA.BR.7197.01 TCGA.B7.A5TJ.01
#> "013" "01222" "0231" "0121" "01222" "022"
#> TCGA.D7.A6EY.01 TCGA.BR.8366.01 TCGA.IN.A7NR.01 TCGA.BR.6706.01 TCGA.IN.7808.01 TCGA.BR.6564.01
#> "0313" "0211" "01114" "0312" "03112" "01111"
#> TCGA.KB.A93H.01 TCGA.KB.A93J.01 TCGA.CD.5798.01 TCGA.CD.8530.01 TCGA.BR.6802.01 TCGA.CG.5719.01
#> "0332" "01222" "01134" "013" "03112" "0114"
#> TCGA.VQ.A8E3.01 TCGA.CD.5801.01 TCGA.FP.A9TM.01 TCGA.BR.7958.01 TCGA.FP.7998.01 TCGA.IN.A6RS.01
#> "022" "0211" "032" "0211" "0312" "032"
#> TCGA.BR.6709.01 TCGA.FP.7916.01 TCGA.R5.A7ZR.01 TCGA.B7.5816.01 TCGA.CG.5721.01 TCGA.SW.A7EA.01
#> "01112" "0211" "01222" "0314" "03111" "022"
#> TCGA.RD.A8NB.01 TCGA.BR.6801.01 TCGA.IN.AB1X.01 TCGA.D7.5579.01 TCGA.CG.5728.01 TCGA.R5.A7ZI.01
#> "0313" "013" "0314" "013" "0313" "013"
#> TCGA.IN.A7NU.01 TCGA.CG.5732.01 TCGA.ZQ.A9CR.01 TCGA.D7.5578.01 TCGA.BR.6803.01 TCGA.BR.8368.01
#> "032" "013" "013" "032" "01111" "022"
#> TCGA.SW.A7EB.01 TCGA.BR.8081.01 TCGA.VQ.A8P5.01 TCGA.CD.8535.01 TCGA.CG.5724.01 TCGA.D7.8574.01
#> "01132" "0231" "032" "022" "03412" "01131"
#> TCGA.HJ.7597.01 TCGA.HF.A5NB.01 TCGA.VQ.A8PB.01 TCGA.R5.A7ZE.01 TCGA.CD.5803.01 TCGA.CG.5725.01
#> "0114" "022" "03412" "01222" "01112" "0121"
#> TCGA.D7.6820.01 TCGA.CD.5802.01 TCGA.R5.A7ZF.01 TCGA.D7.A6F0.01 TCGA.CG.5727.01 TCGA.VQ.A8PC.01
#> "01231" "013" "013" "0121" "032" "03111"
#> TCGA.CD.A486.01 TCGA.RD.A8N2.01 TCGA.IN.A6RI.01 TCGA.HU.8243.01 TCGA.CD.A48C.01 TCGA.RD.A8N5.01
#> "0121" "01113" "0121" "0342" "022" "01131"
#> TCGA.RD.A8N1.01 TCGA.HU.A4GF.01 TCGA.BR.8362.01 TCGA.BR.8285.01 TCGA.CD.8532.01 TCGA.VQ.A8E2.01
#> "013" "01222" "032" "0211" "01121" "013"
#> TCGA.BR.8373.01 TCGA.BR.8361.01 TCGA.BR.8058.01 TCGA.IN.8462.01 TCGA.HU.A4G9.01 TCGA.CD.8524.01
#> "01222" "022" "0114" "03412" "022" "032"
#> TCGA.D7.A748.01 TCGA.CD.8527.01 TCGA.VQ.A8DV.01 TCGA.CD.8528.01 TCGA.BR.A453.01 TCGA.RD.A8N6.01
#> "01115" "013" "01233" "022" "03111" "013"
#> TCGA.HU.8245.01 TCGA.ZA.A8F6.01 TCGA.BR.8367.01 TCGA.BR.8380.01 TCGA.FP.A4BE.01 TCGA.HU.8238.01
#> "01231" "013" "032" "03112" "0233" "03413"
#> TCGA.BR.8078.01 TCGA.HU.8249.01 TCGA.RD.A8N0.01 TCGA.BR.8365.01 TCGA.FP.8211.01 TCGA.RD.A8N4.01
#> "0231" "0331" "01112" "01111" "01122" "01113"
#> TCGA.VQ.A8DU.01 TCGA.VQ.A8DL.01 TCGA.VQ.A8DZ.01 TCGA.D7.8572.01 TCGA.RD.A7BW.01 TCGA.R5.A804.01
#> "01233" "013" "01231" "013" "01116" "0314"
#> TCGA.BR.A4CS.01 TCGA.CD.8531.01 TCGA.CD.A487.01 TCGA.BR.8371.01 TCGA.BR.8059.01 TCGA.D7.A6ET.01
#> "032" "0212" "013" "01131" "013" "0312"
#> TCGA.FP.8099.01 TCGA.D7.8579.01 TCGA.BR.8297.01 TCGA.D7.8576.01 TCGA.VQ.A8DT.01 TCGA.FP.A8CX.01
#> "0333" "0313" "032" "0114" "022" "013"
#> TCGA.HU.A4GH.01 TCGA.CD.8526.01 TCGA.HU.A4G6.01 TCGA.D7.8578.01 TCGA.HU.A4G3.01 TCGA.D7.A74A.01
#> "0121" "013" "0211" "013" "022" "022"
#> TCGA.RD.A7C1.01 TCGA.F1.A448.01 TCGA.D7.8575.01 TCGA.BR.8372.01 TCGA.VQ.A8P3.01 TCGA.RD.A8MW.01
#> "032" "03112" "03411" "022" "03412" "013"
#> TCGA.BR.8286.01 TCGA.BR.8369.01 TCGA.BR.8364.01 TCGA.HU.8244.01 TCGA.KB.A6F7.01 TCGA.FP.A4BF.01
#> "03412" "032" "01111" "022" "0121" "032"
#> TCGA.R5.A805.01 TCGA.IN.A6RL.01 TCGA.IN.A6RR.01 TCGA.BR.A4CR.01 TCGA.CD.A489.01 TCGA.HU.A4GY.01
#> "032" "0342" "022" "013" "01121" "0114"
#> TCGA.BR.8289.01 TCGA.FP.8209.01 TCGA.BR.8296.01 TCGA.CD.A48A.01 TCGA.BR.8060.01 TCGA.BR.8077.01
#> "0342" "01131" "0314" "0331" "0121" "01222"
#> TCGA.CD.8534.01 TCGA.BR.7959.01 TCGA.VQ.A8P2.01 TCGA.EQ.8122.01 TCGA.D7.8573.01 TCGA.BR.A44T.01
#> "032" "032" "022" "01222" "0212" "01112"
#> TCGA.RD.A8MV.01 TCGA.CD.8536.01 TCGA.BR.8360.01 TCGA.BR.8291.01 TCGA.FP.8210.01 TCGA.RD.A7BS.01
#> "03111" "032" "0232" "013" "01131" "01134"
#> TCGA.BR.A44U.01 TCGA.CD.8529.01
#> "03413" "013"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 2372))
#> TCGA.VQ.A94P.01 TCGA.D7.6521.01 TCGA.VQ.A8PE.01 TCGA.D7.6519.01 TCGA.BR.6452.01 TCGA.BR.8485.01
#> "01133" "01121" "01233" "013" "0231" "01232"
#> TCGA.VQ.A8PO.01 TCGA.VQ.AA69.01 TCGA.BR.8683.01 TCGA.BR.8486.01 TCGA.D7.6522.01 TCGA.CG.5716.01
#> "022" "0212" "032" "01232" "01131" "0314"
#> TCGA.BR.8589.01 TCGA.BR.8382.01 TCGA.VQ.AA68.01 TCGA.VQ.A8PJ.01 TCGA.VQ.A8PH.01 TCGA.HU.8604.01
#> "0211" "0231" "0341" "01222" "01233" "0231"
#> TCGA.BR.8676.01 TCGA.CG.4441.01 TCGA.D7.6520.01 TCGA.VQ.AA64.01 TCGA.D7.6527.01 TCGA.VQ.A8PM.01
#> "0212" "0342" "0121" "01122" "01231" "013"
#> TCGA.VQ.A923.01 TCGA.BR.8384.01 TCGA.BR.6453.01 TCGA.VQ.A928.01 TCGA.VQ.A8E0.01 TCGA.BR.8679.01
#> "0212" "03111" "03112" "01122" "01122" "022"
#> TCGA.VQ.A91S.01 TCGA.BR.8678.01 TCGA.D7.6528.01 TCGA.VQ.A8E7.01 TCGA.BR.8680.01 TCGA.BR.8483.01
#> "032" "01221" "0332" "0341" "0341" "0331"
#> TCGA.BR.6566.01 TCGA.VQ.A91X.01 TCGA.VQ.A91Q.01 TCGA.VQ.A92D.01 TCGA.VQ.A91Z.01 TCGA.BR.6455.01
#> "032" "0332" "01122" "022" "01221" "0212"
#> TCGA.BR.8591.01 TCGA.HU.8608.01 TCGA.VQ.A94U.01 TCGA.VQ.A94T.01 TCGA.VQ.A91A.01 TCGA.VQ.A91D.01
#> "0233" "0211" "0333" "01123" "032" "0233"
#> TCGA.D7.6518.01 TCGA.BR.8484.01 TCGA.VQ.A91N.01 TCGA.VQ.A91E.01 TCGA.VQ.A8PY.01 TCGA.HU.8602.01
#> "03111" "013" "01222" "032" "032" "0231"
#> TCGA.BR.8381.01 TCGA.BR.6452.11 TCGA.IN.8663.01 TCGA.VQ.A8PS.01 TCGA.VQ.A91W.01 TCGA.BR.6454.01
#> "0211" "0314" "022" "01122" "0212" "01121"
#> TCGA.BR.8682.01 TCGA.VQ.A91V.01 TCGA.VQ.A8PZ.01 TCGA.BR.8590.01 TCGA.F1.6177.01 TCGA.VQ.A8PQ.01
#> "032" "0333" "0314" "01133" "022" "01112"
#> TCGA.VQ.A91U.01 TCGA.VQ.AA6I.01 TCGA.CG.4437.01 TCGA.VQ.A8PP.01 TCGA.BR.6565.01 TCGA.VQ.A91Y.01
#> "01222" "022" "0232" "0232" "0121" "013"
#> TCGA.VQ.A8PF.01 TCGA.BR.6456.01 TCGA.BR.6458.01 TCGA.VQ.A925.01 TCGA.VQ.A927.01 TCGA.BR.8592.01
#> "0211" "013" "032" "013" "01132" "0313"
#> TCGA.BR.6566.11 TCGA.IN.AB1V.01 TCGA.VQ.AA6F.01 TCGA.VQ.AA6J.01 TCGA.BR.8487.01 TCGA.D7.6525.01
#> "01114" "013" "01121" "01121" "022" "032"
#> TCGA.VQ.A94O.01 TCGA.BR.8588.01 TCGA.HU.8610.01 TCGA.D7.6526.01 TCGA.VQ.A8PD.01 TCGA.D7.6524.01
#> "0121" "0313" "03111" "01231" "03112" "0314"
#> TCGA.3M.AB46.01 TCGA.3M.AB47.01 TCGA.BR.8677.01 TCGA.BR.6457.01 TCGA.BR.8687.01 TCGA.VQ.A91K.01
#> "01222" "03112" "0114" "03111" "013" "022"
#> TCGA.BR.8690.01 TCGA.BR.8686.01 TCGA.FP.8631.01 TCGA.VQ.A922.01 TCGA.BR.A452.01 TCGA.IN.A6RO.01
#> "013" "0211" "0121" "0121" "01121" "022"
#> TCGA.BR.A4QI.01 TCGA.D7.A6EV.01 TCGA.HU.A4G2.01 TCGA.BR.A4IY.01 TCGA.VQ.A8PU.01 TCGA.BR.A4J4.01
#> "0231" "0341" "0211" "0211" "01123" "0211"
#> TCGA.VQ.A94R.01 TCGA.HU.A4H4.01 TCGA.BR.7707.01 TCGA.FP.7829.01 TCGA.BR.A4J5.01 TCGA.HU.A4H0.01
#> "022" "032" "022" "022" "03113" "0211"
#> TCGA.HU.A4HD.01 TCGA.KB.A6F5.01 TCGA.VQ.AA6K.01 TCGA.HF.7133.01 TCGA.F1.6875.01 TCGA.MX.A666.01
#> "0121" "013" "01121" "013" "01221" "0121"
#> TCGA.BR.7717.01 TCGA.BR.A4PF.01 TCGA.BR.A4IU.01 TCGA.VQ.A8PX.01 TCGA.BR.A4IV.01 TCGA.D7.A6EX.01
#> "0341" "0232" "0313" "01121" "01133" "013"
#> TCGA.BR.A4IZ.01 TCGA.BR.A4J9.01 TCGA.CD.A4MJ.01 TCGA.B7.A5TN.01 TCGA.BR.7715.01 TCGA.BR.7704.01
#> "01115" "01133" "0233" "01222" "0332" "01232"
#> TCGA.BR.A4J1.01 TCGA.HU.A4GP.01 TCGA.D7.A4YY.01 TCGA.VQ.AA6G.01 TCGA.HU.A4GJ.01 TCGA.CD.A4MI.01
#> "0121" "022" "022" "022" "0314" "0232"
#> TCGA.BR.7196.01 TCGA.BR.6563.01 TCGA.VQ.A924.01 TCGA.BR.7716.01 TCGA.FP.7735.01 TCGA.BR.7723.01
#> "0312" "03111" "0233" "013" "013" "013"
#> TCGA.HU.A4H8.01 TCGA.IN.A6RJ.01 TCGA.HU.A4H3.01 TCGA.EQ.A4SO.01 TCGA.CD.A4MH.01 TCGA.BR.A4J7.01
#> "022" "03113" "022" "01122" "01232" "01121"
#> TCGA.HF.7131.01 TCGA.D7.A74B.01 TCGA.BR.A4PE.01 TCGA.BR.A4J8.01 TCGA.HU.A4GX.01 TCGA.HU.A4G8.01
#> "01231" "01116" "022" "0231" "032" "0341"
#> TCGA.HU.A4GT.01 TCGA.HU.A4GC.01 TCGA.BR.A4CQ.01 TCGA.D7.A6F2.01 TCGA.RD.A7BT.01 TCGA.BR.A4J6.01
#> "022" "0341" "022" "01222" "01222" "0114"
#> TCGA.HU.A4GQ.01 TCGA.HF.7136.01 TCGA.BR.A4QM.01 TCGA.BR.A4PD.01 TCGA.VQ.A8PK.01 TCGA.B7.A5TK.01
#> "0232" "013" "0232" "01222" "0121" "0312"
#> TCGA.D7.A4YX.01 TCGA.D7.A4Z0.01 TCGA.VQ.A8PT.01 TCGA.IN.A6RN.01 TCGA.CD.A4MG.01 TCGA.D7.A747.01
#> "0211" "0313" "022" "0121" "022" "01133"
#> TCGA.R5.A7O7.01 TCGA.F1.A72C.01 TCGA.BR.A4J2.01 TCGA.MX.A663.01 TCGA.D7.A4YV.01 TCGA.HU.A4GD.01
#> "03113" "01121" "03113" "013" "0231" "0331"
#> TCGA.BR.A4QL.01 TCGA.BR.7703.01 TCGA.VQ.AA6B.01 TCGA.VQ.AA6D.01 TCGA.D7.A6EZ.01 TCGA.D7.A4YU.01
#> "022" "022" "0332" "01232" "0211" "0232"
#> TCGA.VQ.AA6A.01 TCGA.IN.7806.01 TCGA.HU.A4HB.01 TCGA.HU.A4H2.01 TCGA.IN.A6RP.01 TCGA.HU.A4H5.01
#> "01231" "01222" "03113" "0342" "022" "01231"
#> TCGA.HU.A4GU.01 TCGA.MX.A5UJ.01 TCGA.HU.A4GN.01 TCGA.CD.5804.01 TCGA.HU.A4H6.01 TCGA.HF.7132.01
#> "022" "022" "0232" "013" "0231" "0232"
#> TCGA.D7.A4YT.01 TCGA.HF.7134.01 TCGA.BR.6852.01 TCGA.BR.8370.01 TCGA.EQ.5647.01 TCGA.IN.A7NT.01
#> "013" "022" "0314" "0233" "013" "032"
#> TCGA.RD.A8N9.01 TCGA.D7.5577.01 TCGA.CG.5717.01 TCGA.D7.6818.01 TCGA.CG.5734.01 TCGA.VQ.A8P8.01
#> "0114" "0211" "01134" "013" "03111" "0314"
#> TCGA.BR.6707.01 TCGA.B7.5818.01 TCGA.CD.8525.01 TCGA.BR.6705.01 TCGA.BR.4288.01 TCGA.CD.5813.01
#> "0211" "0211" "013" "0313" "013" "01121"
#> TCGA.CG.5723.01 TCGA.CD.5800.01 TCGA.CG.5718.01 TCGA.BR.8080.01 TCGA.CG.5733.01 TCGA.D7.6817.01
#> "01121" "013" "01232" "0114" "022" "01231"
#> TCGA.KB.A93G.01 TCGA.CD.5799.01 TCGA.BR.7851.01 TCGA.BR.7722.01 TCGA.MX.A5UG.01 TCGA.CD.8533.01
#> "01133" "013" "0232" "01121" "03111" "0331"
#> TCGA.BR.7957.01 TCGA.CG.5722.01 TCGA.F1.6874.01 TCGA.CG.5730.01 TCGA.CG.5726.01 TCGA.IP.7968.01
#> "0313" "0312" "032" "0331" "022" "0331"
#> TCGA.BR.8363.01 TCGA.BR.7901.01 TCGA.D7.6822.01 TCGA.BR.6710.01 TCGA.CG.5720.01 TCGA.D7.8570.01
#> "0231" "0121" "0341" "01132" "022" "0211"
#> TCGA.B7.A5TI.01 TCGA.D7.6815.01 TCGA.BR.8284.01 TCGA.BR.8295.01 TCGA.BR.7197.01 TCGA.B7.A5TJ.01
#> "013" "01222" "0231" "0121" "01222" "022"
#> TCGA.D7.A6EY.01 TCGA.BR.8366.01 TCGA.IN.A7NR.01 TCGA.BR.6706.01 TCGA.IN.7808.01 TCGA.BR.6564.01
#> "0313" "0211" "01114" "0312" "03112" "01111"
#> TCGA.KB.A93H.01 TCGA.KB.A93J.01 TCGA.CD.5798.01 TCGA.CD.8530.01 TCGA.BR.6802.01 TCGA.CG.5719.01
#> "0332" "01222" "01134" "013" "03112" "0114"
#> TCGA.VQ.A8E3.01 TCGA.CD.5801.01 TCGA.FP.A9TM.01 TCGA.BR.7958.01 TCGA.FP.7998.01 TCGA.IN.A6RS.01
#> "022" "0211" "032" "0211" "0312" "032"
#> TCGA.BR.6709.01 TCGA.FP.7916.01 TCGA.R5.A7ZR.01 TCGA.B7.5816.01 TCGA.CG.5721.01 TCGA.SW.A7EA.01
#> "01112" "0211" "01222" "0314" "03111" "022"
#> TCGA.RD.A8NB.01 TCGA.BR.6801.01 TCGA.IN.AB1X.01 TCGA.D7.5579.01 TCGA.CG.5728.01 TCGA.R5.A7ZI.01
#> "0313" "013" "0314" "013" "0313" "013"
#> TCGA.IN.A7NU.01 TCGA.CG.5732.01 TCGA.ZQ.A9CR.01 TCGA.D7.5578.01 TCGA.BR.6803.01 TCGA.BR.8368.01
#> "032" "013" "013" "032" "01111" "022"
#> TCGA.SW.A7EB.01 TCGA.BR.8081.01 TCGA.VQ.A8P5.01 TCGA.CD.8535.01 TCGA.CG.5724.01 TCGA.D7.8574.01
#> "01132" "0231" "032" "022" "0341" "01131"
#> TCGA.HJ.7597.01 TCGA.HF.A5NB.01 TCGA.VQ.A8PB.01 TCGA.R5.A7ZE.01 TCGA.CD.5803.01 TCGA.CG.5725.01
#> "0114" "022" "0341" "01222" "01112" "0121"
#> TCGA.D7.6820.01 TCGA.CD.5802.01 TCGA.R5.A7ZF.01 TCGA.D7.A6F0.01 TCGA.CG.5727.01 TCGA.VQ.A8PC.01
#> "01231" "013" "013" "0121" "032" "03111"
#> TCGA.CD.A486.01 TCGA.RD.A8N2.01 TCGA.IN.A6RI.01 TCGA.HU.8243.01 TCGA.CD.A48C.01 TCGA.RD.A8N5.01
#> "0121" "01113" "0121" "0342" "022" "01131"
#> TCGA.RD.A8N1.01 TCGA.HU.A4GF.01 TCGA.BR.8362.01 TCGA.BR.8285.01 TCGA.CD.8532.01 TCGA.VQ.A8E2.01
#> "013" "01222" "032" "0211" "01121" "013"
#> TCGA.BR.8373.01 TCGA.BR.8361.01 TCGA.BR.8058.01 TCGA.IN.8462.01 TCGA.HU.A4G9.01 TCGA.CD.8524.01
#> "01222" "022" "0114" "0341" "022" "032"
#> TCGA.D7.A748.01 TCGA.CD.8527.01 TCGA.VQ.A8DV.01 TCGA.CD.8528.01 TCGA.BR.A453.01 TCGA.RD.A8N6.01
#> "01115" "013" "01233" "022" "03111" "013"
#> TCGA.HU.8245.01 TCGA.ZA.A8F6.01 TCGA.BR.8367.01 TCGA.BR.8380.01 TCGA.FP.A4BE.01 TCGA.HU.8238.01
#> "01231" "013" "032" "03112" "0233" "0341"
#> TCGA.BR.8078.01 TCGA.HU.8249.01 TCGA.RD.A8N0.01 TCGA.BR.8365.01 TCGA.FP.8211.01 TCGA.RD.A8N4.01
#> "0231" "0331" "01112" "01111" "01122" "01113"
#> TCGA.VQ.A8DU.01 TCGA.VQ.A8DL.01 TCGA.VQ.A8DZ.01 TCGA.D7.8572.01 TCGA.RD.A7BW.01 TCGA.R5.A804.01
#> "01233" "013" "01231" "013" "01116" "0314"
#> TCGA.BR.A4CS.01 TCGA.CD.8531.01 TCGA.CD.A487.01 TCGA.BR.8371.01 TCGA.BR.8059.01 TCGA.D7.A6ET.01
#> "032" "0212" "013" "01131" "013" "0312"
#> TCGA.FP.8099.01 TCGA.D7.8579.01 TCGA.BR.8297.01 TCGA.D7.8576.01 TCGA.VQ.A8DT.01 TCGA.FP.A8CX.01
#> "0333" "0313" "032" "0114" "022" "013"
#> TCGA.HU.A4GH.01 TCGA.CD.8526.01 TCGA.HU.A4G6.01 TCGA.D7.8578.01 TCGA.HU.A4G3.01 TCGA.D7.A74A.01
#> "0121" "013" "0211" "013" "022" "022"
#> TCGA.RD.A7C1.01 TCGA.F1.A448.01 TCGA.D7.8575.01 TCGA.BR.8372.01 TCGA.VQ.A8P3.01 TCGA.RD.A8MW.01
#> "032" "03112" "0341" "022" "0341" "013"
#> TCGA.BR.8286.01 TCGA.BR.8369.01 TCGA.BR.8364.01 TCGA.HU.8244.01 TCGA.KB.A6F7.01 TCGA.FP.A4BF.01
#> "0341" "032" "01111" "022" "0121" "032"
#> TCGA.R5.A805.01 TCGA.IN.A6RL.01 TCGA.IN.A6RR.01 TCGA.BR.A4CR.01 TCGA.CD.A489.01 TCGA.HU.A4GY.01
#> "032" "0342" "022" "013" "01121" "0114"
#> TCGA.BR.8289.01 TCGA.FP.8209.01 TCGA.BR.8296.01 TCGA.CD.A48A.01 TCGA.BR.8060.01 TCGA.BR.8077.01
#> "0342" "01131" "0314" "0331" "0121" "01222"
#> TCGA.CD.8534.01 TCGA.BR.7959.01 TCGA.VQ.A8P2.01 TCGA.EQ.8122.01 TCGA.D7.8573.01 TCGA.BR.A44T.01
#> "032" "032" "022" "01222" "0212" "01112"
#> TCGA.RD.A8MV.01 TCGA.CD.8536.01 TCGA.BR.8360.01 TCGA.BR.8291.01 TCGA.FP.8210.01 TCGA.RD.A7BS.01
#> "03111" "032" "0232" "013" "01131" "01134"
#> TCGA.BR.A44U.01 TCGA.CD.8529.01
#> "0341" "013"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 2422))
#> TCGA.VQ.A94P.01 TCGA.D7.6521.01 TCGA.VQ.A8PE.01 TCGA.D7.6519.01 TCGA.BR.6452.01 TCGA.BR.8485.01
#> "01133" "01121" "01233" "013" "0231" "01232"
#> TCGA.VQ.A8PO.01 TCGA.VQ.AA69.01 TCGA.BR.8683.01 TCGA.BR.8486.01 TCGA.D7.6522.01 TCGA.CG.5716.01
#> "022" "0212" "032" "01232" "01131" "0314"
#> TCGA.BR.8589.01 TCGA.BR.8382.01 TCGA.VQ.AA68.01 TCGA.VQ.A8PJ.01 TCGA.VQ.A8PH.01 TCGA.HU.8604.01
#> "0211" "0231" "0341" "0122" "01233" "0231"
#> TCGA.BR.8676.01 TCGA.CG.4441.01 TCGA.D7.6520.01 TCGA.VQ.AA64.01 TCGA.D7.6527.01 TCGA.VQ.A8PM.01
#> "0212" "0342" "0121" "01122" "01231" "013"
#> TCGA.VQ.A923.01 TCGA.BR.8384.01 TCGA.BR.6453.01 TCGA.VQ.A928.01 TCGA.VQ.A8E0.01 TCGA.BR.8679.01
#> "0212" "03111" "03112" "01122" "01122" "022"
#> TCGA.VQ.A91S.01 TCGA.BR.8678.01 TCGA.D7.6528.01 TCGA.VQ.A8E7.01 TCGA.BR.8680.01 TCGA.BR.8483.01
#> "032" "0122" "0332" "0341" "0341" "0331"
#> TCGA.BR.6566.01 TCGA.VQ.A91X.01 TCGA.VQ.A91Q.01 TCGA.VQ.A92D.01 TCGA.VQ.A91Z.01 TCGA.BR.6455.01
#> "032" "0332" "01122" "022" "0122" "0212"
#> TCGA.BR.8591.01 TCGA.HU.8608.01 TCGA.VQ.A94U.01 TCGA.VQ.A94T.01 TCGA.VQ.A91A.01 TCGA.VQ.A91D.01
#> "0233" "0211" "0333" "01123" "032" "0233"
#> TCGA.D7.6518.01 TCGA.BR.8484.01 TCGA.VQ.A91N.01 TCGA.VQ.A91E.01 TCGA.VQ.A8PY.01 TCGA.HU.8602.01
#> "03111" "013" "0122" "032" "032" "0231"
#> TCGA.BR.8381.01 TCGA.BR.6452.11 TCGA.IN.8663.01 TCGA.VQ.A8PS.01 TCGA.VQ.A91W.01 TCGA.BR.6454.01
#> "0211" "0314" "022" "01122" "0212" "01121"
#> TCGA.BR.8682.01 TCGA.VQ.A91V.01 TCGA.VQ.A8PZ.01 TCGA.BR.8590.01 TCGA.F1.6177.01 TCGA.VQ.A8PQ.01
#> "032" "0333" "0314" "01133" "022" "01112"
#> TCGA.VQ.A91U.01 TCGA.VQ.AA6I.01 TCGA.CG.4437.01 TCGA.VQ.A8PP.01 TCGA.BR.6565.01 TCGA.VQ.A91Y.01
#> "0122" "022" "0232" "0232" "0121" "013"
#> TCGA.VQ.A8PF.01 TCGA.BR.6456.01 TCGA.BR.6458.01 TCGA.VQ.A925.01 TCGA.VQ.A927.01 TCGA.BR.8592.01
#> "0211" "013" "032" "013" "01132" "0313"
#> TCGA.BR.6566.11 TCGA.IN.AB1V.01 TCGA.VQ.AA6F.01 TCGA.VQ.AA6J.01 TCGA.BR.8487.01 TCGA.D7.6525.01
#> "01114" "013" "01121" "01121" "022" "032"
#> TCGA.VQ.A94O.01 TCGA.BR.8588.01 TCGA.HU.8610.01 TCGA.D7.6526.01 TCGA.VQ.A8PD.01 TCGA.D7.6524.01
#> "0121" "0313" "03111" "01231" "03112" "0314"
#> TCGA.3M.AB46.01 TCGA.3M.AB47.01 TCGA.BR.8677.01 TCGA.BR.6457.01 TCGA.BR.8687.01 TCGA.VQ.A91K.01
#> "0122" "03112" "0114" "03111" "013" "022"
#> TCGA.BR.8690.01 TCGA.BR.8686.01 TCGA.FP.8631.01 TCGA.VQ.A922.01 TCGA.BR.A452.01 TCGA.IN.A6RO.01
#> "013" "0211" "0121" "0121" "01121" "022"
#> TCGA.BR.A4QI.01 TCGA.D7.A6EV.01 TCGA.HU.A4G2.01 TCGA.BR.A4IY.01 TCGA.VQ.A8PU.01 TCGA.BR.A4J4.01
#> "0231" "0341" "0211" "0211" "01123" "0211"
#> TCGA.VQ.A94R.01 TCGA.HU.A4H4.01 TCGA.BR.7707.01 TCGA.FP.7829.01 TCGA.BR.A4J5.01 TCGA.HU.A4H0.01
#> "022" "032" "022" "022" "03113" "0211"
#> TCGA.HU.A4HD.01 TCGA.KB.A6F5.01 TCGA.VQ.AA6K.01 TCGA.HF.7133.01 TCGA.F1.6875.01 TCGA.MX.A666.01
#> "0121" "013" "01121" "013" "0122" "0121"
#> TCGA.BR.7717.01 TCGA.BR.A4PF.01 TCGA.BR.A4IU.01 TCGA.VQ.A8PX.01 TCGA.BR.A4IV.01 TCGA.D7.A6EX.01
#> "0341" "0232" "0313" "01121" "01133" "013"
#> TCGA.BR.A4IZ.01 TCGA.BR.A4J9.01 TCGA.CD.A4MJ.01 TCGA.B7.A5TN.01 TCGA.BR.7715.01 TCGA.BR.7704.01
#> "01115" "01133" "0233" "0122" "0332" "01232"
#> TCGA.BR.A4J1.01 TCGA.HU.A4GP.01 TCGA.D7.A4YY.01 TCGA.VQ.AA6G.01 TCGA.HU.A4GJ.01 TCGA.CD.A4MI.01
#> "0121" "022" "022" "022" "0314" "0232"
#> TCGA.BR.7196.01 TCGA.BR.6563.01 TCGA.VQ.A924.01 TCGA.BR.7716.01 TCGA.FP.7735.01 TCGA.BR.7723.01
#> "0312" "03111" "0233" "013" "013" "013"
#> TCGA.HU.A4H8.01 TCGA.IN.A6RJ.01 TCGA.HU.A4H3.01 TCGA.EQ.A4SO.01 TCGA.CD.A4MH.01 TCGA.BR.A4J7.01
#> "022" "03113" "022" "01122" "01232" "01121"
#> TCGA.HF.7131.01 TCGA.D7.A74B.01 TCGA.BR.A4PE.01 TCGA.BR.A4J8.01 TCGA.HU.A4GX.01 TCGA.HU.A4G8.01
#> "01231" "01116" "022" "0231" "032" "0341"
#> TCGA.HU.A4GT.01 TCGA.HU.A4GC.01 TCGA.BR.A4CQ.01 TCGA.D7.A6F2.01 TCGA.RD.A7BT.01 TCGA.BR.A4J6.01
#> "022" "0341" "022" "0122" "0122" "0114"
#> TCGA.HU.A4GQ.01 TCGA.HF.7136.01 TCGA.BR.A4QM.01 TCGA.BR.A4PD.01 TCGA.VQ.A8PK.01 TCGA.B7.A5TK.01
#> "0232" "013" "0232" "0122" "0121" "0312"
#> TCGA.D7.A4YX.01 TCGA.D7.A4Z0.01 TCGA.VQ.A8PT.01 TCGA.IN.A6RN.01 TCGA.CD.A4MG.01 TCGA.D7.A747.01
#> "0211" "0313" "022" "0121" "022" "01133"
#> TCGA.R5.A7O7.01 TCGA.F1.A72C.01 TCGA.BR.A4J2.01 TCGA.MX.A663.01 TCGA.D7.A4YV.01 TCGA.HU.A4GD.01
#> "03113" "01121" "03113" "013" "0231" "0331"
#> TCGA.BR.A4QL.01 TCGA.BR.7703.01 TCGA.VQ.AA6B.01 TCGA.VQ.AA6D.01 TCGA.D7.A6EZ.01 TCGA.D7.A4YU.01
#> "022" "022" "0332" "01232" "0211" "0232"
#> TCGA.VQ.AA6A.01 TCGA.IN.7806.01 TCGA.HU.A4HB.01 TCGA.HU.A4H2.01 TCGA.IN.A6RP.01 TCGA.HU.A4H5.01
#> "01231" "0122" "03113" "0342" "022" "01231"
#> TCGA.HU.A4GU.01 TCGA.MX.A5UJ.01 TCGA.HU.A4GN.01 TCGA.CD.5804.01 TCGA.HU.A4H6.01 TCGA.HF.7132.01
#> "022" "022" "0232" "013" "0231" "0232"
#> TCGA.D7.A4YT.01 TCGA.HF.7134.01 TCGA.BR.6852.01 TCGA.BR.8370.01 TCGA.EQ.5647.01 TCGA.IN.A7NT.01
#> "013" "022" "0314" "0233" "013" "032"
#> TCGA.RD.A8N9.01 TCGA.D7.5577.01 TCGA.CG.5717.01 TCGA.D7.6818.01 TCGA.CG.5734.01 TCGA.VQ.A8P8.01
#> "0114" "0211" "01134" "013" "03111" "0314"
#> TCGA.BR.6707.01 TCGA.B7.5818.01 TCGA.CD.8525.01 TCGA.BR.6705.01 TCGA.BR.4288.01 TCGA.CD.5813.01
#> "0211" "0211" "013" "0313" "013" "01121"
#> TCGA.CG.5723.01 TCGA.CD.5800.01 TCGA.CG.5718.01 TCGA.BR.8080.01 TCGA.CG.5733.01 TCGA.D7.6817.01
#> "01121" "013" "01232" "0114" "022" "01231"
#> TCGA.KB.A93G.01 TCGA.CD.5799.01 TCGA.BR.7851.01 TCGA.BR.7722.01 TCGA.MX.A5UG.01 TCGA.CD.8533.01
#> "01133" "013" "0232" "01121" "03111" "0331"
#> TCGA.BR.7957.01 TCGA.CG.5722.01 TCGA.F1.6874.01 TCGA.CG.5730.01 TCGA.CG.5726.01 TCGA.IP.7968.01
#> "0313" "0312" "032" "0331" "022" "0331"
#> TCGA.BR.8363.01 TCGA.BR.7901.01 TCGA.D7.6822.01 TCGA.BR.6710.01 TCGA.CG.5720.01 TCGA.D7.8570.01
#> "0231" "0121" "0341" "01132" "022" "0211"
#> TCGA.B7.A5TI.01 TCGA.D7.6815.01 TCGA.BR.8284.01 TCGA.BR.8295.01 TCGA.BR.7197.01 TCGA.B7.A5TJ.01
#> "013" "0122" "0231" "0121" "0122" "022"
#> TCGA.D7.A6EY.01 TCGA.BR.8366.01 TCGA.IN.A7NR.01 TCGA.BR.6706.01 TCGA.IN.7808.01 TCGA.BR.6564.01
#> "0313" "0211" "01114" "0312" "03112" "01111"
#> TCGA.KB.A93H.01 TCGA.KB.A93J.01 TCGA.CD.5798.01 TCGA.CD.8530.01 TCGA.BR.6802.01 TCGA.CG.5719.01
#> "0332" "0122" "01134" "013" "03112" "0114"
#> TCGA.VQ.A8E3.01 TCGA.CD.5801.01 TCGA.FP.A9TM.01 TCGA.BR.7958.01 TCGA.FP.7998.01 TCGA.IN.A6RS.01
#> "022" "0211" "032" "0211" "0312" "032"
#> TCGA.BR.6709.01 TCGA.FP.7916.01 TCGA.R5.A7ZR.01 TCGA.B7.5816.01 TCGA.CG.5721.01 TCGA.SW.A7EA.01
#> "01112" "0211" "0122" "0314" "03111" "022"
#> TCGA.RD.A8NB.01 TCGA.BR.6801.01 TCGA.IN.AB1X.01 TCGA.D7.5579.01 TCGA.CG.5728.01 TCGA.R5.A7ZI.01
#> "0313" "013" "0314" "013" "0313" "013"
#> TCGA.IN.A7NU.01 TCGA.CG.5732.01 TCGA.ZQ.A9CR.01 TCGA.D7.5578.01 TCGA.BR.6803.01 TCGA.BR.8368.01
#> "032" "013" "013" "032" "01111" "022"
#> TCGA.SW.A7EB.01 TCGA.BR.8081.01 TCGA.VQ.A8P5.01 TCGA.CD.8535.01 TCGA.CG.5724.01 TCGA.D7.8574.01
#> "01132" "0231" "032" "022" "0341" "01131"
#> TCGA.HJ.7597.01 TCGA.HF.A5NB.01 TCGA.VQ.A8PB.01 TCGA.R5.A7ZE.01 TCGA.CD.5803.01 TCGA.CG.5725.01
#> "0114" "022" "0341" "0122" "01112" "0121"
#> TCGA.D7.6820.01 TCGA.CD.5802.01 TCGA.R5.A7ZF.01 TCGA.D7.A6F0.01 TCGA.CG.5727.01 TCGA.VQ.A8PC.01
#> "01231" "013" "013" "0121" "032" "03111"
#> TCGA.CD.A486.01 TCGA.RD.A8N2.01 TCGA.IN.A6RI.01 TCGA.HU.8243.01 TCGA.CD.A48C.01 TCGA.RD.A8N5.01
#> "0121" "01113" "0121" "0342" "022" "01131"
#> TCGA.RD.A8N1.01 TCGA.HU.A4GF.01 TCGA.BR.8362.01 TCGA.BR.8285.01 TCGA.CD.8532.01 TCGA.VQ.A8E2.01
#> "013" "0122" "032" "0211" "01121" "013"
#> TCGA.BR.8373.01 TCGA.BR.8361.01 TCGA.BR.8058.01 TCGA.IN.8462.01 TCGA.HU.A4G9.01 TCGA.CD.8524.01
#> "0122" "022" "0114" "0341" "022" "032"
#> TCGA.D7.A748.01 TCGA.CD.8527.01 TCGA.VQ.A8DV.01 TCGA.CD.8528.01 TCGA.BR.A453.01 TCGA.RD.A8N6.01
#> "01115" "013" "01233" "022" "03111" "013"
#> TCGA.HU.8245.01 TCGA.ZA.A8F6.01 TCGA.BR.8367.01 TCGA.BR.8380.01 TCGA.FP.A4BE.01 TCGA.HU.8238.01
#> "01231" "013" "032" "03112" "0233" "0341"
#> TCGA.BR.8078.01 TCGA.HU.8249.01 TCGA.RD.A8N0.01 TCGA.BR.8365.01 TCGA.FP.8211.01 TCGA.RD.A8N4.01
#> "0231" "0331" "01112" "01111" "01122" "01113"
#> TCGA.VQ.A8DU.01 TCGA.VQ.A8DL.01 TCGA.VQ.A8DZ.01 TCGA.D7.8572.01 TCGA.RD.A7BW.01 TCGA.R5.A804.01
#> "01233" "013" "01231" "013" "01116" "0314"
#> TCGA.BR.A4CS.01 TCGA.CD.8531.01 TCGA.CD.A487.01 TCGA.BR.8371.01 TCGA.BR.8059.01 TCGA.D7.A6ET.01
#> "032" "0212" "013" "01131" "013" "0312"
#> TCGA.FP.8099.01 TCGA.D7.8579.01 TCGA.BR.8297.01 TCGA.D7.8576.01 TCGA.VQ.A8DT.01 TCGA.FP.A8CX.01
#> "0333" "0313" "032" "0114" "022" "013"
#> TCGA.HU.A4GH.01 TCGA.CD.8526.01 TCGA.HU.A4G6.01 TCGA.D7.8578.01 TCGA.HU.A4G3.01 TCGA.D7.A74A.01
#> "0121" "013" "0211" "013" "022" "022"
#> TCGA.RD.A7C1.01 TCGA.F1.A448.01 TCGA.D7.8575.01 TCGA.BR.8372.01 TCGA.VQ.A8P3.01 TCGA.RD.A8MW.01
#> "032" "03112" "0341" "022" "0341" "013"
#> TCGA.BR.8286.01 TCGA.BR.8369.01 TCGA.BR.8364.01 TCGA.HU.8244.01 TCGA.KB.A6F7.01 TCGA.FP.A4BF.01
#> "0341" "032" "01111" "022" "0121" "032"
#> TCGA.R5.A805.01 TCGA.IN.A6RL.01 TCGA.IN.A6RR.01 TCGA.BR.A4CR.01 TCGA.CD.A489.01 TCGA.HU.A4GY.01
#> "032" "0342" "022" "013" "01121" "0114"
#> TCGA.BR.8289.01 TCGA.FP.8209.01 TCGA.BR.8296.01 TCGA.CD.A48A.01 TCGA.BR.8060.01 TCGA.BR.8077.01
#> "0342" "01131" "0314" "0331" "0121" "0122"
#> TCGA.CD.8534.01 TCGA.BR.7959.01 TCGA.VQ.A8P2.01 TCGA.EQ.8122.01 TCGA.D7.8573.01 TCGA.BR.A44T.01
#> "032" "032" "022" "0122" "0212" "01112"
#> TCGA.RD.A8MV.01 TCGA.CD.8536.01 TCGA.BR.8360.01 TCGA.BR.8291.01 TCGA.FP.8210.01 TCGA.RD.A7BS.01
#> "03111" "032" "0232" "013" "01131" "01134"
#> TCGA.BR.A44U.01 TCGA.CD.8529.01
#> "0341" "013"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 2448))
#> TCGA.VQ.A94P.01 TCGA.D7.6521.01 TCGA.VQ.A8PE.01 TCGA.D7.6519.01 TCGA.BR.6452.01 TCGA.BR.8485.01
#> "01133" "01121" "0123" "013" "0231" "0123"
#> TCGA.VQ.A8PO.01 TCGA.VQ.AA69.01 TCGA.BR.8683.01 TCGA.BR.8486.01 TCGA.D7.6522.01 TCGA.CG.5716.01
#> "022" "0212" "032" "0123" "01131" "0314"
#> TCGA.BR.8589.01 TCGA.BR.8382.01 TCGA.VQ.AA68.01 TCGA.VQ.A8PJ.01 TCGA.VQ.A8PH.01 TCGA.HU.8604.01
#> "0211" "0231" "0341" "0122" "0123" "0231"
#> TCGA.BR.8676.01 TCGA.CG.4441.01 TCGA.D7.6520.01 TCGA.VQ.AA64.01 TCGA.D7.6527.01 TCGA.VQ.A8PM.01
#> "0212" "0342" "0121" "01122" "0123" "013"
#> TCGA.VQ.A923.01 TCGA.BR.8384.01 TCGA.BR.6453.01 TCGA.VQ.A928.01 TCGA.VQ.A8E0.01 TCGA.BR.8679.01
#> "0212" "03111" "03112" "01122" "01122" "022"
#> TCGA.VQ.A91S.01 TCGA.BR.8678.01 TCGA.D7.6528.01 TCGA.VQ.A8E7.01 TCGA.BR.8680.01 TCGA.BR.8483.01
#> "032" "0122" "0332" "0341" "0341" "0331"
#> TCGA.BR.6566.01 TCGA.VQ.A91X.01 TCGA.VQ.A91Q.01 TCGA.VQ.A92D.01 TCGA.VQ.A91Z.01 TCGA.BR.6455.01
#> "032" "0332" "01122" "022" "0122" "0212"
#> TCGA.BR.8591.01 TCGA.HU.8608.01 TCGA.VQ.A94U.01 TCGA.VQ.A94T.01 TCGA.VQ.A91A.01 TCGA.VQ.A91D.01
#> "0233" "0211" "0333" "01123" "032" "0233"
#> TCGA.D7.6518.01 TCGA.BR.8484.01 TCGA.VQ.A91N.01 TCGA.VQ.A91E.01 TCGA.VQ.A8PY.01 TCGA.HU.8602.01
#> "03111" "013" "0122" "032" "032" "0231"
#> TCGA.BR.8381.01 TCGA.BR.6452.11 TCGA.IN.8663.01 TCGA.VQ.A8PS.01 TCGA.VQ.A91W.01 TCGA.BR.6454.01
#> "0211" "0314" "022" "01122" "0212" "01121"
#> TCGA.BR.8682.01 TCGA.VQ.A91V.01 TCGA.VQ.A8PZ.01 TCGA.BR.8590.01 TCGA.F1.6177.01 TCGA.VQ.A8PQ.01
#> "032" "0333" "0314" "01133" "022" "01112"
#> TCGA.VQ.A91U.01 TCGA.VQ.AA6I.01 TCGA.CG.4437.01 TCGA.VQ.A8PP.01 TCGA.BR.6565.01 TCGA.VQ.A91Y.01
#> "0122" "022" "0232" "0232" "0121" "013"
#> TCGA.VQ.A8PF.01 TCGA.BR.6456.01 TCGA.BR.6458.01 TCGA.VQ.A925.01 TCGA.VQ.A927.01 TCGA.BR.8592.01
#> "0211" "013" "032" "013" "01132" "0313"
#> TCGA.BR.6566.11 TCGA.IN.AB1V.01 TCGA.VQ.AA6F.01 TCGA.VQ.AA6J.01 TCGA.BR.8487.01 TCGA.D7.6525.01
#> "01114" "013" "01121" "01121" "022" "032"
#> TCGA.VQ.A94O.01 TCGA.BR.8588.01 TCGA.HU.8610.01 TCGA.D7.6526.01 TCGA.VQ.A8PD.01 TCGA.D7.6524.01
#> "0121" "0313" "03111" "0123" "03112" "0314"
#> TCGA.3M.AB46.01 TCGA.3M.AB47.01 TCGA.BR.8677.01 TCGA.BR.6457.01 TCGA.BR.8687.01 TCGA.VQ.A91K.01
#> "0122" "03112" "0114" "03111" "013" "022"
#> TCGA.BR.8690.01 TCGA.BR.8686.01 TCGA.FP.8631.01 TCGA.VQ.A922.01 TCGA.BR.A452.01 TCGA.IN.A6RO.01
#> "013" "0211" "0121" "0121" "01121" "022"
#> TCGA.BR.A4QI.01 TCGA.D7.A6EV.01 TCGA.HU.A4G2.01 TCGA.BR.A4IY.01 TCGA.VQ.A8PU.01 TCGA.BR.A4J4.01
#> "0231" "0341" "0211" "0211" "01123" "0211"
#> TCGA.VQ.A94R.01 TCGA.HU.A4H4.01 TCGA.BR.7707.01 TCGA.FP.7829.01 TCGA.BR.A4J5.01 TCGA.HU.A4H0.01
#> "022" "032" "022" "022" "03113" "0211"
#> TCGA.HU.A4HD.01 TCGA.KB.A6F5.01 TCGA.VQ.AA6K.01 TCGA.HF.7133.01 TCGA.F1.6875.01 TCGA.MX.A666.01
#> "0121" "013" "01121" "013" "0122" "0121"
#> TCGA.BR.7717.01 TCGA.BR.A4PF.01 TCGA.BR.A4IU.01 TCGA.VQ.A8PX.01 TCGA.BR.A4IV.01 TCGA.D7.A6EX.01
#> "0341" "0232" "0313" "01121" "01133" "013"
#> TCGA.BR.A4IZ.01 TCGA.BR.A4J9.01 TCGA.CD.A4MJ.01 TCGA.B7.A5TN.01 TCGA.BR.7715.01 TCGA.BR.7704.01
#> "01115" "01133" "0233" "0122" "0332" "0123"
#> TCGA.BR.A4J1.01 TCGA.HU.A4GP.01 TCGA.D7.A4YY.01 TCGA.VQ.AA6G.01 TCGA.HU.A4GJ.01 TCGA.CD.A4MI.01
#> "0121" "022" "022" "022" "0314" "0232"
#> TCGA.BR.7196.01 TCGA.BR.6563.01 TCGA.VQ.A924.01 TCGA.BR.7716.01 TCGA.FP.7735.01 TCGA.BR.7723.01
#> "0312" "03111" "0233" "013" "013" "013"
#> TCGA.HU.A4H8.01 TCGA.IN.A6RJ.01 TCGA.HU.A4H3.01 TCGA.EQ.A4SO.01 TCGA.CD.A4MH.01 TCGA.BR.A4J7.01
#> "022" "03113" "022" "01122" "0123" "01121"
#> TCGA.HF.7131.01 TCGA.D7.A74B.01 TCGA.BR.A4PE.01 TCGA.BR.A4J8.01 TCGA.HU.A4GX.01 TCGA.HU.A4G8.01
#> "0123" "01116" "022" "0231" "032" "0341"
#> TCGA.HU.A4GT.01 TCGA.HU.A4GC.01 TCGA.BR.A4CQ.01 TCGA.D7.A6F2.01 TCGA.RD.A7BT.01 TCGA.BR.A4J6.01
#> "022" "0341" "022" "0122" "0122" "0114"
#> TCGA.HU.A4GQ.01 TCGA.HF.7136.01 TCGA.BR.A4QM.01 TCGA.BR.A4PD.01 TCGA.VQ.A8PK.01 TCGA.B7.A5TK.01
#> "0232" "013" "0232" "0122" "0121" "0312"
#> TCGA.D7.A4YX.01 TCGA.D7.A4Z0.01 TCGA.VQ.A8PT.01 TCGA.IN.A6RN.01 TCGA.CD.A4MG.01 TCGA.D7.A747.01
#> "0211" "0313" "022" "0121" "022" "01133"
#> TCGA.R5.A7O7.01 TCGA.F1.A72C.01 TCGA.BR.A4J2.01 TCGA.MX.A663.01 TCGA.D7.A4YV.01 TCGA.HU.A4GD.01
#> "03113" "01121" "03113" "013" "0231" "0331"
#> TCGA.BR.A4QL.01 TCGA.BR.7703.01 TCGA.VQ.AA6B.01 TCGA.VQ.AA6D.01 TCGA.D7.A6EZ.01 TCGA.D7.A4YU.01
#> "022" "022" "0332" "0123" "0211" "0232"
#> TCGA.VQ.AA6A.01 TCGA.IN.7806.01 TCGA.HU.A4HB.01 TCGA.HU.A4H2.01 TCGA.IN.A6RP.01 TCGA.HU.A4H5.01
#> "0123" "0122" "03113" "0342" "022" "0123"
#> TCGA.HU.A4GU.01 TCGA.MX.A5UJ.01 TCGA.HU.A4GN.01 TCGA.CD.5804.01 TCGA.HU.A4H6.01 TCGA.HF.7132.01
#> "022" "022" "0232" "013" "0231" "0232"
#> TCGA.D7.A4YT.01 TCGA.HF.7134.01 TCGA.BR.6852.01 TCGA.BR.8370.01 TCGA.EQ.5647.01 TCGA.IN.A7NT.01
#> "013" "022" "0314" "0233" "013" "032"
#> TCGA.RD.A8N9.01 TCGA.D7.5577.01 TCGA.CG.5717.01 TCGA.D7.6818.01 TCGA.CG.5734.01 TCGA.VQ.A8P8.01
#> "0114" "0211" "01134" "013" "03111" "0314"
#> TCGA.BR.6707.01 TCGA.B7.5818.01 TCGA.CD.8525.01 TCGA.BR.6705.01 TCGA.BR.4288.01 TCGA.CD.5813.01
#> "0211" "0211" "013" "0313" "013" "01121"
#> TCGA.CG.5723.01 TCGA.CD.5800.01 TCGA.CG.5718.01 TCGA.BR.8080.01 TCGA.CG.5733.01 TCGA.D7.6817.01
#> "01121" "013" "0123" "0114" "022" "0123"
#> TCGA.KB.A93G.01 TCGA.CD.5799.01 TCGA.BR.7851.01 TCGA.BR.7722.01 TCGA.MX.A5UG.01 TCGA.CD.8533.01
#> "01133" "013" "0232" "01121" "03111" "0331"
#> TCGA.BR.7957.01 TCGA.CG.5722.01 TCGA.F1.6874.01 TCGA.CG.5730.01 TCGA.CG.5726.01 TCGA.IP.7968.01
#> "0313" "0312" "032" "0331" "022" "0331"
#> TCGA.BR.8363.01 TCGA.BR.7901.01 TCGA.D7.6822.01 TCGA.BR.6710.01 TCGA.CG.5720.01 TCGA.D7.8570.01
#> "0231" "0121" "0341" "01132" "022" "0211"
#> TCGA.B7.A5TI.01 TCGA.D7.6815.01 TCGA.BR.8284.01 TCGA.BR.8295.01 TCGA.BR.7197.01 TCGA.B7.A5TJ.01
#> "013" "0122" "0231" "0121" "0122" "022"
#> TCGA.D7.A6EY.01 TCGA.BR.8366.01 TCGA.IN.A7NR.01 TCGA.BR.6706.01 TCGA.IN.7808.01 TCGA.BR.6564.01
#> "0313" "0211" "01114" "0312" "03112" "01111"
#> TCGA.KB.A93H.01 TCGA.KB.A93J.01 TCGA.CD.5798.01 TCGA.CD.8530.01 TCGA.BR.6802.01 TCGA.CG.5719.01
#> "0332" "0122" "01134" "013" "03112" "0114"
#> TCGA.VQ.A8E3.01 TCGA.CD.5801.01 TCGA.FP.A9TM.01 TCGA.BR.7958.01 TCGA.FP.7998.01 TCGA.IN.A6RS.01
#> "022" "0211" "032" "0211" "0312" "032"
#> TCGA.BR.6709.01 TCGA.FP.7916.01 TCGA.R5.A7ZR.01 TCGA.B7.5816.01 TCGA.CG.5721.01 TCGA.SW.A7EA.01
#> "01112" "0211" "0122" "0314" "03111" "022"
#> TCGA.RD.A8NB.01 TCGA.BR.6801.01 TCGA.IN.AB1X.01 TCGA.D7.5579.01 TCGA.CG.5728.01 TCGA.R5.A7ZI.01
#> "0313" "013" "0314" "013" "0313" "013"
#> TCGA.IN.A7NU.01 TCGA.CG.5732.01 TCGA.ZQ.A9CR.01 TCGA.D7.5578.01 TCGA.BR.6803.01 TCGA.BR.8368.01
#> "032" "013" "013" "032" "01111" "022"
#> TCGA.SW.A7EB.01 TCGA.BR.8081.01 TCGA.VQ.A8P5.01 TCGA.CD.8535.01 TCGA.CG.5724.01 TCGA.D7.8574.01
#> "01132" "0231" "032" "022" "0341" "01131"
#> TCGA.HJ.7597.01 TCGA.HF.A5NB.01 TCGA.VQ.A8PB.01 TCGA.R5.A7ZE.01 TCGA.CD.5803.01 TCGA.CG.5725.01
#> "0114" "022" "0341" "0122" "01112" "0121"
#> TCGA.D7.6820.01 TCGA.CD.5802.01 TCGA.R5.A7ZF.01 TCGA.D7.A6F0.01 TCGA.CG.5727.01 TCGA.VQ.A8PC.01
#> "0123" "013" "013" "0121" "032" "03111"
#> TCGA.CD.A486.01 TCGA.RD.A8N2.01 TCGA.IN.A6RI.01 TCGA.HU.8243.01 TCGA.CD.A48C.01 TCGA.RD.A8N5.01
#> "0121" "01113" "0121" "0342" "022" "01131"
#> TCGA.RD.A8N1.01 TCGA.HU.A4GF.01 TCGA.BR.8362.01 TCGA.BR.8285.01 TCGA.CD.8532.01 TCGA.VQ.A8E2.01
#> "013" "0122" "032" "0211" "01121" "013"
#> TCGA.BR.8373.01 TCGA.BR.8361.01 TCGA.BR.8058.01 TCGA.IN.8462.01 TCGA.HU.A4G9.01 TCGA.CD.8524.01
#> "0122" "022" "0114" "0341" "022" "032"
#> TCGA.D7.A748.01 TCGA.CD.8527.01 TCGA.VQ.A8DV.01 TCGA.CD.8528.01 TCGA.BR.A453.01 TCGA.RD.A8N6.01
#> "01115" "013" "0123" "022" "03111" "013"
#> TCGA.HU.8245.01 TCGA.ZA.A8F6.01 TCGA.BR.8367.01 TCGA.BR.8380.01 TCGA.FP.A4BE.01 TCGA.HU.8238.01
#> "0123" "013" "032" "03112" "0233" "0341"
#> TCGA.BR.8078.01 TCGA.HU.8249.01 TCGA.RD.A8N0.01 TCGA.BR.8365.01 TCGA.FP.8211.01 TCGA.RD.A8N4.01
#> "0231" "0331" "01112" "01111" "01122" "01113"
#> TCGA.VQ.A8DU.01 TCGA.VQ.A8DL.01 TCGA.VQ.A8DZ.01 TCGA.D7.8572.01 TCGA.RD.A7BW.01 TCGA.R5.A804.01
#> "0123" "013" "0123" "013" "01116" "0314"
#> TCGA.BR.A4CS.01 TCGA.CD.8531.01 TCGA.CD.A487.01 TCGA.BR.8371.01 TCGA.BR.8059.01 TCGA.D7.A6ET.01
#> "032" "0212" "013" "01131" "013" "0312"
#> TCGA.FP.8099.01 TCGA.D7.8579.01 TCGA.BR.8297.01 TCGA.D7.8576.01 TCGA.VQ.A8DT.01 TCGA.FP.A8CX.01
#> "0333" "0313" "032" "0114" "022" "013"
#> TCGA.HU.A4GH.01 TCGA.CD.8526.01 TCGA.HU.A4G6.01 TCGA.D7.8578.01 TCGA.HU.A4G3.01 TCGA.D7.A74A.01
#> "0121" "013" "0211" "013" "022" "022"
#> TCGA.RD.A7C1.01 TCGA.F1.A448.01 TCGA.D7.8575.01 TCGA.BR.8372.01 TCGA.VQ.A8P3.01 TCGA.RD.A8MW.01
#> "032" "03112" "0341" "022" "0341" "013"
#> TCGA.BR.8286.01 TCGA.BR.8369.01 TCGA.BR.8364.01 TCGA.HU.8244.01 TCGA.KB.A6F7.01 TCGA.FP.A4BF.01
#> "0341" "032" "01111" "022" "0121" "032"
#> TCGA.R5.A805.01 TCGA.IN.A6RL.01 TCGA.IN.A6RR.01 TCGA.BR.A4CR.01 TCGA.CD.A489.01 TCGA.HU.A4GY.01
#> "032" "0342" "022" "013" "01121" "0114"
#> TCGA.BR.8289.01 TCGA.FP.8209.01 TCGA.BR.8296.01 TCGA.CD.A48A.01 TCGA.BR.8060.01 TCGA.BR.8077.01
#> "0342" "01131" "0314" "0331" "0121" "0122"
#> TCGA.CD.8534.01 TCGA.BR.7959.01 TCGA.VQ.A8P2.01 TCGA.EQ.8122.01 TCGA.D7.8573.01 TCGA.BR.A44T.01
#> "032" "032" "022" "0122" "0212" "01112"
#> TCGA.RD.A8MV.01 TCGA.CD.8536.01 TCGA.BR.8360.01 TCGA.BR.8291.01 TCGA.FP.8210.01 TCGA.RD.A7BS.01
#> "03111" "032" "0232" "013" "01131" "01134"
#> TCGA.BR.A44U.01 TCGA.CD.8529.01
#> "0341" "013"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 2546))
#> TCGA.VQ.A94P.01 TCGA.D7.6521.01 TCGA.VQ.A8PE.01 TCGA.D7.6519.01 TCGA.BR.6452.01 TCGA.BR.8485.01
#> "01133" "01121" "0123" "013" "0231" "0123"
#> TCGA.VQ.A8PO.01 TCGA.VQ.AA69.01 TCGA.BR.8683.01 TCGA.BR.8486.01 TCGA.D7.6522.01 TCGA.CG.5716.01
#> "022" "0212" "032" "0123" "01131" "0314"
#> TCGA.BR.8589.01 TCGA.BR.8382.01 TCGA.VQ.AA68.01 TCGA.VQ.A8PJ.01 TCGA.VQ.A8PH.01 TCGA.HU.8604.01
#> "0211" "0231" "0341" "0122" "0123" "0231"
#> TCGA.BR.8676.01 TCGA.CG.4441.01 TCGA.D7.6520.01 TCGA.VQ.AA64.01 TCGA.D7.6527.01 TCGA.VQ.A8PM.01
#> "0212" "0342" "0121" "01122" "0123" "013"
#> TCGA.VQ.A923.01 TCGA.BR.8384.01 TCGA.BR.6453.01 TCGA.VQ.A928.01 TCGA.VQ.A8E0.01 TCGA.BR.8679.01
#> "0212" "03111" "03112" "01122" "01122" "022"
#> TCGA.VQ.A91S.01 TCGA.BR.8678.01 TCGA.D7.6528.01 TCGA.VQ.A8E7.01 TCGA.BR.8680.01 TCGA.BR.8483.01
#> "032" "0122" "0332" "0341" "0341" "0331"
#> TCGA.BR.6566.01 TCGA.VQ.A91X.01 TCGA.VQ.A91Q.01 TCGA.VQ.A92D.01 TCGA.VQ.A91Z.01 TCGA.BR.6455.01
#> "032" "0332" "01122" "022" "0122" "0212"
#> TCGA.BR.8591.01 TCGA.HU.8608.01 TCGA.VQ.A94U.01 TCGA.VQ.A94T.01 TCGA.VQ.A91A.01 TCGA.VQ.A91D.01
#> "0233" "0211" "0333" "01123" "032" "0233"
#> TCGA.D7.6518.01 TCGA.BR.8484.01 TCGA.VQ.A91N.01 TCGA.VQ.A91E.01 TCGA.VQ.A8PY.01 TCGA.HU.8602.01
#> "03111" "013" "0122" "032" "032" "0231"
#> TCGA.BR.8381.01 TCGA.BR.6452.11 TCGA.IN.8663.01 TCGA.VQ.A8PS.01 TCGA.VQ.A91W.01 TCGA.BR.6454.01
#> "0211" "0314" "022" "01122" "0212" "01121"
#> TCGA.BR.8682.01 TCGA.VQ.A91V.01 TCGA.VQ.A8PZ.01 TCGA.BR.8590.01 TCGA.F1.6177.01 TCGA.VQ.A8PQ.01
#> "032" "0333" "0314" "01133" "022" "01112"
#> TCGA.VQ.A91U.01 TCGA.VQ.AA6I.01 TCGA.CG.4437.01 TCGA.VQ.A8PP.01 TCGA.BR.6565.01 TCGA.VQ.A91Y.01
#> "0122" "022" "0232" "0232" "0121" "013"
#> TCGA.VQ.A8PF.01 TCGA.BR.6456.01 TCGA.BR.6458.01 TCGA.VQ.A925.01 TCGA.VQ.A927.01 TCGA.BR.8592.01
#> "0211" "013" "032" "013" "01132" "0313"
#> TCGA.BR.6566.11 TCGA.IN.AB1V.01 TCGA.VQ.AA6F.01 TCGA.VQ.AA6J.01 TCGA.BR.8487.01 TCGA.D7.6525.01
#> "01114" "013" "01121" "01121" "022" "032"
#> TCGA.VQ.A94O.01 TCGA.BR.8588.01 TCGA.HU.8610.01 TCGA.D7.6526.01 TCGA.VQ.A8PD.01 TCGA.D7.6524.01
#> "0121" "0313" "03111" "0123" "03112" "0314"
#> TCGA.3M.AB46.01 TCGA.3M.AB47.01 TCGA.BR.8677.01 TCGA.BR.6457.01 TCGA.BR.8687.01 TCGA.VQ.A91K.01
#> "0122" "03112" "0114" "03111" "013" "022"
#> TCGA.BR.8690.01 TCGA.BR.8686.01 TCGA.FP.8631.01 TCGA.VQ.A922.01 TCGA.BR.A452.01 TCGA.IN.A6RO.01
#> "013" "0211" "0121" "0121" "01121" "022"
#> TCGA.BR.A4QI.01 TCGA.D7.A6EV.01 TCGA.HU.A4G2.01 TCGA.BR.A4IY.01 TCGA.VQ.A8PU.01 TCGA.BR.A4J4.01
#> "0231" "0341" "0211" "0211" "01123" "0211"
#> TCGA.VQ.A94R.01 TCGA.HU.A4H4.01 TCGA.BR.7707.01 TCGA.FP.7829.01 TCGA.BR.A4J5.01 TCGA.HU.A4H0.01
#> "022" "032" "022" "022" "03113" "0211"
#> TCGA.HU.A4HD.01 TCGA.KB.A6F5.01 TCGA.VQ.AA6K.01 TCGA.HF.7133.01 TCGA.F1.6875.01 TCGA.MX.A666.01
#> "0121" "013" "01121" "013" "0122" "0121"
#> TCGA.BR.7717.01 TCGA.BR.A4PF.01 TCGA.BR.A4IU.01 TCGA.VQ.A8PX.01 TCGA.BR.A4IV.01 TCGA.D7.A6EX.01
#> "0341" "0232" "0313" "01121" "01133" "013"
#> TCGA.BR.A4IZ.01 TCGA.BR.A4J9.01 TCGA.CD.A4MJ.01 TCGA.B7.A5TN.01 TCGA.BR.7715.01 TCGA.BR.7704.01
#> "01115" "01133" "0233" "0122" "0332" "0123"
#> TCGA.BR.A4J1.01 TCGA.HU.A4GP.01 TCGA.D7.A4YY.01 TCGA.VQ.AA6G.01 TCGA.HU.A4GJ.01 TCGA.CD.A4MI.01
#> "0121" "022" "022" "022" "0314" "0232"
#> TCGA.BR.7196.01 TCGA.BR.6563.01 TCGA.VQ.A924.01 TCGA.BR.7716.01 TCGA.FP.7735.01 TCGA.BR.7723.01
#> "0312" "03111" "0233" "013" "013" "013"
#> TCGA.HU.A4H8.01 TCGA.IN.A6RJ.01 TCGA.HU.A4H3.01 TCGA.EQ.A4SO.01 TCGA.CD.A4MH.01 TCGA.BR.A4J7.01
#> "022" "03113" "022" "01122" "0123" "01121"
#> TCGA.HF.7131.01 TCGA.D7.A74B.01 TCGA.BR.A4PE.01 TCGA.BR.A4J8.01 TCGA.HU.A4GX.01 TCGA.HU.A4G8.01
#> "0123" "01116" "022" "0231" "032" "0341"
#> TCGA.HU.A4GT.01 TCGA.HU.A4GC.01 TCGA.BR.A4CQ.01 TCGA.D7.A6F2.01 TCGA.RD.A7BT.01 TCGA.BR.A4J6.01
#> "022" "0341" "022" "0122" "0122" "0114"
#> TCGA.HU.A4GQ.01 TCGA.HF.7136.01 TCGA.BR.A4QM.01 TCGA.BR.A4PD.01 TCGA.VQ.A8PK.01 TCGA.B7.A5TK.01
#> "0232" "013" "0232" "0122" "0121" "0312"
#> TCGA.D7.A4YX.01 TCGA.D7.A4Z0.01 TCGA.VQ.A8PT.01 TCGA.IN.A6RN.01 TCGA.CD.A4MG.01 TCGA.D7.A747.01
#> "0211" "0313" "022" "0121" "022" "01133"
#> TCGA.R5.A7O7.01 TCGA.F1.A72C.01 TCGA.BR.A4J2.01 TCGA.MX.A663.01 TCGA.D7.A4YV.01 TCGA.HU.A4GD.01
#> "03113" "01121" "03113" "013" "0231" "0331"
#> TCGA.BR.A4QL.01 TCGA.BR.7703.01 TCGA.VQ.AA6B.01 TCGA.VQ.AA6D.01 TCGA.D7.A6EZ.01 TCGA.D7.A4YU.01
#> "022" "022" "0332" "0123" "0211" "0232"
#> TCGA.VQ.AA6A.01 TCGA.IN.7806.01 TCGA.HU.A4HB.01 TCGA.HU.A4H2.01 TCGA.IN.A6RP.01 TCGA.HU.A4H5.01
#> "0123" "0122" "03113" "0342" "022" "0123"
#> TCGA.HU.A4GU.01 TCGA.MX.A5UJ.01 TCGA.HU.A4GN.01 TCGA.CD.5804.01 TCGA.HU.A4H6.01 TCGA.HF.7132.01
#> "022" "022" "0232" "013" "0231" "0232"
#> TCGA.D7.A4YT.01 TCGA.HF.7134.01 TCGA.BR.6852.01 TCGA.BR.8370.01 TCGA.EQ.5647.01 TCGA.IN.A7NT.01
#> "013" "022" "0314" "0233" "013" "032"
#> TCGA.RD.A8N9.01 TCGA.D7.5577.01 TCGA.CG.5717.01 TCGA.D7.6818.01 TCGA.CG.5734.01 TCGA.VQ.A8P8.01
#> "0114" "0211" "01134" "013" "03111" "0314"
#> TCGA.BR.6707.01 TCGA.B7.5818.01 TCGA.CD.8525.01 TCGA.BR.6705.01 TCGA.BR.4288.01 TCGA.CD.5813.01
#> "0211" "0211" "013" "0313" "013" "01121"
#> TCGA.CG.5723.01 TCGA.CD.5800.01 TCGA.CG.5718.01 TCGA.BR.8080.01 TCGA.CG.5733.01 TCGA.D7.6817.01
#> "01121" "013" "0123" "0114" "022" "0123"
#> TCGA.KB.A93G.01 TCGA.CD.5799.01 TCGA.BR.7851.01 TCGA.BR.7722.01 TCGA.MX.A5UG.01 TCGA.CD.8533.01
#> "01133" "013" "0232" "01121" "03111" "0331"
#> TCGA.BR.7957.01 TCGA.CG.5722.01 TCGA.F1.6874.01 TCGA.CG.5730.01 TCGA.CG.5726.01 TCGA.IP.7968.01
#> "0313" "0312" "032" "0331" "022" "0331"
#> TCGA.BR.8363.01 TCGA.BR.7901.01 TCGA.D7.6822.01 TCGA.BR.6710.01 TCGA.CG.5720.01 TCGA.D7.8570.01
#> "0231" "0121" "0341" "01132" "022" "0211"
#> TCGA.B7.A5TI.01 TCGA.D7.6815.01 TCGA.BR.8284.01 TCGA.BR.8295.01 TCGA.BR.7197.01 TCGA.B7.A5TJ.01
#> "013" "0122" "0231" "0121" "0122" "022"
#> TCGA.D7.A6EY.01 TCGA.BR.8366.01 TCGA.IN.A7NR.01 TCGA.BR.6706.01 TCGA.IN.7808.01 TCGA.BR.6564.01
#> "0313" "0211" "01114" "0312" "03112" "01111"
#> TCGA.KB.A93H.01 TCGA.KB.A93J.01 TCGA.CD.5798.01 TCGA.CD.8530.01 TCGA.BR.6802.01 TCGA.CG.5719.01
#> "0332" "0122" "01134" "013" "03112" "0114"
#> TCGA.VQ.A8E3.01 TCGA.CD.5801.01 TCGA.FP.A9TM.01 TCGA.BR.7958.01 TCGA.FP.7998.01 TCGA.IN.A6RS.01
#> "022" "0211" "032" "0211" "0312" "032"
#> TCGA.BR.6709.01 TCGA.FP.7916.01 TCGA.R5.A7ZR.01 TCGA.B7.5816.01 TCGA.CG.5721.01 TCGA.SW.A7EA.01
#> "01112" "0211" "0122" "0314" "03111" "022"
#> TCGA.RD.A8NB.01 TCGA.BR.6801.01 TCGA.IN.AB1X.01 TCGA.D7.5579.01 TCGA.CG.5728.01 TCGA.R5.A7ZI.01
#> "0313" "013" "0314" "013" "0313" "013"
#> TCGA.IN.A7NU.01 TCGA.CG.5732.01 TCGA.ZQ.A9CR.01 TCGA.D7.5578.01 TCGA.BR.6803.01 TCGA.BR.8368.01
#> "032" "013" "013" "032" "01111" "022"
#> TCGA.SW.A7EB.01 TCGA.BR.8081.01 TCGA.VQ.A8P5.01 TCGA.CD.8535.01 TCGA.CG.5724.01 TCGA.D7.8574.01
#> "01132" "0231" "032" "022" "0341" "01131"
#> TCGA.HJ.7597.01 TCGA.HF.A5NB.01 TCGA.VQ.A8PB.01 TCGA.R5.A7ZE.01 TCGA.CD.5803.01 TCGA.CG.5725.01
#> "0114" "022" "0341" "0122" "01112" "0121"
#> TCGA.D7.6820.01 TCGA.CD.5802.01 TCGA.R5.A7ZF.01 TCGA.D7.A6F0.01 TCGA.CG.5727.01 TCGA.VQ.A8PC.01
#> "0123" "013" "013" "0121" "032" "03111"
#> TCGA.CD.A486.01 TCGA.RD.A8N2.01 TCGA.IN.A6RI.01 TCGA.HU.8243.01 TCGA.CD.A48C.01 TCGA.RD.A8N5.01
#> "0121" "01113" "0121" "0342" "022" "01131"
#> TCGA.RD.A8N1.01 TCGA.HU.A4GF.01 TCGA.BR.8362.01 TCGA.BR.8285.01 TCGA.CD.8532.01 TCGA.VQ.A8E2.01
#> "013" "0122" "032" "0211" "01121" "013"
#> TCGA.BR.8373.01 TCGA.BR.8361.01 TCGA.BR.8058.01 TCGA.IN.8462.01 TCGA.HU.A4G9.01 TCGA.CD.8524.01
#> "0122" "022" "0114" "0341" "022" "032"
#> TCGA.D7.A748.01 TCGA.CD.8527.01 TCGA.VQ.A8DV.01 TCGA.CD.8528.01 TCGA.BR.A453.01 TCGA.RD.A8N6.01
#> "01115" "013" "0123" "022" "03111" "013"
#> TCGA.HU.8245.01 TCGA.ZA.A8F6.01 TCGA.BR.8367.01 TCGA.BR.8380.01 TCGA.FP.A4BE.01 TCGA.HU.8238.01
#> "0123" "013" "032" "03112" "0233" "0341"
#> TCGA.BR.8078.01 TCGA.HU.8249.01 TCGA.RD.A8N0.01 TCGA.BR.8365.01 TCGA.FP.8211.01 TCGA.RD.A8N4.01
#> "0231" "0331" "01112" "01111" "01122" "01113"
#> TCGA.VQ.A8DU.01 TCGA.VQ.A8DL.01 TCGA.VQ.A8DZ.01 TCGA.D7.8572.01 TCGA.RD.A7BW.01 TCGA.R5.A804.01
#> "0123" "013" "0123" "013" "01116" "0314"
#> TCGA.BR.A4CS.01 TCGA.CD.8531.01 TCGA.CD.A487.01 TCGA.BR.8371.01 TCGA.BR.8059.01 TCGA.D7.A6ET.01
#> "032" "0212" "013" "01131" "013" "0312"
#> TCGA.FP.8099.01 TCGA.D7.8579.01 TCGA.BR.8297.01 TCGA.D7.8576.01 TCGA.VQ.A8DT.01 TCGA.FP.A8CX.01
#> "0333" "0313" "032" "0114" "022" "013"
#> TCGA.HU.A4GH.01 TCGA.CD.8526.01 TCGA.HU.A4G6.01 TCGA.D7.8578.01 TCGA.HU.A4G3.01 TCGA.D7.A74A.01
#> "0121" "013" "0211" "013" "022" "022"
#> TCGA.RD.A7C1.01 TCGA.F1.A448.01 TCGA.D7.8575.01 TCGA.BR.8372.01 TCGA.VQ.A8P3.01 TCGA.RD.A8MW.01
#> "032" "03112" "0341" "022" "0341" "013"
#> TCGA.BR.8286.01 TCGA.BR.8369.01 TCGA.BR.8364.01 TCGA.HU.8244.01 TCGA.KB.A6F7.01 TCGA.FP.A4BF.01
#> "0341" "032" "01111" "022" "0121" "032"
#> TCGA.R5.A805.01 TCGA.IN.A6RL.01 TCGA.IN.A6RR.01 TCGA.BR.A4CR.01 TCGA.CD.A489.01 TCGA.HU.A4GY.01
#> "032" "0342" "022" "013" "01121" "0114"
#> TCGA.BR.8289.01 TCGA.FP.8209.01 TCGA.BR.8296.01 TCGA.CD.A48A.01 TCGA.BR.8060.01 TCGA.BR.8077.01
#> "0342" "01131" "0314" "0331" "0121" "0122"
#> TCGA.CD.8534.01 TCGA.BR.7959.01 TCGA.VQ.A8P2.01 TCGA.EQ.8122.01 TCGA.D7.8573.01 TCGA.BR.A44T.01
#> "032" "032" "022" "0122" "0212" "01112"
#> TCGA.RD.A8MV.01 TCGA.CD.8536.01 TCGA.BR.8360.01 TCGA.BR.8291.01 TCGA.FP.8210.01 TCGA.RD.A7BS.01
#> "03111" "032" "0232" "013" "01131" "01134"
#> TCGA.BR.A44U.01 TCGA.CD.8529.01
#> "0341" "013"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 2903))
#> TCGA.VQ.A94P.01 TCGA.D7.6521.01 TCGA.VQ.A8PE.01 TCGA.D7.6519.01 TCGA.BR.6452.01 TCGA.BR.8485.01
#> "01133" "01121" "0123" "013" "0231" "0123"
#> TCGA.VQ.A8PO.01 TCGA.VQ.AA69.01 TCGA.BR.8683.01 TCGA.BR.8486.01 TCGA.D7.6522.01 TCGA.CG.5716.01
#> "022" "0212" "032" "0123" "01131" "0314"
#> TCGA.BR.8589.01 TCGA.BR.8382.01 TCGA.VQ.AA68.01 TCGA.VQ.A8PJ.01 TCGA.VQ.A8PH.01 TCGA.HU.8604.01
#> "0211" "0231" "0341" "0122" "0123" "0231"
#> TCGA.BR.8676.01 TCGA.CG.4441.01 TCGA.D7.6520.01 TCGA.VQ.AA64.01 TCGA.D7.6527.01 TCGA.VQ.A8PM.01
#> "0212" "0342" "0121" "01122" "0123" "013"
#> TCGA.VQ.A923.01 TCGA.BR.8384.01 TCGA.BR.6453.01 TCGA.VQ.A928.01 TCGA.VQ.A8E0.01 TCGA.BR.8679.01
#> "0212" "0311" "0311" "01122" "01122" "022"
#> TCGA.VQ.A91S.01 TCGA.BR.8678.01 TCGA.D7.6528.01 TCGA.VQ.A8E7.01 TCGA.BR.8680.01 TCGA.BR.8483.01
#> "032" "0122" "0332" "0341" "0341" "0331"
#> TCGA.BR.6566.01 TCGA.VQ.A91X.01 TCGA.VQ.A91Q.01 TCGA.VQ.A92D.01 TCGA.VQ.A91Z.01 TCGA.BR.6455.01
#> "032" "0332" "01122" "022" "0122" "0212"
#> TCGA.BR.8591.01 TCGA.HU.8608.01 TCGA.VQ.A94U.01 TCGA.VQ.A94T.01 TCGA.VQ.A91A.01 TCGA.VQ.A91D.01
#> "0233" "0211" "0333" "01123" "032" "0233"
#> TCGA.D7.6518.01 TCGA.BR.8484.01 TCGA.VQ.A91N.01 TCGA.VQ.A91E.01 TCGA.VQ.A8PY.01 TCGA.HU.8602.01
#> "0311" "013" "0122" "032" "032" "0231"
#> TCGA.BR.8381.01 TCGA.BR.6452.11 TCGA.IN.8663.01 TCGA.VQ.A8PS.01 TCGA.VQ.A91W.01 TCGA.BR.6454.01
#> "0211" "0314" "022" "01122" "0212" "01121"
#> TCGA.BR.8682.01 TCGA.VQ.A91V.01 TCGA.VQ.A8PZ.01 TCGA.BR.8590.01 TCGA.F1.6177.01 TCGA.VQ.A8PQ.01
#> "032" "0333" "0314" "01133" "022" "01112"
#> TCGA.VQ.A91U.01 TCGA.VQ.AA6I.01 TCGA.CG.4437.01 TCGA.VQ.A8PP.01 TCGA.BR.6565.01 TCGA.VQ.A91Y.01
#> "0122" "022" "0232" "0232" "0121" "013"
#> TCGA.VQ.A8PF.01 TCGA.BR.6456.01 TCGA.BR.6458.01 TCGA.VQ.A925.01 TCGA.VQ.A927.01 TCGA.BR.8592.01
#> "0211" "013" "032" "013" "01132" "0313"
#> TCGA.BR.6566.11 TCGA.IN.AB1V.01 TCGA.VQ.AA6F.01 TCGA.VQ.AA6J.01 TCGA.BR.8487.01 TCGA.D7.6525.01
#> "01114" "013" "01121" "01121" "022" "032"
#> TCGA.VQ.A94O.01 TCGA.BR.8588.01 TCGA.HU.8610.01 TCGA.D7.6526.01 TCGA.VQ.A8PD.01 TCGA.D7.6524.01
#> "0121" "0313" "0311" "0123" "0311" "0314"
#> TCGA.3M.AB46.01 TCGA.3M.AB47.01 TCGA.BR.8677.01 TCGA.BR.6457.01 TCGA.BR.8687.01 TCGA.VQ.A91K.01
#> "0122" "0311" "0114" "0311" "013" "022"
#> TCGA.BR.8690.01 TCGA.BR.8686.01 TCGA.FP.8631.01 TCGA.VQ.A922.01 TCGA.BR.A452.01 TCGA.IN.A6RO.01
#> "013" "0211" "0121" "0121" "01121" "022"
#> TCGA.BR.A4QI.01 TCGA.D7.A6EV.01 TCGA.HU.A4G2.01 TCGA.BR.A4IY.01 TCGA.VQ.A8PU.01 TCGA.BR.A4J4.01
#> "0231" "0341" "0211" "0211" "01123" "0211"
#> TCGA.VQ.A94R.01 TCGA.HU.A4H4.01 TCGA.BR.7707.01 TCGA.FP.7829.01 TCGA.BR.A4J5.01 TCGA.HU.A4H0.01
#> "022" "032" "022" "022" "0311" "0211"
#> TCGA.HU.A4HD.01 TCGA.KB.A6F5.01 TCGA.VQ.AA6K.01 TCGA.HF.7133.01 TCGA.F1.6875.01 TCGA.MX.A666.01
#> "0121" "013" "01121" "013" "0122" "0121"
#> TCGA.BR.7717.01 TCGA.BR.A4PF.01 TCGA.BR.A4IU.01 TCGA.VQ.A8PX.01 TCGA.BR.A4IV.01 TCGA.D7.A6EX.01
#> "0341" "0232" "0313" "01121" "01133" "013"
#> TCGA.BR.A4IZ.01 TCGA.BR.A4J9.01 TCGA.CD.A4MJ.01 TCGA.B7.A5TN.01 TCGA.BR.7715.01 TCGA.BR.7704.01
#> "01115" "01133" "0233" "0122" "0332" "0123"
#> TCGA.BR.A4J1.01 TCGA.HU.A4GP.01 TCGA.D7.A4YY.01 TCGA.VQ.AA6G.01 TCGA.HU.A4GJ.01 TCGA.CD.A4MI.01
#> "0121" "022" "022" "022" "0314" "0232"
#> TCGA.BR.7196.01 TCGA.BR.6563.01 TCGA.VQ.A924.01 TCGA.BR.7716.01 TCGA.FP.7735.01 TCGA.BR.7723.01
#> "0312" "0311" "0233" "013" "013" "013"
#> TCGA.HU.A4H8.01 TCGA.IN.A6RJ.01 TCGA.HU.A4H3.01 TCGA.EQ.A4SO.01 TCGA.CD.A4MH.01 TCGA.BR.A4J7.01
#> "022" "0311" "022" "01122" "0123" "01121"
#> TCGA.HF.7131.01 TCGA.D7.A74B.01 TCGA.BR.A4PE.01 TCGA.BR.A4J8.01 TCGA.HU.A4GX.01 TCGA.HU.A4G8.01
#> "0123" "01116" "022" "0231" "032" "0341"
#> TCGA.HU.A4GT.01 TCGA.HU.A4GC.01 TCGA.BR.A4CQ.01 TCGA.D7.A6F2.01 TCGA.RD.A7BT.01 TCGA.BR.A4J6.01
#> "022" "0341" "022" "0122" "0122" "0114"
#> TCGA.HU.A4GQ.01 TCGA.HF.7136.01 TCGA.BR.A4QM.01 TCGA.BR.A4PD.01 TCGA.VQ.A8PK.01 TCGA.B7.A5TK.01
#> "0232" "013" "0232" "0122" "0121" "0312"
#> TCGA.D7.A4YX.01 TCGA.D7.A4Z0.01 TCGA.VQ.A8PT.01 TCGA.IN.A6RN.01 TCGA.CD.A4MG.01 TCGA.D7.A747.01
#> "0211" "0313" "022" "0121" "022" "01133"
#> TCGA.R5.A7O7.01 TCGA.F1.A72C.01 TCGA.BR.A4J2.01 TCGA.MX.A663.01 TCGA.D7.A4YV.01 TCGA.HU.A4GD.01
#> "0311" "01121" "0311" "013" "0231" "0331"
#> TCGA.BR.A4QL.01 TCGA.BR.7703.01 TCGA.VQ.AA6B.01 TCGA.VQ.AA6D.01 TCGA.D7.A6EZ.01 TCGA.D7.A4YU.01
#> "022" "022" "0332" "0123" "0211" "0232"
#> TCGA.VQ.AA6A.01 TCGA.IN.7806.01 TCGA.HU.A4HB.01 TCGA.HU.A4H2.01 TCGA.IN.A6RP.01 TCGA.HU.A4H5.01
#> "0123" "0122" "0311" "0342" "022" "0123"
#> TCGA.HU.A4GU.01 TCGA.MX.A5UJ.01 TCGA.HU.A4GN.01 TCGA.CD.5804.01 TCGA.HU.A4H6.01 TCGA.HF.7132.01
#> "022" "022" "0232" "013" "0231" "0232"
#> TCGA.D7.A4YT.01 TCGA.HF.7134.01 TCGA.BR.6852.01 TCGA.BR.8370.01 TCGA.EQ.5647.01 TCGA.IN.A7NT.01
#> "013" "022" "0314" "0233" "013" "032"
#> TCGA.RD.A8N9.01 TCGA.D7.5577.01 TCGA.CG.5717.01 TCGA.D7.6818.01 TCGA.CG.5734.01 TCGA.VQ.A8P8.01
#> "0114" "0211" "01134" "013" "0311" "0314"
#> TCGA.BR.6707.01 TCGA.B7.5818.01 TCGA.CD.8525.01 TCGA.BR.6705.01 TCGA.BR.4288.01 TCGA.CD.5813.01
#> "0211" "0211" "013" "0313" "013" "01121"
#> TCGA.CG.5723.01 TCGA.CD.5800.01 TCGA.CG.5718.01 TCGA.BR.8080.01 TCGA.CG.5733.01 TCGA.D7.6817.01
#> "01121" "013" "0123" "0114" "022" "0123"
#> TCGA.KB.A93G.01 TCGA.CD.5799.01 TCGA.BR.7851.01 TCGA.BR.7722.01 TCGA.MX.A5UG.01 TCGA.CD.8533.01
#> "01133" "013" "0232" "01121" "0311" "0331"
#> TCGA.BR.7957.01 TCGA.CG.5722.01 TCGA.F1.6874.01 TCGA.CG.5730.01 TCGA.CG.5726.01 TCGA.IP.7968.01
#> "0313" "0312" "032" "0331" "022" "0331"
#> TCGA.BR.8363.01 TCGA.BR.7901.01 TCGA.D7.6822.01 TCGA.BR.6710.01 TCGA.CG.5720.01 TCGA.D7.8570.01
#> "0231" "0121" "0341" "01132" "022" "0211"
#> TCGA.B7.A5TI.01 TCGA.D7.6815.01 TCGA.BR.8284.01 TCGA.BR.8295.01 TCGA.BR.7197.01 TCGA.B7.A5TJ.01
#> "013" "0122" "0231" "0121" "0122" "022"
#> TCGA.D7.A6EY.01 TCGA.BR.8366.01 TCGA.IN.A7NR.01 TCGA.BR.6706.01 TCGA.IN.7808.01 TCGA.BR.6564.01
#> "0313" "0211" "01114" "0312" "0311" "01111"
#> TCGA.KB.A93H.01 TCGA.KB.A93J.01 TCGA.CD.5798.01 TCGA.CD.8530.01 TCGA.BR.6802.01 TCGA.CG.5719.01
#> "0332" "0122" "01134" "013" "0311" "0114"
#> TCGA.VQ.A8E3.01 TCGA.CD.5801.01 TCGA.FP.A9TM.01 TCGA.BR.7958.01 TCGA.FP.7998.01 TCGA.IN.A6RS.01
#> "022" "0211" "032" "0211" "0312" "032"
#> TCGA.BR.6709.01 TCGA.FP.7916.01 TCGA.R5.A7ZR.01 TCGA.B7.5816.01 TCGA.CG.5721.01 TCGA.SW.A7EA.01
#> "01112" "0211" "0122" "0314" "0311" "022"
#> TCGA.RD.A8NB.01 TCGA.BR.6801.01 TCGA.IN.AB1X.01 TCGA.D7.5579.01 TCGA.CG.5728.01 TCGA.R5.A7ZI.01
#> "0313" "013" "0314" "013" "0313" "013"
#> TCGA.IN.A7NU.01 TCGA.CG.5732.01 TCGA.ZQ.A9CR.01 TCGA.D7.5578.01 TCGA.BR.6803.01 TCGA.BR.8368.01
#> "032" "013" "013" "032" "01111" "022"
#> TCGA.SW.A7EB.01 TCGA.BR.8081.01 TCGA.VQ.A8P5.01 TCGA.CD.8535.01 TCGA.CG.5724.01 TCGA.D7.8574.01
#> "01132" "0231" "032" "022" "0341" "01131"
#> TCGA.HJ.7597.01 TCGA.HF.A5NB.01 TCGA.VQ.A8PB.01 TCGA.R5.A7ZE.01 TCGA.CD.5803.01 TCGA.CG.5725.01
#> "0114" "022" "0341" "0122" "01112" "0121"
#> TCGA.D7.6820.01 TCGA.CD.5802.01 TCGA.R5.A7ZF.01 TCGA.D7.A6F0.01 TCGA.CG.5727.01 TCGA.VQ.A8PC.01
#> "0123" "013" "013" "0121" "032" "0311"
#> TCGA.CD.A486.01 TCGA.RD.A8N2.01 TCGA.IN.A6RI.01 TCGA.HU.8243.01 TCGA.CD.A48C.01 TCGA.RD.A8N5.01
#> "0121" "01113" "0121" "0342" "022" "01131"
#> TCGA.RD.A8N1.01 TCGA.HU.A4GF.01 TCGA.BR.8362.01 TCGA.BR.8285.01 TCGA.CD.8532.01 TCGA.VQ.A8E2.01
#> "013" "0122" "032" "0211" "01121" "013"
#> TCGA.BR.8373.01 TCGA.BR.8361.01 TCGA.BR.8058.01 TCGA.IN.8462.01 TCGA.HU.A4G9.01 TCGA.CD.8524.01
#> "0122" "022" "0114" "0341" "022" "032"
#> TCGA.D7.A748.01 TCGA.CD.8527.01 TCGA.VQ.A8DV.01 TCGA.CD.8528.01 TCGA.BR.A453.01 TCGA.RD.A8N6.01
#> "01115" "013" "0123" "022" "0311" "013"
#> TCGA.HU.8245.01 TCGA.ZA.A8F6.01 TCGA.BR.8367.01 TCGA.BR.8380.01 TCGA.FP.A4BE.01 TCGA.HU.8238.01
#> "0123" "013" "032" "0311" "0233" "0341"
#> TCGA.BR.8078.01 TCGA.HU.8249.01 TCGA.RD.A8N0.01 TCGA.BR.8365.01 TCGA.FP.8211.01 TCGA.RD.A8N4.01
#> "0231" "0331" "01112" "01111" "01122" "01113"
#> TCGA.VQ.A8DU.01 TCGA.VQ.A8DL.01 TCGA.VQ.A8DZ.01 TCGA.D7.8572.01 TCGA.RD.A7BW.01 TCGA.R5.A804.01
#> "0123" "013" "0123" "013" "01116" "0314"
#> TCGA.BR.A4CS.01 TCGA.CD.8531.01 TCGA.CD.A487.01 TCGA.BR.8371.01 TCGA.BR.8059.01 TCGA.D7.A6ET.01
#> "032" "0212" "013" "01131" "013" "0312"
#> TCGA.FP.8099.01 TCGA.D7.8579.01 TCGA.BR.8297.01 TCGA.D7.8576.01 TCGA.VQ.A8DT.01 TCGA.FP.A8CX.01
#> "0333" "0313" "032" "0114" "022" "013"
#> TCGA.HU.A4GH.01 TCGA.CD.8526.01 TCGA.HU.A4G6.01 TCGA.D7.8578.01 TCGA.HU.A4G3.01 TCGA.D7.A74A.01
#> "0121" "013" "0211" "013" "022" "022"
#> TCGA.RD.A7C1.01 TCGA.F1.A448.01 TCGA.D7.8575.01 TCGA.BR.8372.01 TCGA.VQ.A8P3.01 TCGA.RD.A8MW.01
#> "032" "0311" "0341" "022" "0341" "013"
#> TCGA.BR.8286.01 TCGA.BR.8369.01 TCGA.BR.8364.01 TCGA.HU.8244.01 TCGA.KB.A6F7.01 TCGA.FP.A4BF.01
#> "0341" "032" "01111" "022" "0121" "032"
#> TCGA.R5.A805.01 TCGA.IN.A6RL.01 TCGA.IN.A6RR.01 TCGA.BR.A4CR.01 TCGA.CD.A489.01 TCGA.HU.A4GY.01
#> "032" "0342" "022" "013" "01121" "0114"
#> TCGA.BR.8289.01 TCGA.FP.8209.01 TCGA.BR.8296.01 TCGA.CD.A48A.01 TCGA.BR.8060.01 TCGA.BR.8077.01
#> "0342" "01131" "0314" "0331" "0121" "0122"
#> TCGA.CD.8534.01 TCGA.BR.7959.01 TCGA.VQ.A8P2.01 TCGA.EQ.8122.01 TCGA.D7.8573.01 TCGA.BR.A44T.01
#> "032" "032" "022" "0122" "0212" "01112"
#> TCGA.RD.A8MV.01 TCGA.CD.8536.01 TCGA.BR.8360.01 TCGA.BR.8291.01 TCGA.FP.8210.01 TCGA.RD.A7BS.01
#> "0311" "032" "0232" "013" "01131" "01134"
#> TCGA.BR.A44U.01 TCGA.CD.8529.01
#> "0341" "013"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 3226))
#> TCGA.VQ.A94P.01 TCGA.D7.6521.01 TCGA.VQ.A8PE.01 TCGA.D7.6519.01 TCGA.BR.6452.01 TCGA.BR.8485.01
#> "01133" "01121" "0123" "013" "0231" "0123"
#> TCGA.VQ.A8PO.01 TCGA.VQ.AA69.01 TCGA.BR.8683.01 TCGA.BR.8486.01 TCGA.D7.6522.01 TCGA.CG.5716.01
#> "022" "0212" "032" "0123" "01131" "0314"
#> TCGA.BR.8589.01 TCGA.BR.8382.01 TCGA.VQ.AA68.01 TCGA.VQ.A8PJ.01 TCGA.VQ.A8PH.01 TCGA.HU.8604.01
#> "0211" "0231" "0341" "0122" "0123" "0231"
#> TCGA.BR.8676.01 TCGA.CG.4441.01 TCGA.D7.6520.01 TCGA.VQ.AA64.01 TCGA.D7.6527.01 TCGA.VQ.A8PM.01
#> "0212" "0342" "0121" "01122" "0123" "013"
#> TCGA.VQ.A923.01 TCGA.BR.8384.01 TCGA.BR.6453.01 TCGA.VQ.A928.01 TCGA.VQ.A8E0.01 TCGA.BR.8679.01
#> "0212" "0311" "0311" "01122" "01122" "022"
#> TCGA.VQ.A91S.01 TCGA.BR.8678.01 TCGA.D7.6528.01 TCGA.VQ.A8E7.01 TCGA.BR.8680.01 TCGA.BR.8483.01
#> "032" "0122" "0332" "0341" "0341" "0331"
#> TCGA.BR.6566.01 TCGA.VQ.A91X.01 TCGA.VQ.A91Q.01 TCGA.VQ.A92D.01 TCGA.VQ.A91Z.01 TCGA.BR.6455.01
#> "032" "0332" "01122" "022" "0122" "0212"
#> TCGA.BR.8591.01 TCGA.HU.8608.01 TCGA.VQ.A94U.01 TCGA.VQ.A94T.01 TCGA.VQ.A91A.01 TCGA.VQ.A91D.01
#> "0233" "0211" "0333" "01123" "032" "0233"
#> TCGA.D7.6518.01 TCGA.BR.8484.01 TCGA.VQ.A91N.01 TCGA.VQ.A91E.01 TCGA.VQ.A8PY.01 TCGA.HU.8602.01
#> "0311" "013" "0122" "032" "032" "0231"
#> TCGA.BR.8381.01 TCGA.BR.6452.11 TCGA.IN.8663.01 TCGA.VQ.A8PS.01 TCGA.VQ.A91W.01 TCGA.BR.6454.01
#> "0211" "0314" "022" "01122" "0212" "01121"
#> TCGA.BR.8682.01 TCGA.VQ.A91V.01 TCGA.VQ.A8PZ.01 TCGA.BR.8590.01 TCGA.F1.6177.01 TCGA.VQ.A8PQ.01
#> "032" "0333" "0314" "01133" "022" "01112"
#> TCGA.VQ.A91U.01 TCGA.VQ.AA6I.01 TCGA.CG.4437.01 TCGA.VQ.A8PP.01 TCGA.BR.6565.01 TCGA.VQ.A91Y.01
#> "0122" "022" "0232" "0232" "0121" "013"
#> TCGA.VQ.A8PF.01 TCGA.BR.6456.01 TCGA.BR.6458.01 TCGA.VQ.A925.01 TCGA.VQ.A927.01 TCGA.BR.8592.01
#> "0211" "013" "032" "013" "01132" "0313"
#> TCGA.BR.6566.11 TCGA.IN.AB1V.01 TCGA.VQ.AA6F.01 TCGA.VQ.AA6J.01 TCGA.BR.8487.01 TCGA.D7.6525.01
#> "01114" "013" "01121" "01121" "022" "032"
#> TCGA.VQ.A94O.01 TCGA.BR.8588.01 TCGA.HU.8610.01 TCGA.D7.6526.01 TCGA.VQ.A8PD.01 TCGA.D7.6524.01
#> "0121" "0313" "0311" "0123" "0311" "0314"
#> TCGA.3M.AB46.01 TCGA.3M.AB47.01 TCGA.BR.8677.01 TCGA.BR.6457.01 TCGA.BR.8687.01 TCGA.VQ.A91K.01
#> "0122" "0311" "0114" "0311" "013" "022"
#> TCGA.BR.8690.01 TCGA.BR.8686.01 TCGA.FP.8631.01 TCGA.VQ.A922.01 TCGA.BR.A452.01 TCGA.IN.A6RO.01
#> "013" "0211" "0121" "0121" "01121" "022"
#> TCGA.BR.A4QI.01 TCGA.D7.A6EV.01 TCGA.HU.A4G2.01 TCGA.BR.A4IY.01 TCGA.VQ.A8PU.01 TCGA.BR.A4J4.01
#> "0231" "0341" "0211" "0211" "01123" "0211"
#> TCGA.VQ.A94R.01 TCGA.HU.A4H4.01 TCGA.BR.7707.01 TCGA.FP.7829.01 TCGA.BR.A4J5.01 TCGA.HU.A4H0.01
#> "022" "032" "022" "022" "0311" "0211"
#> TCGA.HU.A4HD.01 TCGA.KB.A6F5.01 TCGA.VQ.AA6K.01 TCGA.HF.7133.01 TCGA.F1.6875.01 TCGA.MX.A666.01
#> "0121" "013" "01121" "013" "0122" "0121"
#> TCGA.BR.7717.01 TCGA.BR.A4PF.01 TCGA.BR.A4IU.01 TCGA.VQ.A8PX.01 TCGA.BR.A4IV.01 TCGA.D7.A6EX.01
#> "0341" "0232" "0313" "01121" "01133" "013"
#> TCGA.BR.A4IZ.01 TCGA.BR.A4J9.01 TCGA.CD.A4MJ.01 TCGA.B7.A5TN.01 TCGA.BR.7715.01 TCGA.BR.7704.01
#> "01115" "01133" "0233" "0122" "0332" "0123"
#> TCGA.BR.A4J1.01 TCGA.HU.A4GP.01 TCGA.D7.A4YY.01 TCGA.VQ.AA6G.01 TCGA.HU.A4GJ.01 TCGA.CD.A4MI.01
#> "0121" "022" "022" "022" "0314" "0232"
#> TCGA.BR.7196.01 TCGA.BR.6563.01 TCGA.VQ.A924.01 TCGA.BR.7716.01 TCGA.FP.7735.01 TCGA.BR.7723.01
#> "0312" "0311" "0233" "013" "013" "013"
#> TCGA.HU.A4H8.01 TCGA.IN.A6RJ.01 TCGA.HU.A4H3.01 TCGA.EQ.A4SO.01 TCGA.CD.A4MH.01 TCGA.BR.A4J7.01
#> "022" "0311" "022" "01122" "0123" "01121"
#> TCGA.HF.7131.01 TCGA.D7.A74B.01 TCGA.BR.A4PE.01 TCGA.BR.A4J8.01 TCGA.HU.A4GX.01 TCGA.HU.A4G8.01
#> "0123" "01116" "022" "0231" "032" "0341"
#> TCGA.HU.A4GT.01 TCGA.HU.A4GC.01 TCGA.BR.A4CQ.01 TCGA.D7.A6F2.01 TCGA.RD.A7BT.01 TCGA.BR.A4J6.01
#> "022" "0341" "022" "0122" "0122" "0114"
#> TCGA.HU.A4GQ.01 TCGA.HF.7136.01 TCGA.BR.A4QM.01 TCGA.BR.A4PD.01 TCGA.VQ.A8PK.01 TCGA.B7.A5TK.01
#> "0232" "013" "0232" "0122" "0121" "0312"
#> TCGA.D7.A4YX.01 TCGA.D7.A4Z0.01 TCGA.VQ.A8PT.01 TCGA.IN.A6RN.01 TCGA.CD.A4MG.01 TCGA.D7.A747.01
#> "0211" "0313" "022" "0121" "022" "01133"
#> TCGA.R5.A7O7.01 TCGA.F1.A72C.01 TCGA.BR.A4J2.01 TCGA.MX.A663.01 TCGA.D7.A4YV.01 TCGA.HU.A4GD.01
#> "0311" "01121" "0311" "013" "0231" "0331"
#> TCGA.BR.A4QL.01 TCGA.BR.7703.01 TCGA.VQ.AA6B.01 TCGA.VQ.AA6D.01 TCGA.D7.A6EZ.01 TCGA.D7.A4YU.01
#> "022" "022" "0332" "0123" "0211" "0232"
#> TCGA.VQ.AA6A.01 TCGA.IN.7806.01 TCGA.HU.A4HB.01 TCGA.HU.A4H2.01 TCGA.IN.A6RP.01 TCGA.HU.A4H5.01
#> "0123" "0122" "0311" "0342" "022" "0123"
#> TCGA.HU.A4GU.01 TCGA.MX.A5UJ.01 TCGA.HU.A4GN.01 TCGA.CD.5804.01 TCGA.HU.A4H6.01 TCGA.HF.7132.01
#> "022" "022" "0232" "013" "0231" "0232"
#> TCGA.D7.A4YT.01 TCGA.HF.7134.01 TCGA.BR.6852.01 TCGA.BR.8370.01 TCGA.EQ.5647.01 TCGA.IN.A7NT.01
#> "013" "022" "0314" "0233" "013" "032"
#> TCGA.RD.A8N9.01 TCGA.D7.5577.01 TCGA.CG.5717.01 TCGA.D7.6818.01 TCGA.CG.5734.01 TCGA.VQ.A8P8.01
#> "0114" "0211" "01134" "013" "0311" "0314"
#> TCGA.BR.6707.01 TCGA.B7.5818.01 TCGA.CD.8525.01 TCGA.BR.6705.01 TCGA.BR.4288.01 TCGA.CD.5813.01
#> "0211" "0211" "013" "0313" "013" "01121"
#> TCGA.CG.5723.01 TCGA.CD.5800.01 TCGA.CG.5718.01 TCGA.BR.8080.01 TCGA.CG.5733.01 TCGA.D7.6817.01
#> "01121" "013" "0123" "0114" "022" "0123"
#> TCGA.KB.A93G.01 TCGA.CD.5799.01 TCGA.BR.7851.01 TCGA.BR.7722.01 TCGA.MX.A5UG.01 TCGA.CD.8533.01
#> "01133" "013" "0232" "01121" "0311" "0331"
#> TCGA.BR.7957.01 TCGA.CG.5722.01 TCGA.F1.6874.01 TCGA.CG.5730.01 TCGA.CG.5726.01 TCGA.IP.7968.01
#> "0313" "0312" "032" "0331" "022" "0331"
#> TCGA.BR.8363.01 TCGA.BR.7901.01 TCGA.D7.6822.01 TCGA.BR.6710.01 TCGA.CG.5720.01 TCGA.D7.8570.01
#> "0231" "0121" "0341" "01132" "022" "0211"
#> TCGA.B7.A5TI.01 TCGA.D7.6815.01 TCGA.BR.8284.01 TCGA.BR.8295.01 TCGA.BR.7197.01 TCGA.B7.A5TJ.01
#> "013" "0122" "0231" "0121" "0122" "022"
#> TCGA.D7.A6EY.01 TCGA.BR.8366.01 TCGA.IN.A7NR.01 TCGA.BR.6706.01 TCGA.IN.7808.01 TCGA.BR.6564.01
#> "0313" "0211" "01114" "0312" "0311" "01111"
#> TCGA.KB.A93H.01 TCGA.KB.A93J.01 TCGA.CD.5798.01 TCGA.CD.8530.01 TCGA.BR.6802.01 TCGA.CG.5719.01
#> "0332" "0122" "01134" "013" "0311" "0114"
#> TCGA.VQ.A8E3.01 TCGA.CD.5801.01 TCGA.FP.A9TM.01 TCGA.BR.7958.01 TCGA.FP.7998.01 TCGA.IN.A6RS.01
#> "022" "0211" "032" "0211" "0312" "032"
#> TCGA.BR.6709.01 TCGA.FP.7916.01 TCGA.R5.A7ZR.01 TCGA.B7.5816.01 TCGA.CG.5721.01 TCGA.SW.A7EA.01
#> "01112" "0211" "0122" "0314" "0311" "022"
#> TCGA.RD.A8NB.01 TCGA.BR.6801.01 TCGA.IN.AB1X.01 TCGA.D7.5579.01 TCGA.CG.5728.01 TCGA.R5.A7ZI.01
#> "0313" "013" "0314" "013" "0313" "013"
#> TCGA.IN.A7NU.01 TCGA.CG.5732.01 TCGA.ZQ.A9CR.01 TCGA.D7.5578.01 TCGA.BR.6803.01 TCGA.BR.8368.01
#> "032" "013" "013" "032" "01111" "022"
#> TCGA.SW.A7EB.01 TCGA.BR.8081.01 TCGA.VQ.A8P5.01 TCGA.CD.8535.01 TCGA.CG.5724.01 TCGA.D7.8574.01
#> "01132" "0231" "032" "022" "0341" "01131"
#> TCGA.HJ.7597.01 TCGA.HF.A5NB.01 TCGA.VQ.A8PB.01 TCGA.R5.A7ZE.01 TCGA.CD.5803.01 TCGA.CG.5725.01
#> "0114" "022" "0341" "0122" "01112" "0121"
#> TCGA.D7.6820.01 TCGA.CD.5802.01 TCGA.R5.A7ZF.01 TCGA.D7.A6F0.01 TCGA.CG.5727.01 TCGA.VQ.A8PC.01
#> "0123" "013" "013" "0121" "032" "0311"
#> TCGA.CD.A486.01 TCGA.RD.A8N2.01 TCGA.IN.A6RI.01 TCGA.HU.8243.01 TCGA.CD.A48C.01 TCGA.RD.A8N5.01
#> "0121" "01113" "0121" "0342" "022" "01131"
#> TCGA.RD.A8N1.01 TCGA.HU.A4GF.01 TCGA.BR.8362.01 TCGA.BR.8285.01 TCGA.CD.8532.01 TCGA.VQ.A8E2.01
#> "013" "0122" "032" "0211" "01121" "013"
#> TCGA.BR.8373.01 TCGA.BR.8361.01 TCGA.BR.8058.01 TCGA.IN.8462.01 TCGA.HU.A4G9.01 TCGA.CD.8524.01
#> "0122" "022" "0114" "0341" "022" "032"
#> TCGA.D7.A748.01 TCGA.CD.8527.01 TCGA.VQ.A8DV.01 TCGA.CD.8528.01 TCGA.BR.A453.01 TCGA.RD.A8N6.01
#> "01115" "013" "0123" "022" "0311" "013"
#> TCGA.HU.8245.01 TCGA.ZA.A8F6.01 TCGA.BR.8367.01 TCGA.BR.8380.01 TCGA.FP.A4BE.01 TCGA.HU.8238.01
#> "0123" "013" "032" "0311" "0233" "0341"
#> TCGA.BR.8078.01 TCGA.HU.8249.01 TCGA.RD.A8N0.01 TCGA.BR.8365.01 TCGA.FP.8211.01 TCGA.RD.A8N4.01
#> "0231" "0331" "01112" "01111" "01122" "01113"
#> TCGA.VQ.A8DU.01 TCGA.VQ.A8DL.01 TCGA.VQ.A8DZ.01 TCGA.D7.8572.01 TCGA.RD.A7BW.01 TCGA.R5.A804.01
#> "0123" "013" "0123" "013" "01116" "0314"
#> TCGA.BR.A4CS.01 TCGA.CD.8531.01 TCGA.CD.A487.01 TCGA.BR.8371.01 TCGA.BR.8059.01 TCGA.D7.A6ET.01
#> "032" "0212" "013" "01131" "013" "0312"
#> TCGA.FP.8099.01 TCGA.D7.8579.01 TCGA.BR.8297.01 TCGA.D7.8576.01 TCGA.VQ.A8DT.01 TCGA.FP.A8CX.01
#> "0333" "0313" "032" "0114" "022" "013"
#> TCGA.HU.A4GH.01 TCGA.CD.8526.01 TCGA.HU.A4G6.01 TCGA.D7.8578.01 TCGA.HU.A4G3.01 TCGA.D7.A74A.01
#> "0121" "013" "0211" "013" "022" "022"
#> TCGA.RD.A7C1.01 TCGA.F1.A448.01 TCGA.D7.8575.01 TCGA.BR.8372.01 TCGA.VQ.A8P3.01 TCGA.RD.A8MW.01
#> "032" "0311" "0341" "022" "0341" "013"
#> TCGA.BR.8286.01 TCGA.BR.8369.01 TCGA.BR.8364.01 TCGA.HU.8244.01 TCGA.KB.A6F7.01 TCGA.FP.A4BF.01
#> "0341" "032" "01111" "022" "0121" "032"
#> TCGA.R5.A805.01 TCGA.IN.A6RL.01 TCGA.IN.A6RR.01 TCGA.BR.A4CR.01 TCGA.CD.A489.01 TCGA.HU.A4GY.01
#> "032" "0342" "022" "013" "01121" "0114"
#> TCGA.BR.8289.01 TCGA.FP.8209.01 TCGA.BR.8296.01 TCGA.CD.A48A.01 TCGA.BR.8060.01 TCGA.BR.8077.01
#> "0342" "01131" "0314" "0331" "0121" "0122"
#> TCGA.CD.8534.01 TCGA.BR.7959.01 TCGA.VQ.A8P2.01 TCGA.EQ.8122.01 TCGA.D7.8573.01 TCGA.BR.A44T.01
#> "032" "032" "022" "0122" "0212" "01112"
#> TCGA.RD.A8MV.01 TCGA.CD.8536.01 TCGA.BR.8360.01 TCGA.BR.8291.01 TCGA.FP.8210.01 TCGA.RD.A7BS.01
#> "0311" "032" "0232" "013" "01131" "01134"
#> TCGA.BR.A44U.01 TCGA.CD.8529.01
#> "0341" "013"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 3913))
#> TCGA.VQ.A94P.01 TCGA.D7.6521.01 TCGA.VQ.A8PE.01 TCGA.D7.6519.01 TCGA.BR.6452.01 TCGA.BR.8485.01
#> "01133" "01121" "0123" "013" "0231" "0123"
#> TCGA.VQ.A8PO.01 TCGA.VQ.AA69.01 TCGA.BR.8683.01 TCGA.BR.8486.01 TCGA.D7.6522.01 TCGA.CG.5716.01
#> "022" "021" "032" "0123" "01131" "0314"
#> TCGA.BR.8589.01 TCGA.BR.8382.01 TCGA.VQ.AA68.01 TCGA.VQ.A8PJ.01 TCGA.VQ.A8PH.01 TCGA.HU.8604.01
#> "021" "0231" "0341" "0122" "0123" "0231"
#> TCGA.BR.8676.01 TCGA.CG.4441.01 TCGA.D7.6520.01 TCGA.VQ.AA64.01 TCGA.D7.6527.01 TCGA.VQ.A8PM.01
#> "021" "0342" "0121" "01122" "0123" "013"
#> TCGA.VQ.A923.01 TCGA.BR.8384.01 TCGA.BR.6453.01 TCGA.VQ.A928.01 TCGA.VQ.A8E0.01 TCGA.BR.8679.01
#> "021" "0311" "0311" "01122" "01122" "022"
#> TCGA.VQ.A91S.01 TCGA.BR.8678.01 TCGA.D7.6528.01 TCGA.VQ.A8E7.01 TCGA.BR.8680.01 TCGA.BR.8483.01
#> "032" "0122" "0332" "0341" "0341" "0331"
#> TCGA.BR.6566.01 TCGA.VQ.A91X.01 TCGA.VQ.A91Q.01 TCGA.VQ.A92D.01 TCGA.VQ.A91Z.01 TCGA.BR.6455.01
#> "032" "0332" "01122" "022" "0122" "021"
#> TCGA.BR.8591.01 TCGA.HU.8608.01 TCGA.VQ.A94U.01 TCGA.VQ.A94T.01 TCGA.VQ.A91A.01 TCGA.VQ.A91D.01
#> "0233" "021" "0333" "01123" "032" "0233"
#> TCGA.D7.6518.01 TCGA.BR.8484.01 TCGA.VQ.A91N.01 TCGA.VQ.A91E.01 TCGA.VQ.A8PY.01 TCGA.HU.8602.01
#> "0311" "013" "0122" "032" "032" "0231"
#> TCGA.BR.8381.01 TCGA.BR.6452.11 TCGA.IN.8663.01 TCGA.VQ.A8PS.01 TCGA.VQ.A91W.01 TCGA.BR.6454.01
#> "021" "0314" "022" "01122" "021" "01121"
#> TCGA.BR.8682.01 TCGA.VQ.A91V.01 TCGA.VQ.A8PZ.01 TCGA.BR.8590.01 TCGA.F1.6177.01 TCGA.VQ.A8PQ.01
#> "032" "0333" "0314" "01133" "022" "01112"
#> TCGA.VQ.A91U.01 TCGA.VQ.AA6I.01 TCGA.CG.4437.01 TCGA.VQ.A8PP.01 TCGA.BR.6565.01 TCGA.VQ.A91Y.01
#> "0122" "022" "0232" "0232" "0121" "013"
#> TCGA.VQ.A8PF.01 TCGA.BR.6456.01 TCGA.BR.6458.01 TCGA.VQ.A925.01 TCGA.VQ.A927.01 TCGA.BR.8592.01
#> "021" "013" "032" "013" "01132" "0313"
#> TCGA.BR.6566.11 TCGA.IN.AB1V.01 TCGA.VQ.AA6F.01 TCGA.VQ.AA6J.01 TCGA.BR.8487.01 TCGA.D7.6525.01
#> "01114" "013" "01121" "01121" "022" "032"
#> TCGA.VQ.A94O.01 TCGA.BR.8588.01 TCGA.HU.8610.01 TCGA.D7.6526.01 TCGA.VQ.A8PD.01 TCGA.D7.6524.01
#> "0121" "0313" "0311" "0123" "0311" "0314"
#> TCGA.3M.AB46.01 TCGA.3M.AB47.01 TCGA.BR.8677.01 TCGA.BR.6457.01 TCGA.BR.8687.01 TCGA.VQ.A91K.01
#> "0122" "0311" "0114" "0311" "013" "022"
#> TCGA.BR.8690.01 TCGA.BR.8686.01 TCGA.FP.8631.01 TCGA.VQ.A922.01 TCGA.BR.A452.01 TCGA.IN.A6RO.01
#> "013" "021" "0121" "0121" "01121" "022"
#> TCGA.BR.A4QI.01 TCGA.D7.A6EV.01 TCGA.HU.A4G2.01 TCGA.BR.A4IY.01 TCGA.VQ.A8PU.01 TCGA.BR.A4J4.01
#> "0231" "0341" "021" "021" "01123" "021"
#> TCGA.VQ.A94R.01 TCGA.HU.A4H4.01 TCGA.BR.7707.01 TCGA.FP.7829.01 TCGA.BR.A4J5.01 TCGA.HU.A4H0.01
#> "022" "032" "022" "022" "0311" "021"
#> TCGA.HU.A4HD.01 TCGA.KB.A6F5.01 TCGA.VQ.AA6K.01 TCGA.HF.7133.01 TCGA.F1.6875.01 TCGA.MX.A666.01
#> "0121" "013" "01121" "013" "0122" "0121"
#> TCGA.BR.7717.01 TCGA.BR.A4PF.01 TCGA.BR.A4IU.01 TCGA.VQ.A8PX.01 TCGA.BR.A4IV.01 TCGA.D7.A6EX.01
#> "0341" "0232" "0313" "01121" "01133" "013"
#> TCGA.BR.A4IZ.01 TCGA.BR.A4J9.01 TCGA.CD.A4MJ.01 TCGA.B7.A5TN.01 TCGA.BR.7715.01 TCGA.BR.7704.01
#> "01115" "01133" "0233" "0122" "0332" "0123"
#> TCGA.BR.A4J1.01 TCGA.HU.A4GP.01 TCGA.D7.A4YY.01 TCGA.VQ.AA6G.01 TCGA.HU.A4GJ.01 TCGA.CD.A4MI.01
#> "0121" "022" "022" "022" "0314" "0232"
#> TCGA.BR.7196.01 TCGA.BR.6563.01 TCGA.VQ.A924.01 TCGA.BR.7716.01 TCGA.FP.7735.01 TCGA.BR.7723.01
#> "0312" "0311" "0233" "013" "013" "013"
#> TCGA.HU.A4H8.01 TCGA.IN.A6RJ.01 TCGA.HU.A4H3.01 TCGA.EQ.A4SO.01 TCGA.CD.A4MH.01 TCGA.BR.A4J7.01
#> "022" "0311" "022" "01122" "0123" "01121"
#> TCGA.HF.7131.01 TCGA.D7.A74B.01 TCGA.BR.A4PE.01 TCGA.BR.A4J8.01 TCGA.HU.A4GX.01 TCGA.HU.A4G8.01
#> "0123" "01116" "022" "0231" "032" "0341"
#> TCGA.HU.A4GT.01 TCGA.HU.A4GC.01 TCGA.BR.A4CQ.01 TCGA.D7.A6F2.01 TCGA.RD.A7BT.01 TCGA.BR.A4J6.01
#> "022" "0341" "022" "0122" "0122" "0114"
#> TCGA.HU.A4GQ.01 TCGA.HF.7136.01 TCGA.BR.A4QM.01 TCGA.BR.A4PD.01 TCGA.VQ.A8PK.01 TCGA.B7.A5TK.01
#> "0232" "013" "0232" "0122" "0121" "0312"
#> TCGA.D7.A4YX.01 TCGA.D7.A4Z0.01 TCGA.VQ.A8PT.01 TCGA.IN.A6RN.01 TCGA.CD.A4MG.01 TCGA.D7.A747.01
#> "021" "0313" "022" "0121" "022" "01133"
#> TCGA.R5.A7O7.01 TCGA.F1.A72C.01 TCGA.BR.A4J2.01 TCGA.MX.A663.01 TCGA.D7.A4YV.01 TCGA.HU.A4GD.01
#> "0311" "01121" "0311" "013" "0231" "0331"
#> TCGA.BR.A4QL.01 TCGA.BR.7703.01 TCGA.VQ.AA6B.01 TCGA.VQ.AA6D.01 TCGA.D7.A6EZ.01 TCGA.D7.A4YU.01
#> "022" "022" "0332" "0123" "021" "0232"
#> TCGA.VQ.AA6A.01 TCGA.IN.7806.01 TCGA.HU.A4HB.01 TCGA.HU.A4H2.01 TCGA.IN.A6RP.01 TCGA.HU.A4H5.01
#> "0123" "0122" "0311" "0342" "022" "0123"
#> TCGA.HU.A4GU.01 TCGA.MX.A5UJ.01 TCGA.HU.A4GN.01 TCGA.CD.5804.01 TCGA.HU.A4H6.01 TCGA.HF.7132.01
#> "022" "022" "0232" "013" "0231" "0232"
#> TCGA.D7.A4YT.01 TCGA.HF.7134.01 TCGA.BR.6852.01 TCGA.BR.8370.01 TCGA.EQ.5647.01 TCGA.IN.A7NT.01
#> "013" "022" "0314" "0233" "013" "032"
#> TCGA.RD.A8N9.01 TCGA.D7.5577.01 TCGA.CG.5717.01 TCGA.D7.6818.01 TCGA.CG.5734.01 TCGA.VQ.A8P8.01
#> "0114" "021" "01134" "013" "0311" "0314"
#> TCGA.BR.6707.01 TCGA.B7.5818.01 TCGA.CD.8525.01 TCGA.BR.6705.01 TCGA.BR.4288.01 TCGA.CD.5813.01
#> "021" "021" "013" "0313" "013" "01121"
#> TCGA.CG.5723.01 TCGA.CD.5800.01 TCGA.CG.5718.01 TCGA.BR.8080.01 TCGA.CG.5733.01 TCGA.D7.6817.01
#> "01121" "013" "0123" "0114" "022" "0123"
#> TCGA.KB.A93G.01 TCGA.CD.5799.01 TCGA.BR.7851.01 TCGA.BR.7722.01 TCGA.MX.A5UG.01 TCGA.CD.8533.01
#> "01133" "013" "0232" "01121" "0311" "0331"
#> TCGA.BR.7957.01 TCGA.CG.5722.01 TCGA.F1.6874.01 TCGA.CG.5730.01 TCGA.CG.5726.01 TCGA.IP.7968.01
#> "0313" "0312" "032" "0331" "022" "0331"
#> TCGA.BR.8363.01 TCGA.BR.7901.01 TCGA.D7.6822.01 TCGA.BR.6710.01 TCGA.CG.5720.01 TCGA.D7.8570.01
#> "0231" "0121" "0341" "01132" "022" "021"
#> TCGA.B7.A5TI.01 TCGA.D7.6815.01 TCGA.BR.8284.01 TCGA.BR.8295.01 TCGA.BR.7197.01 TCGA.B7.A5TJ.01
#> "013" "0122" "0231" "0121" "0122" "022"
#> TCGA.D7.A6EY.01 TCGA.BR.8366.01 TCGA.IN.A7NR.01 TCGA.BR.6706.01 TCGA.IN.7808.01 TCGA.BR.6564.01
#> "0313" "021" "01114" "0312" "0311" "01111"
#> TCGA.KB.A93H.01 TCGA.KB.A93J.01 TCGA.CD.5798.01 TCGA.CD.8530.01 TCGA.BR.6802.01 TCGA.CG.5719.01
#> "0332" "0122" "01134" "013" "0311" "0114"
#> TCGA.VQ.A8E3.01 TCGA.CD.5801.01 TCGA.FP.A9TM.01 TCGA.BR.7958.01 TCGA.FP.7998.01 TCGA.IN.A6RS.01
#> "022" "021" "032" "021" "0312" "032"
#> TCGA.BR.6709.01 TCGA.FP.7916.01 TCGA.R5.A7ZR.01 TCGA.B7.5816.01 TCGA.CG.5721.01 TCGA.SW.A7EA.01
#> "01112" "021" "0122" "0314" "0311" "022"
#> TCGA.RD.A8NB.01 TCGA.BR.6801.01 TCGA.IN.AB1X.01 TCGA.D7.5579.01 TCGA.CG.5728.01 TCGA.R5.A7ZI.01
#> "0313" "013" "0314" "013" "0313" "013"
#> TCGA.IN.A7NU.01 TCGA.CG.5732.01 TCGA.ZQ.A9CR.01 TCGA.D7.5578.01 TCGA.BR.6803.01 TCGA.BR.8368.01
#> "032" "013" "013" "032" "01111" "022"
#> TCGA.SW.A7EB.01 TCGA.BR.8081.01 TCGA.VQ.A8P5.01 TCGA.CD.8535.01 TCGA.CG.5724.01 TCGA.D7.8574.01
#> "01132" "0231" "032" "022" "0341" "01131"
#> TCGA.HJ.7597.01 TCGA.HF.A5NB.01 TCGA.VQ.A8PB.01 TCGA.R5.A7ZE.01 TCGA.CD.5803.01 TCGA.CG.5725.01
#> "0114" "022" "0341" "0122" "01112" "0121"
#> TCGA.D7.6820.01 TCGA.CD.5802.01 TCGA.R5.A7ZF.01 TCGA.D7.A6F0.01 TCGA.CG.5727.01 TCGA.VQ.A8PC.01
#> "0123" "013" "013" "0121" "032" "0311"
#> TCGA.CD.A486.01 TCGA.RD.A8N2.01 TCGA.IN.A6RI.01 TCGA.HU.8243.01 TCGA.CD.A48C.01 TCGA.RD.A8N5.01
#> "0121" "01113" "0121" "0342" "022" "01131"
#> TCGA.RD.A8N1.01 TCGA.HU.A4GF.01 TCGA.BR.8362.01 TCGA.BR.8285.01 TCGA.CD.8532.01 TCGA.VQ.A8E2.01
#> "013" "0122" "032" "021" "01121" "013"
#> TCGA.BR.8373.01 TCGA.BR.8361.01 TCGA.BR.8058.01 TCGA.IN.8462.01 TCGA.HU.A4G9.01 TCGA.CD.8524.01
#> "0122" "022" "0114" "0341" "022" "032"
#> TCGA.D7.A748.01 TCGA.CD.8527.01 TCGA.VQ.A8DV.01 TCGA.CD.8528.01 TCGA.BR.A453.01 TCGA.RD.A8N6.01
#> "01115" "013" "0123" "022" "0311" "013"
#> TCGA.HU.8245.01 TCGA.ZA.A8F6.01 TCGA.BR.8367.01 TCGA.BR.8380.01 TCGA.FP.A4BE.01 TCGA.HU.8238.01
#> "0123" "013" "032" "0311" "0233" "0341"
#> TCGA.BR.8078.01 TCGA.HU.8249.01 TCGA.RD.A8N0.01 TCGA.BR.8365.01 TCGA.FP.8211.01 TCGA.RD.A8N4.01
#> "0231" "0331" "01112" "01111" "01122" "01113"
#> TCGA.VQ.A8DU.01 TCGA.VQ.A8DL.01 TCGA.VQ.A8DZ.01 TCGA.D7.8572.01 TCGA.RD.A7BW.01 TCGA.R5.A804.01
#> "0123" "013" "0123" "013" "01116" "0314"
#> TCGA.BR.A4CS.01 TCGA.CD.8531.01 TCGA.CD.A487.01 TCGA.BR.8371.01 TCGA.BR.8059.01 TCGA.D7.A6ET.01
#> "032" "021" "013" "01131" "013" "0312"
#> TCGA.FP.8099.01 TCGA.D7.8579.01 TCGA.BR.8297.01 TCGA.D7.8576.01 TCGA.VQ.A8DT.01 TCGA.FP.A8CX.01
#> "0333" "0313" "032" "0114" "022" "013"
#> TCGA.HU.A4GH.01 TCGA.CD.8526.01 TCGA.HU.A4G6.01 TCGA.D7.8578.01 TCGA.HU.A4G3.01 TCGA.D7.A74A.01
#> "0121" "013" "021" "013" "022" "022"
#> TCGA.RD.A7C1.01 TCGA.F1.A448.01 TCGA.D7.8575.01 TCGA.BR.8372.01 TCGA.VQ.A8P3.01 TCGA.RD.A8MW.01
#> "032" "0311" "0341" "022" "0341" "013"
#> TCGA.BR.8286.01 TCGA.BR.8369.01 TCGA.BR.8364.01 TCGA.HU.8244.01 TCGA.KB.A6F7.01 TCGA.FP.A4BF.01
#> "0341" "032" "01111" "022" "0121" "032"
#> TCGA.R5.A805.01 TCGA.IN.A6RL.01 TCGA.IN.A6RR.01 TCGA.BR.A4CR.01 TCGA.CD.A489.01 TCGA.HU.A4GY.01
#> "032" "0342" "022" "013" "01121" "0114"
#> TCGA.BR.8289.01 TCGA.FP.8209.01 TCGA.BR.8296.01 TCGA.CD.A48A.01 TCGA.BR.8060.01 TCGA.BR.8077.01
#> "0342" "01131" "0314" "0331" "0121" "0122"
#> TCGA.CD.8534.01 TCGA.BR.7959.01 TCGA.VQ.A8P2.01 TCGA.EQ.8122.01 TCGA.D7.8573.01 TCGA.BR.A44T.01
#> "032" "032" "022" "0122" "021" "01112"
#> TCGA.RD.A8MV.01 TCGA.CD.8536.01 TCGA.BR.8360.01 TCGA.BR.8291.01 TCGA.FP.8210.01 TCGA.RD.A7BS.01
#> "0311" "032" "0232" "013" "01131" "01134"
#> TCGA.BR.A44U.01 TCGA.CD.8529.01
#> "0341" "013"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 4126))
#> TCGA.VQ.A94P.01 TCGA.D7.6521.01 TCGA.VQ.A8PE.01 TCGA.D7.6519.01 TCGA.BR.6452.01 TCGA.BR.8485.01
#> "01133" "01121" "0123" "013" "023" "0123"
#> TCGA.VQ.A8PO.01 TCGA.VQ.AA69.01 TCGA.BR.8683.01 TCGA.BR.8486.01 TCGA.D7.6522.01 TCGA.CG.5716.01
#> "022" "021" "032" "0123" "01131" "0314"
#> TCGA.BR.8589.01 TCGA.BR.8382.01 TCGA.VQ.AA68.01 TCGA.VQ.A8PJ.01 TCGA.VQ.A8PH.01 TCGA.HU.8604.01
#> "021" "023" "0341" "0122" "0123" "023"
#> TCGA.BR.8676.01 TCGA.CG.4441.01 TCGA.D7.6520.01 TCGA.VQ.AA64.01 TCGA.D7.6527.01 TCGA.VQ.A8PM.01
#> "021" "0342" "0121" "01122" "0123" "013"
#> TCGA.VQ.A923.01 TCGA.BR.8384.01 TCGA.BR.6453.01 TCGA.VQ.A928.01 TCGA.VQ.A8E0.01 TCGA.BR.8679.01
#> "021" "0311" "0311" "01122" "01122" "022"
#> TCGA.VQ.A91S.01 TCGA.BR.8678.01 TCGA.D7.6528.01 TCGA.VQ.A8E7.01 TCGA.BR.8680.01 TCGA.BR.8483.01
#> "032" "0122" "0332" "0341" "0341" "0331"
#> TCGA.BR.6566.01 TCGA.VQ.A91X.01 TCGA.VQ.A91Q.01 TCGA.VQ.A92D.01 TCGA.VQ.A91Z.01 TCGA.BR.6455.01
#> "032" "0332" "01122" "022" "0122" "021"
#> TCGA.BR.8591.01 TCGA.HU.8608.01 TCGA.VQ.A94U.01 TCGA.VQ.A94T.01 TCGA.VQ.A91A.01 TCGA.VQ.A91D.01
#> "023" "021" "0333" "01123" "032" "023"
#> TCGA.D7.6518.01 TCGA.BR.8484.01 TCGA.VQ.A91N.01 TCGA.VQ.A91E.01 TCGA.VQ.A8PY.01 TCGA.HU.8602.01
#> "0311" "013" "0122" "032" "032" "023"
#> TCGA.BR.8381.01 TCGA.BR.6452.11 TCGA.IN.8663.01 TCGA.VQ.A8PS.01 TCGA.VQ.A91W.01 TCGA.BR.6454.01
#> "021" "0314" "022" "01122" "021" "01121"
#> TCGA.BR.8682.01 TCGA.VQ.A91V.01 TCGA.VQ.A8PZ.01 TCGA.BR.8590.01 TCGA.F1.6177.01 TCGA.VQ.A8PQ.01
#> "032" "0333" "0314" "01133" "022" "01112"
#> TCGA.VQ.A91U.01 TCGA.VQ.AA6I.01 TCGA.CG.4437.01 TCGA.VQ.A8PP.01 TCGA.BR.6565.01 TCGA.VQ.A91Y.01
#> "0122" "022" "023" "023" "0121" "013"
#> TCGA.VQ.A8PF.01 TCGA.BR.6456.01 TCGA.BR.6458.01 TCGA.VQ.A925.01 TCGA.VQ.A927.01 TCGA.BR.8592.01
#> "021" "013" "032" "013" "01132" "0313"
#> TCGA.BR.6566.11 TCGA.IN.AB1V.01 TCGA.VQ.AA6F.01 TCGA.VQ.AA6J.01 TCGA.BR.8487.01 TCGA.D7.6525.01
#> "01114" "013" "01121" "01121" "022" "032"
#> TCGA.VQ.A94O.01 TCGA.BR.8588.01 TCGA.HU.8610.01 TCGA.D7.6526.01 TCGA.VQ.A8PD.01 TCGA.D7.6524.01
#> "0121" "0313" "0311" "0123" "0311" "0314"
#> TCGA.3M.AB46.01 TCGA.3M.AB47.01 TCGA.BR.8677.01 TCGA.BR.6457.01 TCGA.BR.8687.01 TCGA.VQ.A91K.01
#> "0122" "0311" "0114" "0311" "013" "022"
#> TCGA.BR.8690.01 TCGA.BR.8686.01 TCGA.FP.8631.01 TCGA.VQ.A922.01 TCGA.BR.A452.01 TCGA.IN.A6RO.01
#> "013" "021" "0121" "0121" "01121" "022"
#> TCGA.BR.A4QI.01 TCGA.D7.A6EV.01 TCGA.HU.A4G2.01 TCGA.BR.A4IY.01 TCGA.VQ.A8PU.01 TCGA.BR.A4J4.01
#> "023" "0341" "021" "021" "01123" "021"
#> TCGA.VQ.A94R.01 TCGA.HU.A4H4.01 TCGA.BR.7707.01 TCGA.FP.7829.01 TCGA.BR.A4J5.01 TCGA.HU.A4H0.01
#> "022" "032" "022" "022" "0311" "021"
#> TCGA.HU.A4HD.01 TCGA.KB.A6F5.01 TCGA.VQ.AA6K.01 TCGA.HF.7133.01 TCGA.F1.6875.01 TCGA.MX.A666.01
#> "0121" "013" "01121" "013" "0122" "0121"
#> TCGA.BR.7717.01 TCGA.BR.A4PF.01 TCGA.BR.A4IU.01 TCGA.VQ.A8PX.01 TCGA.BR.A4IV.01 TCGA.D7.A6EX.01
#> "0341" "023" "0313" "01121" "01133" "013"
#> TCGA.BR.A4IZ.01 TCGA.BR.A4J9.01 TCGA.CD.A4MJ.01 TCGA.B7.A5TN.01 TCGA.BR.7715.01 TCGA.BR.7704.01
#> "01115" "01133" "023" "0122" "0332" "0123"
#> TCGA.BR.A4J1.01 TCGA.HU.A4GP.01 TCGA.D7.A4YY.01 TCGA.VQ.AA6G.01 TCGA.HU.A4GJ.01 TCGA.CD.A4MI.01
#> "0121" "022" "022" "022" "0314" "023"
#> TCGA.BR.7196.01 TCGA.BR.6563.01 TCGA.VQ.A924.01 TCGA.BR.7716.01 TCGA.FP.7735.01 TCGA.BR.7723.01
#> "0312" "0311" "023" "013" "013" "013"
#> TCGA.HU.A4H8.01 TCGA.IN.A6RJ.01 TCGA.HU.A4H3.01 TCGA.EQ.A4SO.01 TCGA.CD.A4MH.01 TCGA.BR.A4J7.01
#> "022" "0311" "022" "01122" "0123" "01121"
#> TCGA.HF.7131.01 TCGA.D7.A74B.01 TCGA.BR.A4PE.01 TCGA.BR.A4J8.01 TCGA.HU.A4GX.01 TCGA.HU.A4G8.01
#> "0123" "01116" "022" "023" "032" "0341"
#> TCGA.HU.A4GT.01 TCGA.HU.A4GC.01 TCGA.BR.A4CQ.01 TCGA.D7.A6F2.01 TCGA.RD.A7BT.01 TCGA.BR.A4J6.01
#> "022" "0341" "022" "0122" "0122" "0114"
#> TCGA.HU.A4GQ.01 TCGA.HF.7136.01 TCGA.BR.A4QM.01 TCGA.BR.A4PD.01 TCGA.VQ.A8PK.01 TCGA.B7.A5TK.01
#> "023" "013" "023" "0122" "0121" "0312"
#> TCGA.D7.A4YX.01 TCGA.D7.A4Z0.01 TCGA.VQ.A8PT.01 TCGA.IN.A6RN.01 TCGA.CD.A4MG.01 TCGA.D7.A747.01
#> "021" "0313" "022" "0121" "022" "01133"
#> TCGA.R5.A7O7.01 TCGA.F1.A72C.01 TCGA.BR.A4J2.01 TCGA.MX.A663.01 TCGA.D7.A4YV.01 TCGA.HU.A4GD.01
#> "0311" "01121" "0311" "013" "023" "0331"
#> TCGA.BR.A4QL.01 TCGA.BR.7703.01 TCGA.VQ.AA6B.01 TCGA.VQ.AA6D.01 TCGA.D7.A6EZ.01 TCGA.D7.A4YU.01
#> "022" "022" "0332" "0123" "021" "023"
#> TCGA.VQ.AA6A.01 TCGA.IN.7806.01 TCGA.HU.A4HB.01 TCGA.HU.A4H2.01 TCGA.IN.A6RP.01 TCGA.HU.A4H5.01
#> "0123" "0122" "0311" "0342" "022" "0123"
#> TCGA.HU.A4GU.01 TCGA.MX.A5UJ.01 TCGA.HU.A4GN.01 TCGA.CD.5804.01 TCGA.HU.A4H6.01 TCGA.HF.7132.01
#> "022" "022" "023" "013" "023" "023"
#> TCGA.D7.A4YT.01 TCGA.HF.7134.01 TCGA.BR.6852.01 TCGA.BR.8370.01 TCGA.EQ.5647.01 TCGA.IN.A7NT.01
#> "013" "022" "0314" "023" "013" "032"
#> TCGA.RD.A8N9.01 TCGA.D7.5577.01 TCGA.CG.5717.01 TCGA.D7.6818.01 TCGA.CG.5734.01 TCGA.VQ.A8P8.01
#> "0114" "021" "01134" "013" "0311" "0314"
#> TCGA.BR.6707.01 TCGA.B7.5818.01 TCGA.CD.8525.01 TCGA.BR.6705.01 TCGA.BR.4288.01 TCGA.CD.5813.01
#> "021" "021" "013" "0313" "013" "01121"
#> TCGA.CG.5723.01 TCGA.CD.5800.01 TCGA.CG.5718.01 TCGA.BR.8080.01 TCGA.CG.5733.01 TCGA.D7.6817.01
#> "01121" "013" "0123" "0114" "022" "0123"
#> TCGA.KB.A93G.01 TCGA.CD.5799.01 TCGA.BR.7851.01 TCGA.BR.7722.01 TCGA.MX.A5UG.01 TCGA.CD.8533.01
#> "01133" "013" "023" "01121" "0311" "0331"
#> TCGA.BR.7957.01 TCGA.CG.5722.01 TCGA.F1.6874.01 TCGA.CG.5730.01 TCGA.CG.5726.01 TCGA.IP.7968.01
#> "0313" "0312" "032" "0331" "022" "0331"
#> TCGA.BR.8363.01 TCGA.BR.7901.01 TCGA.D7.6822.01 TCGA.BR.6710.01 TCGA.CG.5720.01 TCGA.D7.8570.01
#> "023" "0121" "0341" "01132" "022" "021"
#> TCGA.B7.A5TI.01 TCGA.D7.6815.01 TCGA.BR.8284.01 TCGA.BR.8295.01 TCGA.BR.7197.01 TCGA.B7.A5TJ.01
#> "013" "0122" "023" "0121" "0122" "022"
#> TCGA.D7.A6EY.01 TCGA.BR.8366.01 TCGA.IN.A7NR.01 TCGA.BR.6706.01 TCGA.IN.7808.01 TCGA.BR.6564.01
#> "0313" "021" "01114" "0312" "0311" "01111"
#> TCGA.KB.A93H.01 TCGA.KB.A93J.01 TCGA.CD.5798.01 TCGA.CD.8530.01 TCGA.BR.6802.01 TCGA.CG.5719.01
#> "0332" "0122" "01134" "013" "0311" "0114"
#> TCGA.VQ.A8E3.01 TCGA.CD.5801.01 TCGA.FP.A9TM.01 TCGA.BR.7958.01 TCGA.FP.7998.01 TCGA.IN.A6RS.01
#> "022" "021" "032" "021" "0312" "032"
#> TCGA.BR.6709.01 TCGA.FP.7916.01 TCGA.R5.A7ZR.01 TCGA.B7.5816.01 TCGA.CG.5721.01 TCGA.SW.A7EA.01
#> "01112" "021" "0122" "0314" "0311" "022"
#> TCGA.RD.A8NB.01 TCGA.BR.6801.01 TCGA.IN.AB1X.01 TCGA.D7.5579.01 TCGA.CG.5728.01 TCGA.R5.A7ZI.01
#> "0313" "013" "0314" "013" "0313" "013"
#> TCGA.IN.A7NU.01 TCGA.CG.5732.01 TCGA.ZQ.A9CR.01 TCGA.D7.5578.01 TCGA.BR.6803.01 TCGA.BR.8368.01
#> "032" "013" "013" "032" "01111" "022"
#> TCGA.SW.A7EB.01 TCGA.BR.8081.01 TCGA.VQ.A8P5.01 TCGA.CD.8535.01 TCGA.CG.5724.01 TCGA.D7.8574.01
#> "01132" "023" "032" "022" "0341" "01131"
#> TCGA.HJ.7597.01 TCGA.HF.A5NB.01 TCGA.VQ.A8PB.01 TCGA.R5.A7ZE.01 TCGA.CD.5803.01 TCGA.CG.5725.01
#> "0114" "022" "0341" "0122" "01112" "0121"
#> TCGA.D7.6820.01 TCGA.CD.5802.01 TCGA.R5.A7ZF.01 TCGA.D7.A6F0.01 TCGA.CG.5727.01 TCGA.VQ.A8PC.01
#> "0123" "013" "013" "0121" "032" "0311"
#> TCGA.CD.A486.01 TCGA.RD.A8N2.01 TCGA.IN.A6RI.01 TCGA.HU.8243.01 TCGA.CD.A48C.01 TCGA.RD.A8N5.01
#> "0121" "01113" "0121" "0342" "022" "01131"
#> TCGA.RD.A8N1.01 TCGA.HU.A4GF.01 TCGA.BR.8362.01 TCGA.BR.8285.01 TCGA.CD.8532.01 TCGA.VQ.A8E2.01
#> "013" "0122" "032" "021" "01121" "013"
#> TCGA.BR.8373.01 TCGA.BR.8361.01 TCGA.BR.8058.01 TCGA.IN.8462.01 TCGA.HU.A4G9.01 TCGA.CD.8524.01
#> "0122" "022" "0114" "0341" "022" "032"
#> TCGA.D7.A748.01 TCGA.CD.8527.01 TCGA.VQ.A8DV.01 TCGA.CD.8528.01 TCGA.BR.A453.01 TCGA.RD.A8N6.01
#> "01115" "013" "0123" "022" "0311" "013"
#> TCGA.HU.8245.01 TCGA.ZA.A8F6.01 TCGA.BR.8367.01 TCGA.BR.8380.01 TCGA.FP.A4BE.01 TCGA.HU.8238.01
#> "0123" "013" "032" "0311" "023" "0341"
#> TCGA.BR.8078.01 TCGA.HU.8249.01 TCGA.RD.A8N0.01 TCGA.BR.8365.01 TCGA.FP.8211.01 TCGA.RD.A8N4.01
#> "023" "0331" "01112" "01111" "01122" "01113"
#> TCGA.VQ.A8DU.01 TCGA.VQ.A8DL.01 TCGA.VQ.A8DZ.01 TCGA.D7.8572.01 TCGA.RD.A7BW.01 TCGA.R5.A804.01
#> "0123" "013" "0123" "013" "01116" "0314"
#> TCGA.BR.A4CS.01 TCGA.CD.8531.01 TCGA.CD.A487.01 TCGA.BR.8371.01 TCGA.BR.8059.01 TCGA.D7.A6ET.01
#> "032" "021" "013" "01131" "013" "0312"
#> TCGA.FP.8099.01 TCGA.D7.8579.01 TCGA.BR.8297.01 TCGA.D7.8576.01 TCGA.VQ.A8DT.01 TCGA.FP.A8CX.01
#> "0333" "0313" "032" "0114" "022" "013"
#> TCGA.HU.A4GH.01 TCGA.CD.8526.01 TCGA.HU.A4G6.01 TCGA.D7.8578.01 TCGA.HU.A4G3.01 TCGA.D7.A74A.01
#> "0121" "013" "021" "013" "022" "022"
#> TCGA.RD.A7C1.01 TCGA.F1.A448.01 TCGA.D7.8575.01 TCGA.BR.8372.01 TCGA.VQ.A8P3.01 TCGA.RD.A8MW.01
#> "032" "0311" "0341" "022" "0341" "013"
#> TCGA.BR.8286.01 TCGA.BR.8369.01 TCGA.BR.8364.01 TCGA.HU.8244.01 TCGA.KB.A6F7.01 TCGA.FP.A4BF.01
#> "0341" "032" "01111" "022" "0121" "032"
#> TCGA.R5.A805.01 TCGA.IN.A6RL.01 TCGA.IN.A6RR.01 TCGA.BR.A4CR.01 TCGA.CD.A489.01 TCGA.HU.A4GY.01
#> "032" "0342" "022" "013" "01121" "0114"
#> TCGA.BR.8289.01 TCGA.FP.8209.01 TCGA.BR.8296.01 TCGA.CD.A48A.01 TCGA.BR.8060.01 TCGA.BR.8077.01
#> "0342" "01131" "0314" "0331" "0121" "0122"
#> TCGA.CD.8534.01 TCGA.BR.7959.01 TCGA.VQ.A8P2.01 TCGA.EQ.8122.01 TCGA.D7.8573.01 TCGA.BR.A44T.01
#> "032" "032" "022" "0122" "021" "01112"
#> TCGA.RD.A8MV.01 TCGA.CD.8536.01 TCGA.BR.8360.01 TCGA.BR.8291.01 TCGA.FP.8210.01 TCGA.RD.A7BS.01
#> "0311" "032" "023" "013" "01131" "01134"
#> TCGA.BR.A44U.01 TCGA.CD.8529.01
#> "0341" "013"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 6100))
#> TCGA.VQ.A94P.01 TCGA.D7.6521.01 TCGA.VQ.A8PE.01 TCGA.D7.6519.01 TCGA.BR.6452.01 TCGA.BR.8485.01
#> "01133" "0112" "0123" "013" "023" "0123"
#> TCGA.VQ.A8PO.01 TCGA.VQ.AA69.01 TCGA.BR.8683.01 TCGA.BR.8486.01 TCGA.D7.6522.01 TCGA.CG.5716.01
#> "022" "021" "032" "0123" "01131" "0314"
#> TCGA.BR.8589.01 TCGA.BR.8382.01 TCGA.VQ.AA68.01 TCGA.VQ.A8PJ.01 TCGA.VQ.A8PH.01 TCGA.HU.8604.01
#> "021" "023" "0341" "0122" "0123" "023"
#> TCGA.BR.8676.01 TCGA.CG.4441.01 TCGA.D7.6520.01 TCGA.VQ.AA64.01 TCGA.D7.6527.01 TCGA.VQ.A8PM.01
#> "021" "0342" "0121" "0112" "0123" "013"
#> TCGA.VQ.A923.01 TCGA.BR.8384.01 TCGA.BR.6453.01 TCGA.VQ.A928.01 TCGA.VQ.A8E0.01 TCGA.BR.8679.01
#> "021" "0311" "0311" "0112" "0112" "022"
#> TCGA.VQ.A91S.01 TCGA.BR.8678.01 TCGA.D7.6528.01 TCGA.VQ.A8E7.01 TCGA.BR.8680.01 TCGA.BR.8483.01
#> "032" "0122" "0332" "0341" "0341" "0331"
#> TCGA.BR.6566.01 TCGA.VQ.A91X.01 TCGA.VQ.A91Q.01 TCGA.VQ.A92D.01 TCGA.VQ.A91Z.01 TCGA.BR.6455.01
#> "032" "0332" "0112" "022" "0122" "021"
#> TCGA.BR.8591.01 TCGA.HU.8608.01 TCGA.VQ.A94U.01 TCGA.VQ.A94T.01 TCGA.VQ.A91A.01 TCGA.VQ.A91D.01
#> "023" "021" "0333" "0112" "032" "023"
#> TCGA.D7.6518.01 TCGA.BR.8484.01 TCGA.VQ.A91N.01 TCGA.VQ.A91E.01 TCGA.VQ.A8PY.01 TCGA.HU.8602.01
#> "0311" "013" "0122" "032" "032" "023"
#> TCGA.BR.8381.01 TCGA.BR.6452.11 TCGA.IN.8663.01 TCGA.VQ.A8PS.01 TCGA.VQ.A91W.01 TCGA.BR.6454.01
#> "021" "0314" "022" "0112" "021" "0112"
#> TCGA.BR.8682.01 TCGA.VQ.A91V.01 TCGA.VQ.A8PZ.01 TCGA.BR.8590.01 TCGA.F1.6177.01 TCGA.VQ.A8PQ.01
#> "032" "0333" "0314" "01133" "022" "01112"
#> TCGA.VQ.A91U.01 TCGA.VQ.AA6I.01 TCGA.CG.4437.01 TCGA.VQ.A8PP.01 TCGA.BR.6565.01 TCGA.VQ.A91Y.01
#> "0122" "022" "023" "023" "0121" "013"
#> TCGA.VQ.A8PF.01 TCGA.BR.6456.01 TCGA.BR.6458.01 TCGA.VQ.A925.01 TCGA.VQ.A927.01 TCGA.BR.8592.01
#> "021" "013" "032" "013" "01132" "0313"
#> TCGA.BR.6566.11 TCGA.IN.AB1V.01 TCGA.VQ.AA6F.01 TCGA.VQ.AA6J.01 TCGA.BR.8487.01 TCGA.D7.6525.01
#> "01114" "013" "0112" "0112" "022" "032"
#> TCGA.VQ.A94O.01 TCGA.BR.8588.01 TCGA.HU.8610.01 TCGA.D7.6526.01 TCGA.VQ.A8PD.01 TCGA.D7.6524.01
#> "0121" "0313" "0311" "0123" "0311" "0314"
#> TCGA.3M.AB46.01 TCGA.3M.AB47.01 TCGA.BR.8677.01 TCGA.BR.6457.01 TCGA.BR.8687.01 TCGA.VQ.A91K.01
#> "0122" "0311" "0114" "0311" "013" "022"
#> TCGA.BR.8690.01 TCGA.BR.8686.01 TCGA.FP.8631.01 TCGA.VQ.A922.01 TCGA.BR.A452.01 TCGA.IN.A6RO.01
#> "013" "021" "0121" "0121" "0112" "022"
#> TCGA.BR.A4QI.01 TCGA.D7.A6EV.01 TCGA.HU.A4G2.01 TCGA.BR.A4IY.01 TCGA.VQ.A8PU.01 TCGA.BR.A4J4.01
#> "023" "0341" "021" "021" "0112" "021"
#> TCGA.VQ.A94R.01 TCGA.HU.A4H4.01 TCGA.BR.7707.01 TCGA.FP.7829.01 TCGA.BR.A4J5.01 TCGA.HU.A4H0.01
#> "022" "032" "022" "022" "0311" "021"
#> TCGA.HU.A4HD.01 TCGA.KB.A6F5.01 TCGA.VQ.AA6K.01 TCGA.HF.7133.01 TCGA.F1.6875.01 TCGA.MX.A666.01
#> "0121" "013" "0112" "013" "0122" "0121"
#> TCGA.BR.7717.01 TCGA.BR.A4PF.01 TCGA.BR.A4IU.01 TCGA.VQ.A8PX.01 TCGA.BR.A4IV.01 TCGA.D7.A6EX.01
#> "0341" "023" "0313" "0112" "01133" "013"
#> TCGA.BR.A4IZ.01 TCGA.BR.A4J9.01 TCGA.CD.A4MJ.01 TCGA.B7.A5TN.01 TCGA.BR.7715.01 TCGA.BR.7704.01
#> "01115" "01133" "023" "0122" "0332" "0123"
#> TCGA.BR.A4J1.01 TCGA.HU.A4GP.01 TCGA.D7.A4YY.01 TCGA.VQ.AA6G.01 TCGA.HU.A4GJ.01 TCGA.CD.A4MI.01
#> "0121" "022" "022" "022" "0314" "023"
#> TCGA.BR.7196.01 TCGA.BR.6563.01 TCGA.VQ.A924.01 TCGA.BR.7716.01 TCGA.FP.7735.01 TCGA.BR.7723.01
#> "0312" "0311" "023" "013" "013" "013"
#> TCGA.HU.A4H8.01 TCGA.IN.A6RJ.01 TCGA.HU.A4H3.01 TCGA.EQ.A4SO.01 TCGA.CD.A4MH.01 TCGA.BR.A4J7.01
#> "022" "0311" "022" "0112" "0123" "0112"
#> TCGA.HF.7131.01 TCGA.D7.A74B.01 TCGA.BR.A4PE.01 TCGA.BR.A4J8.01 TCGA.HU.A4GX.01 TCGA.HU.A4G8.01
#> "0123" "01116" "022" "023" "032" "0341"
#> TCGA.HU.A4GT.01 TCGA.HU.A4GC.01 TCGA.BR.A4CQ.01 TCGA.D7.A6F2.01 TCGA.RD.A7BT.01 TCGA.BR.A4J6.01
#> "022" "0341" "022" "0122" "0122" "0114"
#> TCGA.HU.A4GQ.01 TCGA.HF.7136.01 TCGA.BR.A4QM.01 TCGA.BR.A4PD.01 TCGA.VQ.A8PK.01 TCGA.B7.A5TK.01
#> "023" "013" "023" "0122" "0121" "0312"
#> TCGA.D7.A4YX.01 TCGA.D7.A4Z0.01 TCGA.VQ.A8PT.01 TCGA.IN.A6RN.01 TCGA.CD.A4MG.01 TCGA.D7.A747.01
#> "021" "0313" "022" "0121" "022" "01133"
#> TCGA.R5.A7O7.01 TCGA.F1.A72C.01 TCGA.BR.A4J2.01 TCGA.MX.A663.01 TCGA.D7.A4YV.01 TCGA.HU.A4GD.01
#> "0311" "0112" "0311" "013" "023" "0331"
#> TCGA.BR.A4QL.01 TCGA.BR.7703.01 TCGA.VQ.AA6B.01 TCGA.VQ.AA6D.01 TCGA.D7.A6EZ.01 TCGA.D7.A4YU.01
#> "022" "022" "0332" "0123" "021" "023"
#> TCGA.VQ.AA6A.01 TCGA.IN.7806.01 TCGA.HU.A4HB.01 TCGA.HU.A4H2.01 TCGA.IN.A6RP.01 TCGA.HU.A4H5.01
#> "0123" "0122" "0311" "0342" "022" "0123"
#> TCGA.HU.A4GU.01 TCGA.MX.A5UJ.01 TCGA.HU.A4GN.01 TCGA.CD.5804.01 TCGA.HU.A4H6.01 TCGA.HF.7132.01
#> "022" "022" "023" "013" "023" "023"
#> TCGA.D7.A4YT.01 TCGA.HF.7134.01 TCGA.BR.6852.01 TCGA.BR.8370.01 TCGA.EQ.5647.01 TCGA.IN.A7NT.01
#> "013" "022" "0314" "023" "013" "032"
#> TCGA.RD.A8N9.01 TCGA.D7.5577.01 TCGA.CG.5717.01 TCGA.D7.6818.01 TCGA.CG.5734.01 TCGA.VQ.A8P8.01
#> "0114" "021" "01134" "013" "0311" "0314"
#> TCGA.BR.6707.01 TCGA.B7.5818.01 TCGA.CD.8525.01 TCGA.BR.6705.01 TCGA.BR.4288.01 TCGA.CD.5813.01
#> "021" "021" "013" "0313" "013" "0112"
#> TCGA.CG.5723.01 TCGA.CD.5800.01 TCGA.CG.5718.01 TCGA.BR.8080.01 TCGA.CG.5733.01 TCGA.D7.6817.01
#> "0112" "013" "0123" "0114" "022" "0123"
#> TCGA.KB.A93G.01 TCGA.CD.5799.01 TCGA.BR.7851.01 TCGA.BR.7722.01 TCGA.MX.A5UG.01 TCGA.CD.8533.01
#> "01133" "013" "023" "0112" "0311" "0331"
#> TCGA.BR.7957.01 TCGA.CG.5722.01 TCGA.F1.6874.01 TCGA.CG.5730.01 TCGA.CG.5726.01 TCGA.IP.7968.01
#> "0313" "0312" "032" "0331" "022" "0331"
#> TCGA.BR.8363.01 TCGA.BR.7901.01 TCGA.D7.6822.01 TCGA.BR.6710.01 TCGA.CG.5720.01 TCGA.D7.8570.01
#> "023" "0121" "0341" "01132" "022" "021"
#> TCGA.B7.A5TI.01 TCGA.D7.6815.01 TCGA.BR.8284.01 TCGA.BR.8295.01 TCGA.BR.7197.01 TCGA.B7.A5TJ.01
#> "013" "0122" "023" "0121" "0122" "022"
#> TCGA.D7.A6EY.01 TCGA.BR.8366.01 TCGA.IN.A7NR.01 TCGA.BR.6706.01 TCGA.IN.7808.01 TCGA.BR.6564.01
#> "0313" "021" "01114" "0312" "0311" "01111"
#> TCGA.KB.A93H.01 TCGA.KB.A93J.01 TCGA.CD.5798.01 TCGA.CD.8530.01 TCGA.BR.6802.01 TCGA.CG.5719.01
#> "0332" "0122" "01134" "013" "0311" "0114"
#> TCGA.VQ.A8E3.01 TCGA.CD.5801.01 TCGA.FP.A9TM.01 TCGA.BR.7958.01 TCGA.FP.7998.01 TCGA.IN.A6RS.01
#> "022" "021" "032" "021" "0312" "032"
#> TCGA.BR.6709.01 TCGA.FP.7916.01 TCGA.R5.A7ZR.01 TCGA.B7.5816.01 TCGA.CG.5721.01 TCGA.SW.A7EA.01
#> "01112" "021" "0122" "0314" "0311" "022"
#> TCGA.RD.A8NB.01 TCGA.BR.6801.01 TCGA.IN.AB1X.01 TCGA.D7.5579.01 TCGA.CG.5728.01 TCGA.R5.A7ZI.01
#> "0313" "013" "0314" "013" "0313" "013"
#> TCGA.IN.A7NU.01 TCGA.CG.5732.01 TCGA.ZQ.A9CR.01 TCGA.D7.5578.01 TCGA.BR.6803.01 TCGA.BR.8368.01
#> "032" "013" "013" "032" "01111" "022"
#> TCGA.SW.A7EB.01 TCGA.BR.8081.01 TCGA.VQ.A8P5.01 TCGA.CD.8535.01 TCGA.CG.5724.01 TCGA.D7.8574.01
#> "01132" "023" "032" "022" "0341" "01131"
#> TCGA.HJ.7597.01 TCGA.HF.A5NB.01 TCGA.VQ.A8PB.01 TCGA.R5.A7ZE.01 TCGA.CD.5803.01 TCGA.CG.5725.01
#> "0114" "022" "0341" "0122" "01112" "0121"
#> TCGA.D7.6820.01 TCGA.CD.5802.01 TCGA.R5.A7ZF.01 TCGA.D7.A6F0.01 TCGA.CG.5727.01 TCGA.VQ.A8PC.01
#> "0123" "013" "013" "0121" "032" "0311"
#> TCGA.CD.A486.01 TCGA.RD.A8N2.01 TCGA.IN.A6RI.01 TCGA.HU.8243.01 TCGA.CD.A48C.01 TCGA.RD.A8N5.01
#> "0121" "01113" "0121" "0342" "022" "01131"
#> TCGA.RD.A8N1.01 TCGA.HU.A4GF.01 TCGA.BR.8362.01 TCGA.BR.8285.01 TCGA.CD.8532.01 TCGA.VQ.A8E2.01
#> "013" "0122" "032" "021" "0112" "013"
#> TCGA.BR.8373.01 TCGA.BR.8361.01 TCGA.BR.8058.01 TCGA.IN.8462.01 TCGA.HU.A4G9.01 TCGA.CD.8524.01
#> "0122" "022" "0114" "0341" "022" "032"
#> TCGA.D7.A748.01 TCGA.CD.8527.01 TCGA.VQ.A8DV.01 TCGA.CD.8528.01 TCGA.BR.A453.01 TCGA.RD.A8N6.01
#> "01115" "013" "0123" "022" "0311" "013"
#> TCGA.HU.8245.01 TCGA.ZA.A8F6.01 TCGA.BR.8367.01 TCGA.BR.8380.01 TCGA.FP.A4BE.01 TCGA.HU.8238.01
#> "0123" "013" "032" "0311" "023" "0341"
#> TCGA.BR.8078.01 TCGA.HU.8249.01 TCGA.RD.A8N0.01 TCGA.BR.8365.01 TCGA.FP.8211.01 TCGA.RD.A8N4.01
#> "023" "0331" "01112" "01111" "0112" "01113"
#> TCGA.VQ.A8DU.01 TCGA.VQ.A8DL.01 TCGA.VQ.A8DZ.01 TCGA.D7.8572.01 TCGA.RD.A7BW.01 TCGA.R5.A804.01
#> "0123" "013" "0123" "013" "01116" "0314"
#> TCGA.BR.A4CS.01 TCGA.CD.8531.01 TCGA.CD.A487.01 TCGA.BR.8371.01 TCGA.BR.8059.01 TCGA.D7.A6ET.01
#> "032" "021" "013" "01131" "013" "0312"
#> TCGA.FP.8099.01 TCGA.D7.8579.01 TCGA.BR.8297.01 TCGA.D7.8576.01 TCGA.VQ.A8DT.01 TCGA.FP.A8CX.01
#> "0333" "0313" "032" "0114" "022" "013"
#> TCGA.HU.A4GH.01 TCGA.CD.8526.01 TCGA.HU.A4G6.01 TCGA.D7.8578.01 TCGA.HU.A4G3.01 TCGA.D7.A74A.01
#> "0121" "013" "021" "013" "022" "022"
#> TCGA.RD.A7C1.01 TCGA.F1.A448.01 TCGA.D7.8575.01 TCGA.BR.8372.01 TCGA.VQ.A8P3.01 TCGA.RD.A8MW.01
#> "032" "0311" "0341" "022" "0341" "013"
#> TCGA.BR.8286.01 TCGA.BR.8369.01 TCGA.BR.8364.01 TCGA.HU.8244.01 TCGA.KB.A6F7.01 TCGA.FP.A4BF.01
#> "0341" "032" "01111" "022" "0121" "032"
#> TCGA.R5.A805.01 TCGA.IN.A6RL.01 TCGA.IN.A6RR.01 TCGA.BR.A4CR.01 TCGA.CD.A489.01 TCGA.HU.A4GY.01
#> "032" "0342" "022" "013" "0112" "0114"
#> TCGA.BR.8289.01 TCGA.FP.8209.01 TCGA.BR.8296.01 TCGA.CD.A48A.01 TCGA.BR.8060.01 TCGA.BR.8077.01
#> "0342" "01131" "0314" "0331" "0121" "0122"
#> TCGA.CD.8534.01 TCGA.BR.7959.01 TCGA.VQ.A8P2.01 TCGA.EQ.8122.01 TCGA.D7.8573.01 TCGA.BR.A44T.01
#> "032" "032" "022" "0122" "021" "01112"
#> TCGA.RD.A8MV.01 TCGA.CD.8536.01 TCGA.BR.8360.01 TCGA.BR.8291.01 TCGA.FP.8210.01 TCGA.RD.A7BS.01
#> "0311" "032" "023" "013" "01131" "01134"
#> TCGA.BR.A44U.01 TCGA.CD.8529.01
#> "0341" "013"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 6799))
#> TCGA.VQ.A94P.01 TCGA.D7.6521.01 TCGA.VQ.A8PE.01 TCGA.D7.6519.01 TCGA.BR.6452.01 TCGA.BR.8485.01
#> "01133" "0112" "0123" "013" "023" "0123"
#> TCGA.VQ.A8PO.01 TCGA.VQ.AA69.01 TCGA.BR.8683.01 TCGA.BR.8486.01 TCGA.D7.6522.01 TCGA.CG.5716.01
#> "022" "021" "032" "0123" "01131" "0314"
#> TCGA.BR.8589.01 TCGA.BR.8382.01 TCGA.VQ.AA68.01 TCGA.VQ.A8PJ.01 TCGA.VQ.A8PH.01 TCGA.HU.8604.01
#> "021" "023" "034" "0122" "0123" "023"
#> TCGA.BR.8676.01 TCGA.CG.4441.01 TCGA.D7.6520.01 TCGA.VQ.AA64.01 TCGA.D7.6527.01 TCGA.VQ.A8PM.01
#> "021" "034" "0121" "0112" "0123" "013"
#> TCGA.VQ.A923.01 TCGA.BR.8384.01 TCGA.BR.6453.01 TCGA.VQ.A928.01 TCGA.VQ.A8E0.01 TCGA.BR.8679.01
#> "021" "0311" "0311" "0112" "0112" "022"
#> TCGA.VQ.A91S.01 TCGA.BR.8678.01 TCGA.D7.6528.01 TCGA.VQ.A8E7.01 TCGA.BR.8680.01 TCGA.BR.8483.01
#> "032" "0122" "0332" "034" "034" "0331"
#> TCGA.BR.6566.01 TCGA.VQ.A91X.01 TCGA.VQ.A91Q.01 TCGA.VQ.A92D.01 TCGA.VQ.A91Z.01 TCGA.BR.6455.01
#> "032" "0332" "0112" "022" "0122" "021"
#> TCGA.BR.8591.01 TCGA.HU.8608.01 TCGA.VQ.A94U.01 TCGA.VQ.A94T.01 TCGA.VQ.A91A.01 TCGA.VQ.A91D.01
#> "023" "021" "0333" "0112" "032" "023"
#> TCGA.D7.6518.01 TCGA.BR.8484.01 TCGA.VQ.A91N.01 TCGA.VQ.A91E.01 TCGA.VQ.A8PY.01 TCGA.HU.8602.01
#> "0311" "013" "0122" "032" "032" "023"
#> TCGA.BR.8381.01 TCGA.BR.6452.11 TCGA.IN.8663.01 TCGA.VQ.A8PS.01 TCGA.VQ.A91W.01 TCGA.BR.6454.01
#> "021" "0314" "022" "0112" "021" "0112"
#> TCGA.BR.8682.01 TCGA.VQ.A91V.01 TCGA.VQ.A8PZ.01 TCGA.BR.8590.01 TCGA.F1.6177.01 TCGA.VQ.A8PQ.01
#> "032" "0333" "0314" "01133" "022" "01112"
#> TCGA.VQ.A91U.01 TCGA.VQ.AA6I.01 TCGA.CG.4437.01 TCGA.VQ.A8PP.01 TCGA.BR.6565.01 TCGA.VQ.A91Y.01
#> "0122" "022" "023" "023" "0121" "013"
#> TCGA.VQ.A8PF.01 TCGA.BR.6456.01 TCGA.BR.6458.01 TCGA.VQ.A925.01 TCGA.VQ.A927.01 TCGA.BR.8592.01
#> "021" "013" "032" "013" "01132" "0313"
#> TCGA.BR.6566.11 TCGA.IN.AB1V.01 TCGA.VQ.AA6F.01 TCGA.VQ.AA6J.01 TCGA.BR.8487.01 TCGA.D7.6525.01
#> "01114" "013" "0112" "0112" "022" "032"
#> TCGA.VQ.A94O.01 TCGA.BR.8588.01 TCGA.HU.8610.01 TCGA.D7.6526.01 TCGA.VQ.A8PD.01 TCGA.D7.6524.01
#> "0121" "0313" "0311" "0123" "0311" "0314"
#> TCGA.3M.AB46.01 TCGA.3M.AB47.01 TCGA.BR.8677.01 TCGA.BR.6457.01 TCGA.BR.8687.01 TCGA.VQ.A91K.01
#> "0122" "0311" "0114" "0311" "013" "022"
#> TCGA.BR.8690.01 TCGA.BR.8686.01 TCGA.FP.8631.01 TCGA.VQ.A922.01 TCGA.BR.A452.01 TCGA.IN.A6RO.01
#> "013" "021" "0121" "0121" "0112" "022"
#> TCGA.BR.A4QI.01 TCGA.D7.A6EV.01 TCGA.HU.A4G2.01 TCGA.BR.A4IY.01 TCGA.VQ.A8PU.01 TCGA.BR.A4J4.01
#> "023" "034" "021" "021" "0112" "021"
#> TCGA.VQ.A94R.01 TCGA.HU.A4H4.01 TCGA.BR.7707.01 TCGA.FP.7829.01 TCGA.BR.A4J5.01 TCGA.HU.A4H0.01
#> "022" "032" "022" "022" "0311" "021"
#> TCGA.HU.A4HD.01 TCGA.KB.A6F5.01 TCGA.VQ.AA6K.01 TCGA.HF.7133.01 TCGA.F1.6875.01 TCGA.MX.A666.01
#> "0121" "013" "0112" "013" "0122" "0121"
#> TCGA.BR.7717.01 TCGA.BR.A4PF.01 TCGA.BR.A4IU.01 TCGA.VQ.A8PX.01 TCGA.BR.A4IV.01 TCGA.D7.A6EX.01
#> "034" "023" "0313" "0112" "01133" "013"
#> TCGA.BR.A4IZ.01 TCGA.BR.A4J9.01 TCGA.CD.A4MJ.01 TCGA.B7.A5TN.01 TCGA.BR.7715.01 TCGA.BR.7704.01
#> "01115" "01133" "023" "0122" "0332" "0123"
#> TCGA.BR.A4J1.01 TCGA.HU.A4GP.01 TCGA.D7.A4YY.01 TCGA.VQ.AA6G.01 TCGA.HU.A4GJ.01 TCGA.CD.A4MI.01
#> "0121" "022" "022" "022" "0314" "023"
#> TCGA.BR.7196.01 TCGA.BR.6563.01 TCGA.VQ.A924.01 TCGA.BR.7716.01 TCGA.FP.7735.01 TCGA.BR.7723.01
#> "0312" "0311" "023" "013" "013" "013"
#> TCGA.HU.A4H8.01 TCGA.IN.A6RJ.01 TCGA.HU.A4H3.01 TCGA.EQ.A4SO.01 TCGA.CD.A4MH.01 TCGA.BR.A4J7.01
#> "022" "0311" "022" "0112" "0123" "0112"
#> TCGA.HF.7131.01 TCGA.D7.A74B.01 TCGA.BR.A4PE.01 TCGA.BR.A4J8.01 TCGA.HU.A4GX.01 TCGA.HU.A4G8.01
#> "0123" "01116" "022" "023" "032" "034"
#> TCGA.HU.A4GT.01 TCGA.HU.A4GC.01 TCGA.BR.A4CQ.01 TCGA.D7.A6F2.01 TCGA.RD.A7BT.01 TCGA.BR.A4J6.01
#> "022" "034" "022" "0122" "0122" "0114"
#> TCGA.HU.A4GQ.01 TCGA.HF.7136.01 TCGA.BR.A4QM.01 TCGA.BR.A4PD.01 TCGA.VQ.A8PK.01 TCGA.B7.A5TK.01
#> "023" "013" "023" "0122" "0121" "0312"
#> TCGA.D7.A4YX.01 TCGA.D7.A4Z0.01 TCGA.VQ.A8PT.01 TCGA.IN.A6RN.01 TCGA.CD.A4MG.01 TCGA.D7.A747.01
#> "021" "0313" "022" "0121" "022" "01133"
#> TCGA.R5.A7O7.01 TCGA.F1.A72C.01 TCGA.BR.A4J2.01 TCGA.MX.A663.01 TCGA.D7.A4YV.01 TCGA.HU.A4GD.01
#> "0311" "0112" "0311" "013" "023" "0331"
#> TCGA.BR.A4QL.01 TCGA.BR.7703.01 TCGA.VQ.AA6B.01 TCGA.VQ.AA6D.01 TCGA.D7.A6EZ.01 TCGA.D7.A4YU.01
#> "022" "022" "0332" "0123" "021" "023"
#> TCGA.VQ.AA6A.01 TCGA.IN.7806.01 TCGA.HU.A4HB.01 TCGA.HU.A4H2.01 TCGA.IN.A6RP.01 TCGA.HU.A4H5.01
#> "0123" "0122" "0311" "034" "022" "0123"
#> TCGA.HU.A4GU.01 TCGA.MX.A5UJ.01 TCGA.HU.A4GN.01 TCGA.CD.5804.01 TCGA.HU.A4H6.01 TCGA.HF.7132.01
#> "022" "022" "023" "013" "023" "023"
#> TCGA.D7.A4YT.01 TCGA.HF.7134.01 TCGA.BR.6852.01 TCGA.BR.8370.01 TCGA.EQ.5647.01 TCGA.IN.A7NT.01
#> "013" "022" "0314" "023" "013" "032"
#> TCGA.RD.A8N9.01 TCGA.D7.5577.01 TCGA.CG.5717.01 TCGA.D7.6818.01 TCGA.CG.5734.01 TCGA.VQ.A8P8.01
#> "0114" "021" "01134" "013" "0311" "0314"
#> TCGA.BR.6707.01 TCGA.B7.5818.01 TCGA.CD.8525.01 TCGA.BR.6705.01 TCGA.BR.4288.01 TCGA.CD.5813.01
#> "021" "021" "013" "0313" "013" "0112"
#> TCGA.CG.5723.01 TCGA.CD.5800.01 TCGA.CG.5718.01 TCGA.BR.8080.01 TCGA.CG.5733.01 TCGA.D7.6817.01
#> "0112" "013" "0123" "0114" "022" "0123"
#> TCGA.KB.A93G.01 TCGA.CD.5799.01 TCGA.BR.7851.01 TCGA.BR.7722.01 TCGA.MX.A5UG.01 TCGA.CD.8533.01
#> "01133" "013" "023" "0112" "0311" "0331"
#> TCGA.BR.7957.01 TCGA.CG.5722.01 TCGA.F1.6874.01 TCGA.CG.5730.01 TCGA.CG.5726.01 TCGA.IP.7968.01
#> "0313" "0312" "032" "0331" "022" "0331"
#> TCGA.BR.8363.01 TCGA.BR.7901.01 TCGA.D7.6822.01 TCGA.BR.6710.01 TCGA.CG.5720.01 TCGA.D7.8570.01
#> "023" "0121" "034" "01132" "022" "021"
#> TCGA.B7.A5TI.01 TCGA.D7.6815.01 TCGA.BR.8284.01 TCGA.BR.8295.01 TCGA.BR.7197.01 TCGA.B7.A5TJ.01
#> "013" "0122" "023" "0121" "0122" "022"
#> TCGA.D7.A6EY.01 TCGA.BR.8366.01 TCGA.IN.A7NR.01 TCGA.BR.6706.01 TCGA.IN.7808.01 TCGA.BR.6564.01
#> "0313" "021" "01114" "0312" "0311" "01111"
#> TCGA.KB.A93H.01 TCGA.KB.A93J.01 TCGA.CD.5798.01 TCGA.CD.8530.01 TCGA.BR.6802.01 TCGA.CG.5719.01
#> "0332" "0122" "01134" "013" "0311" "0114"
#> TCGA.VQ.A8E3.01 TCGA.CD.5801.01 TCGA.FP.A9TM.01 TCGA.BR.7958.01 TCGA.FP.7998.01 TCGA.IN.A6RS.01
#> "022" "021" "032" "021" "0312" "032"
#> TCGA.BR.6709.01 TCGA.FP.7916.01 TCGA.R5.A7ZR.01 TCGA.B7.5816.01 TCGA.CG.5721.01 TCGA.SW.A7EA.01
#> "01112" "021" "0122" "0314" "0311" "022"
#> TCGA.RD.A8NB.01 TCGA.BR.6801.01 TCGA.IN.AB1X.01 TCGA.D7.5579.01 TCGA.CG.5728.01 TCGA.R5.A7ZI.01
#> "0313" "013" "0314" "013" "0313" "013"
#> TCGA.IN.A7NU.01 TCGA.CG.5732.01 TCGA.ZQ.A9CR.01 TCGA.D7.5578.01 TCGA.BR.6803.01 TCGA.BR.8368.01
#> "032" "013" "013" "032" "01111" "022"
#> TCGA.SW.A7EB.01 TCGA.BR.8081.01 TCGA.VQ.A8P5.01 TCGA.CD.8535.01 TCGA.CG.5724.01 TCGA.D7.8574.01
#> "01132" "023" "032" "022" "034" "01131"
#> TCGA.HJ.7597.01 TCGA.HF.A5NB.01 TCGA.VQ.A8PB.01 TCGA.R5.A7ZE.01 TCGA.CD.5803.01 TCGA.CG.5725.01
#> "0114" "022" "034" "0122" "01112" "0121"
#> TCGA.D7.6820.01 TCGA.CD.5802.01 TCGA.R5.A7ZF.01 TCGA.D7.A6F0.01 TCGA.CG.5727.01 TCGA.VQ.A8PC.01
#> "0123" "013" "013" "0121" "032" "0311"
#> TCGA.CD.A486.01 TCGA.RD.A8N2.01 TCGA.IN.A6RI.01 TCGA.HU.8243.01 TCGA.CD.A48C.01 TCGA.RD.A8N5.01
#> "0121" "01113" "0121" "034" "022" "01131"
#> TCGA.RD.A8N1.01 TCGA.HU.A4GF.01 TCGA.BR.8362.01 TCGA.BR.8285.01 TCGA.CD.8532.01 TCGA.VQ.A8E2.01
#> "013" "0122" "032" "021" "0112" "013"
#> TCGA.BR.8373.01 TCGA.BR.8361.01 TCGA.BR.8058.01 TCGA.IN.8462.01 TCGA.HU.A4G9.01 TCGA.CD.8524.01
#> "0122" "022" "0114" "034" "022" "032"
#> TCGA.D7.A748.01 TCGA.CD.8527.01 TCGA.VQ.A8DV.01 TCGA.CD.8528.01 TCGA.BR.A453.01 TCGA.RD.A8N6.01
#> "01115" "013" "0123" "022" "0311" "013"
#> TCGA.HU.8245.01 TCGA.ZA.A8F6.01 TCGA.BR.8367.01 TCGA.BR.8380.01 TCGA.FP.A4BE.01 TCGA.HU.8238.01
#> "0123" "013" "032" "0311" "023" "034"
#> TCGA.BR.8078.01 TCGA.HU.8249.01 TCGA.RD.A8N0.01 TCGA.BR.8365.01 TCGA.FP.8211.01 TCGA.RD.A8N4.01
#> "023" "0331" "01112" "01111" "0112" "01113"
#> TCGA.VQ.A8DU.01 TCGA.VQ.A8DL.01 TCGA.VQ.A8DZ.01 TCGA.D7.8572.01 TCGA.RD.A7BW.01 TCGA.R5.A804.01
#> "0123" "013" "0123" "013" "01116" "0314"
#> TCGA.BR.A4CS.01 TCGA.CD.8531.01 TCGA.CD.A487.01 TCGA.BR.8371.01 TCGA.BR.8059.01 TCGA.D7.A6ET.01
#> "032" "021" "013" "01131" "013" "0312"
#> TCGA.FP.8099.01 TCGA.D7.8579.01 TCGA.BR.8297.01 TCGA.D7.8576.01 TCGA.VQ.A8DT.01 TCGA.FP.A8CX.01
#> "0333" "0313" "032" "0114" "022" "013"
#> TCGA.HU.A4GH.01 TCGA.CD.8526.01 TCGA.HU.A4G6.01 TCGA.D7.8578.01 TCGA.HU.A4G3.01 TCGA.D7.A74A.01
#> "0121" "013" "021" "013" "022" "022"
#> TCGA.RD.A7C1.01 TCGA.F1.A448.01 TCGA.D7.8575.01 TCGA.BR.8372.01 TCGA.VQ.A8P3.01 TCGA.RD.A8MW.01
#> "032" "0311" "034" "022" "034" "013"
#> TCGA.BR.8286.01 TCGA.BR.8369.01 TCGA.BR.8364.01 TCGA.HU.8244.01 TCGA.KB.A6F7.01 TCGA.FP.A4BF.01
#> "034" "032" "01111" "022" "0121" "032"
#> TCGA.R5.A805.01 TCGA.IN.A6RL.01 TCGA.IN.A6RR.01 TCGA.BR.A4CR.01 TCGA.CD.A489.01 TCGA.HU.A4GY.01
#> "032" "034" "022" "013" "0112" "0114"
#> TCGA.BR.8289.01 TCGA.FP.8209.01 TCGA.BR.8296.01 TCGA.CD.A48A.01 TCGA.BR.8060.01 TCGA.BR.8077.01
#> "034" "01131" "0314" "0331" "0121" "0122"
#> TCGA.CD.8534.01 TCGA.BR.7959.01 TCGA.VQ.A8P2.01 TCGA.EQ.8122.01 TCGA.D7.8573.01 TCGA.BR.A44T.01
#> "032" "032" "022" "0122" "021" "01112"
#> TCGA.RD.A8MV.01 TCGA.CD.8536.01 TCGA.BR.8360.01 TCGA.BR.8291.01 TCGA.FP.8210.01 TCGA.RD.A7BS.01
#> "0311" "032" "023" "013" "01131" "01134"
#> TCGA.BR.A44U.01 TCGA.CD.8529.01
#> "034" "013"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 7619))
#> TCGA.VQ.A94P.01 TCGA.D7.6521.01 TCGA.VQ.A8PE.01 TCGA.D7.6519.01 TCGA.BR.6452.01 TCGA.BR.8485.01
#> "01133" "0112" "012" "013" "023" "012"
#> TCGA.VQ.A8PO.01 TCGA.VQ.AA69.01 TCGA.BR.8683.01 TCGA.BR.8486.01 TCGA.D7.6522.01 TCGA.CG.5716.01
#> "022" "021" "032" "012" "01131" "0314"
#> TCGA.BR.8589.01 TCGA.BR.8382.01 TCGA.VQ.AA68.01 TCGA.VQ.A8PJ.01 TCGA.VQ.A8PH.01 TCGA.HU.8604.01
#> "021" "023" "034" "012" "012" "023"
#> TCGA.BR.8676.01 TCGA.CG.4441.01 TCGA.D7.6520.01 TCGA.VQ.AA64.01 TCGA.D7.6527.01 TCGA.VQ.A8PM.01
#> "021" "034" "012" "0112" "012" "013"
#> TCGA.VQ.A923.01 TCGA.BR.8384.01 TCGA.BR.6453.01 TCGA.VQ.A928.01 TCGA.VQ.A8E0.01 TCGA.BR.8679.01
#> "021" "0311" "0311" "0112" "0112" "022"
#> TCGA.VQ.A91S.01 TCGA.BR.8678.01 TCGA.D7.6528.01 TCGA.VQ.A8E7.01 TCGA.BR.8680.01 TCGA.BR.8483.01
#> "032" "012" "0332" "034" "034" "0331"
#> TCGA.BR.6566.01 TCGA.VQ.A91X.01 TCGA.VQ.A91Q.01 TCGA.VQ.A92D.01 TCGA.VQ.A91Z.01 TCGA.BR.6455.01
#> "032" "0332" "0112" "022" "012" "021"
#> TCGA.BR.8591.01 TCGA.HU.8608.01 TCGA.VQ.A94U.01 TCGA.VQ.A94T.01 TCGA.VQ.A91A.01 TCGA.VQ.A91D.01
#> "023" "021" "0333" "0112" "032" "023"
#> TCGA.D7.6518.01 TCGA.BR.8484.01 TCGA.VQ.A91N.01 TCGA.VQ.A91E.01 TCGA.VQ.A8PY.01 TCGA.HU.8602.01
#> "0311" "013" "012" "032" "032" "023"
#> TCGA.BR.8381.01 TCGA.BR.6452.11 TCGA.IN.8663.01 TCGA.VQ.A8PS.01 TCGA.VQ.A91W.01 TCGA.BR.6454.01
#> "021" "0314" "022" "0112" "021" "0112"
#> TCGA.BR.8682.01 TCGA.VQ.A91V.01 TCGA.VQ.A8PZ.01 TCGA.BR.8590.01 TCGA.F1.6177.01 TCGA.VQ.A8PQ.01
#> "032" "0333" "0314" "01133" "022" "01112"
#> TCGA.VQ.A91U.01 TCGA.VQ.AA6I.01 TCGA.CG.4437.01 TCGA.VQ.A8PP.01 TCGA.BR.6565.01 TCGA.VQ.A91Y.01
#> "012" "022" "023" "023" "012" "013"
#> TCGA.VQ.A8PF.01 TCGA.BR.6456.01 TCGA.BR.6458.01 TCGA.VQ.A925.01 TCGA.VQ.A927.01 TCGA.BR.8592.01
#> "021" "013" "032" "013" "01132" "0313"
#> TCGA.BR.6566.11 TCGA.IN.AB1V.01 TCGA.VQ.AA6F.01 TCGA.VQ.AA6J.01 TCGA.BR.8487.01 TCGA.D7.6525.01
#> "01114" "013" "0112" "0112" "022" "032"
#> TCGA.VQ.A94O.01 TCGA.BR.8588.01 TCGA.HU.8610.01 TCGA.D7.6526.01 TCGA.VQ.A8PD.01 TCGA.D7.6524.01
#> "012" "0313" "0311" "012" "0311" "0314"
#> TCGA.3M.AB46.01 TCGA.3M.AB47.01 TCGA.BR.8677.01 TCGA.BR.6457.01 TCGA.BR.8687.01 TCGA.VQ.A91K.01
#> "012" "0311" "0114" "0311" "013" "022"
#> TCGA.BR.8690.01 TCGA.BR.8686.01 TCGA.FP.8631.01 TCGA.VQ.A922.01 TCGA.BR.A452.01 TCGA.IN.A6RO.01
#> "013" "021" "012" "012" "0112" "022"
#> TCGA.BR.A4QI.01 TCGA.D7.A6EV.01 TCGA.HU.A4G2.01 TCGA.BR.A4IY.01 TCGA.VQ.A8PU.01 TCGA.BR.A4J4.01
#> "023" "034" "021" "021" "0112" "021"
#> TCGA.VQ.A94R.01 TCGA.HU.A4H4.01 TCGA.BR.7707.01 TCGA.FP.7829.01 TCGA.BR.A4J5.01 TCGA.HU.A4H0.01
#> "022" "032" "022" "022" "0311" "021"
#> TCGA.HU.A4HD.01 TCGA.KB.A6F5.01 TCGA.VQ.AA6K.01 TCGA.HF.7133.01 TCGA.F1.6875.01 TCGA.MX.A666.01
#> "012" "013" "0112" "013" "012" "012"
#> TCGA.BR.7717.01 TCGA.BR.A4PF.01 TCGA.BR.A4IU.01 TCGA.VQ.A8PX.01 TCGA.BR.A4IV.01 TCGA.D7.A6EX.01
#> "034" "023" "0313" "0112" "01133" "013"
#> TCGA.BR.A4IZ.01 TCGA.BR.A4J9.01 TCGA.CD.A4MJ.01 TCGA.B7.A5TN.01 TCGA.BR.7715.01 TCGA.BR.7704.01
#> "01115" "01133" "023" "012" "0332" "012"
#> TCGA.BR.A4J1.01 TCGA.HU.A4GP.01 TCGA.D7.A4YY.01 TCGA.VQ.AA6G.01 TCGA.HU.A4GJ.01 TCGA.CD.A4MI.01
#> "012" "022" "022" "022" "0314" "023"
#> TCGA.BR.7196.01 TCGA.BR.6563.01 TCGA.VQ.A924.01 TCGA.BR.7716.01 TCGA.FP.7735.01 TCGA.BR.7723.01
#> "0312" "0311" "023" "013" "013" "013"
#> TCGA.HU.A4H8.01 TCGA.IN.A6RJ.01 TCGA.HU.A4H3.01 TCGA.EQ.A4SO.01 TCGA.CD.A4MH.01 TCGA.BR.A4J7.01
#> "022" "0311" "022" "0112" "012" "0112"
#> TCGA.HF.7131.01 TCGA.D7.A74B.01 TCGA.BR.A4PE.01 TCGA.BR.A4J8.01 TCGA.HU.A4GX.01 TCGA.HU.A4G8.01
#> "012" "01116" "022" "023" "032" "034"
#> TCGA.HU.A4GT.01 TCGA.HU.A4GC.01 TCGA.BR.A4CQ.01 TCGA.D7.A6F2.01 TCGA.RD.A7BT.01 TCGA.BR.A4J6.01
#> "022" "034" "022" "012" "012" "0114"
#> TCGA.HU.A4GQ.01 TCGA.HF.7136.01 TCGA.BR.A4QM.01 TCGA.BR.A4PD.01 TCGA.VQ.A8PK.01 TCGA.B7.A5TK.01
#> "023" "013" "023" "012" "012" "0312"
#> TCGA.D7.A4YX.01 TCGA.D7.A4Z0.01 TCGA.VQ.A8PT.01 TCGA.IN.A6RN.01 TCGA.CD.A4MG.01 TCGA.D7.A747.01
#> "021" "0313" "022" "012" "022" "01133"
#> TCGA.R5.A7O7.01 TCGA.F1.A72C.01 TCGA.BR.A4J2.01 TCGA.MX.A663.01 TCGA.D7.A4YV.01 TCGA.HU.A4GD.01
#> "0311" "0112" "0311" "013" "023" "0331"
#> TCGA.BR.A4QL.01 TCGA.BR.7703.01 TCGA.VQ.AA6B.01 TCGA.VQ.AA6D.01 TCGA.D7.A6EZ.01 TCGA.D7.A4YU.01
#> "022" "022" "0332" "012" "021" "023"
#> TCGA.VQ.AA6A.01 TCGA.IN.7806.01 TCGA.HU.A4HB.01 TCGA.HU.A4H2.01 TCGA.IN.A6RP.01 TCGA.HU.A4H5.01
#> "012" "012" "0311" "034" "022" "012"
#> TCGA.HU.A4GU.01 TCGA.MX.A5UJ.01 TCGA.HU.A4GN.01 TCGA.CD.5804.01 TCGA.HU.A4H6.01 TCGA.HF.7132.01
#> "022" "022" "023" "013" "023" "023"
#> TCGA.D7.A4YT.01 TCGA.HF.7134.01 TCGA.BR.6852.01 TCGA.BR.8370.01 TCGA.EQ.5647.01 TCGA.IN.A7NT.01
#> "013" "022" "0314" "023" "013" "032"
#> TCGA.RD.A8N9.01 TCGA.D7.5577.01 TCGA.CG.5717.01 TCGA.D7.6818.01 TCGA.CG.5734.01 TCGA.VQ.A8P8.01
#> "0114" "021" "01134" "013" "0311" "0314"
#> TCGA.BR.6707.01 TCGA.B7.5818.01 TCGA.CD.8525.01 TCGA.BR.6705.01 TCGA.BR.4288.01 TCGA.CD.5813.01
#> "021" "021" "013" "0313" "013" "0112"
#> TCGA.CG.5723.01 TCGA.CD.5800.01 TCGA.CG.5718.01 TCGA.BR.8080.01 TCGA.CG.5733.01 TCGA.D7.6817.01
#> "0112" "013" "012" "0114" "022" "012"
#> TCGA.KB.A93G.01 TCGA.CD.5799.01 TCGA.BR.7851.01 TCGA.BR.7722.01 TCGA.MX.A5UG.01 TCGA.CD.8533.01
#> "01133" "013" "023" "0112" "0311" "0331"
#> TCGA.BR.7957.01 TCGA.CG.5722.01 TCGA.F1.6874.01 TCGA.CG.5730.01 TCGA.CG.5726.01 TCGA.IP.7968.01
#> "0313" "0312" "032" "0331" "022" "0331"
#> TCGA.BR.8363.01 TCGA.BR.7901.01 TCGA.D7.6822.01 TCGA.BR.6710.01 TCGA.CG.5720.01 TCGA.D7.8570.01
#> "023" "012" "034" "01132" "022" "021"
#> TCGA.B7.A5TI.01 TCGA.D7.6815.01 TCGA.BR.8284.01 TCGA.BR.8295.01 TCGA.BR.7197.01 TCGA.B7.A5TJ.01
#> "013" "012" "023" "012" "012" "022"
#> TCGA.D7.A6EY.01 TCGA.BR.8366.01 TCGA.IN.A7NR.01 TCGA.BR.6706.01 TCGA.IN.7808.01 TCGA.BR.6564.01
#> "0313" "021" "01114" "0312" "0311" "01111"
#> TCGA.KB.A93H.01 TCGA.KB.A93J.01 TCGA.CD.5798.01 TCGA.CD.8530.01 TCGA.BR.6802.01 TCGA.CG.5719.01
#> "0332" "012" "01134" "013" "0311" "0114"
#> TCGA.VQ.A8E3.01 TCGA.CD.5801.01 TCGA.FP.A9TM.01 TCGA.BR.7958.01 TCGA.FP.7998.01 TCGA.IN.A6RS.01
#> "022" "021" "032" "021" "0312" "032"
#> TCGA.BR.6709.01 TCGA.FP.7916.01 TCGA.R5.A7ZR.01 TCGA.B7.5816.01 TCGA.CG.5721.01 TCGA.SW.A7EA.01
#> "01112" "021" "012" "0314" "0311" "022"
#> TCGA.RD.A8NB.01 TCGA.BR.6801.01 TCGA.IN.AB1X.01 TCGA.D7.5579.01 TCGA.CG.5728.01 TCGA.R5.A7ZI.01
#> "0313" "013" "0314" "013" "0313" "013"
#> TCGA.IN.A7NU.01 TCGA.CG.5732.01 TCGA.ZQ.A9CR.01 TCGA.D7.5578.01 TCGA.BR.6803.01 TCGA.BR.8368.01
#> "032" "013" "013" "032" "01111" "022"
#> TCGA.SW.A7EB.01 TCGA.BR.8081.01 TCGA.VQ.A8P5.01 TCGA.CD.8535.01 TCGA.CG.5724.01 TCGA.D7.8574.01
#> "01132" "023" "032" "022" "034" "01131"
#> TCGA.HJ.7597.01 TCGA.HF.A5NB.01 TCGA.VQ.A8PB.01 TCGA.R5.A7ZE.01 TCGA.CD.5803.01 TCGA.CG.5725.01
#> "0114" "022" "034" "012" "01112" "012"
#> TCGA.D7.6820.01 TCGA.CD.5802.01 TCGA.R5.A7ZF.01 TCGA.D7.A6F0.01 TCGA.CG.5727.01 TCGA.VQ.A8PC.01
#> "012" "013" "013" "012" "032" "0311"
#> TCGA.CD.A486.01 TCGA.RD.A8N2.01 TCGA.IN.A6RI.01 TCGA.HU.8243.01 TCGA.CD.A48C.01 TCGA.RD.A8N5.01
#> "012" "01113" "012" "034" "022" "01131"
#> TCGA.RD.A8N1.01 TCGA.HU.A4GF.01 TCGA.BR.8362.01 TCGA.BR.8285.01 TCGA.CD.8532.01 TCGA.VQ.A8E2.01
#> "013" "012" "032" "021" "0112" "013"
#> TCGA.BR.8373.01 TCGA.BR.8361.01 TCGA.BR.8058.01 TCGA.IN.8462.01 TCGA.HU.A4G9.01 TCGA.CD.8524.01
#> "012" "022" "0114" "034" "022" "032"
#> TCGA.D7.A748.01 TCGA.CD.8527.01 TCGA.VQ.A8DV.01 TCGA.CD.8528.01 TCGA.BR.A453.01 TCGA.RD.A8N6.01
#> "01115" "013" "012" "022" "0311" "013"
#> TCGA.HU.8245.01 TCGA.ZA.A8F6.01 TCGA.BR.8367.01 TCGA.BR.8380.01 TCGA.FP.A4BE.01 TCGA.HU.8238.01
#> "012" "013" "032" "0311" "023" "034"
#> TCGA.BR.8078.01 TCGA.HU.8249.01 TCGA.RD.A8N0.01 TCGA.BR.8365.01 TCGA.FP.8211.01 TCGA.RD.A8N4.01
#> "023" "0331" "01112" "01111" "0112" "01113"
#> TCGA.VQ.A8DU.01 TCGA.VQ.A8DL.01 TCGA.VQ.A8DZ.01 TCGA.D7.8572.01 TCGA.RD.A7BW.01 TCGA.R5.A804.01
#> "012" "013" "012" "013" "01116" "0314"
#> TCGA.BR.A4CS.01 TCGA.CD.8531.01 TCGA.CD.A487.01 TCGA.BR.8371.01 TCGA.BR.8059.01 TCGA.D7.A6ET.01
#> "032" "021" "013" "01131" "013" "0312"
#> TCGA.FP.8099.01 TCGA.D7.8579.01 TCGA.BR.8297.01 TCGA.D7.8576.01 TCGA.VQ.A8DT.01 TCGA.FP.A8CX.01
#> "0333" "0313" "032" "0114" "022" "013"
#> TCGA.HU.A4GH.01 TCGA.CD.8526.01 TCGA.HU.A4G6.01 TCGA.D7.8578.01 TCGA.HU.A4G3.01 TCGA.D7.A74A.01
#> "012" "013" "021" "013" "022" "022"
#> TCGA.RD.A7C1.01 TCGA.F1.A448.01 TCGA.D7.8575.01 TCGA.BR.8372.01 TCGA.VQ.A8P3.01 TCGA.RD.A8MW.01
#> "032" "0311" "034" "022" "034" "013"
#> TCGA.BR.8286.01 TCGA.BR.8369.01 TCGA.BR.8364.01 TCGA.HU.8244.01 TCGA.KB.A6F7.01 TCGA.FP.A4BF.01
#> "034" "032" "01111" "022" "012" "032"
#> TCGA.R5.A805.01 TCGA.IN.A6RL.01 TCGA.IN.A6RR.01 TCGA.BR.A4CR.01 TCGA.CD.A489.01 TCGA.HU.A4GY.01
#> "032" "034" "022" "013" "0112" "0114"
#> TCGA.BR.8289.01 TCGA.FP.8209.01 TCGA.BR.8296.01 TCGA.CD.A48A.01 TCGA.BR.8060.01 TCGA.BR.8077.01
#> "034" "01131" "0314" "0331" "012" "012"
#> TCGA.CD.8534.01 TCGA.BR.7959.01 TCGA.VQ.A8P2.01 TCGA.EQ.8122.01 TCGA.D7.8573.01 TCGA.BR.A44T.01
#> "032" "032" "022" "012" "021" "01112"
#> TCGA.RD.A8MV.01 TCGA.CD.8536.01 TCGA.BR.8360.01 TCGA.BR.8291.01 TCGA.FP.8210.01 TCGA.RD.A7BS.01
#> "0311" "032" "023" "013" "01131" "01134"
#> TCGA.BR.A44U.01 TCGA.CD.8529.01
#> "034" "013"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 7939))
#> TCGA.VQ.A94P.01 TCGA.D7.6521.01 TCGA.VQ.A8PE.01 TCGA.D7.6519.01 TCGA.BR.6452.01 TCGA.BR.8485.01
#> "011" "011" "012" "013" "023" "012"
#> TCGA.VQ.A8PO.01 TCGA.VQ.AA69.01 TCGA.BR.8683.01 TCGA.BR.8486.01 TCGA.D7.6522.01 TCGA.CG.5716.01
#> "022" "021" "032" "012" "011" "0314"
#> TCGA.BR.8589.01 TCGA.BR.8382.01 TCGA.VQ.AA68.01 TCGA.VQ.A8PJ.01 TCGA.VQ.A8PH.01 TCGA.HU.8604.01
#> "021" "023" "034" "012" "012" "023"
#> TCGA.BR.8676.01 TCGA.CG.4441.01 TCGA.D7.6520.01 TCGA.VQ.AA64.01 TCGA.D7.6527.01 TCGA.VQ.A8PM.01
#> "021" "034" "012" "011" "012" "013"
#> TCGA.VQ.A923.01 TCGA.BR.8384.01 TCGA.BR.6453.01 TCGA.VQ.A928.01 TCGA.VQ.A8E0.01 TCGA.BR.8679.01
#> "021" "0311" "0311" "011" "011" "022"
#> TCGA.VQ.A91S.01 TCGA.BR.8678.01 TCGA.D7.6528.01 TCGA.VQ.A8E7.01 TCGA.BR.8680.01 TCGA.BR.8483.01
#> "032" "012" "0332" "034" "034" "0331"
#> TCGA.BR.6566.01 TCGA.VQ.A91X.01 TCGA.VQ.A91Q.01 TCGA.VQ.A92D.01 TCGA.VQ.A91Z.01 TCGA.BR.6455.01
#> "032" "0332" "011" "022" "012" "021"
#> TCGA.BR.8591.01 TCGA.HU.8608.01 TCGA.VQ.A94U.01 TCGA.VQ.A94T.01 TCGA.VQ.A91A.01 TCGA.VQ.A91D.01
#> "023" "021" "0333" "011" "032" "023"
#> TCGA.D7.6518.01 TCGA.BR.8484.01 TCGA.VQ.A91N.01 TCGA.VQ.A91E.01 TCGA.VQ.A8PY.01 TCGA.HU.8602.01
#> "0311" "013" "012" "032" "032" "023"
#> TCGA.BR.8381.01 TCGA.BR.6452.11 TCGA.IN.8663.01 TCGA.VQ.A8PS.01 TCGA.VQ.A91W.01 TCGA.BR.6454.01
#> "021" "0314" "022" "011" "021" "011"
#> TCGA.BR.8682.01 TCGA.VQ.A91V.01 TCGA.VQ.A8PZ.01 TCGA.BR.8590.01 TCGA.F1.6177.01 TCGA.VQ.A8PQ.01
#> "032" "0333" "0314" "011" "022" "011"
#> TCGA.VQ.A91U.01 TCGA.VQ.AA6I.01 TCGA.CG.4437.01 TCGA.VQ.A8PP.01 TCGA.BR.6565.01 TCGA.VQ.A91Y.01
#> "012" "022" "023" "023" "012" "013"
#> TCGA.VQ.A8PF.01 TCGA.BR.6456.01 TCGA.BR.6458.01 TCGA.VQ.A925.01 TCGA.VQ.A927.01 TCGA.BR.8592.01
#> "021" "013" "032" "013" "011" "0313"
#> TCGA.BR.6566.11 TCGA.IN.AB1V.01 TCGA.VQ.AA6F.01 TCGA.VQ.AA6J.01 TCGA.BR.8487.01 TCGA.D7.6525.01
#> "011" "013" "011" "011" "022" "032"
#> TCGA.VQ.A94O.01 TCGA.BR.8588.01 TCGA.HU.8610.01 TCGA.D7.6526.01 TCGA.VQ.A8PD.01 TCGA.D7.6524.01
#> "012" "0313" "0311" "012" "0311" "0314"
#> TCGA.3M.AB46.01 TCGA.3M.AB47.01 TCGA.BR.8677.01 TCGA.BR.6457.01 TCGA.BR.8687.01 TCGA.VQ.A91K.01
#> "012" "0311" "011" "0311" "013" "022"
#> TCGA.BR.8690.01 TCGA.BR.8686.01 TCGA.FP.8631.01 TCGA.VQ.A922.01 TCGA.BR.A452.01 TCGA.IN.A6RO.01
#> "013" "021" "012" "012" "011" "022"
#> TCGA.BR.A4QI.01 TCGA.D7.A6EV.01 TCGA.HU.A4G2.01 TCGA.BR.A4IY.01 TCGA.VQ.A8PU.01 TCGA.BR.A4J4.01
#> "023" "034" "021" "021" "011" "021"
#> TCGA.VQ.A94R.01 TCGA.HU.A4H4.01 TCGA.BR.7707.01 TCGA.FP.7829.01 TCGA.BR.A4J5.01 TCGA.HU.A4H0.01
#> "022" "032" "022" "022" "0311" "021"
#> TCGA.HU.A4HD.01 TCGA.KB.A6F5.01 TCGA.VQ.AA6K.01 TCGA.HF.7133.01 TCGA.F1.6875.01 TCGA.MX.A666.01
#> "012" "013" "011" "013" "012" "012"
#> TCGA.BR.7717.01 TCGA.BR.A4PF.01 TCGA.BR.A4IU.01 TCGA.VQ.A8PX.01 TCGA.BR.A4IV.01 TCGA.D7.A6EX.01
#> "034" "023" "0313" "011" "011" "013"
#> TCGA.BR.A4IZ.01 TCGA.BR.A4J9.01 TCGA.CD.A4MJ.01 TCGA.B7.A5TN.01 TCGA.BR.7715.01 TCGA.BR.7704.01
#> "011" "011" "023" "012" "0332" "012"
#> TCGA.BR.A4J1.01 TCGA.HU.A4GP.01 TCGA.D7.A4YY.01 TCGA.VQ.AA6G.01 TCGA.HU.A4GJ.01 TCGA.CD.A4MI.01
#> "012" "022" "022" "022" "0314" "023"
#> TCGA.BR.7196.01 TCGA.BR.6563.01 TCGA.VQ.A924.01 TCGA.BR.7716.01 TCGA.FP.7735.01 TCGA.BR.7723.01
#> "0312" "0311" "023" "013" "013" "013"
#> TCGA.HU.A4H8.01 TCGA.IN.A6RJ.01 TCGA.HU.A4H3.01 TCGA.EQ.A4SO.01 TCGA.CD.A4MH.01 TCGA.BR.A4J7.01
#> "022" "0311" "022" "011" "012" "011"
#> TCGA.HF.7131.01 TCGA.D7.A74B.01 TCGA.BR.A4PE.01 TCGA.BR.A4J8.01 TCGA.HU.A4GX.01 TCGA.HU.A4G8.01
#> "012" "011" "022" "023" "032" "034"
#> TCGA.HU.A4GT.01 TCGA.HU.A4GC.01 TCGA.BR.A4CQ.01 TCGA.D7.A6F2.01 TCGA.RD.A7BT.01 TCGA.BR.A4J6.01
#> "022" "034" "022" "012" "012" "011"
#> TCGA.HU.A4GQ.01 TCGA.HF.7136.01 TCGA.BR.A4QM.01 TCGA.BR.A4PD.01 TCGA.VQ.A8PK.01 TCGA.B7.A5TK.01
#> "023" "013" "023" "012" "012" "0312"
#> TCGA.D7.A4YX.01 TCGA.D7.A4Z0.01 TCGA.VQ.A8PT.01 TCGA.IN.A6RN.01 TCGA.CD.A4MG.01 TCGA.D7.A747.01
#> "021" "0313" "022" "012" "022" "011"
#> TCGA.R5.A7O7.01 TCGA.F1.A72C.01 TCGA.BR.A4J2.01 TCGA.MX.A663.01 TCGA.D7.A4YV.01 TCGA.HU.A4GD.01
#> "0311" "011" "0311" "013" "023" "0331"
#> TCGA.BR.A4QL.01 TCGA.BR.7703.01 TCGA.VQ.AA6B.01 TCGA.VQ.AA6D.01 TCGA.D7.A6EZ.01 TCGA.D7.A4YU.01
#> "022" "022" "0332" "012" "021" "023"
#> TCGA.VQ.AA6A.01 TCGA.IN.7806.01 TCGA.HU.A4HB.01 TCGA.HU.A4H2.01 TCGA.IN.A6RP.01 TCGA.HU.A4H5.01
#> "012" "012" "0311" "034" "022" "012"
#> TCGA.HU.A4GU.01 TCGA.MX.A5UJ.01 TCGA.HU.A4GN.01 TCGA.CD.5804.01 TCGA.HU.A4H6.01 TCGA.HF.7132.01
#> "022" "022" "023" "013" "023" "023"
#> TCGA.D7.A4YT.01 TCGA.HF.7134.01 TCGA.BR.6852.01 TCGA.BR.8370.01 TCGA.EQ.5647.01 TCGA.IN.A7NT.01
#> "013" "022" "0314" "023" "013" "032"
#> TCGA.RD.A8N9.01 TCGA.D7.5577.01 TCGA.CG.5717.01 TCGA.D7.6818.01 TCGA.CG.5734.01 TCGA.VQ.A8P8.01
#> "011" "021" "011" "013" "0311" "0314"
#> TCGA.BR.6707.01 TCGA.B7.5818.01 TCGA.CD.8525.01 TCGA.BR.6705.01 TCGA.BR.4288.01 TCGA.CD.5813.01
#> "021" "021" "013" "0313" "013" "011"
#> TCGA.CG.5723.01 TCGA.CD.5800.01 TCGA.CG.5718.01 TCGA.BR.8080.01 TCGA.CG.5733.01 TCGA.D7.6817.01
#> "011" "013" "012" "011" "022" "012"
#> TCGA.KB.A93G.01 TCGA.CD.5799.01 TCGA.BR.7851.01 TCGA.BR.7722.01 TCGA.MX.A5UG.01 TCGA.CD.8533.01
#> "011" "013" "023" "011" "0311" "0331"
#> TCGA.BR.7957.01 TCGA.CG.5722.01 TCGA.F1.6874.01 TCGA.CG.5730.01 TCGA.CG.5726.01 TCGA.IP.7968.01
#> "0313" "0312" "032" "0331" "022" "0331"
#> TCGA.BR.8363.01 TCGA.BR.7901.01 TCGA.D7.6822.01 TCGA.BR.6710.01 TCGA.CG.5720.01 TCGA.D7.8570.01
#> "023" "012" "034" "011" "022" "021"
#> TCGA.B7.A5TI.01 TCGA.D7.6815.01 TCGA.BR.8284.01 TCGA.BR.8295.01 TCGA.BR.7197.01 TCGA.B7.A5TJ.01
#> "013" "012" "023" "012" "012" "022"
#> TCGA.D7.A6EY.01 TCGA.BR.8366.01 TCGA.IN.A7NR.01 TCGA.BR.6706.01 TCGA.IN.7808.01 TCGA.BR.6564.01
#> "0313" "021" "011" "0312" "0311" "011"
#> TCGA.KB.A93H.01 TCGA.KB.A93J.01 TCGA.CD.5798.01 TCGA.CD.8530.01 TCGA.BR.6802.01 TCGA.CG.5719.01
#> "0332" "012" "011" "013" "0311" "011"
#> TCGA.VQ.A8E3.01 TCGA.CD.5801.01 TCGA.FP.A9TM.01 TCGA.BR.7958.01 TCGA.FP.7998.01 TCGA.IN.A6RS.01
#> "022" "021" "032" "021" "0312" "032"
#> TCGA.BR.6709.01 TCGA.FP.7916.01 TCGA.R5.A7ZR.01 TCGA.B7.5816.01 TCGA.CG.5721.01 TCGA.SW.A7EA.01
#> "011" "021" "012" "0314" "0311" "022"
#> TCGA.RD.A8NB.01 TCGA.BR.6801.01 TCGA.IN.AB1X.01 TCGA.D7.5579.01 TCGA.CG.5728.01 TCGA.R5.A7ZI.01
#> "0313" "013" "0314" "013" "0313" "013"
#> TCGA.IN.A7NU.01 TCGA.CG.5732.01 TCGA.ZQ.A9CR.01 TCGA.D7.5578.01 TCGA.BR.6803.01 TCGA.BR.8368.01
#> "032" "013" "013" "032" "011" "022"
#> TCGA.SW.A7EB.01 TCGA.BR.8081.01 TCGA.VQ.A8P5.01 TCGA.CD.8535.01 TCGA.CG.5724.01 TCGA.D7.8574.01
#> "011" "023" "032" "022" "034" "011"
#> TCGA.HJ.7597.01 TCGA.HF.A5NB.01 TCGA.VQ.A8PB.01 TCGA.R5.A7ZE.01 TCGA.CD.5803.01 TCGA.CG.5725.01
#> "011" "022" "034" "012" "011" "012"
#> TCGA.D7.6820.01 TCGA.CD.5802.01 TCGA.R5.A7ZF.01 TCGA.D7.A6F0.01 TCGA.CG.5727.01 TCGA.VQ.A8PC.01
#> "012" "013" "013" "012" "032" "0311"
#> TCGA.CD.A486.01 TCGA.RD.A8N2.01 TCGA.IN.A6RI.01 TCGA.HU.8243.01 TCGA.CD.A48C.01 TCGA.RD.A8N5.01
#> "012" "011" "012" "034" "022" "011"
#> TCGA.RD.A8N1.01 TCGA.HU.A4GF.01 TCGA.BR.8362.01 TCGA.BR.8285.01 TCGA.CD.8532.01 TCGA.VQ.A8E2.01
#> "013" "012" "032" "021" "011" "013"
#> TCGA.BR.8373.01 TCGA.BR.8361.01 TCGA.BR.8058.01 TCGA.IN.8462.01 TCGA.HU.A4G9.01 TCGA.CD.8524.01
#> "012" "022" "011" "034" "022" "032"
#> TCGA.D7.A748.01 TCGA.CD.8527.01 TCGA.VQ.A8DV.01 TCGA.CD.8528.01 TCGA.BR.A453.01 TCGA.RD.A8N6.01
#> "011" "013" "012" "022" "0311" "013"
#> TCGA.HU.8245.01 TCGA.ZA.A8F6.01 TCGA.BR.8367.01 TCGA.BR.8380.01 TCGA.FP.A4BE.01 TCGA.HU.8238.01
#> "012" "013" "032" "0311" "023" "034"
#> TCGA.BR.8078.01 TCGA.HU.8249.01 TCGA.RD.A8N0.01 TCGA.BR.8365.01 TCGA.FP.8211.01 TCGA.RD.A8N4.01
#> "023" "0331" "011" "011" "011" "011"
#> TCGA.VQ.A8DU.01 TCGA.VQ.A8DL.01 TCGA.VQ.A8DZ.01 TCGA.D7.8572.01 TCGA.RD.A7BW.01 TCGA.R5.A804.01
#> "012" "013" "012" "013" "011" "0314"
#> TCGA.BR.A4CS.01 TCGA.CD.8531.01 TCGA.CD.A487.01 TCGA.BR.8371.01 TCGA.BR.8059.01 TCGA.D7.A6ET.01
#> "032" "021" "013" "011" "013" "0312"
#> TCGA.FP.8099.01 TCGA.D7.8579.01 TCGA.BR.8297.01 TCGA.D7.8576.01 TCGA.VQ.A8DT.01 TCGA.FP.A8CX.01
#> "0333" "0313" "032" "011" "022" "013"
#> TCGA.HU.A4GH.01 TCGA.CD.8526.01 TCGA.HU.A4G6.01 TCGA.D7.8578.01 TCGA.HU.A4G3.01 TCGA.D7.A74A.01
#> "012" "013" "021" "013" "022" "022"
#> TCGA.RD.A7C1.01 TCGA.F1.A448.01 TCGA.D7.8575.01 TCGA.BR.8372.01 TCGA.VQ.A8P3.01 TCGA.RD.A8MW.01
#> "032" "0311" "034" "022" "034" "013"
#> TCGA.BR.8286.01 TCGA.BR.8369.01 TCGA.BR.8364.01 TCGA.HU.8244.01 TCGA.KB.A6F7.01 TCGA.FP.A4BF.01
#> "034" "032" "011" "022" "012" "032"
#> TCGA.R5.A805.01 TCGA.IN.A6RL.01 TCGA.IN.A6RR.01 TCGA.BR.A4CR.01 TCGA.CD.A489.01 TCGA.HU.A4GY.01
#> "032" "034" "022" "013" "011" "011"
#> TCGA.BR.8289.01 TCGA.FP.8209.01 TCGA.BR.8296.01 TCGA.CD.A48A.01 TCGA.BR.8060.01 TCGA.BR.8077.01
#> "034" "011" "0314" "0331" "012" "012"
#> TCGA.CD.8534.01 TCGA.BR.7959.01 TCGA.VQ.A8P2.01 TCGA.EQ.8122.01 TCGA.D7.8573.01 TCGA.BR.A44T.01
#> "032" "032" "022" "012" "021" "011"
#> TCGA.RD.A8MV.01 TCGA.CD.8536.01 TCGA.BR.8360.01 TCGA.BR.8291.01 TCGA.FP.8210.01 TCGA.RD.A7BS.01
#> "0311" "032" "023" "013" "011" "011"
#> TCGA.BR.A44U.01 TCGA.CD.8529.01
#> "034" "013"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 10459))
#> TCGA.VQ.A94P.01 TCGA.D7.6521.01 TCGA.VQ.A8PE.01 TCGA.D7.6519.01 TCGA.BR.6452.01 TCGA.BR.8485.01
#> "011" "011" "012" "013" "023" "012"
#> TCGA.VQ.A8PO.01 TCGA.VQ.AA69.01 TCGA.BR.8683.01 TCGA.BR.8486.01 TCGA.D7.6522.01 TCGA.CG.5716.01
#> "022" "021" "032" "012" "011" "0314"
#> TCGA.BR.8589.01 TCGA.BR.8382.01 TCGA.VQ.AA68.01 TCGA.VQ.A8PJ.01 TCGA.VQ.A8PH.01 TCGA.HU.8604.01
#> "021" "023" "034" "012" "012" "023"
#> TCGA.BR.8676.01 TCGA.CG.4441.01 TCGA.D7.6520.01 TCGA.VQ.AA64.01 TCGA.D7.6527.01 TCGA.VQ.A8PM.01
#> "021" "034" "012" "011" "012" "013"
#> TCGA.VQ.A923.01 TCGA.BR.8384.01 TCGA.BR.6453.01 TCGA.VQ.A928.01 TCGA.VQ.A8E0.01 TCGA.BR.8679.01
#> "021" "0311" "0311" "011" "011" "022"
#> TCGA.VQ.A91S.01 TCGA.BR.8678.01 TCGA.D7.6528.01 TCGA.VQ.A8E7.01 TCGA.BR.8680.01 TCGA.BR.8483.01
#> "032" "012" "033" "034" "034" "033"
#> TCGA.BR.6566.01 TCGA.VQ.A91X.01 TCGA.VQ.A91Q.01 TCGA.VQ.A92D.01 TCGA.VQ.A91Z.01 TCGA.BR.6455.01
#> "032" "033" "011" "022" "012" "021"
#> TCGA.BR.8591.01 TCGA.HU.8608.01 TCGA.VQ.A94U.01 TCGA.VQ.A94T.01 TCGA.VQ.A91A.01 TCGA.VQ.A91D.01
#> "023" "021" "033" "011" "032" "023"
#> TCGA.D7.6518.01 TCGA.BR.8484.01 TCGA.VQ.A91N.01 TCGA.VQ.A91E.01 TCGA.VQ.A8PY.01 TCGA.HU.8602.01
#> "0311" "013" "012" "032" "032" "023"
#> TCGA.BR.8381.01 TCGA.BR.6452.11 TCGA.IN.8663.01 TCGA.VQ.A8PS.01 TCGA.VQ.A91W.01 TCGA.BR.6454.01
#> "021" "0314" "022" "011" "021" "011"
#> TCGA.BR.8682.01 TCGA.VQ.A91V.01 TCGA.VQ.A8PZ.01 TCGA.BR.8590.01 TCGA.F1.6177.01 TCGA.VQ.A8PQ.01
#> "032" "033" "0314" "011" "022" "011"
#> TCGA.VQ.A91U.01 TCGA.VQ.AA6I.01 TCGA.CG.4437.01 TCGA.VQ.A8PP.01 TCGA.BR.6565.01 TCGA.VQ.A91Y.01
#> "012" "022" "023" "023" "012" "013"
#> TCGA.VQ.A8PF.01 TCGA.BR.6456.01 TCGA.BR.6458.01 TCGA.VQ.A925.01 TCGA.VQ.A927.01 TCGA.BR.8592.01
#> "021" "013" "032" "013" "011" "0313"
#> TCGA.BR.6566.11 TCGA.IN.AB1V.01 TCGA.VQ.AA6F.01 TCGA.VQ.AA6J.01 TCGA.BR.8487.01 TCGA.D7.6525.01
#> "011" "013" "011" "011" "022" "032"
#> TCGA.VQ.A94O.01 TCGA.BR.8588.01 TCGA.HU.8610.01 TCGA.D7.6526.01 TCGA.VQ.A8PD.01 TCGA.D7.6524.01
#> "012" "0313" "0311" "012" "0311" "0314"
#> TCGA.3M.AB46.01 TCGA.3M.AB47.01 TCGA.BR.8677.01 TCGA.BR.6457.01 TCGA.BR.8687.01 TCGA.VQ.A91K.01
#> "012" "0311" "011" "0311" "013" "022"
#> TCGA.BR.8690.01 TCGA.BR.8686.01 TCGA.FP.8631.01 TCGA.VQ.A922.01 TCGA.BR.A452.01 TCGA.IN.A6RO.01
#> "013" "021" "012" "012" "011" "022"
#> TCGA.BR.A4QI.01 TCGA.D7.A6EV.01 TCGA.HU.A4G2.01 TCGA.BR.A4IY.01 TCGA.VQ.A8PU.01 TCGA.BR.A4J4.01
#> "023" "034" "021" "021" "011" "021"
#> TCGA.VQ.A94R.01 TCGA.HU.A4H4.01 TCGA.BR.7707.01 TCGA.FP.7829.01 TCGA.BR.A4J5.01 TCGA.HU.A4H0.01
#> "022" "032" "022" "022" "0311" "021"
#> TCGA.HU.A4HD.01 TCGA.KB.A6F5.01 TCGA.VQ.AA6K.01 TCGA.HF.7133.01 TCGA.F1.6875.01 TCGA.MX.A666.01
#> "012" "013" "011" "013" "012" "012"
#> TCGA.BR.7717.01 TCGA.BR.A4PF.01 TCGA.BR.A4IU.01 TCGA.VQ.A8PX.01 TCGA.BR.A4IV.01 TCGA.D7.A6EX.01
#> "034" "023" "0313" "011" "011" "013"
#> TCGA.BR.A4IZ.01 TCGA.BR.A4J9.01 TCGA.CD.A4MJ.01 TCGA.B7.A5TN.01 TCGA.BR.7715.01 TCGA.BR.7704.01
#> "011" "011" "023" "012" "033" "012"
#> TCGA.BR.A4J1.01 TCGA.HU.A4GP.01 TCGA.D7.A4YY.01 TCGA.VQ.AA6G.01 TCGA.HU.A4GJ.01 TCGA.CD.A4MI.01
#> "012" "022" "022" "022" "0314" "023"
#> TCGA.BR.7196.01 TCGA.BR.6563.01 TCGA.VQ.A924.01 TCGA.BR.7716.01 TCGA.FP.7735.01 TCGA.BR.7723.01
#> "0312" "0311" "023" "013" "013" "013"
#> TCGA.HU.A4H8.01 TCGA.IN.A6RJ.01 TCGA.HU.A4H3.01 TCGA.EQ.A4SO.01 TCGA.CD.A4MH.01 TCGA.BR.A4J7.01
#> "022" "0311" "022" "011" "012" "011"
#> TCGA.HF.7131.01 TCGA.D7.A74B.01 TCGA.BR.A4PE.01 TCGA.BR.A4J8.01 TCGA.HU.A4GX.01 TCGA.HU.A4G8.01
#> "012" "011" "022" "023" "032" "034"
#> TCGA.HU.A4GT.01 TCGA.HU.A4GC.01 TCGA.BR.A4CQ.01 TCGA.D7.A6F2.01 TCGA.RD.A7BT.01 TCGA.BR.A4J6.01
#> "022" "034" "022" "012" "012" "011"
#> TCGA.HU.A4GQ.01 TCGA.HF.7136.01 TCGA.BR.A4QM.01 TCGA.BR.A4PD.01 TCGA.VQ.A8PK.01 TCGA.B7.A5TK.01
#> "023" "013" "023" "012" "012" "0312"
#> TCGA.D7.A4YX.01 TCGA.D7.A4Z0.01 TCGA.VQ.A8PT.01 TCGA.IN.A6RN.01 TCGA.CD.A4MG.01 TCGA.D7.A747.01
#> "021" "0313" "022" "012" "022" "011"
#> TCGA.R5.A7O7.01 TCGA.F1.A72C.01 TCGA.BR.A4J2.01 TCGA.MX.A663.01 TCGA.D7.A4YV.01 TCGA.HU.A4GD.01
#> "0311" "011" "0311" "013" "023" "033"
#> TCGA.BR.A4QL.01 TCGA.BR.7703.01 TCGA.VQ.AA6B.01 TCGA.VQ.AA6D.01 TCGA.D7.A6EZ.01 TCGA.D7.A4YU.01
#> "022" "022" "033" "012" "021" "023"
#> TCGA.VQ.AA6A.01 TCGA.IN.7806.01 TCGA.HU.A4HB.01 TCGA.HU.A4H2.01 TCGA.IN.A6RP.01 TCGA.HU.A4H5.01
#> "012" "012" "0311" "034" "022" "012"
#> TCGA.HU.A4GU.01 TCGA.MX.A5UJ.01 TCGA.HU.A4GN.01 TCGA.CD.5804.01 TCGA.HU.A4H6.01 TCGA.HF.7132.01
#> "022" "022" "023" "013" "023" "023"
#> TCGA.D7.A4YT.01 TCGA.HF.7134.01 TCGA.BR.6852.01 TCGA.BR.8370.01 TCGA.EQ.5647.01 TCGA.IN.A7NT.01
#> "013" "022" "0314" "023" "013" "032"
#> TCGA.RD.A8N9.01 TCGA.D7.5577.01 TCGA.CG.5717.01 TCGA.D7.6818.01 TCGA.CG.5734.01 TCGA.VQ.A8P8.01
#> "011" "021" "011" "013" "0311" "0314"
#> TCGA.BR.6707.01 TCGA.B7.5818.01 TCGA.CD.8525.01 TCGA.BR.6705.01 TCGA.BR.4288.01 TCGA.CD.5813.01
#> "021" "021" "013" "0313" "013" "011"
#> TCGA.CG.5723.01 TCGA.CD.5800.01 TCGA.CG.5718.01 TCGA.BR.8080.01 TCGA.CG.5733.01 TCGA.D7.6817.01
#> "011" "013" "012" "011" "022" "012"
#> TCGA.KB.A93G.01 TCGA.CD.5799.01 TCGA.BR.7851.01 TCGA.BR.7722.01 TCGA.MX.A5UG.01 TCGA.CD.8533.01
#> "011" "013" "023" "011" "0311" "033"
#> TCGA.BR.7957.01 TCGA.CG.5722.01 TCGA.F1.6874.01 TCGA.CG.5730.01 TCGA.CG.5726.01 TCGA.IP.7968.01
#> "0313" "0312" "032" "033" "022" "033"
#> TCGA.BR.8363.01 TCGA.BR.7901.01 TCGA.D7.6822.01 TCGA.BR.6710.01 TCGA.CG.5720.01 TCGA.D7.8570.01
#> "023" "012" "034" "011" "022" "021"
#> TCGA.B7.A5TI.01 TCGA.D7.6815.01 TCGA.BR.8284.01 TCGA.BR.8295.01 TCGA.BR.7197.01 TCGA.B7.A5TJ.01
#> "013" "012" "023" "012" "012" "022"
#> TCGA.D7.A6EY.01 TCGA.BR.8366.01 TCGA.IN.A7NR.01 TCGA.BR.6706.01 TCGA.IN.7808.01 TCGA.BR.6564.01
#> "0313" "021" "011" "0312" "0311" "011"
#> TCGA.KB.A93H.01 TCGA.KB.A93J.01 TCGA.CD.5798.01 TCGA.CD.8530.01 TCGA.BR.6802.01 TCGA.CG.5719.01
#> "033" "012" "011" "013" "0311" "011"
#> TCGA.VQ.A8E3.01 TCGA.CD.5801.01 TCGA.FP.A9TM.01 TCGA.BR.7958.01 TCGA.FP.7998.01 TCGA.IN.A6RS.01
#> "022" "021" "032" "021" "0312" "032"
#> TCGA.BR.6709.01 TCGA.FP.7916.01 TCGA.R5.A7ZR.01 TCGA.B7.5816.01 TCGA.CG.5721.01 TCGA.SW.A7EA.01
#> "011" "021" "012" "0314" "0311" "022"
#> TCGA.RD.A8NB.01 TCGA.BR.6801.01 TCGA.IN.AB1X.01 TCGA.D7.5579.01 TCGA.CG.5728.01 TCGA.R5.A7ZI.01
#> "0313" "013" "0314" "013" "0313" "013"
#> TCGA.IN.A7NU.01 TCGA.CG.5732.01 TCGA.ZQ.A9CR.01 TCGA.D7.5578.01 TCGA.BR.6803.01 TCGA.BR.8368.01
#> "032" "013" "013" "032" "011" "022"
#> TCGA.SW.A7EB.01 TCGA.BR.8081.01 TCGA.VQ.A8P5.01 TCGA.CD.8535.01 TCGA.CG.5724.01 TCGA.D7.8574.01
#> "011" "023" "032" "022" "034" "011"
#> TCGA.HJ.7597.01 TCGA.HF.A5NB.01 TCGA.VQ.A8PB.01 TCGA.R5.A7ZE.01 TCGA.CD.5803.01 TCGA.CG.5725.01
#> "011" "022" "034" "012" "011" "012"
#> TCGA.D7.6820.01 TCGA.CD.5802.01 TCGA.R5.A7ZF.01 TCGA.D7.A6F0.01 TCGA.CG.5727.01 TCGA.VQ.A8PC.01
#> "012" "013" "013" "012" "032" "0311"
#> TCGA.CD.A486.01 TCGA.RD.A8N2.01 TCGA.IN.A6RI.01 TCGA.HU.8243.01 TCGA.CD.A48C.01 TCGA.RD.A8N5.01
#> "012" "011" "012" "034" "022" "011"
#> TCGA.RD.A8N1.01 TCGA.HU.A4GF.01 TCGA.BR.8362.01 TCGA.BR.8285.01 TCGA.CD.8532.01 TCGA.VQ.A8E2.01
#> "013" "012" "032" "021" "011" "013"
#> TCGA.BR.8373.01 TCGA.BR.8361.01 TCGA.BR.8058.01 TCGA.IN.8462.01 TCGA.HU.A4G9.01 TCGA.CD.8524.01
#> "012" "022" "011" "034" "022" "032"
#> TCGA.D7.A748.01 TCGA.CD.8527.01 TCGA.VQ.A8DV.01 TCGA.CD.8528.01 TCGA.BR.A453.01 TCGA.RD.A8N6.01
#> "011" "013" "012" "022" "0311" "013"
#> TCGA.HU.8245.01 TCGA.ZA.A8F6.01 TCGA.BR.8367.01 TCGA.BR.8380.01 TCGA.FP.A4BE.01 TCGA.HU.8238.01
#> "012" "013" "032" "0311" "023" "034"
#> TCGA.BR.8078.01 TCGA.HU.8249.01 TCGA.RD.A8N0.01 TCGA.BR.8365.01 TCGA.FP.8211.01 TCGA.RD.A8N4.01
#> "023" "033" "011" "011" "011" "011"
#> TCGA.VQ.A8DU.01 TCGA.VQ.A8DL.01 TCGA.VQ.A8DZ.01 TCGA.D7.8572.01 TCGA.RD.A7BW.01 TCGA.R5.A804.01
#> "012" "013" "012" "013" "011" "0314"
#> TCGA.BR.A4CS.01 TCGA.CD.8531.01 TCGA.CD.A487.01 TCGA.BR.8371.01 TCGA.BR.8059.01 TCGA.D7.A6ET.01
#> "032" "021" "013" "011" "013" "0312"
#> TCGA.FP.8099.01 TCGA.D7.8579.01 TCGA.BR.8297.01 TCGA.D7.8576.01 TCGA.VQ.A8DT.01 TCGA.FP.A8CX.01
#> "033" "0313" "032" "011" "022" "013"
#> TCGA.HU.A4GH.01 TCGA.CD.8526.01 TCGA.HU.A4G6.01 TCGA.D7.8578.01 TCGA.HU.A4G3.01 TCGA.D7.A74A.01
#> "012" "013" "021" "013" "022" "022"
#> TCGA.RD.A7C1.01 TCGA.F1.A448.01 TCGA.D7.8575.01 TCGA.BR.8372.01 TCGA.VQ.A8P3.01 TCGA.RD.A8MW.01
#> "032" "0311" "034" "022" "034" "013"
#> TCGA.BR.8286.01 TCGA.BR.8369.01 TCGA.BR.8364.01 TCGA.HU.8244.01 TCGA.KB.A6F7.01 TCGA.FP.A4BF.01
#> "034" "032" "011" "022" "012" "032"
#> TCGA.R5.A805.01 TCGA.IN.A6RL.01 TCGA.IN.A6RR.01 TCGA.BR.A4CR.01 TCGA.CD.A489.01 TCGA.HU.A4GY.01
#> "032" "034" "022" "013" "011" "011"
#> TCGA.BR.8289.01 TCGA.FP.8209.01 TCGA.BR.8296.01 TCGA.CD.A48A.01 TCGA.BR.8060.01 TCGA.BR.8077.01
#> "034" "011" "0314" "033" "012" "012"
#> TCGA.CD.8534.01 TCGA.BR.7959.01 TCGA.VQ.A8P2.01 TCGA.EQ.8122.01 TCGA.D7.8573.01 TCGA.BR.A44T.01
#> "032" "032" "022" "012" "021" "011"
#> TCGA.RD.A8MV.01 TCGA.CD.8536.01 TCGA.BR.8360.01 TCGA.BR.8291.01 TCGA.FP.8210.01 TCGA.RD.A7BS.01
#> "0311" "032" "023" "013" "011" "011"
#> TCGA.BR.A44U.01 TCGA.CD.8529.01
#> "034" "013"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 11163))
#> TCGA.VQ.A94P.01 TCGA.D7.6521.01 TCGA.VQ.A8PE.01 TCGA.D7.6519.01 TCGA.BR.6452.01 TCGA.BR.8485.01
#> "011" "011" "012" "013" "023" "012"
#> TCGA.VQ.A8PO.01 TCGA.VQ.AA69.01 TCGA.BR.8683.01 TCGA.BR.8486.01 TCGA.D7.6522.01 TCGA.CG.5716.01
#> "022" "021" "032" "012" "011" "0314"
#> TCGA.BR.8589.01 TCGA.BR.8382.01 TCGA.VQ.AA68.01 TCGA.VQ.A8PJ.01 TCGA.VQ.A8PH.01 TCGA.HU.8604.01
#> "021" "023" "034" "012" "012" "023"
#> TCGA.BR.8676.01 TCGA.CG.4441.01 TCGA.D7.6520.01 TCGA.VQ.AA64.01 TCGA.D7.6527.01 TCGA.VQ.A8PM.01
#> "021" "034" "012" "011" "012" "013"
#> TCGA.VQ.A923.01 TCGA.BR.8384.01 TCGA.BR.6453.01 TCGA.VQ.A928.01 TCGA.VQ.A8E0.01 TCGA.BR.8679.01
#> "021" "0311" "0311" "011" "011" "022"
#> TCGA.VQ.A91S.01 TCGA.BR.8678.01 TCGA.D7.6528.01 TCGA.VQ.A8E7.01 TCGA.BR.8680.01 TCGA.BR.8483.01
#> "032" "012" "033" "034" "034" "033"
#> TCGA.BR.6566.01 TCGA.VQ.A91X.01 TCGA.VQ.A91Q.01 TCGA.VQ.A92D.01 TCGA.VQ.A91Z.01 TCGA.BR.6455.01
#> "032" "033" "011" "022" "012" "021"
#> TCGA.BR.8591.01 TCGA.HU.8608.01 TCGA.VQ.A94U.01 TCGA.VQ.A94T.01 TCGA.VQ.A91A.01 TCGA.VQ.A91D.01
#> "023" "021" "033" "011" "032" "023"
#> TCGA.D7.6518.01 TCGA.BR.8484.01 TCGA.VQ.A91N.01 TCGA.VQ.A91E.01 TCGA.VQ.A8PY.01 TCGA.HU.8602.01
#> "0311" "013" "012" "032" "032" "023"
#> TCGA.BR.8381.01 TCGA.BR.6452.11 TCGA.IN.8663.01 TCGA.VQ.A8PS.01 TCGA.VQ.A91W.01 TCGA.BR.6454.01
#> "021" "0314" "022" "011" "021" "011"
#> TCGA.BR.8682.01 TCGA.VQ.A91V.01 TCGA.VQ.A8PZ.01 TCGA.BR.8590.01 TCGA.F1.6177.01 TCGA.VQ.A8PQ.01
#> "032" "033" "0314" "011" "022" "011"
#> TCGA.VQ.A91U.01 TCGA.VQ.AA6I.01 TCGA.CG.4437.01 TCGA.VQ.A8PP.01 TCGA.BR.6565.01 TCGA.VQ.A91Y.01
#> "012" "022" "023" "023" "012" "013"
#> TCGA.VQ.A8PF.01 TCGA.BR.6456.01 TCGA.BR.6458.01 TCGA.VQ.A925.01 TCGA.VQ.A927.01 TCGA.BR.8592.01
#> "021" "013" "032" "013" "011" "0313"
#> TCGA.BR.6566.11 TCGA.IN.AB1V.01 TCGA.VQ.AA6F.01 TCGA.VQ.AA6J.01 TCGA.BR.8487.01 TCGA.D7.6525.01
#> "011" "013" "011" "011" "022" "032"
#> TCGA.VQ.A94O.01 TCGA.BR.8588.01 TCGA.HU.8610.01 TCGA.D7.6526.01 TCGA.VQ.A8PD.01 TCGA.D7.6524.01
#> "012" "0313" "0311" "012" "0311" "0314"
#> TCGA.3M.AB46.01 TCGA.3M.AB47.01 TCGA.BR.8677.01 TCGA.BR.6457.01 TCGA.BR.8687.01 TCGA.VQ.A91K.01
#> "012" "0311" "011" "0311" "013" "022"
#> TCGA.BR.8690.01 TCGA.BR.8686.01 TCGA.FP.8631.01 TCGA.VQ.A922.01 TCGA.BR.A452.01 TCGA.IN.A6RO.01
#> "013" "021" "012" "012" "011" "022"
#> TCGA.BR.A4QI.01 TCGA.D7.A6EV.01 TCGA.HU.A4G2.01 TCGA.BR.A4IY.01 TCGA.VQ.A8PU.01 TCGA.BR.A4J4.01
#> "023" "034" "021" "021" "011" "021"
#> TCGA.VQ.A94R.01 TCGA.HU.A4H4.01 TCGA.BR.7707.01 TCGA.FP.7829.01 TCGA.BR.A4J5.01 TCGA.HU.A4H0.01
#> "022" "032" "022" "022" "0311" "021"
#> TCGA.HU.A4HD.01 TCGA.KB.A6F5.01 TCGA.VQ.AA6K.01 TCGA.HF.7133.01 TCGA.F1.6875.01 TCGA.MX.A666.01
#> "012" "013" "011" "013" "012" "012"
#> TCGA.BR.7717.01 TCGA.BR.A4PF.01 TCGA.BR.A4IU.01 TCGA.VQ.A8PX.01 TCGA.BR.A4IV.01 TCGA.D7.A6EX.01
#> "034" "023" "0313" "011" "011" "013"
#> TCGA.BR.A4IZ.01 TCGA.BR.A4J9.01 TCGA.CD.A4MJ.01 TCGA.B7.A5TN.01 TCGA.BR.7715.01 TCGA.BR.7704.01
#> "011" "011" "023" "012" "033" "012"
#> TCGA.BR.A4J1.01 TCGA.HU.A4GP.01 TCGA.D7.A4YY.01 TCGA.VQ.AA6G.01 TCGA.HU.A4GJ.01 TCGA.CD.A4MI.01
#> "012" "022" "022" "022" "0314" "023"
#> TCGA.BR.7196.01 TCGA.BR.6563.01 TCGA.VQ.A924.01 TCGA.BR.7716.01 TCGA.FP.7735.01 TCGA.BR.7723.01
#> "0312" "0311" "023" "013" "013" "013"
#> TCGA.HU.A4H8.01 TCGA.IN.A6RJ.01 TCGA.HU.A4H3.01 TCGA.EQ.A4SO.01 TCGA.CD.A4MH.01 TCGA.BR.A4J7.01
#> "022" "0311" "022" "011" "012" "011"
#> TCGA.HF.7131.01 TCGA.D7.A74B.01 TCGA.BR.A4PE.01 TCGA.BR.A4J8.01 TCGA.HU.A4GX.01 TCGA.HU.A4G8.01
#> "012" "011" "022" "023" "032" "034"
#> TCGA.HU.A4GT.01 TCGA.HU.A4GC.01 TCGA.BR.A4CQ.01 TCGA.D7.A6F2.01 TCGA.RD.A7BT.01 TCGA.BR.A4J6.01
#> "022" "034" "022" "012" "012" "011"
#> TCGA.HU.A4GQ.01 TCGA.HF.7136.01 TCGA.BR.A4QM.01 TCGA.BR.A4PD.01 TCGA.VQ.A8PK.01 TCGA.B7.A5TK.01
#> "023" "013" "023" "012" "012" "0312"
#> TCGA.D7.A4YX.01 TCGA.D7.A4Z0.01 TCGA.VQ.A8PT.01 TCGA.IN.A6RN.01 TCGA.CD.A4MG.01 TCGA.D7.A747.01
#> "021" "0313" "022" "012" "022" "011"
#> TCGA.R5.A7O7.01 TCGA.F1.A72C.01 TCGA.BR.A4J2.01 TCGA.MX.A663.01 TCGA.D7.A4YV.01 TCGA.HU.A4GD.01
#> "0311" "011" "0311" "013" "023" "033"
#> TCGA.BR.A4QL.01 TCGA.BR.7703.01 TCGA.VQ.AA6B.01 TCGA.VQ.AA6D.01 TCGA.D7.A6EZ.01 TCGA.D7.A4YU.01
#> "022" "022" "033" "012" "021" "023"
#> TCGA.VQ.AA6A.01 TCGA.IN.7806.01 TCGA.HU.A4HB.01 TCGA.HU.A4H2.01 TCGA.IN.A6RP.01 TCGA.HU.A4H5.01
#> "012" "012" "0311" "034" "022" "012"
#> TCGA.HU.A4GU.01 TCGA.MX.A5UJ.01 TCGA.HU.A4GN.01 TCGA.CD.5804.01 TCGA.HU.A4H6.01 TCGA.HF.7132.01
#> "022" "022" "023" "013" "023" "023"
#> TCGA.D7.A4YT.01 TCGA.HF.7134.01 TCGA.BR.6852.01 TCGA.BR.8370.01 TCGA.EQ.5647.01 TCGA.IN.A7NT.01
#> "013" "022" "0314" "023" "013" "032"
#> TCGA.RD.A8N9.01 TCGA.D7.5577.01 TCGA.CG.5717.01 TCGA.D7.6818.01 TCGA.CG.5734.01 TCGA.VQ.A8P8.01
#> "011" "021" "011" "013" "0311" "0314"
#> TCGA.BR.6707.01 TCGA.B7.5818.01 TCGA.CD.8525.01 TCGA.BR.6705.01 TCGA.BR.4288.01 TCGA.CD.5813.01
#> "021" "021" "013" "0313" "013" "011"
#> TCGA.CG.5723.01 TCGA.CD.5800.01 TCGA.CG.5718.01 TCGA.BR.8080.01 TCGA.CG.5733.01 TCGA.D7.6817.01
#> "011" "013" "012" "011" "022" "012"
#> TCGA.KB.A93G.01 TCGA.CD.5799.01 TCGA.BR.7851.01 TCGA.BR.7722.01 TCGA.MX.A5UG.01 TCGA.CD.8533.01
#> "011" "013" "023" "011" "0311" "033"
#> TCGA.BR.7957.01 TCGA.CG.5722.01 TCGA.F1.6874.01 TCGA.CG.5730.01 TCGA.CG.5726.01 TCGA.IP.7968.01
#> "0313" "0312" "032" "033" "022" "033"
#> TCGA.BR.8363.01 TCGA.BR.7901.01 TCGA.D7.6822.01 TCGA.BR.6710.01 TCGA.CG.5720.01 TCGA.D7.8570.01
#> "023" "012" "034" "011" "022" "021"
#> TCGA.B7.A5TI.01 TCGA.D7.6815.01 TCGA.BR.8284.01 TCGA.BR.8295.01 TCGA.BR.7197.01 TCGA.B7.A5TJ.01
#> "013" "012" "023" "012" "012" "022"
#> TCGA.D7.A6EY.01 TCGA.BR.8366.01 TCGA.IN.A7NR.01 TCGA.BR.6706.01 TCGA.IN.7808.01 TCGA.BR.6564.01
#> "0313" "021" "011" "0312" "0311" "011"
#> TCGA.KB.A93H.01 TCGA.KB.A93J.01 TCGA.CD.5798.01 TCGA.CD.8530.01 TCGA.BR.6802.01 TCGA.CG.5719.01
#> "033" "012" "011" "013" "0311" "011"
#> TCGA.VQ.A8E3.01 TCGA.CD.5801.01 TCGA.FP.A9TM.01 TCGA.BR.7958.01 TCGA.FP.7998.01 TCGA.IN.A6RS.01
#> "022" "021" "032" "021" "0312" "032"
#> TCGA.BR.6709.01 TCGA.FP.7916.01 TCGA.R5.A7ZR.01 TCGA.B7.5816.01 TCGA.CG.5721.01 TCGA.SW.A7EA.01
#> "011" "021" "012" "0314" "0311" "022"
#> TCGA.RD.A8NB.01 TCGA.BR.6801.01 TCGA.IN.AB1X.01 TCGA.D7.5579.01 TCGA.CG.5728.01 TCGA.R5.A7ZI.01
#> "0313" "013" "0314" "013" "0313" "013"
#> TCGA.IN.A7NU.01 TCGA.CG.5732.01 TCGA.ZQ.A9CR.01 TCGA.D7.5578.01 TCGA.BR.6803.01 TCGA.BR.8368.01
#> "032" "013" "013" "032" "011" "022"
#> TCGA.SW.A7EB.01 TCGA.BR.8081.01 TCGA.VQ.A8P5.01 TCGA.CD.8535.01 TCGA.CG.5724.01 TCGA.D7.8574.01
#> "011" "023" "032" "022" "034" "011"
#> TCGA.HJ.7597.01 TCGA.HF.A5NB.01 TCGA.VQ.A8PB.01 TCGA.R5.A7ZE.01 TCGA.CD.5803.01 TCGA.CG.5725.01
#> "011" "022" "034" "012" "011" "012"
#> TCGA.D7.6820.01 TCGA.CD.5802.01 TCGA.R5.A7ZF.01 TCGA.D7.A6F0.01 TCGA.CG.5727.01 TCGA.VQ.A8PC.01
#> "012" "013" "013" "012" "032" "0311"
#> TCGA.CD.A486.01 TCGA.RD.A8N2.01 TCGA.IN.A6RI.01 TCGA.HU.8243.01 TCGA.CD.A48C.01 TCGA.RD.A8N5.01
#> "012" "011" "012" "034" "022" "011"
#> TCGA.RD.A8N1.01 TCGA.HU.A4GF.01 TCGA.BR.8362.01 TCGA.BR.8285.01 TCGA.CD.8532.01 TCGA.VQ.A8E2.01
#> "013" "012" "032" "021" "011" "013"
#> TCGA.BR.8373.01 TCGA.BR.8361.01 TCGA.BR.8058.01 TCGA.IN.8462.01 TCGA.HU.A4G9.01 TCGA.CD.8524.01
#> "012" "022" "011" "034" "022" "032"
#> TCGA.D7.A748.01 TCGA.CD.8527.01 TCGA.VQ.A8DV.01 TCGA.CD.8528.01 TCGA.BR.A453.01 TCGA.RD.A8N6.01
#> "011" "013" "012" "022" "0311" "013"
#> TCGA.HU.8245.01 TCGA.ZA.A8F6.01 TCGA.BR.8367.01 TCGA.BR.8380.01 TCGA.FP.A4BE.01 TCGA.HU.8238.01
#> "012" "013" "032" "0311" "023" "034"
#> TCGA.BR.8078.01 TCGA.HU.8249.01 TCGA.RD.A8N0.01 TCGA.BR.8365.01 TCGA.FP.8211.01 TCGA.RD.A8N4.01
#> "023" "033" "011" "011" "011" "011"
#> TCGA.VQ.A8DU.01 TCGA.VQ.A8DL.01 TCGA.VQ.A8DZ.01 TCGA.D7.8572.01 TCGA.RD.A7BW.01 TCGA.R5.A804.01
#> "012" "013" "012" "013" "011" "0314"
#> TCGA.BR.A4CS.01 TCGA.CD.8531.01 TCGA.CD.A487.01 TCGA.BR.8371.01 TCGA.BR.8059.01 TCGA.D7.A6ET.01
#> "032" "021" "013" "011" "013" "0312"
#> TCGA.FP.8099.01 TCGA.D7.8579.01 TCGA.BR.8297.01 TCGA.D7.8576.01 TCGA.VQ.A8DT.01 TCGA.FP.A8CX.01
#> "033" "0313" "032" "011" "022" "013"
#> TCGA.HU.A4GH.01 TCGA.CD.8526.01 TCGA.HU.A4G6.01 TCGA.D7.8578.01 TCGA.HU.A4G3.01 TCGA.D7.A74A.01
#> "012" "013" "021" "013" "022" "022"
#> TCGA.RD.A7C1.01 TCGA.F1.A448.01 TCGA.D7.8575.01 TCGA.BR.8372.01 TCGA.VQ.A8P3.01 TCGA.RD.A8MW.01
#> "032" "0311" "034" "022" "034" "013"
#> TCGA.BR.8286.01 TCGA.BR.8369.01 TCGA.BR.8364.01 TCGA.HU.8244.01 TCGA.KB.A6F7.01 TCGA.FP.A4BF.01
#> "034" "032" "011" "022" "012" "032"
#> TCGA.R5.A805.01 TCGA.IN.A6RL.01 TCGA.IN.A6RR.01 TCGA.BR.A4CR.01 TCGA.CD.A489.01 TCGA.HU.A4GY.01
#> "032" "034" "022" "013" "011" "011"
#> TCGA.BR.8289.01 TCGA.FP.8209.01 TCGA.BR.8296.01 TCGA.CD.A48A.01 TCGA.BR.8060.01 TCGA.BR.8077.01
#> "034" "011" "0314" "033" "012" "012"
#> TCGA.CD.8534.01 TCGA.BR.7959.01 TCGA.VQ.A8P2.01 TCGA.EQ.8122.01 TCGA.D7.8573.01 TCGA.BR.A44T.01
#> "032" "032" "022" "012" "021" "011"
#> TCGA.RD.A8MV.01 TCGA.CD.8536.01 TCGA.BR.8360.01 TCGA.BR.8291.01 TCGA.FP.8210.01 TCGA.RD.A7BS.01
#> "0311" "032" "023" "013" "011" "011"
#> TCGA.BR.A44U.01 TCGA.CD.8529.01
#> "034" "013"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 16188))
#> TCGA.VQ.A94P.01 TCGA.D7.6521.01 TCGA.VQ.A8PE.01 TCGA.D7.6519.01 TCGA.BR.6452.01 TCGA.BR.8485.01
#> "011" "011" "012" "013" "023" "012"
#> TCGA.VQ.A8PO.01 TCGA.VQ.AA69.01 TCGA.BR.8683.01 TCGA.BR.8486.01 TCGA.D7.6522.01 TCGA.CG.5716.01
#> "022" "021" "032" "012" "011" "031"
#> TCGA.BR.8589.01 TCGA.BR.8382.01 TCGA.VQ.AA68.01 TCGA.VQ.A8PJ.01 TCGA.VQ.A8PH.01 TCGA.HU.8604.01
#> "021" "023" "034" "012" "012" "023"
#> TCGA.BR.8676.01 TCGA.CG.4441.01 TCGA.D7.6520.01 TCGA.VQ.AA64.01 TCGA.D7.6527.01 TCGA.VQ.A8PM.01
#> "021" "034" "012" "011" "012" "013"
#> TCGA.VQ.A923.01 TCGA.BR.8384.01 TCGA.BR.6453.01 TCGA.VQ.A928.01 TCGA.VQ.A8E0.01 TCGA.BR.8679.01
#> "021" "031" "031" "011" "011" "022"
#> TCGA.VQ.A91S.01 TCGA.BR.8678.01 TCGA.D7.6528.01 TCGA.VQ.A8E7.01 TCGA.BR.8680.01 TCGA.BR.8483.01
#> "032" "012" "033" "034" "034" "033"
#> TCGA.BR.6566.01 TCGA.VQ.A91X.01 TCGA.VQ.A91Q.01 TCGA.VQ.A92D.01 TCGA.VQ.A91Z.01 TCGA.BR.6455.01
#> "032" "033" "011" "022" "012" "021"
#> TCGA.BR.8591.01 TCGA.HU.8608.01 TCGA.VQ.A94U.01 TCGA.VQ.A94T.01 TCGA.VQ.A91A.01 TCGA.VQ.A91D.01
#> "023" "021" "033" "011" "032" "023"
#> TCGA.D7.6518.01 TCGA.BR.8484.01 TCGA.VQ.A91N.01 TCGA.VQ.A91E.01 TCGA.VQ.A8PY.01 TCGA.HU.8602.01
#> "031" "013" "012" "032" "032" "023"
#> TCGA.BR.8381.01 TCGA.BR.6452.11 TCGA.IN.8663.01 TCGA.VQ.A8PS.01 TCGA.VQ.A91W.01 TCGA.BR.6454.01
#> "021" "031" "022" "011" "021" "011"
#> TCGA.BR.8682.01 TCGA.VQ.A91V.01 TCGA.VQ.A8PZ.01 TCGA.BR.8590.01 TCGA.F1.6177.01 TCGA.VQ.A8PQ.01
#> "032" "033" "031" "011" "022" "011"
#> TCGA.VQ.A91U.01 TCGA.VQ.AA6I.01 TCGA.CG.4437.01 TCGA.VQ.A8PP.01 TCGA.BR.6565.01 TCGA.VQ.A91Y.01
#> "012" "022" "023" "023" "012" "013"
#> TCGA.VQ.A8PF.01 TCGA.BR.6456.01 TCGA.BR.6458.01 TCGA.VQ.A925.01 TCGA.VQ.A927.01 TCGA.BR.8592.01
#> "021" "013" "032" "013" "011" "031"
#> TCGA.BR.6566.11 TCGA.IN.AB1V.01 TCGA.VQ.AA6F.01 TCGA.VQ.AA6J.01 TCGA.BR.8487.01 TCGA.D7.6525.01
#> "011" "013" "011" "011" "022" "032"
#> TCGA.VQ.A94O.01 TCGA.BR.8588.01 TCGA.HU.8610.01 TCGA.D7.6526.01 TCGA.VQ.A8PD.01 TCGA.D7.6524.01
#> "012" "031" "031" "012" "031" "031"
#> TCGA.3M.AB46.01 TCGA.3M.AB47.01 TCGA.BR.8677.01 TCGA.BR.6457.01 TCGA.BR.8687.01 TCGA.VQ.A91K.01
#> "012" "031" "011" "031" "013" "022"
#> TCGA.BR.8690.01 TCGA.BR.8686.01 TCGA.FP.8631.01 TCGA.VQ.A922.01 TCGA.BR.A452.01 TCGA.IN.A6RO.01
#> "013" "021" "012" "012" "011" "022"
#> TCGA.BR.A4QI.01 TCGA.D7.A6EV.01 TCGA.HU.A4G2.01 TCGA.BR.A4IY.01 TCGA.VQ.A8PU.01 TCGA.BR.A4J4.01
#> "023" "034" "021" "021" "011" "021"
#> TCGA.VQ.A94R.01 TCGA.HU.A4H4.01 TCGA.BR.7707.01 TCGA.FP.7829.01 TCGA.BR.A4J5.01 TCGA.HU.A4H0.01
#> "022" "032" "022" "022" "031" "021"
#> TCGA.HU.A4HD.01 TCGA.KB.A6F5.01 TCGA.VQ.AA6K.01 TCGA.HF.7133.01 TCGA.F1.6875.01 TCGA.MX.A666.01
#> "012" "013" "011" "013" "012" "012"
#> TCGA.BR.7717.01 TCGA.BR.A4PF.01 TCGA.BR.A4IU.01 TCGA.VQ.A8PX.01 TCGA.BR.A4IV.01 TCGA.D7.A6EX.01
#> "034" "023" "031" "011" "011" "013"
#> TCGA.BR.A4IZ.01 TCGA.BR.A4J9.01 TCGA.CD.A4MJ.01 TCGA.B7.A5TN.01 TCGA.BR.7715.01 TCGA.BR.7704.01
#> "011" "011" "023" "012" "033" "012"
#> TCGA.BR.A4J1.01 TCGA.HU.A4GP.01 TCGA.D7.A4YY.01 TCGA.VQ.AA6G.01 TCGA.HU.A4GJ.01 TCGA.CD.A4MI.01
#> "012" "022" "022" "022" "031" "023"
#> TCGA.BR.7196.01 TCGA.BR.6563.01 TCGA.VQ.A924.01 TCGA.BR.7716.01 TCGA.FP.7735.01 TCGA.BR.7723.01
#> "031" "031" "023" "013" "013" "013"
#> TCGA.HU.A4H8.01 TCGA.IN.A6RJ.01 TCGA.HU.A4H3.01 TCGA.EQ.A4SO.01 TCGA.CD.A4MH.01 TCGA.BR.A4J7.01
#> "022" "031" "022" "011" "012" "011"
#> TCGA.HF.7131.01 TCGA.D7.A74B.01 TCGA.BR.A4PE.01 TCGA.BR.A4J8.01 TCGA.HU.A4GX.01 TCGA.HU.A4G8.01
#> "012" "011" "022" "023" "032" "034"
#> TCGA.HU.A4GT.01 TCGA.HU.A4GC.01 TCGA.BR.A4CQ.01 TCGA.D7.A6F2.01 TCGA.RD.A7BT.01 TCGA.BR.A4J6.01
#> "022" "034" "022" "012" "012" "011"
#> TCGA.HU.A4GQ.01 TCGA.HF.7136.01 TCGA.BR.A4QM.01 TCGA.BR.A4PD.01 TCGA.VQ.A8PK.01 TCGA.B7.A5TK.01
#> "023" "013" "023" "012" "012" "031"
#> TCGA.D7.A4YX.01 TCGA.D7.A4Z0.01 TCGA.VQ.A8PT.01 TCGA.IN.A6RN.01 TCGA.CD.A4MG.01 TCGA.D7.A747.01
#> "021" "031" "022" "012" "022" "011"
#> TCGA.R5.A7O7.01 TCGA.F1.A72C.01 TCGA.BR.A4J2.01 TCGA.MX.A663.01 TCGA.D7.A4YV.01 TCGA.HU.A4GD.01
#> "031" "011" "031" "013" "023" "033"
#> TCGA.BR.A4QL.01 TCGA.BR.7703.01 TCGA.VQ.AA6B.01 TCGA.VQ.AA6D.01 TCGA.D7.A6EZ.01 TCGA.D7.A4YU.01
#> "022" "022" "033" "012" "021" "023"
#> TCGA.VQ.AA6A.01 TCGA.IN.7806.01 TCGA.HU.A4HB.01 TCGA.HU.A4H2.01 TCGA.IN.A6RP.01 TCGA.HU.A4H5.01
#> "012" "012" "031" "034" "022" "012"
#> TCGA.HU.A4GU.01 TCGA.MX.A5UJ.01 TCGA.HU.A4GN.01 TCGA.CD.5804.01 TCGA.HU.A4H6.01 TCGA.HF.7132.01
#> "022" "022" "023" "013" "023" "023"
#> TCGA.D7.A4YT.01 TCGA.HF.7134.01 TCGA.BR.6852.01 TCGA.BR.8370.01 TCGA.EQ.5647.01 TCGA.IN.A7NT.01
#> "013" "022" "031" "023" "013" "032"
#> TCGA.RD.A8N9.01 TCGA.D7.5577.01 TCGA.CG.5717.01 TCGA.D7.6818.01 TCGA.CG.5734.01 TCGA.VQ.A8P8.01
#> "011" "021" "011" "013" "031" "031"
#> TCGA.BR.6707.01 TCGA.B7.5818.01 TCGA.CD.8525.01 TCGA.BR.6705.01 TCGA.BR.4288.01 TCGA.CD.5813.01
#> "021" "021" "013" "031" "013" "011"
#> TCGA.CG.5723.01 TCGA.CD.5800.01 TCGA.CG.5718.01 TCGA.BR.8080.01 TCGA.CG.5733.01 TCGA.D7.6817.01
#> "011" "013" "012" "011" "022" "012"
#> TCGA.KB.A93G.01 TCGA.CD.5799.01 TCGA.BR.7851.01 TCGA.BR.7722.01 TCGA.MX.A5UG.01 TCGA.CD.8533.01
#> "011" "013" "023" "011" "031" "033"
#> TCGA.BR.7957.01 TCGA.CG.5722.01 TCGA.F1.6874.01 TCGA.CG.5730.01 TCGA.CG.5726.01 TCGA.IP.7968.01
#> "031" "031" "032" "033" "022" "033"
#> TCGA.BR.8363.01 TCGA.BR.7901.01 TCGA.D7.6822.01 TCGA.BR.6710.01 TCGA.CG.5720.01 TCGA.D7.8570.01
#> "023" "012" "034" "011" "022" "021"
#> TCGA.B7.A5TI.01 TCGA.D7.6815.01 TCGA.BR.8284.01 TCGA.BR.8295.01 TCGA.BR.7197.01 TCGA.B7.A5TJ.01
#> "013" "012" "023" "012" "012" "022"
#> TCGA.D7.A6EY.01 TCGA.BR.8366.01 TCGA.IN.A7NR.01 TCGA.BR.6706.01 TCGA.IN.7808.01 TCGA.BR.6564.01
#> "031" "021" "011" "031" "031" "011"
#> TCGA.KB.A93H.01 TCGA.KB.A93J.01 TCGA.CD.5798.01 TCGA.CD.8530.01 TCGA.BR.6802.01 TCGA.CG.5719.01
#> "033" "012" "011" "013" "031" "011"
#> TCGA.VQ.A8E3.01 TCGA.CD.5801.01 TCGA.FP.A9TM.01 TCGA.BR.7958.01 TCGA.FP.7998.01 TCGA.IN.A6RS.01
#> "022" "021" "032" "021" "031" "032"
#> TCGA.BR.6709.01 TCGA.FP.7916.01 TCGA.R5.A7ZR.01 TCGA.B7.5816.01 TCGA.CG.5721.01 TCGA.SW.A7EA.01
#> "011" "021" "012" "031" "031" "022"
#> TCGA.RD.A8NB.01 TCGA.BR.6801.01 TCGA.IN.AB1X.01 TCGA.D7.5579.01 TCGA.CG.5728.01 TCGA.R5.A7ZI.01
#> "031" "013" "031" "013" "031" "013"
#> TCGA.IN.A7NU.01 TCGA.CG.5732.01 TCGA.ZQ.A9CR.01 TCGA.D7.5578.01 TCGA.BR.6803.01 TCGA.BR.8368.01
#> "032" "013" "013" "032" "011" "022"
#> TCGA.SW.A7EB.01 TCGA.BR.8081.01 TCGA.VQ.A8P5.01 TCGA.CD.8535.01 TCGA.CG.5724.01 TCGA.D7.8574.01
#> "011" "023" "032" "022" "034" "011"
#> TCGA.HJ.7597.01 TCGA.HF.A5NB.01 TCGA.VQ.A8PB.01 TCGA.R5.A7ZE.01 TCGA.CD.5803.01 TCGA.CG.5725.01
#> "011" "022" "034" "012" "011" "012"
#> TCGA.D7.6820.01 TCGA.CD.5802.01 TCGA.R5.A7ZF.01 TCGA.D7.A6F0.01 TCGA.CG.5727.01 TCGA.VQ.A8PC.01
#> "012" "013" "013" "012" "032" "031"
#> TCGA.CD.A486.01 TCGA.RD.A8N2.01 TCGA.IN.A6RI.01 TCGA.HU.8243.01 TCGA.CD.A48C.01 TCGA.RD.A8N5.01
#> "012" "011" "012" "034" "022" "011"
#> TCGA.RD.A8N1.01 TCGA.HU.A4GF.01 TCGA.BR.8362.01 TCGA.BR.8285.01 TCGA.CD.8532.01 TCGA.VQ.A8E2.01
#> "013" "012" "032" "021" "011" "013"
#> TCGA.BR.8373.01 TCGA.BR.8361.01 TCGA.BR.8058.01 TCGA.IN.8462.01 TCGA.HU.A4G9.01 TCGA.CD.8524.01
#> "012" "022" "011" "034" "022" "032"
#> TCGA.D7.A748.01 TCGA.CD.8527.01 TCGA.VQ.A8DV.01 TCGA.CD.8528.01 TCGA.BR.A453.01 TCGA.RD.A8N6.01
#> "011" "013" "012" "022" "031" "013"
#> TCGA.HU.8245.01 TCGA.ZA.A8F6.01 TCGA.BR.8367.01 TCGA.BR.8380.01 TCGA.FP.A4BE.01 TCGA.HU.8238.01
#> "012" "013" "032" "031" "023" "034"
#> TCGA.BR.8078.01 TCGA.HU.8249.01 TCGA.RD.A8N0.01 TCGA.BR.8365.01 TCGA.FP.8211.01 TCGA.RD.A8N4.01
#> "023" "033" "011" "011" "011" "011"
#> TCGA.VQ.A8DU.01 TCGA.VQ.A8DL.01 TCGA.VQ.A8DZ.01 TCGA.D7.8572.01 TCGA.RD.A7BW.01 TCGA.R5.A804.01
#> "012" "013" "012" "013" "011" "031"
#> TCGA.BR.A4CS.01 TCGA.CD.8531.01 TCGA.CD.A487.01 TCGA.BR.8371.01 TCGA.BR.8059.01 TCGA.D7.A6ET.01
#> "032" "021" "013" "011" "013" "031"
#> TCGA.FP.8099.01 TCGA.D7.8579.01 TCGA.BR.8297.01 TCGA.D7.8576.01 TCGA.VQ.A8DT.01 TCGA.FP.A8CX.01
#> "033" "031" "032" "011" "022" "013"
#> TCGA.HU.A4GH.01 TCGA.CD.8526.01 TCGA.HU.A4G6.01 TCGA.D7.8578.01 TCGA.HU.A4G3.01 TCGA.D7.A74A.01
#> "012" "013" "021" "013" "022" "022"
#> TCGA.RD.A7C1.01 TCGA.F1.A448.01 TCGA.D7.8575.01 TCGA.BR.8372.01 TCGA.VQ.A8P3.01 TCGA.RD.A8MW.01
#> "032" "031" "034" "022" "034" "013"
#> TCGA.BR.8286.01 TCGA.BR.8369.01 TCGA.BR.8364.01 TCGA.HU.8244.01 TCGA.KB.A6F7.01 TCGA.FP.A4BF.01
#> "034" "032" "011" "022" "012" "032"
#> TCGA.R5.A805.01 TCGA.IN.A6RL.01 TCGA.IN.A6RR.01 TCGA.BR.A4CR.01 TCGA.CD.A489.01 TCGA.HU.A4GY.01
#> "032" "034" "022" "013" "011" "011"
#> TCGA.BR.8289.01 TCGA.FP.8209.01 TCGA.BR.8296.01 TCGA.CD.A48A.01 TCGA.BR.8060.01 TCGA.BR.8077.01
#> "034" "011" "031" "033" "012" "012"
#> TCGA.CD.8534.01 TCGA.BR.7959.01 TCGA.VQ.A8P2.01 TCGA.EQ.8122.01 TCGA.D7.8573.01 TCGA.BR.A44T.01
#> "032" "032" "022" "012" "021" "011"
#> TCGA.RD.A8MV.01 TCGA.CD.8536.01 TCGA.BR.8360.01 TCGA.BR.8291.01 TCGA.FP.8210.01 TCGA.RD.A7BS.01
#> "031" "032" "023" "013" "011" "011"
#> TCGA.BR.A44U.01 TCGA.CD.8529.01
#> "034" "013"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 17153))
#> TCGA.VQ.A94P.01 TCGA.D7.6521.01 TCGA.VQ.A8PE.01 TCGA.D7.6519.01 TCGA.BR.6452.01 TCGA.BR.8485.01
#> "011" "011" "012" "013" "023" "012"
#> TCGA.VQ.A8PO.01 TCGA.VQ.AA69.01 TCGA.BR.8683.01 TCGA.BR.8486.01 TCGA.D7.6522.01 TCGA.CG.5716.01
#> "022" "021" "03" "012" "011" "03"
#> TCGA.BR.8589.01 TCGA.BR.8382.01 TCGA.VQ.AA68.01 TCGA.VQ.A8PJ.01 TCGA.VQ.A8PH.01 TCGA.HU.8604.01
#> "021" "023" "03" "012" "012" "023"
#> TCGA.BR.8676.01 TCGA.CG.4441.01 TCGA.D7.6520.01 TCGA.VQ.AA64.01 TCGA.D7.6527.01 TCGA.VQ.A8PM.01
#> "021" "03" "012" "011" "012" "013"
#> TCGA.VQ.A923.01 TCGA.BR.8384.01 TCGA.BR.6453.01 TCGA.VQ.A928.01 TCGA.VQ.A8E0.01 TCGA.BR.8679.01
#> "021" "03" "03" "011" "011" "022"
#> TCGA.VQ.A91S.01 TCGA.BR.8678.01 TCGA.D7.6528.01 TCGA.VQ.A8E7.01 TCGA.BR.8680.01 TCGA.BR.8483.01
#> "03" "012" "03" "03" "03" "03"
#> TCGA.BR.6566.01 TCGA.VQ.A91X.01 TCGA.VQ.A91Q.01 TCGA.VQ.A92D.01 TCGA.VQ.A91Z.01 TCGA.BR.6455.01
#> "03" "03" "011" "022" "012" "021"
#> TCGA.BR.8591.01 TCGA.HU.8608.01 TCGA.VQ.A94U.01 TCGA.VQ.A94T.01 TCGA.VQ.A91A.01 TCGA.VQ.A91D.01
#> "023" "021" "03" "011" "03" "023"
#> TCGA.D7.6518.01 TCGA.BR.8484.01 TCGA.VQ.A91N.01 TCGA.VQ.A91E.01 TCGA.VQ.A8PY.01 TCGA.HU.8602.01
#> "03" "013" "012" "03" "03" "023"
#> TCGA.BR.8381.01 TCGA.BR.6452.11 TCGA.IN.8663.01 TCGA.VQ.A8PS.01 TCGA.VQ.A91W.01 TCGA.BR.6454.01
#> "021" "03" "022" "011" "021" "011"
#> TCGA.BR.8682.01 TCGA.VQ.A91V.01 TCGA.VQ.A8PZ.01 TCGA.BR.8590.01 TCGA.F1.6177.01 TCGA.VQ.A8PQ.01
#> "03" "03" "03" "011" "022" "011"
#> TCGA.VQ.A91U.01 TCGA.VQ.AA6I.01 TCGA.CG.4437.01 TCGA.VQ.A8PP.01 TCGA.BR.6565.01 TCGA.VQ.A91Y.01
#> "012" "022" "023" "023" "012" "013"
#> TCGA.VQ.A8PF.01 TCGA.BR.6456.01 TCGA.BR.6458.01 TCGA.VQ.A925.01 TCGA.VQ.A927.01 TCGA.BR.8592.01
#> "021" "013" "03" "013" "011" "03"
#> TCGA.BR.6566.11 TCGA.IN.AB1V.01 TCGA.VQ.AA6F.01 TCGA.VQ.AA6J.01 TCGA.BR.8487.01 TCGA.D7.6525.01
#> "011" "013" "011" "011" "022" "03"
#> TCGA.VQ.A94O.01 TCGA.BR.8588.01 TCGA.HU.8610.01 TCGA.D7.6526.01 TCGA.VQ.A8PD.01 TCGA.D7.6524.01
#> "012" "03" "03" "012" "03" "03"
#> TCGA.3M.AB46.01 TCGA.3M.AB47.01 TCGA.BR.8677.01 TCGA.BR.6457.01 TCGA.BR.8687.01 TCGA.VQ.A91K.01
#> "012" "03" "011" "03" "013" "022"
#> TCGA.BR.8690.01 TCGA.BR.8686.01 TCGA.FP.8631.01 TCGA.VQ.A922.01 TCGA.BR.A452.01 TCGA.IN.A6RO.01
#> "013" "021" "012" "012" "011" "022"
#> TCGA.BR.A4QI.01 TCGA.D7.A6EV.01 TCGA.HU.A4G2.01 TCGA.BR.A4IY.01 TCGA.VQ.A8PU.01 TCGA.BR.A4J4.01
#> "023" "03" "021" "021" "011" "021"
#> TCGA.VQ.A94R.01 TCGA.HU.A4H4.01 TCGA.BR.7707.01 TCGA.FP.7829.01 TCGA.BR.A4J5.01 TCGA.HU.A4H0.01
#> "022" "03" "022" "022" "03" "021"
#> TCGA.HU.A4HD.01 TCGA.KB.A6F5.01 TCGA.VQ.AA6K.01 TCGA.HF.7133.01 TCGA.F1.6875.01 TCGA.MX.A666.01
#> "012" "013" "011" "013" "012" "012"
#> TCGA.BR.7717.01 TCGA.BR.A4PF.01 TCGA.BR.A4IU.01 TCGA.VQ.A8PX.01 TCGA.BR.A4IV.01 TCGA.D7.A6EX.01
#> "03" "023" "03" "011" "011" "013"
#> TCGA.BR.A4IZ.01 TCGA.BR.A4J9.01 TCGA.CD.A4MJ.01 TCGA.B7.A5TN.01 TCGA.BR.7715.01 TCGA.BR.7704.01
#> "011" "011" "023" "012" "03" "012"
#> TCGA.BR.A4J1.01 TCGA.HU.A4GP.01 TCGA.D7.A4YY.01 TCGA.VQ.AA6G.01 TCGA.HU.A4GJ.01 TCGA.CD.A4MI.01
#> "012" "022" "022" "022" "03" "023"
#> TCGA.BR.7196.01 TCGA.BR.6563.01 TCGA.VQ.A924.01 TCGA.BR.7716.01 TCGA.FP.7735.01 TCGA.BR.7723.01
#> "03" "03" "023" "013" "013" "013"
#> TCGA.HU.A4H8.01 TCGA.IN.A6RJ.01 TCGA.HU.A4H3.01 TCGA.EQ.A4SO.01 TCGA.CD.A4MH.01 TCGA.BR.A4J7.01
#> "022" "03" "022" "011" "012" "011"
#> TCGA.HF.7131.01 TCGA.D7.A74B.01 TCGA.BR.A4PE.01 TCGA.BR.A4J8.01 TCGA.HU.A4GX.01 TCGA.HU.A4G8.01
#> "012" "011" "022" "023" "03" "03"
#> TCGA.HU.A4GT.01 TCGA.HU.A4GC.01 TCGA.BR.A4CQ.01 TCGA.D7.A6F2.01 TCGA.RD.A7BT.01 TCGA.BR.A4J6.01
#> "022" "03" "022" "012" "012" "011"
#> TCGA.HU.A4GQ.01 TCGA.HF.7136.01 TCGA.BR.A4QM.01 TCGA.BR.A4PD.01 TCGA.VQ.A8PK.01 TCGA.B7.A5TK.01
#> "023" "013" "023" "012" "012" "03"
#> TCGA.D7.A4YX.01 TCGA.D7.A4Z0.01 TCGA.VQ.A8PT.01 TCGA.IN.A6RN.01 TCGA.CD.A4MG.01 TCGA.D7.A747.01
#> "021" "03" "022" "012" "022" "011"
#> TCGA.R5.A7O7.01 TCGA.F1.A72C.01 TCGA.BR.A4J2.01 TCGA.MX.A663.01 TCGA.D7.A4YV.01 TCGA.HU.A4GD.01
#> "03" "011" "03" "013" "023" "03"
#> TCGA.BR.A4QL.01 TCGA.BR.7703.01 TCGA.VQ.AA6B.01 TCGA.VQ.AA6D.01 TCGA.D7.A6EZ.01 TCGA.D7.A4YU.01
#> "022" "022" "03" "012" "021" "023"
#> TCGA.VQ.AA6A.01 TCGA.IN.7806.01 TCGA.HU.A4HB.01 TCGA.HU.A4H2.01 TCGA.IN.A6RP.01 TCGA.HU.A4H5.01
#> "012" "012" "03" "03" "022" "012"
#> TCGA.HU.A4GU.01 TCGA.MX.A5UJ.01 TCGA.HU.A4GN.01 TCGA.CD.5804.01 TCGA.HU.A4H6.01 TCGA.HF.7132.01
#> "022" "022" "023" "013" "023" "023"
#> TCGA.D7.A4YT.01 TCGA.HF.7134.01 TCGA.BR.6852.01 TCGA.BR.8370.01 TCGA.EQ.5647.01 TCGA.IN.A7NT.01
#> "013" "022" "03" "023" "013" "03"
#> TCGA.RD.A8N9.01 TCGA.D7.5577.01 TCGA.CG.5717.01 TCGA.D7.6818.01 TCGA.CG.5734.01 TCGA.VQ.A8P8.01
#> "011" "021" "011" "013" "03" "03"
#> TCGA.BR.6707.01 TCGA.B7.5818.01 TCGA.CD.8525.01 TCGA.BR.6705.01 TCGA.BR.4288.01 TCGA.CD.5813.01
#> "021" "021" "013" "03" "013" "011"
#> TCGA.CG.5723.01 TCGA.CD.5800.01 TCGA.CG.5718.01 TCGA.BR.8080.01 TCGA.CG.5733.01 TCGA.D7.6817.01
#> "011" "013" "012" "011" "022" "012"
#> TCGA.KB.A93G.01 TCGA.CD.5799.01 TCGA.BR.7851.01 TCGA.BR.7722.01 TCGA.MX.A5UG.01 TCGA.CD.8533.01
#> "011" "013" "023" "011" "03" "03"
#> TCGA.BR.7957.01 TCGA.CG.5722.01 TCGA.F1.6874.01 TCGA.CG.5730.01 TCGA.CG.5726.01 TCGA.IP.7968.01
#> "03" "03" "03" "03" "022" "03"
#> TCGA.BR.8363.01 TCGA.BR.7901.01 TCGA.D7.6822.01 TCGA.BR.6710.01 TCGA.CG.5720.01 TCGA.D7.8570.01
#> "023" "012" "03" "011" "022" "021"
#> TCGA.B7.A5TI.01 TCGA.D7.6815.01 TCGA.BR.8284.01 TCGA.BR.8295.01 TCGA.BR.7197.01 TCGA.B7.A5TJ.01
#> "013" "012" "023" "012" "012" "022"
#> TCGA.D7.A6EY.01 TCGA.BR.8366.01 TCGA.IN.A7NR.01 TCGA.BR.6706.01 TCGA.IN.7808.01 TCGA.BR.6564.01
#> "03" "021" "011" "03" "03" "011"
#> TCGA.KB.A93H.01 TCGA.KB.A93J.01 TCGA.CD.5798.01 TCGA.CD.8530.01 TCGA.BR.6802.01 TCGA.CG.5719.01
#> "03" "012" "011" "013" "03" "011"
#> TCGA.VQ.A8E3.01 TCGA.CD.5801.01 TCGA.FP.A9TM.01 TCGA.BR.7958.01 TCGA.FP.7998.01 TCGA.IN.A6RS.01
#> "022" "021" "03" "021" "03" "03"
#> TCGA.BR.6709.01 TCGA.FP.7916.01 TCGA.R5.A7ZR.01 TCGA.B7.5816.01 TCGA.CG.5721.01 TCGA.SW.A7EA.01
#> "011" "021" "012" "03" "03" "022"
#> TCGA.RD.A8NB.01 TCGA.BR.6801.01 TCGA.IN.AB1X.01 TCGA.D7.5579.01 TCGA.CG.5728.01 TCGA.R5.A7ZI.01
#> "03" "013" "03" "013" "03" "013"
#> TCGA.IN.A7NU.01 TCGA.CG.5732.01 TCGA.ZQ.A9CR.01 TCGA.D7.5578.01 TCGA.BR.6803.01 TCGA.BR.8368.01
#> "03" "013" "013" "03" "011" "022"
#> TCGA.SW.A7EB.01 TCGA.BR.8081.01 TCGA.VQ.A8P5.01 TCGA.CD.8535.01 TCGA.CG.5724.01 TCGA.D7.8574.01
#> "011" "023" "03" "022" "03" "011"
#> TCGA.HJ.7597.01 TCGA.HF.A5NB.01 TCGA.VQ.A8PB.01 TCGA.R5.A7ZE.01 TCGA.CD.5803.01 TCGA.CG.5725.01
#> "011" "022" "03" "012" "011" "012"
#> TCGA.D7.6820.01 TCGA.CD.5802.01 TCGA.R5.A7ZF.01 TCGA.D7.A6F0.01 TCGA.CG.5727.01 TCGA.VQ.A8PC.01
#> "012" "013" "013" "012" "03" "03"
#> TCGA.CD.A486.01 TCGA.RD.A8N2.01 TCGA.IN.A6RI.01 TCGA.HU.8243.01 TCGA.CD.A48C.01 TCGA.RD.A8N5.01
#> "012" "011" "012" "03" "022" "011"
#> TCGA.RD.A8N1.01 TCGA.HU.A4GF.01 TCGA.BR.8362.01 TCGA.BR.8285.01 TCGA.CD.8532.01 TCGA.VQ.A8E2.01
#> "013" "012" "03" "021" "011" "013"
#> TCGA.BR.8373.01 TCGA.BR.8361.01 TCGA.BR.8058.01 TCGA.IN.8462.01 TCGA.HU.A4G9.01 TCGA.CD.8524.01
#> "012" "022" "011" "03" "022" "03"
#> TCGA.D7.A748.01 TCGA.CD.8527.01 TCGA.VQ.A8DV.01 TCGA.CD.8528.01 TCGA.BR.A453.01 TCGA.RD.A8N6.01
#> "011" "013" "012" "022" "03" "013"
#> TCGA.HU.8245.01 TCGA.ZA.A8F6.01 TCGA.BR.8367.01 TCGA.BR.8380.01 TCGA.FP.A4BE.01 TCGA.HU.8238.01
#> "012" "013" "03" "03" "023" "03"
#> TCGA.BR.8078.01 TCGA.HU.8249.01 TCGA.RD.A8N0.01 TCGA.BR.8365.01 TCGA.FP.8211.01 TCGA.RD.A8N4.01
#> "023" "03" "011" "011" "011" "011"
#> TCGA.VQ.A8DU.01 TCGA.VQ.A8DL.01 TCGA.VQ.A8DZ.01 TCGA.D7.8572.01 TCGA.RD.A7BW.01 TCGA.R5.A804.01
#> "012" "013" "012" "013" "011" "03"
#> TCGA.BR.A4CS.01 TCGA.CD.8531.01 TCGA.CD.A487.01 TCGA.BR.8371.01 TCGA.BR.8059.01 TCGA.D7.A6ET.01
#> "03" "021" "013" "011" "013" "03"
#> TCGA.FP.8099.01 TCGA.D7.8579.01 TCGA.BR.8297.01 TCGA.D7.8576.01 TCGA.VQ.A8DT.01 TCGA.FP.A8CX.01
#> "03" "03" "03" "011" "022" "013"
#> TCGA.HU.A4GH.01 TCGA.CD.8526.01 TCGA.HU.A4G6.01 TCGA.D7.8578.01 TCGA.HU.A4G3.01 TCGA.D7.A74A.01
#> "012" "013" "021" "013" "022" "022"
#> TCGA.RD.A7C1.01 TCGA.F1.A448.01 TCGA.D7.8575.01 TCGA.BR.8372.01 TCGA.VQ.A8P3.01 TCGA.RD.A8MW.01
#> "03" "03" "03" "022" "03" "013"
#> TCGA.BR.8286.01 TCGA.BR.8369.01 TCGA.BR.8364.01 TCGA.HU.8244.01 TCGA.KB.A6F7.01 TCGA.FP.A4BF.01
#> "03" "03" "011" "022" "012" "03"
#> TCGA.R5.A805.01 TCGA.IN.A6RL.01 TCGA.IN.A6RR.01 TCGA.BR.A4CR.01 TCGA.CD.A489.01 TCGA.HU.A4GY.01
#> "03" "03" "022" "013" "011" "011"
#> TCGA.BR.8289.01 TCGA.FP.8209.01 TCGA.BR.8296.01 TCGA.CD.A48A.01 TCGA.BR.8060.01 TCGA.BR.8077.01
#> "03" "011" "03" "03" "012" "012"
#> TCGA.CD.8534.01 TCGA.BR.7959.01 TCGA.VQ.A8P2.01 TCGA.EQ.8122.01 TCGA.D7.8573.01 TCGA.BR.A44T.01
#> "03" "03" "022" "012" "021" "011"
#> TCGA.RD.A8MV.01 TCGA.CD.8536.01 TCGA.BR.8360.01 TCGA.BR.8291.01 TCGA.FP.8210.01 TCGA.RD.A7BS.01
#> "03" "03" "023" "013" "011" "011"
#> TCGA.BR.A44U.01 TCGA.CD.8529.01
#> "03" "013"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 19830))
#> TCGA.VQ.A94P.01 TCGA.D7.6521.01 TCGA.VQ.A8PE.01 TCGA.D7.6519.01 TCGA.BR.6452.01 TCGA.BR.8485.01
#> "011" "011" "012" "013" "023" "012"
#> TCGA.VQ.A8PO.01 TCGA.VQ.AA69.01 TCGA.BR.8683.01 TCGA.BR.8486.01 TCGA.D7.6522.01 TCGA.CG.5716.01
#> "022" "021" "03" "012" "011" "03"
#> TCGA.BR.8589.01 TCGA.BR.8382.01 TCGA.VQ.AA68.01 TCGA.VQ.A8PJ.01 TCGA.VQ.A8PH.01 TCGA.HU.8604.01
#> "021" "023" "03" "012" "012" "023"
#> TCGA.BR.8676.01 TCGA.CG.4441.01 TCGA.D7.6520.01 TCGA.VQ.AA64.01 TCGA.D7.6527.01 TCGA.VQ.A8PM.01
#> "021" "03" "012" "011" "012" "013"
#> TCGA.VQ.A923.01 TCGA.BR.8384.01 TCGA.BR.6453.01 TCGA.VQ.A928.01 TCGA.VQ.A8E0.01 TCGA.BR.8679.01
#> "021" "03" "03" "011" "011" "022"
#> TCGA.VQ.A91S.01 TCGA.BR.8678.01 TCGA.D7.6528.01 TCGA.VQ.A8E7.01 TCGA.BR.8680.01 TCGA.BR.8483.01
#> "03" "012" "03" "03" "03" "03"
#> TCGA.BR.6566.01 TCGA.VQ.A91X.01 TCGA.VQ.A91Q.01 TCGA.VQ.A92D.01 TCGA.VQ.A91Z.01 TCGA.BR.6455.01
#> "03" "03" "011" "022" "012" "021"
#> TCGA.BR.8591.01 TCGA.HU.8608.01 TCGA.VQ.A94U.01 TCGA.VQ.A94T.01 TCGA.VQ.A91A.01 TCGA.VQ.A91D.01
#> "023" "021" "03" "011" "03" "023"
#> TCGA.D7.6518.01 TCGA.BR.8484.01 TCGA.VQ.A91N.01 TCGA.VQ.A91E.01 TCGA.VQ.A8PY.01 TCGA.HU.8602.01
#> "03" "013" "012" "03" "03" "023"
#> TCGA.BR.8381.01 TCGA.BR.6452.11 TCGA.IN.8663.01 TCGA.VQ.A8PS.01 TCGA.VQ.A91W.01 TCGA.BR.6454.01
#> "021" "03" "022" "011" "021" "011"
#> TCGA.BR.8682.01 TCGA.VQ.A91V.01 TCGA.VQ.A8PZ.01 TCGA.BR.8590.01 TCGA.F1.6177.01 TCGA.VQ.A8PQ.01
#> "03" "03" "03" "011" "022" "011"
#> TCGA.VQ.A91U.01 TCGA.VQ.AA6I.01 TCGA.CG.4437.01 TCGA.VQ.A8PP.01 TCGA.BR.6565.01 TCGA.VQ.A91Y.01
#> "012" "022" "023" "023" "012" "013"
#> TCGA.VQ.A8PF.01 TCGA.BR.6456.01 TCGA.BR.6458.01 TCGA.VQ.A925.01 TCGA.VQ.A927.01 TCGA.BR.8592.01
#> "021" "013" "03" "013" "011" "03"
#> TCGA.BR.6566.11 TCGA.IN.AB1V.01 TCGA.VQ.AA6F.01 TCGA.VQ.AA6J.01 TCGA.BR.8487.01 TCGA.D7.6525.01
#> "011" "013" "011" "011" "022" "03"
#> TCGA.VQ.A94O.01 TCGA.BR.8588.01 TCGA.HU.8610.01 TCGA.D7.6526.01 TCGA.VQ.A8PD.01 TCGA.D7.6524.01
#> "012" "03" "03" "012" "03" "03"
#> TCGA.3M.AB46.01 TCGA.3M.AB47.01 TCGA.BR.8677.01 TCGA.BR.6457.01 TCGA.BR.8687.01 TCGA.VQ.A91K.01
#> "012" "03" "011" "03" "013" "022"
#> TCGA.BR.8690.01 TCGA.BR.8686.01 TCGA.FP.8631.01 TCGA.VQ.A922.01 TCGA.BR.A452.01 TCGA.IN.A6RO.01
#> "013" "021" "012" "012" "011" "022"
#> TCGA.BR.A4QI.01 TCGA.D7.A6EV.01 TCGA.HU.A4G2.01 TCGA.BR.A4IY.01 TCGA.VQ.A8PU.01 TCGA.BR.A4J4.01
#> "023" "03" "021" "021" "011" "021"
#> TCGA.VQ.A94R.01 TCGA.HU.A4H4.01 TCGA.BR.7707.01 TCGA.FP.7829.01 TCGA.BR.A4J5.01 TCGA.HU.A4H0.01
#> "022" "03" "022" "022" "03" "021"
#> TCGA.HU.A4HD.01 TCGA.KB.A6F5.01 TCGA.VQ.AA6K.01 TCGA.HF.7133.01 TCGA.F1.6875.01 TCGA.MX.A666.01
#> "012" "013" "011" "013" "012" "012"
#> TCGA.BR.7717.01 TCGA.BR.A4PF.01 TCGA.BR.A4IU.01 TCGA.VQ.A8PX.01 TCGA.BR.A4IV.01 TCGA.D7.A6EX.01
#> "03" "023" "03" "011" "011" "013"
#> TCGA.BR.A4IZ.01 TCGA.BR.A4J9.01 TCGA.CD.A4MJ.01 TCGA.B7.A5TN.01 TCGA.BR.7715.01 TCGA.BR.7704.01
#> "011" "011" "023" "012" "03" "012"
#> TCGA.BR.A4J1.01 TCGA.HU.A4GP.01 TCGA.D7.A4YY.01 TCGA.VQ.AA6G.01 TCGA.HU.A4GJ.01 TCGA.CD.A4MI.01
#> "012" "022" "022" "022" "03" "023"
#> TCGA.BR.7196.01 TCGA.BR.6563.01 TCGA.VQ.A924.01 TCGA.BR.7716.01 TCGA.FP.7735.01 TCGA.BR.7723.01
#> "03" "03" "023" "013" "013" "013"
#> TCGA.HU.A4H8.01 TCGA.IN.A6RJ.01 TCGA.HU.A4H3.01 TCGA.EQ.A4SO.01 TCGA.CD.A4MH.01 TCGA.BR.A4J7.01
#> "022" "03" "022" "011" "012" "011"
#> TCGA.HF.7131.01 TCGA.D7.A74B.01 TCGA.BR.A4PE.01 TCGA.BR.A4J8.01 TCGA.HU.A4GX.01 TCGA.HU.A4G8.01
#> "012" "011" "022" "023" "03" "03"
#> TCGA.HU.A4GT.01 TCGA.HU.A4GC.01 TCGA.BR.A4CQ.01 TCGA.D7.A6F2.01 TCGA.RD.A7BT.01 TCGA.BR.A4J6.01
#> "022" "03" "022" "012" "012" "011"
#> TCGA.HU.A4GQ.01 TCGA.HF.7136.01 TCGA.BR.A4QM.01 TCGA.BR.A4PD.01 TCGA.VQ.A8PK.01 TCGA.B7.A5TK.01
#> "023" "013" "023" "012" "012" "03"
#> TCGA.D7.A4YX.01 TCGA.D7.A4Z0.01 TCGA.VQ.A8PT.01 TCGA.IN.A6RN.01 TCGA.CD.A4MG.01 TCGA.D7.A747.01
#> "021" "03" "022" "012" "022" "011"
#> TCGA.R5.A7O7.01 TCGA.F1.A72C.01 TCGA.BR.A4J2.01 TCGA.MX.A663.01 TCGA.D7.A4YV.01 TCGA.HU.A4GD.01
#> "03" "011" "03" "013" "023" "03"
#> TCGA.BR.A4QL.01 TCGA.BR.7703.01 TCGA.VQ.AA6B.01 TCGA.VQ.AA6D.01 TCGA.D7.A6EZ.01 TCGA.D7.A4YU.01
#> "022" "022" "03" "012" "021" "023"
#> TCGA.VQ.AA6A.01 TCGA.IN.7806.01 TCGA.HU.A4HB.01 TCGA.HU.A4H2.01 TCGA.IN.A6RP.01 TCGA.HU.A4H5.01
#> "012" "012" "03" "03" "022" "012"
#> TCGA.HU.A4GU.01 TCGA.MX.A5UJ.01 TCGA.HU.A4GN.01 TCGA.CD.5804.01 TCGA.HU.A4H6.01 TCGA.HF.7132.01
#> "022" "022" "023" "013" "023" "023"
#> TCGA.D7.A4YT.01 TCGA.HF.7134.01 TCGA.BR.6852.01 TCGA.BR.8370.01 TCGA.EQ.5647.01 TCGA.IN.A7NT.01
#> "013" "022" "03" "023" "013" "03"
#> TCGA.RD.A8N9.01 TCGA.D7.5577.01 TCGA.CG.5717.01 TCGA.D7.6818.01 TCGA.CG.5734.01 TCGA.VQ.A8P8.01
#> "011" "021" "011" "013" "03" "03"
#> TCGA.BR.6707.01 TCGA.B7.5818.01 TCGA.CD.8525.01 TCGA.BR.6705.01 TCGA.BR.4288.01 TCGA.CD.5813.01
#> "021" "021" "013" "03" "013" "011"
#> TCGA.CG.5723.01 TCGA.CD.5800.01 TCGA.CG.5718.01 TCGA.BR.8080.01 TCGA.CG.5733.01 TCGA.D7.6817.01
#> "011" "013" "012" "011" "022" "012"
#> TCGA.KB.A93G.01 TCGA.CD.5799.01 TCGA.BR.7851.01 TCGA.BR.7722.01 TCGA.MX.A5UG.01 TCGA.CD.8533.01
#> "011" "013" "023" "011" "03" "03"
#> TCGA.BR.7957.01 TCGA.CG.5722.01 TCGA.F1.6874.01 TCGA.CG.5730.01 TCGA.CG.5726.01 TCGA.IP.7968.01
#> "03" "03" "03" "03" "022" "03"
#> TCGA.BR.8363.01 TCGA.BR.7901.01 TCGA.D7.6822.01 TCGA.BR.6710.01 TCGA.CG.5720.01 TCGA.D7.8570.01
#> "023" "012" "03" "011" "022" "021"
#> TCGA.B7.A5TI.01 TCGA.D7.6815.01 TCGA.BR.8284.01 TCGA.BR.8295.01 TCGA.BR.7197.01 TCGA.B7.A5TJ.01
#> "013" "012" "023" "012" "012" "022"
#> TCGA.D7.A6EY.01 TCGA.BR.8366.01 TCGA.IN.A7NR.01 TCGA.BR.6706.01 TCGA.IN.7808.01 TCGA.BR.6564.01
#> "03" "021" "011" "03" "03" "011"
#> TCGA.KB.A93H.01 TCGA.KB.A93J.01 TCGA.CD.5798.01 TCGA.CD.8530.01 TCGA.BR.6802.01 TCGA.CG.5719.01
#> "03" "012" "011" "013" "03" "011"
#> TCGA.VQ.A8E3.01 TCGA.CD.5801.01 TCGA.FP.A9TM.01 TCGA.BR.7958.01 TCGA.FP.7998.01 TCGA.IN.A6RS.01
#> "022" "021" "03" "021" "03" "03"
#> TCGA.BR.6709.01 TCGA.FP.7916.01 TCGA.R5.A7ZR.01 TCGA.B7.5816.01 TCGA.CG.5721.01 TCGA.SW.A7EA.01
#> "011" "021" "012" "03" "03" "022"
#> TCGA.RD.A8NB.01 TCGA.BR.6801.01 TCGA.IN.AB1X.01 TCGA.D7.5579.01 TCGA.CG.5728.01 TCGA.R5.A7ZI.01
#> "03" "013" "03" "013" "03" "013"
#> TCGA.IN.A7NU.01 TCGA.CG.5732.01 TCGA.ZQ.A9CR.01 TCGA.D7.5578.01 TCGA.BR.6803.01 TCGA.BR.8368.01
#> "03" "013" "013" "03" "011" "022"
#> TCGA.SW.A7EB.01 TCGA.BR.8081.01 TCGA.VQ.A8P5.01 TCGA.CD.8535.01 TCGA.CG.5724.01 TCGA.D7.8574.01
#> "011" "023" "03" "022" "03" "011"
#> TCGA.HJ.7597.01 TCGA.HF.A5NB.01 TCGA.VQ.A8PB.01 TCGA.R5.A7ZE.01 TCGA.CD.5803.01 TCGA.CG.5725.01
#> "011" "022" "03" "012" "011" "012"
#> TCGA.D7.6820.01 TCGA.CD.5802.01 TCGA.R5.A7ZF.01 TCGA.D7.A6F0.01 TCGA.CG.5727.01 TCGA.VQ.A8PC.01
#> "012" "013" "013" "012" "03" "03"
#> TCGA.CD.A486.01 TCGA.RD.A8N2.01 TCGA.IN.A6RI.01 TCGA.HU.8243.01 TCGA.CD.A48C.01 TCGA.RD.A8N5.01
#> "012" "011" "012" "03" "022" "011"
#> TCGA.RD.A8N1.01 TCGA.HU.A4GF.01 TCGA.BR.8362.01 TCGA.BR.8285.01 TCGA.CD.8532.01 TCGA.VQ.A8E2.01
#> "013" "012" "03" "021" "011" "013"
#> TCGA.BR.8373.01 TCGA.BR.8361.01 TCGA.BR.8058.01 TCGA.IN.8462.01 TCGA.HU.A4G9.01 TCGA.CD.8524.01
#> "012" "022" "011" "03" "022" "03"
#> TCGA.D7.A748.01 TCGA.CD.8527.01 TCGA.VQ.A8DV.01 TCGA.CD.8528.01 TCGA.BR.A453.01 TCGA.RD.A8N6.01
#> "011" "013" "012" "022" "03" "013"
#> TCGA.HU.8245.01 TCGA.ZA.A8F6.01 TCGA.BR.8367.01 TCGA.BR.8380.01 TCGA.FP.A4BE.01 TCGA.HU.8238.01
#> "012" "013" "03" "03" "023" "03"
#> TCGA.BR.8078.01 TCGA.HU.8249.01 TCGA.RD.A8N0.01 TCGA.BR.8365.01 TCGA.FP.8211.01 TCGA.RD.A8N4.01
#> "023" "03" "011" "011" "011" "011"
#> TCGA.VQ.A8DU.01 TCGA.VQ.A8DL.01 TCGA.VQ.A8DZ.01 TCGA.D7.8572.01 TCGA.RD.A7BW.01 TCGA.R5.A804.01
#> "012" "013" "012" "013" "011" "03"
#> TCGA.BR.A4CS.01 TCGA.CD.8531.01 TCGA.CD.A487.01 TCGA.BR.8371.01 TCGA.BR.8059.01 TCGA.D7.A6ET.01
#> "03" "021" "013" "011" "013" "03"
#> TCGA.FP.8099.01 TCGA.D7.8579.01 TCGA.BR.8297.01 TCGA.D7.8576.01 TCGA.VQ.A8DT.01 TCGA.FP.A8CX.01
#> "03" "03" "03" "011" "022" "013"
#> TCGA.HU.A4GH.01 TCGA.CD.8526.01 TCGA.HU.A4G6.01 TCGA.D7.8578.01 TCGA.HU.A4G3.01 TCGA.D7.A74A.01
#> "012" "013" "021" "013" "022" "022"
#> TCGA.RD.A7C1.01 TCGA.F1.A448.01 TCGA.D7.8575.01 TCGA.BR.8372.01 TCGA.VQ.A8P3.01 TCGA.RD.A8MW.01
#> "03" "03" "03" "022" "03" "013"
#> TCGA.BR.8286.01 TCGA.BR.8369.01 TCGA.BR.8364.01 TCGA.HU.8244.01 TCGA.KB.A6F7.01 TCGA.FP.A4BF.01
#> "03" "03" "011" "022" "012" "03"
#> TCGA.R5.A805.01 TCGA.IN.A6RL.01 TCGA.IN.A6RR.01 TCGA.BR.A4CR.01 TCGA.CD.A489.01 TCGA.HU.A4GY.01
#> "03" "03" "022" "013" "011" "011"
#> TCGA.BR.8289.01 TCGA.FP.8209.01 TCGA.BR.8296.01 TCGA.CD.A48A.01 TCGA.BR.8060.01 TCGA.BR.8077.01
#> "03" "011" "03" "03" "012" "012"
#> TCGA.CD.8534.01 TCGA.BR.7959.01 TCGA.VQ.A8P2.01 TCGA.EQ.8122.01 TCGA.D7.8573.01 TCGA.BR.A44T.01
#> "03" "03" "022" "012" "021" "011"
#> TCGA.RD.A8MV.01 TCGA.CD.8536.01 TCGA.BR.8360.01 TCGA.BR.8291.01 TCGA.FP.8210.01 TCGA.RD.A7BS.01
#> "03" "03" "023" "013" "011" "011"
#> TCGA.BR.A44U.01 TCGA.CD.8529.01
#> "03" "013"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 26007))
#> TCGA.VQ.A94P.01 TCGA.D7.6521.01 TCGA.VQ.A8PE.01 TCGA.D7.6519.01 TCGA.BR.6452.01 TCGA.BR.8485.01
#> "01" "01" "01" "01" "023" "01"
#> TCGA.VQ.A8PO.01 TCGA.VQ.AA69.01 TCGA.BR.8683.01 TCGA.BR.8486.01 TCGA.D7.6522.01 TCGA.CG.5716.01
#> "022" "021" "03" "01" "01" "03"
#> TCGA.BR.8589.01 TCGA.BR.8382.01 TCGA.VQ.AA68.01 TCGA.VQ.A8PJ.01 TCGA.VQ.A8PH.01 TCGA.HU.8604.01
#> "021" "023" "03" "01" "01" "023"
#> TCGA.BR.8676.01 TCGA.CG.4441.01 TCGA.D7.6520.01 TCGA.VQ.AA64.01 TCGA.D7.6527.01 TCGA.VQ.A8PM.01
#> "021" "03" "01" "01" "01" "01"
#> TCGA.VQ.A923.01 TCGA.BR.8384.01 TCGA.BR.6453.01 TCGA.VQ.A928.01 TCGA.VQ.A8E0.01 TCGA.BR.8679.01
#> "021" "03" "03" "01" "01" "022"
#> TCGA.VQ.A91S.01 TCGA.BR.8678.01 TCGA.D7.6528.01 TCGA.VQ.A8E7.01 TCGA.BR.8680.01 TCGA.BR.8483.01
#> "03" "01" "03" "03" "03" "03"
#> TCGA.BR.6566.01 TCGA.VQ.A91X.01 TCGA.VQ.A91Q.01 TCGA.VQ.A92D.01 TCGA.VQ.A91Z.01 TCGA.BR.6455.01
#> "03" "03" "01" "022" "01" "021"
#> TCGA.BR.8591.01 TCGA.HU.8608.01 TCGA.VQ.A94U.01 TCGA.VQ.A94T.01 TCGA.VQ.A91A.01 TCGA.VQ.A91D.01
#> "023" "021" "03" "01" "03" "023"
#> TCGA.D7.6518.01 TCGA.BR.8484.01 TCGA.VQ.A91N.01 TCGA.VQ.A91E.01 TCGA.VQ.A8PY.01 TCGA.HU.8602.01
#> "03" "01" "01" "03" "03" "023"
#> TCGA.BR.8381.01 TCGA.BR.6452.11 TCGA.IN.8663.01 TCGA.VQ.A8PS.01 TCGA.VQ.A91W.01 TCGA.BR.6454.01
#> "021" "03" "022" "01" "021" "01"
#> TCGA.BR.8682.01 TCGA.VQ.A91V.01 TCGA.VQ.A8PZ.01 TCGA.BR.8590.01 TCGA.F1.6177.01 TCGA.VQ.A8PQ.01
#> "03" "03" "03" "01" "022" "01"
#> TCGA.VQ.A91U.01 TCGA.VQ.AA6I.01 TCGA.CG.4437.01 TCGA.VQ.A8PP.01 TCGA.BR.6565.01 TCGA.VQ.A91Y.01
#> "01" "022" "023" "023" "01" "01"
#> TCGA.VQ.A8PF.01 TCGA.BR.6456.01 TCGA.BR.6458.01 TCGA.VQ.A925.01 TCGA.VQ.A927.01 TCGA.BR.8592.01
#> "021" "01" "03" "01" "01" "03"
#> TCGA.BR.6566.11 TCGA.IN.AB1V.01 TCGA.VQ.AA6F.01 TCGA.VQ.AA6J.01 TCGA.BR.8487.01 TCGA.D7.6525.01
#> "01" "01" "01" "01" "022" "03"
#> TCGA.VQ.A94O.01 TCGA.BR.8588.01 TCGA.HU.8610.01 TCGA.D7.6526.01 TCGA.VQ.A8PD.01 TCGA.D7.6524.01
#> "01" "03" "03" "01" "03" "03"
#> TCGA.3M.AB46.01 TCGA.3M.AB47.01 TCGA.BR.8677.01 TCGA.BR.6457.01 TCGA.BR.8687.01 TCGA.VQ.A91K.01
#> "01" "03" "01" "03" "01" "022"
#> TCGA.BR.8690.01 TCGA.BR.8686.01 TCGA.FP.8631.01 TCGA.VQ.A922.01 TCGA.BR.A452.01 TCGA.IN.A6RO.01
#> "01" "021" "01" "01" "01" "022"
#> TCGA.BR.A4QI.01 TCGA.D7.A6EV.01 TCGA.HU.A4G2.01 TCGA.BR.A4IY.01 TCGA.VQ.A8PU.01 TCGA.BR.A4J4.01
#> "023" "03" "021" "021" "01" "021"
#> TCGA.VQ.A94R.01 TCGA.HU.A4H4.01 TCGA.BR.7707.01 TCGA.FP.7829.01 TCGA.BR.A4J5.01 TCGA.HU.A4H0.01
#> "022" "03" "022" "022" "03" "021"
#> TCGA.HU.A4HD.01 TCGA.KB.A6F5.01 TCGA.VQ.AA6K.01 TCGA.HF.7133.01 TCGA.F1.6875.01 TCGA.MX.A666.01
#> "01" "01" "01" "01" "01" "01"
#> TCGA.BR.7717.01 TCGA.BR.A4PF.01 TCGA.BR.A4IU.01 TCGA.VQ.A8PX.01 TCGA.BR.A4IV.01 TCGA.D7.A6EX.01
#> "03" "023" "03" "01" "01" "01"
#> TCGA.BR.A4IZ.01 TCGA.BR.A4J9.01 TCGA.CD.A4MJ.01 TCGA.B7.A5TN.01 TCGA.BR.7715.01 TCGA.BR.7704.01
#> "01" "01" "023" "01" "03" "01"
#> TCGA.BR.A4J1.01 TCGA.HU.A4GP.01 TCGA.D7.A4YY.01 TCGA.VQ.AA6G.01 TCGA.HU.A4GJ.01 TCGA.CD.A4MI.01
#> "01" "022" "022" "022" "03" "023"
#> TCGA.BR.7196.01 TCGA.BR.6563.01 TCGA.VQ.A924.01 TCGA.BR.7716.01 TCGA.FP.7735.01 TCGA.BR.7723.01
#> "03" "03" "023" "01" "01" "01"
#> TCGA.HU.A4H8.01 TCGA.IN.A6RJ.01 TCGA.HU.A4H3.01 TCGA.EQ.A4SO.01 TCGA.CD.A4MH.01 TCGA.BR.A4J7.01
#> "022" "03" "022" "01" "01" "01"
#> TCGA.HF.7131.01 TCGA.D7.A74B.01 TCGA.BR.A4PE.01 TCGA.BR.A4J8.01 TCGA.HU.A4GX.01 TCGA.HU.A4G8.01
#> "01" "01" "022" "023" "03" "03"
#> TCGA.HU.A4GT.01 TCGA.HU.A4GC.01 TCGA.BR.A4CQ.01 TCGA.D7.A6F2.01 TCGA.RD.A7BT.01 TCGA.BR.A4J6.01
#> "022" "03" "022" "01" "01" "01"
#> TCGA.HU.A4GQ.01 TCGA.HF.7136.01 TCGA.BR.A4QM.01 TCGA.BR.A4PD.01 TCGA.VQ.A8PK.01 TCGA.B7.A5TK.01
#> "023" "01" "023" "01" "01" "03"
#> TCGA.D7.A4YX.01 TCGA.D7.A4Z0.01 TCGA.VQ.A8PT.01 TCGA.IN.A6RN.01 TCGA.CD.A4MG.01 TCGA.D7.A747.01
#> "021" "03" "022" "01" "022" "01"
#> TCGA.R5.A7O7.01 TCGA.F1.A72C.01 TCGA.BR.A4J2.01 TCGA.MX.A663.01 TCGA.D7.A4YV.01 TCGA.HU.A4GD.01
#> "03" "01" "03" "01" "023" "03"
#> TCGA.BR.A4QL.01 TCGA.BR.7703.01 TCGA.VQ.AA6B.01 TCGA.VQ.AA6D.01 TCGA.D7.A6EZ.01 TCGA.D7.A4YU.01
#> "022" "022" "03" "01" "021" "023"
#> TCGA.VQ.AA6A.01 TCGA.IN.7806.01 TCGA.HU.A4HB.01 TCGA.HU.A4H2.01 TCGA.IN.A6RP.01 TCGA.HU.A4H5.01
#> "01" "01" "03" "03" "022" "01"
#> TCGA.HU.A4GU.01 TCGA.MX.A5UJ.01 TCGA.HU.A4GN.01 TCGA.CD.5804.01 TCGA.HU.A4H6.01 TCGA.HF.7132.01
#> "022" "022" "023" "01" "023" "023"
#> TCGA.D7.A4YT.01 TCGA.HF.7134.01 TCGA.BR.6852.01 TCGA.BR.8370.01 TCGA.EQ.5647.01 TCGA.IN.A7NT.01
#> "01" "022" "03" "023" "01" "03"
#> TCGA.RD.A8N9.01 TCGA.D7.5577.01 TCGA.CG.5717.01 TCGA.D7.6818.01 TCGA.CG.5734.01 TCGA.VQ.A8P8.01
#> "01" "021" "01" "01" "03" "03"
#> TCGA.BR.6707.01 TCGA.B7.5818.01 TCGA.CD.8525.01 TCGA.BR.6705.01 TCGA.BR.4288.01 TCGA.CD.5813.01
#> "021" "021" "01" "03" "01" "01"
#> TCGA.CG.5723.01 TCGA.CD.5800.01 TCGA.CG.5718.01 TCGA.BR.8080.01 TCGA.CG.5733.01 TCGA.D7.6817.01
#> "01" "01" "01" "01" "022" "01"
#> TCGA.KB.A93G.01 TCGA.CD.5799.01 TCGA.BR.7851.01 TCGA.BR.7722.01 TCGA.MX.A5UG.01 TCGA.CD.8533.01
#> "01" "01" "023" "01" "03" "03"
#> TCGA.BR.7957.01 TCGA.CG.5722.01 TCGA.F1.6874.01 TCGA.CG.5730.01 TCGA.CG.5726.01 TCGA.IP.7968.01
#> "03" "03" "03" "03" "022" "03"
#> TCGA.BR.8363.01 TCGA.BR.7901.01 TCGA.D7.6822.01 TCGA.BR.6710.01 TCGA.CG.5720.01 TCGA.D7.8570.01
#> "023" "01" "03" "01" "022" "021"
#> TCGA.B7.A5TI.01 TCGA.D7.6815.01 TCGA.BR.8284.01 TCGA.BR.8295.01 TCGA.BR.7197.01 TCGA.B7.A5TJ.01
#> "01" "01" "023" "01" "01" "022"
#> TCGA.D7.A6EY.01 TCGA.BR.8366.01 TCGA.IN.A7NR.01 TCGA.BR.6706.01 TCGA.IN.7808.01 TCGA.BR.6564.01
#> "03" "021" "01" "03" "03" "01"
#> TCGA.KB.A93H.01 TCGA.KB.A93J.01 TCGA.CD.5798.01 TCGA.CD.8530.01 TCGA.BR.6802.01 TCGA.CG.5719.01
#> "03" "01" "01" "01" "03" "01"
#> TCGA.VQ.A8E3.01 TCGA.CD.5801.01 TCGA.FP.A9TM.01 TCGA.BR.7958.01 TCGA.FP.7998.01 TCGA.IN.A6RS.01
#> "022" "021" "03" "021" "03" "03"
#> TCGA.BR.6709.01 TCGA.FP.7916.01 TCGA.R5.A7ZR.01 TCGA.B7.5816.01 TCGA.CG.5721.01 TCGA.SW.A7EA.01
#> "01" "021" "01" "03" "03" "022"
#> TCGA.RD.A8NB.01 TCGA.BR.6801.01 TCGA.IN.AB1X.01 TCGA.D7.5579.01 TCGA.CG.5728.01 TCGA.R5.A7ZI.01
#> "03" "01" "03" "01" "03" "01"
#> TCGA.IN.A7NU.01 TCGA.CG.5732.01 TCGA.ZQ.A9CR.01 TCGA.D7.5578.01 TCGA.BR.6803.01 TCGA.BR.8368.01
#> "03" "01" "01" "03" "01" "022"
#> TCGA.SW.A7EB.01 TCGA.BR.8081.01 TCGA.VQ.A8P5.01 TCGA.CD.8535.01 TCGA.CG.5724.01 TCGA.D7.8574.01
#> "01" "023" "03" "022" "03" "01"
#> TCGA.HJ.7597.01 TCGA.HF.A5NB.01 TCGA.VQ.A8PB.01 TCGA.R5.A7ZE.01 TCGA.CD.5803.01 TCGA.CG.5725.01
#> "01" "022" "03" "01" "01" "01"
#> TCGA.D7.6820.01 TCGA.CD.5802.01 TCGA.R5.A7ZF.01 TCGA.D7.A6F0.01 TCGA.CG.5727.01 TCGA.VQ.A8PC.01
#> "01" "01" "01" "01" "03" "03"
#> TCGA.CD.A486.01 TCGA.RD.A8N2.01 TCGA.IN.A6RI.01 TCGA.HU.8243.01 TCGA.CD.A48C.01 TCGA.RD.A8N5.01
#> "01" "01" "01" "03" "022" "01"
#> TCGA.RD.A8N1.01 TCGA.HU.A4GF.01 TCGA.BR.8362.01 TCGA.BR.8285.01 TCGA.CD.8532.01 TCGA.VQ.A8E2.01
#> "01" "01" "03" "021" "01" "01"
#> TCGA.BR.8373.01 TCGA.BR.8361.01 TCGA.BR.8058.01 TCGA.IN.8462.01 TCGA.HU.A4G9.01 TCGA.CD.8524.01
#> "01" "022" "01" "03" "022" "03"
#> TCGA.D7.A748.01 TCGA.CD.8527.01 TCGA.VQ.A8DV.01 TCGA.CD.8528.01 TCGA.BR.A453.01 TCGA.RD.A8N6.01
#> "01" "01" "01" "022" "03" "01"
#> TCGA.HU.8245.01 TCGA.ZA.A8F6.01 TCGA.BR.8367.01 TCGA.BR.8380.01 TCGA.FP.A4BE.01 TCGA.HU.8238.01
#> "01" "01" "03" "03" "023" "03"
#> TCGA.BR.8078.01 TCGA.HU.8249.01 TCGA.RD.A8N0.01 TCGA.BR.8365.01 TCGA.FP.8211.01 TCGA.RD.A8N4.01
#> "023" "03" "01" "01" "01" "01"
#> TCGA.VQ.A8DU.01 TCGA.VQ.A8DL.01 TCGA.VQ.A8DZ.01 TCGA.D7.8572.01 TCGA.RD.A7BW.01 TCGA.R5.A804.01
#> "01" "01" "01" "01" "01" "03"
#> TCGA.BR.A4CS.01 TCGA.CD.8531.01 TCGA.CD.A487.01 TCGA.BR.8371.01 TCGA.BR.8059.01 TCGA.D7.A6ET.01
#> "03" "021" "01" "01" "01" "03"
#> TCGA.FP.8099.01 TCGA.D7.8579.01 TCGA.BR.8297.01 TCGA.D7.8576.01 TCGA.VQ.A8DT.01 TCGA.FP.A8CX.01
#> "03" "03" "03" "01" "022" "01"
#> TCGA.HU.A4GH.01 TCGA.CD.8526.01 TCGA.HU.A4G6.01 TCGA.D7.8578.01 TCGA.HU.A4G3.01 TCGA.D7.A74A.01
#> "01" "01" "021" "01" "022" "022"
#> TCGA.RD.A7C1.01 TCGA.F1.A448.01 TCGA.D7.8575.01 TCGA.BR.8372.01 TCGA.VQ.A8P3.01 TCGA.RD.A8MW.01
#> "03" "03" "03" "022" "03" "01"
#> TCGA.BR.8286.01 TCGA.BR.8369.01 TCGA.BR.8364.01 TCGA.HU.8244.01 TCGA.KB.A6F7.01 TCGA.FP.A4BF.01
#> "03" "03" "01" "022" "01" "03"
#> TCGA.R5.A805.01 TCGA.IN.A6RL.01 TCGA.IN.A6RR.01 TCGA.BR.A4CR.01 TCGA.CD.A489.01 TCGA.HU.A4GY.01
#> "03" "03" "022" "01" "01" "01"
#> TCGA.BR.8289.01 TCGA.FP.8209.01 TCGA.BR.8296.01 TCGA.CD.A48A.01 TCGA.BR.8060.01 TCGA.BR.8077.01
#> "03" "01" "03" "03" "01" "01"
#> TCGA.CD.8534.01 TCGA.BR.7959.01 TCGA.VQ.A8P2.01 TCGA.EQ.8122.01 TCGA.D7.8573.01 TCGA.BR.A44T.01
#> "03" "03" "022" "01" "021" "01"
#> TCGA.RD.A8MV.01 TCGA.CD.8536.01 TCGA.BR.8360.01 TCGA.BR.8291.01 TCGA.FP.8210.01 TCGA.RD.A7BS.01
#> "03" "03" "023" "01" "01" "01"
#> TCGA.BR.A44U.01 TCGA.CD.8529.01
#> "03" "01"
get_classes(res_rh, merge_node = merge_node_param(min_n_signatures = 29355))
#> TCGA.VQ.A94P.01 TCGA.D7.6521.01 TCGA.VQ.A8PE.01 TCGA.D7.6519.01 TCGA.BR.6452.01 TCGA.BR.8485.01
#> NA NA NA NA NA NA
#> TCGA.VQ.A8PO.01 TCGA.VQ.AA69.01 TCGA.BR.8683.01 TCGA.BR.8486.01 TCGA.D7.6522.01 TCGA.CG.5716.01
#> NA NA NA NA NA NA
#> TCGA.BR.8589.01 TCGA.BR.8382.01 TCGA.VQ.AA68.01 TCGA.VQ.A8PJ.01 TCGA.VQ.A8PH.01 TCGA.HU.8604.01
#> NA NA NA NA NA NA
#> TCGA.BR.8676.01 TCGA.CG.4441.01 TCGA.D7.6520.01 TCGA.VQ.AA64.01 TCGA.D7.6527.01 TCGA.VQ.A8PM.01
#> NA NA NA NA NA NA
#> TCGA.VQ.A923.01 TCGA.BR.8384.01 TCGA.BR.6453.01 TCGA.VQ.A928.01 TCGA.VQ.A8E0.01 TCGA.BR.8679.01
#> NA NA NA NA NA NA
#> TCGA.VQ.A91S.01 TCGA.BR.8678.01 TCGA.D7.6528.01 TCGA.VQ.A8E7.01 TCGA.BR.8680.01 TCGA.BR.8483.01
#> NA NA NA NA NA NA
#> TCGA.BR.6566.01 TCGA.VQ.A91X.01 TCGA.VQ.A91Q.01 TCGA.VQ.A92D.01 TCGA.VQ.A91Z.01 TCGA.BR.6455.01
#> NA NA NA NA NA NA
#> TCGA.BR.8591.01 TCGA.HU.8608.01 TCGA.VQ.A94U.01 TCGA.VQ.A94T.01 TCGA.VQ.A91A.01 TCGA.VQ.A91D.01
#> NA NA NA NA NA NA
#> TCGA.D7.6518.01 TCGA.BR.8484.01 TCGA.VQ.A91N.01 TCGA.VQ.A91E.01 TCGA.VQ.A8PY.01 TCGA.HU.8602.01
#> NA NA NA NA NA NA
#> TCGA.BR.8381.01 TCGA.BR.6452.11 TCGA.IN.8663.01 TCGA.VQ.A8PS.01 TCGA.VQ.A91W.01 TCGA.BR.6454.01
#> NA NA NA NA NA NA
#> TCGA.BR.8682.01 TCGA.VQ.A91V.01 TCGA.VQ.A8PZ.01 TCGA.BR.8590.01 TCGA.F1.6177.01 TCGA.VQ.A8PQ.01
#> NA NA NA NA NA NA
#> TCGA.VQ.A91U.01 TCGA.VQ.AA6I.01 TCGA.CG.4437.01 TCGA.VQ.A8PP.01 TCGA.BR.6565.01 TCGA.VQ.A91Y.01
#> NA NA NA NA NA NA
#> TCGA.VQ.A8PF.01 TCGA.BR.6456.01 TCGA.BR.6458.01 TCGA.VQ.A925.01 TCGA.VQ.A927.01 TCGA.BR.8592.01
#> NA NA NA NA NA NA
#> TCGA.BR.6566.11 TCGA.IN.AB1V.01 TCGA.VQ.AA6F.01 TCGA.VQ.AA6J.01 TCGA.BR.8487.01 TCGA.D7.6525.01
#> NA NA NA NA NA NA
#> TCGA.VQ.A94O.01 TCGA.BR.8588.01 TCGA.HU.8610.01 TCGA.D7.6526.01 TCGA.VQ.A8PD.01 TCGA.D7.6524.01
#> NA NA NA NA NA NA
#> TCGA.3M.AB46.01 TCGA.3M.AB47.01 TCGA.BR.8677.01 TCGA.BR.6457.01 TCGA.BR.8687.01 TCGA.VQ.A91K.01
#> NA NA NA NA NA NA
#> TCGA.BR.8690.01 TCGA.BR.8686.01 TCGA.FP.8631.01 TCGA.VQ.A922.01 TCGA.BR.A452.01 TCGA.IN.A6RO.01
#> NA NA NA NA NA NA
#> TCGA.BR.A4QI.01 TCGA.D7.A6EV.01 TCGA.HU.A4G2.01 TCGA.BR.A4IY.01 TCGA.VQ.A8PU.01 TCGA.BR.A4J4.01
#> NA NA NA NA NA NA
#> TCGA.VQ.A94R.01 TCGA.HU.A4H4.01 TCGA.BR.7707.01 TCGA.FP.7829.01 TCGA.BR.A4J5.01 TCGA.HU.A4H0.01
#> NA NA NA NA NA NA
#> TCGA.HU.A4HD.01 TCGA.KB.A6F5.01 TCGA.VQ.AA6K.01 TCGA.HF.7133.01 TCGA.F1.6875.01 TCGA.MX.A666.01
#> NA NA NA NA NA NA
#> TCGA.BR.7717.01 TCGA.BR.A4PF.01 TCGA.BR.A4IU.01 TCGA.VQ.A8PX.01 TCGA.BR.A4IV.01 TCGA.D7.A6EX.01
#> NA NA NA NA NA NA
#> TCGA.BR.A4IZ.01 TCGA.BR.A4J9.01 TCGA.CD.A4MJ.01 TCGA.B7.A5TN.01 TCGA.BR.7715.01 TCGA.BR.7704.01
#> NA NA NA NA NA NA
#> TCGA.BR.A4J1.01 TCGA.HU.A4GP.01 TCGA.D7.A4YY.01 TCGA.VQ.AA6G.01 TCGA.HU.A4GJ.01 TCGA.CD.A4MI.01
#> NA NA NA NA NA NA
#> TCGA.BR.7196.01 TCGA.BR.6563.01 TCGA.VQ.A924.01 TCGA.BR.7716.01 TCGA.FP.7735.01 TCGA.BR.7723.01
#> NA NA NA NA NA NA
#> TCGA.HU.A4H8.01 TCGA.IN.A6RJ.01 TCGA.HU.A4H3.01 TCGA.EQ.A4SO.01 TCGA.CD.A4MH.01 TCGA.BR.A4J7.01
#> NA NA NA NA NA NA
#> TCGA.HF.7131.01 TCGA.D7.A74B.01 TCGA.BR.A4PE.01 TCGA.BR.A4J8.01 TCGA.HU.A4GX.01 TCGA.HU.A4G8.01
#> NA NA NA NA NA NA
#> TCGA.HU.A4GT.01 TCGA.HU.A4GC.01 TCGA.BR.A4CQ.01 TCGA.D7.A6F2.01 TCGA.RD.A7BT.01 TCGA.BR.A4J6.01
#> NA NA NA NA NA NA
#> TCGA.HU.A4GQ.01 TCGA.HF.7136.01 TCGA.BR.A4QM.01 TCGA.BR.A4PD.01 TCGA.VQ.A8PK.01 TCGA.B7.A5TK.01
#> NA NA NA NA NA NA
#> TCGA.D7.A4YX.01 TCGA.D7.A4Z0.01 TCGA.VQ.A8PT.01 TCGA.IN.A6RN.01 TCGA.CD.A4MG.01 TCGA.D7.A747.01
#> NA NA NA NA NA NA
#> TCGA.R5.A7O7.01 TCGA.F1.A72C.01 TCGA.BR.A4J2.01 TCGA.MX.A663.01 TCGA.D7.A4YV.01 TCGA.HU.A4GD.01
#> NA NA NA NA NA NA
#> TCGA.BR.A4QL.01 TCGA.BR.7703.01 TCGA.VQ.AA6B.01 TCGA.VQ.AA6D.01 TCGA.D7.A6EZ.01 TCGA.D7.A4YU.01
#> NA NA NA NA NA NA
#> TCGA.VQ.AA6A.01 TCGA.IN.7806.01 TCGA.HU.A4HB.01 TCGA.HU.A4H2.01 TCGA.IN.A6RP.01 TCGA.HU.A4H5.01
#> NA NA NA NA NA NA
#> TCGA.HU.A4GU.01 TCGA.MX.A5UJ.01 TCGA.HU.A4GN.01 TCGA.CD.5804.01 TCGA.HU.A4H6.01 TCGA.HF.7132.01
#> NA NA NA NA NA NA
#> TCGA.D7.A4YT.01 TCGA.HF.7134.01 TCGA.BR.6852.01 TCGA.BR.8370.01 TCGA.EQ.5647.01 TCGA.IN.A7NT.01
#> NA NA NA NA NA NA
#> TCGA.RD.A8N9.01 TCGA.D7.5577.01 TCGA.CG.5717.01 TCGA.D7.6818.01 TCGA.CG.5734.01 TCGA.VQ.A8P8.01
#> NA NA NA NA NA NA
#> TCGA.BR.6707.01 TCGA.B7.5818.01 TCGA.CD.8525.01 TCGA.BR.6705.01 TCGA.BR.4288.01 TCGA.CD.5813.01
#> NA NA NA NA NA NA
#> TCGA.CG.5723.01 TCGA.CD.5800.01 TCGA.CG.5718.01 TCGA.BR.8080.01 TCGA.CG.5733.01 TCGA.D7.6817.01
#> NA NA NA NA NA NA
#> TCGA.KB.A93G.01 TCGA.CD.5799.01 TCGA.BR.7851.01 TCGA.BR.7722.01 TCGA.MX.A5UG.01 TCGA.CD.8533.01
#> NA NA NA NA NA NA
#> TCGA.BR.7957.01 TCGA.CG.5722.01 TCGA.F1.6874.01 TCGA.CG.5730.01 TCGA.CG.5726.01 TCGA.IP.7968.01
#> NA NA NA NA NA NA
#> TCGA.BR.8363.01 TCGA.BR.7901.01 TCGA.D7.6822.01 TCGA.BR.6710.01 TCGA.CG.5720.01 TCGA.D7.8570.01
#> NA NA NA NA NA NA
#> TCGA.B7.A5TI.01 TCGA.D7.6815.01 TCGA.BR.8284.01 TCGA.BR.8295.01 TCGA.BR.7197.01 TCGA.B7.A5TJ.01
#> NA NA NA NA NA NA
#> TCGA.D7.A6EY.01 TCGA.BR.8366.01 TCGA.IN.A7NR.01 TCGA.BR.6706.01 TCGA.IN.7808.01 TCGA.BR.6564.01
#> NA NA NA NA NA NA
#> TCGA.KB.A93H.01 TCGA.KB.A93J.01 TCGA.CD.5798.01 TCGA.CD.8530.01 TCGA.BR.6802.01 TCGA.CG.5719.01
#> NA NA NA NA NA NA
#> TCGA.VQ.A8E3.01 TCGA.CD.5801.01 TCGA.FP.A9TM.01 TCGA.BR.7958.01 TCGA.FP.7998.01 TCGA.IN.A6RS.01
#> NA NA NA NA NA NA
#> TCGA.BR.6709.01 TCGA.FP.7916.01 TCGA.R5.A7ZR.01 TCGA.B7.5816.01 TCGA.CG.5721.01 TCGA.SW.A7EA.01
#> NA NA NA NA NA NA
#> TCGA.RD.A8NB.01 TCGA.BR.6801.01 TCGA.IN.AB1X.01 TCGA.D7.5579.01 TCGA.CG.5728.01 TCGA.R5.A7ZI.01
#> NA NA NA NA NA NA
#> TCGA.IN.A7NU.01 TCGA.CG.5732.01 TCGA.ZQ.A9CR.01 TCGA.D7.5578.01 TCGA.BR.6803.01 TCGA.BR.8368.01
#> NA NA NA NA NA NA
#> TCGA.SW.A7EB.01 TCGA.BR.8081.01 TCGA.VQ.A8P5.01 TCGA.CD.8535.01 TCGA.CG.5724.01 TCGA.D7.8574.01
#> NA NA NA NA NA NA
#> TCGA.HJ.7597.01 TCGA.HF.A5NB.01 TCGA.VQ.A8PB.01 TCGA.R5.A7ZE.01 TCGA.CD.5803.01 TCGA.CG.5725.01
#> NA NA NA NA NA NA
#> TCGA.D7.6820.01 TCGA.CD.5802.01 TCGA.R5.A7ZF.01 TCGA.D7.A6F0.01 TCGA.CG.5727.01 TCGA.VQ.A8PC.01
#> NA NA NA NA NA NA
#> TCGA.CD.A486.01 TCGA.RD.A8N2.01 TCGA.IN.A6RI.01 TCGA.HU.8243.01 TCGA.CD.A48C.01 TCGA.RD.A8N5.01
#> NA NA NA NA NA NA
#> TCGA.RD.A8N1.01 TCGA.HU.A4GF.01 TCGA.BR.8362.01 TCGA.BR.8285.01 TCGA.CD.8532.01 TCGA.VQ.A8E2.01
#> NA NA NA NA NA NA
#> TCGA.BR.8373.01 TCGA.BR.8361.01 TCGA.BR.8058.01 TCGA.IN.8462.01 TCGA.HU.A4G9.01 TCGA.CD.8524.01
#> NA NA NA NA NA NA
#> TCGA.D7.A748.01 TCGA.CD.8527.01 TCGA.VQ.A8DV.01 TCGA.CD.8528.01 TCGA.BR.A453.01 TCGA.RD.A8N6.01
#> NA NA NA NA NA NA
#> TCGA.HU.8245.01 TCGA.ZA.A8F6.01 TCGA.BR.8367.01 TCGA.BR.8380.01 TCGA.FP.A4BE.01 TCGA.HU.8238.01
#> NA NA NA NA NA NA
#> TCGA.BR.8078.01 TCGA.HU.8249.01 TCGA.RD.A8N0.01 TCGA.BR.8365.01 TCGA.FP.8211.01 TCGA.RD.A8N4.01
#> NA NA NA NA NA NA
#> TCGA.VQ.A8DU.01 TCGA.VQ.A8DL.01 TCGA.VQ.A8DZ.01 TCGA.D7.8572.01 TCGA.RD.A7BW.01 TCGA.R5.A804.01
#> NA NA NA NA NA NA
#> TCGA.BR.A4CS.01 TCGA.CD.8531.01 TCGA.CD.A487.01 TCGA.BR.8371.01 TCGA.BR.8059.01 TCGA.D7.A6ET.01
#> NA NA NA NA NA NA
#> TCGA.FP.8099.01 TCGA.D7.8579.01 TCGA.BR.8297.01 TCGA.D7.8576.01 TCGA.VQ.A8DT.01 TCGA.FP.A8CX.01
#> NA NA NA NA NA NA
#> TCGA.HU.A4GH.01 TCGA.CD.8526.01 TCGA.HU.A4G6.01 TCGA.D7.8578.01 TCGA.HU.A4G3.01 TCGA.D7.A74A.01
#> NA NA NA NA NA NA
#> TCGA.RD.A7C1.01 TCGA.F1.A448.01 TCGA.D7.8575.01 TCGA.BR.8372.01 TCGA.VQ.A8P3.01 TCGA.RD.A8MW.01
#> NA NA NA NA NA NA
#> TCGA.BR.8286.01 TCGA.BR.8369.01 TCGA.BR.8364.01 TCGA.HU.8244.01 TCGA.KB.A6F7.01 TCGA.FP.A4BF.01
#> NA NA NA NA NA NA
#> TCGA.R5.A805.01 TCGA.IN.A6RL.01 TCGA.IN.A6RR.01 TCGA.BR.A4CR.01 TCGA.CD.A489.01 TCGA.HU.A4GY.01
#> NA NA NA NA NA NA
#> TCGA.BR.8289.01 TCGA.FP.8209.01 TCGA.BR.8296.01 TCGA.CD.A48A.01 TCGA.BR.8060.01 TCGA.BR.8077.01
#> NA NA NA NA NA NA
#> TCGA.CD.8534.01 TCGA.BR.7959.01 TCGA.VQ.A8P2.01 TCGA.EQ.8122.01 TCGA.D7.8573.01 TCGA.BR.A44T.01
#> NA NA NA NA NA NA
#> TCGA.RD.A8MV.01 TCGA.CD.8536.01 TCGA.BR.8360.01 TCGA.BR.8291.01 TCGA.FP.8210.01 TCGA.RD.A7BS.01
#> NA NA NA NA NA NA
#> TCGA.BR.A44U.01 TCGA.CD.8529.01
#> NA NA
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 = 1033),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 1033),
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 = 1377),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 1377),
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 = 1613),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 1613),
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 = 2012),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 2012),
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 = 2116),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 2116),
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 = 2372),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 2372),
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 = 2422),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 2422),
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 = 2448),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 2448),
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 = 2546),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 2546),
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 = 2903),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 2903),
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 = 3226),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 3226),
method = "UMAP", top_value_method = "ATC", top_n = 40000, scale_rows = TRUE)
par(mfrow = c(1, 2))
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 3913),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 3913),
method = "UMAP", top_value_method = "ATC", top_n = 40000, scale_rows = TRUE)
par(mfrow = c(1, 2))
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 4126),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 4126),
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 = 6100),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 6100),
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 = 6799),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 6799),
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 = 7619),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 7619),
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 = 7939),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 7939),
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 = 10459),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 10459),
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 = 11163),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 11163),
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 = 16188),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 16188),
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 = 17153),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 17153),
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 = 19830),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 19830),
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 = 26007),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 26007),
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 = 29355),
method = "UMAP", top_value_method = "SD", top_n = 40000, scale_rows = FALSE)
dimension_reduction(res_rh, merge_node = merge_node_param(min_n_signatures = 29355),
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 = 1033))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 1377))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 1613))
#> Error in lt[[hierarchy[i, 1]]]$AddChildNode({: attempt to apply non-function
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 2012))
#> Error in lt[[hierarchy[i, 1]]]$AddChildNode({: attempt to apply non-function
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 2116))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 2372))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 2422))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 2448))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 2546))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 2903))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 3226))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 3913))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 4126))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 6100))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 6799))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 7619))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 7939))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 10459))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 11163))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 16188))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 17153))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 19830))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 26007))
get_signatures(res_rh, merge_node = merge_node_param(min_n_signatures = 29355))
#> Error in names(x) <- value: 'names' attribute [1] must be the same length as the vector [0]
Compare signatures from different nodes:
compare_signatures(res_rh, verbose = FALSE)
If there are too many signatures, top_signatures = ... can be set to only show the
signatures with the highest FDRs. Note it only works on every node and the final signatures
are the union of all signatures of all nodes.
# code only for demonstration
# e.g. to show the top 500 most significant rows on each node.
tb = get_signature(res_rh, top_signatures = 500)
Child nodes: Node01 , Node02 , Node03 .
The object with results only for a single top-value method and a single partitioning method can be extracted as:
res = res_rh["0"]
A summary of res and all the functions that can be applied to it:
res
#> A 'ConsensusPartition' object with k = 2, 3, 4, 5, 6, 7, 8.
#> On a matrix with 30000 rows and 398 columns.
#> Top rows (1000) are extracted by 'SD' method.
#> Subgroups are detected by 'kmeans' method.
#> Performed in total 350 partitions by row resampling.
#> Best k for subgroups seems to be 3.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_partitions"
#> [7] "compare_signatures" "consensus_heatmap" "dimension_reduction"
#> [10] "functional_enrichment" "get_anno_col" "get_anno"
#> [13] "get_classes" "get_consensus" "get_matrix"
#> [16] "get_membership" "get_param" "get_signatures"
#> [19] "get_stats" "is_best_k" "is_stable_k"
#> [22] "membership_heatmap" "ncol" "nrow"
#> [25] "plot_ecdf" "predict_classes" "rownames"
#> [28] "select_partition_number" "show" "suggest_best_k"
#> [31] "test_to_known_factors" "top_rows_heatmap"
collect_plots() function collects all the plots made from res for all k (number of subgroups)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
The plots are:
k and the heatmap of
predicted classes for each k.k.k.k.All the plots in panels can be made by individual functions and they are plotted later in this section.
select_partition_number() produces several plots showing different
statistics for choosing “optimized” k. There are following statistics:
k;k, the area increased is defined as \(A_k - A_{k-1}\).The detailed explanations of these statistics can be found in the cola vignette.
Generally speaking, higher 1-PAC score, higher mean silhouette score or higher
concordance corresponds to better partition. Rand index and Jaccard index
measure how similar the current partition is compared to partition with k-1.
If they are too similar, we won't accept k is better than k-1.
select_partition_number(res)
The numeric values for all these statistics can be obtained by get_stats().
get_stats(res)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> 2 2 1.000 0.994 0.998 0.4979 0.503 0.503
#> 3 3 0.987 0.954 0.982 0.3054 0.768 0.573
#> 4 4 0.752 0.809 0.900 0.1451 0.806 0.511
#> 5 5 0.824 0.720 0.869 0.0670 0.835 0.465
#> 6 6 0.779 0.733 0.831 0.0381 0.948 0.758
#> 7 7 0.811 0.697 0.823 0.0275 0.973 0.849
#> 8 8 0.827 0.661 0.781 0.0191 0.951 0.714
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.VQ.A94P.01 1 0.000 0.996 1.00 0.00
#> TCGA.D7.6521.01 1 0.000 0.996 1.00 0.00
#> TCGA.VQ.A8PE.01 1 0.000 0.996 1.00 0.00
#> TCGA.D7.6519.01 1 0.000 0.996 1.00 0.00
#> TCGA.BR.6452.01 2 0.000 0.999 0.00 1.00
#> TCGA.BR.8485.01 1 0.000 0.996 1.00 0.00
#> TCGA.VQ.A8PO.01 2 0.000 0.999 0.00 1.00
#> TCGA.VQ.AA69.01 2 0.000 0.999 0.00 1.00
#> TCGA.BR.8683.01 1 0.000 0.996 1.00 0.00
#> TCGA.BR.8486.01 1 0.000 0.996 1.00 0.00
#> TCGA.D7.6522.01 1 0.000 0.996 1.00 0.00
#> TCGA.CG.5716.01 1 0.000 0.996 1.00 0.00
#> TCGA.BR.8589.01 2 0.000 0.999 0.00 1.00
#> TCGA.BR.8382.01 2 0.000 0.999 0.00 1.00
#> TCGA.VQ.AA68.01 2 0.000 0.999 0.00 1.00
#> TCGA.VQ.A8PJ.01 1 0.000 0.996 1.00 0.00
#> TCGA.VQ.A8PH.01 1 0.000 0.996 1.00 0.00
#> TCGA.HU.8604.01 2 0.000 0.999 0.00 1.00
#> TCGA.BR.8676.01 2 0.000 0.999 0.00 1.00
#> TCGA.CG.4441.01 1 0.000 0.996 1.00 0.00
#> TCGA.D7.6520.01 1 0.000 0.996 1.00 0.00
#> TCGA.VQ.AA64.01 1 0.000 0.996 1.00 0.00
#> TCGA.D7.6527.01 1 0.000 0.996 1.00 0.00
#> TCGA.VQ.A8PM.01 1 0.000 0.996 1.00 0.00
#> TCGA.VQ.A923.01 2 0.000 0.999 0.00 1.00
#> TCGA.BR.8384.01 1 0.000 0.996 1.00 0.00
#> TCGA.BR.6453.01 2 0.000 0.999 0.00 1.00
#> TCGA.VQ.A928.01 1 0.000 0.996 1.00 0.00
#> TCGA.VQ.A8E0.01 1 0.000 0.996 1.00 0.00
#> TCGA.BR.8679.01 2 0.000 0.999 0.00 1.00
#> TCGA.VQ.A91S.01 1 0.000 0.996 1.00 0.00
#> TCGA.BR.8678.01 1 0.000 0.996 1.00 0.00
#> TCGA.D7.6528.01 1 0.000 0.996 1.00 0.00
#> TCGA.VQ.A8E7.01 2 0.000 0.999 0.00 1.00
#> TCGA.BR.8680.01 2 0.000 0.999 0.00 1.00
#> TCGA.BR.8483.01 1 0.141 0.976 0.98 0.02
#> TCGA.BR.6566.01 2 0.000 0.999 0.00 1.00
#> TCGA.VQ.A91X.01 2 0.000 0.999 0.00 1.00
#> TCGA.VQ.A91Q.01 1 0.000 0.996 1.00 0.00
#> TCGA.VQ.A92D.01 2 0.000 0.999 0.00 1.00
#> TCGA.VQ.A91Z.01 1 0.000 0.996 1.00 0.00
#> TCGA.BR.6455.01 2 0.000 0.999 0.00 1.00
#> TCGA.BR.8591.01 2 0.000 0.999 0.00 1.00
#> TCGA.HU.8608.01 2 0.000 0.999 0.00 1.00
#> TCGA.VQ.A94U.01 2 0.000 0.999 0.00 1.00
#> TCGA.VQ.A94T.01 1 0.000 0.996 1.00 0.00
#> TCGA.VQ.A91A.01 2 0.000 0.999 0.00 1.00
#> TCGA.VQ.A91D.01 2 0.000 0.999 0.00 1.00
#> TCGA.D7.6518.01 1 0.000 0.996 1.00 0.00
#> TCGA.BR.8484.01 1 0.000 0.996 1.00 0.00
#> TCGA.VQ.A91N.01 1 0.000 0.996 1.00 0.00
#> TCGA.VQ.A91E.01 2 0.000 0.999 0.00 1.00
#> TCGA.VQ.A8PY.01 2 0.000 0.999 0.00 1.00
#> TCGA.HU.8602.01 2 0.000 0.999 0.00 1.00
#> TCGA.BR.8381.01 2 0.000 0.999 0.00 1.00
#> TCGA.BR.6452.11 1 0.000 0.996 1.00 0.00
#> TCGA.IN.8663.01 2 0.000 0.999 0.00 1.00
#> TCGA.VQ.A8PS.01 1 0.000 0.996 1.00 0.00
#> TCGA.VQ.A91W.01 2 0.000 0.999 0.00 1.00
#> TCGA.BR.6454.01 1 0.000 0.996 1.00 0.00
#> TCGA.BR.8682.01 2 0.000 0.999 0.00 1.00
#> TCGA.VQ.A91V.01 2 0.000 0.999 0.00 1.00
#> TCGA.VQ.A8PZ.01 2 0.000 0.999 0.00 1.00
#> TCGA.BR.8590.01 1 0.000 0.996 1.00 0.00
#> TCGA.F1.6177.01 2 0.000 0.999 0.00 1.00
#> TCGA.VQ.A8PQ.01 1 0.000 0.996 1.00 0.00
#> TCGA.VQ.A91U.01 1 0.000 0.996 1.00 0.00
#> TCGA.VQ.AA6I.01 2 0.000 0.999 0.00 1.00
#> TCGA.CG.4437.01 2 0.000 0.999 0.00 1.00
#> TCGA.VQ.A8PP.01 2 0.000 0.999 0.00 1.00
#> TCGA.BR.6565.01 1 0.000 0.996 1.00 0.00
#> TCGA.VQ.A91Y.01 1 0.000 0.996 1.00 0.00
#> TCGA.VQ.A8PF.01 2 0.000 0.999 0.00 1.00
#> TCGA.BR.6456.01 1 0.000 0.996 1.00 0.00
#> TCGA.BR.6458.01 2 0.000 0.999 0.00 1.00
#> TCGA.VQ.A925.01 1 0.000 0.996 1.00 0.00
#> TCGA.VQ.A927.01 1 0.000 0.996 1.00 0.00
#> TCGA.BR.8592.01 1 0.000 0.996 1.00 0.00
#> TCGA.BR.6566.11 1 0.000 0.996 1.00 0.00
#> TCGA.IN.AB1V.01 1 0.000 0.996 1.00 0.00
#> TCGA.VQ.AA6F.01 1 0.000 0.996 1.00 0.00
#> TCGA.VQ.AA6J.01 1 0.000 0.996 1.00 0.00
#> TCGA.BR.8487.01 2 0.000 0.999 0.00 1.00
#> TCGA.D7.6525.01 2 0.000 0.999 0.00 1.00
#> TCGA.VQ.A94O.01 1 0.000 0.996 1.00 0.00
#> TCGA.BR.8588.01 2 0.000 0.999 0.00 1.00
#> TCGA.HU.8610.01 1 0.000 0.996 1.00 0.00
#> TCGA.D7.6526.01 1 0.000 0.996 1.00 0.00
#> TCGA.VQ.A8PD.01 1 0.000 0.996 1.00 0.00
#> TCGA.D7.6524.01 2 0.000 0.999 0.00 1.00
#> TCGA.3M.AB46.01 1 0.000 0.996 1.00 0.00
#> TCGA.3M.AB47.01 2 0.000 0.999 0.00 1.00
#> TCGA.BR.8677.01 1 0.000 0.996 1.00 0.00
#> TCGA.BR.6457.01 1 0.000 0.996 1.00 0.00
#> TCGA.BR.8687.01 1 0.000 0.996 1.00 0.00
#> TCGA.VQ.A91K.01 2 0.000 0.999 0.00 1.00
#> TCGA.BR.8690.01 1 0.000 0.996 1.00 0.00
#> TCGA.BR.8686.01 2 0.000 0.999 0.00 1.00
#> TCGA.FP.8631.01 1 0.000 0.996 1.00 0.00
#> TCGA.VQ.A922.01 1 0.000 0.996 1.00 0.00
#> TCGA.BR.A452.01 1 0.000 0.996 1.00 0.00
#> TCGA.IN.A6RO.01 2 0.000 0.999 0.00 1.00
#> TCGA.BR.A4QI.01 2 0.000 0.999 0.00 1.00
#> TCGA.D7.A6EV.01 2 0.000 0.999 0.00 1.00
#> TCGA.HU.A4G2.01 2 0.000 0.999 0.00 1.00
#> TCGA.BR.A4IY.01 2 0.000 0.999 0.00 1.00
#> TCGA.VQ.A8PU.01 1 0.000 0.996 1.00 0.00
#> TCGA.BR.A4J4.01 2 0.000 0.999 0.00 1.00
#> TCGA.VQ.A94R.01 2 0.000 0.999 0.00 1.00
#> TCGA.HU.A4H4.01 2 0.000 0.999 0.00 1.00
#> TCGA.BR.7707.01 2 0.000 0.999 0.00 1.00
#> TCGA.FP.7829.01 2 0.000 0.999 0.00 1.00
#> TCGA.BR.A4J5.01 2 0.000 0.999 0.00 1.00
#> TCGA.HU.A4H0.01 2 0.000 0.999 0.00 1.00
#> TCGA.HU.A4HD.01 1 0.000 0.996 1.00 0.00
#> TCGA.KB.A6F5.01 1 0.000 0.996 1.00 0.00
#> TCGA.VQ.AA6K.01 1 0.000 0.996 1.00 0.00
#> TCGA.HF.7133.01 1 0.000 0.996 1.00 0.00
#> TCGA.F1.6875.01 1 0.000 0.996 1.00 0.00
#> TCGA.MX.A666.01 1 0.000 0.996 1.00 0.00
#> TCGA.BR.7717.01 2 0.000 0.999 0.00 1.00
#> TCGA.BR.A4PF.01 2 0.000 0.999 0.00 1.00
#> TCGA.BR.A4IU.01 2 0.000 0.999 0.00 1.00
#> TCGA.VQ.A8PX.01 1 0.000 0.996 1.00 0.00
#> TCGA.BR.A4IV.01 1 0.000 0.996 1.00 0.00
#> TCGA.D7.A6EX.01 1 0.000 0.996 1.00 0.00
#> TCGA.BR.A4IZ.01 1 0.000 0.996 1.00 0.00
#> TCGA.BR.A4J9.01 1 0.000 0.996 1.00 0.00
#> TCGA.CD.A4MJ.01 2 0.000 0.999 0.00 1.00
#> TCGA.B7.A5TN.01 1 0.000 0.996 1.00 0.00
#> TCGA.BR.7715.01 2 0.000 0.999 0.00 1.00
#> TCGA.BR.7704.01 1 0.000 0.996 1.00 0.00
#> TCGA.BR.A4J1.01 1 0.000 0.996 1.00 0.00
#> TCGA.HU.A4GP.01 2 0.000 0.999 0.00 1.00
#> TCGA.D7.A4YY.01 2 0.000 0.999 0.00 1.00
#> TCGA.VQ.AA6G.01 2 0.000 0.999 0.00 1.00
#> TCGA.HU.A4GJ.01 2 0.000 0.999 0.00 1.00
#> TCGA.CD.A4MI.01 2 0.000 0.999 0.00 1.00
#> TCGA.BR.7196.01 2 0.000 0.999 0.00 1.00
#> TCGA.BR.6563.01 1 0.000 0.996 1.00 0.00
#> TCGA.VQ.A924.01 2 0.000 0.999 0.00 1.00
#> TCGA.BR.7716.01 1 0.000 0.996 1.00 0.00
#> TCGA.FP.7735.01 1 0.000 0.996 1.00 0.00
#> TCGA.BR.7723.01 1 0.000 0.996 1.00 0.00
#> TCGA.HU.A4H8.01 2 0.000 0.999 0.00 1.00
#> TCGA.IN.A6RJ.01 1 0.000 0.996 1.00 0.00
#> TCGA.HU.A4H3.01 2 0.000 0.999 0.00 1.00
#> TCGA.EQ.A4SO.01 1 0.000 0.996 1.00 0.00
#> TCGA.CD.A4MH.01 1 0.000 0.996 1.00 0.00
#> TCGA.BR.A4J7.01 1 0.000 0.996 1.00 0.00
#> TCGA.HF.7131.01 1 0.000 0.996 1.00 0.00
#> TCGA.D7.A74B.01 1 0.000 0.996 1.00 0.00
#> TCGA.BR.A4PE.01 2 0.000 0.999 0.00 1.00
#> TCGA.BR.A4J8.01 2 0.000 0.999 0.00 1.00
#> TCGA.HU.A4GX.01 1 0.000 0.996 1.00 0.00
#> TCGA.HU.A4G8.01 2 0.000 0.999 0.00 1.00
#> TCGA.HU.A4GT.01 2 0.000 0.999 0.00 1.00
#> TCGA.HU.A4GC.01 2 0.000 0.999 0.00 1.00
#> TCGA.BR.A4CQ.01 2 0.000 0.999 0.00 1.00
#> TCGA.D7.A6F2.01 1 0.000 0.996 1.00 0.00
#> TCGA.RD.A7BT.01 1 0.000 0.996 1.00 0.00
#> TCGA.BR.A4J6.01 1 0.000 0.996 1.00 0.00
#> TCGA.HU.A4GQ.01 2 0.000 0.999 0.00 1.00
#> TCGA.HF.7136.01 1 0.000 0.996 1.00 0.00
#> TCGA.BR.A4QM.01 2 0.000 0.999 0.00 1.00
#> TCGA.BR.A4PD.01 1 0.000 0.996 1.00 0.00
#> TCGA.VQ.A8PK.01 1 0.000 0.996 1.00 0.00
#> TCGA.B7.A5TK.01 2 0.000 0.999 0.00 1.00
#> TCGA.D7.A4YX.01 2 0.000 0.999 0.00 1.00
#> TCGA.D7.A4Z0.01 2 0.000 0.999 0.00 1.00
#> TCGA.VQ.A8PT.01 2 0.000 0.999 0.00 1.00
#> TCGA.IN.A6RN.01 1 0.000 0.996 1.00 0.00
#> TCGA.CD.A4MG.01 2 0.000 0.999 0.00 1.00
#> TCGA.D7.A747.01 1 0.000 0.996 1.00 0.00
#> TCGA.R5.A7O7.01 1 0.000 0.996 1.00 0.00
#> TCGA.F1.A72C.01 1 0.000 0.996 1.00 0.00
#> TCGA.BR.A4J2.01 1 0.000 0.996 1.00 0.00
#> TCGA.MX.A663.01 1 0.000 0.996 1.00 0.00
#> TCGA.D7.A4YV.01 2 0.000 0.999 0.00 1.00
#> TCGA.HU.A4GD.01 1 0.000 0.996 1.00 0.00
#> TCGA.BR.A4QL.01 2 0.000 0.999 0.00 1.00
#> TCGA.BR.7703.01 2 0.000 0.999 0.00 1.00
#> TCGA.VQ.AA6B.01 2 0.000 0.999 0.00 1.00
#> TCGA.VQ.AA6D.01 1 0.000 0.996 1.00 0.00
#> TCGA.D7.A6EZ.01 2 0.000 0.999 0.00 1.00
#> TCGA.D7.A4YU.01 2 0.000 0.999 0.00 1.00
#> TCGA.VQ.AA6A.01 1 0.000 0.996 1.00 0.00
#> TCGA.IN.7806.01 1 0.000 0.996 1.00 0.00
#> TCGA.HU.A4HB.01 1 0.000 0.996 1.00 0.00
#> TCGA.HU.A4H2.01 2 0.000 0.999 0.00 1.00
#> TCGA.IN.A6RP.01 2 0.000 0.999 0.00 1.00
#> TCGA.HU.A4H5.01 1 0.000 0.996 1.00 0.00
#> TCGA.HU.A4GU.01 2 0.000 0.999 0.00 1.00
#> TCGA.MX.A5UJ.01 2 0.000 0.999 0.00 1.00
#> TCGA.HU.A4GN.01 2 0.000 0.999 0.00 1.00
#> TCGA.CD.5804.01 1 0.000 0.996 1.00 0.00
#> TCGA.HU.A4H6.01 2 0.000 0.999 0.00 1.00
#> TCGA.HF.7132.01 2 0.000 0.999 0.00 1.00
#> TCGA.D7.A4YT.01 1 0.000 0.996 1.00 0.00
#> TCGA.HF.7134.01 2 0.000 0.999 0.00 1.00
#> TCGA.BR.6852.01 2 0.000 0.999 0.00 1.00
#> TCGA.BR.8370.01 2 0.000 0.999 0.00 1.00
#> TCGA.EQ.5647.01 1 0.000 0.996 1.00 0.00
#> TCGA.IN.A7NT.01 1 0.000 0.996 1.00 0.00
#> TCGA.RD.A8N9.01 1 0.000 0.996 1.00 0.00
#> TCGA.D7.5577.01 2 0.000 0.999 0.00 1.00
#> TCGA.CG.5717.01 1 0.000 0.996 1.00 0.00
#> TCGA.D7.6818.01 1 0.000 0.996 1.00 0.00
#> TCGA.CG.5734.01 1 0.000 0.996 1.00 0.00
#> TCGA.VQ.A8P8.01 2 0.000 0.999 0.00 1.00
#> TCGA.BR.6707.01 2 0.000 0.999 0.00 1.00
#> TCGA.B7.5818.01 2 0.000 0.999 0.00 1.00
#> TCGA.CD.8525.01 1 0.000 0.996 1.00 0.00
#> TCGA.BR.6705.01 1 0.000 0.996 1.00 0.00
#> TCGA.BR.4288.01 1 0.000 0.996 1.00 0.00
#> TCGA.CD.5813.01 1 0.000 0.996 1.00 0.00
#> TCGA.CG.5723.01 1 0.000 0.996 1.00 0.00
#> TCGA.CD.5800.01 1 0.000 0.996 1.00 0.00
#> TCGA.CG.5718.01 1 0.000 0.996 1.00 0.00
#> TCGA.BR.8080.01 1 0.000 0.996 1.00 0.00
#> TCGA.CG.5733.01 2 0.000 0.999 0.00 1.00
#> TCGA.D7.6817.01 1 0.000 0.996 1.00 0.00
#> TCGA.KB.A93G.01 1 0.000 0.996 1.00 0.00
#> TCGA.CD.5799.01 1 0.000 0.996 1.00 0.00
#> TCGA.BR.7851.01 2 0.000 0.999 0.00 1.00
#> TCGA.BR.7722.01 1 0.000 0.996 1.00 0.00
#> TCGA.MX.A5UG.01 1 0.000 0.996 1.00 0.00
#> TCGA.CD.8533.01 2 0.000 0.999 0.00 1.00
#> TCGA.BR.7957.01 1 0.000 0.996 1.00 0.00
#> TCGA.CG.5722.01 2 0.000 0.999 0.00 1.00
#> TCGA.F1.6874.01 1 0.000 0.996 1.00 0.00
#> TCGA.CG.5730.01 1 0.000 0.996 1.00 0.00
#> TCGA.CG.5726.01 2 0.000 0.999 0.00 1.00
#> TCGA.IP.7968.01 1 0.000 0.996 1.00 0.00
#> TCGA.BR.8363.01 2 0.000 0.999 0.00 1.00
#> TCGA.BR.7901.01 1 0.000 0.996 1.00 0.00
#> TCGA.D7.6822.01 2 0.000 0.999 0.00 1.00
#> TCGA.BR.6710.01 1 0.000 0.996 1.00 0.00
#> TCGA.CG.5720.01 2 0.000 0.999 0.00 1.00
#> TCGA.D7.8570.01 2 0.000 0.999 0.00 1.00
#> TCGA.B7.A5TI.01 1 0.000 0.996 1.00 0.00
#> TCGA.D7.6815.01 1 0.000 0.996 1.00 0.00
#> TCGA.BR.8284.01 2 0.000 0.999 0.00 1.00
#> TCGA.BR.8295.01 1 0.000 0.996 1.00 0.00
#> TCGA.BR.7197.01 1 0.000 0.996 1.00 0.00
#> TCGA.B7.A5TJ.01 2 0.000 0.999 0.00 1.00
#> TCGA.D7.A6EY.01 1 0.469 0.887 0.90 0.10
#> TCGA.BR.8366.01 2 0.000 0.999 0.00 1.00
#> TCGA.IN.A7NR.01 1 0.000 0.996 1.00 0.00
#> TCGA.BR.6706.01 2 0.000 0.999 0.00 1.00
#> TCGA.IN.7808.01 2 0.000 0.999 0.00 1.00
#> TCGA.BR.6564.01 1 0.000 0.996 1.00 0.00
#> TCGA.KB.A93H.01 1 0.000 0.996 1.00 0.00
#> TCGA.KB.A93J.01 1 0.000 0.996 1.00 0.00
#> TCGA.CD.5798.01 1 0.000 0.996 1.00 0.00
#> TCGA.CD.8530.01 1 0.000 0.996 1.00 0.00
#> TCGA.BR.6802.01 2 0.000 0.999 0.00 1.00
#> TCGA.CG.5719.01 1 0.000 0.996 1.00 0.00
#> TCGA.VQ.A8E3.01 2 0.000 0.999 0.00 1.00
#> TCGA.CD.5801.01 2 0.000 0.999 0.00 1.00
#> TCGA.FP.A9TM.01 2 0.000 0.999 0.00 1.00
#> TCGA.BR.7958.01 2 0.000 0.999 0.00 1.00
#> TCGA.FP.7998.01 2 0.000 0.999 0.00 1.00
#> TCGA.IN.A6RS.01 2 0.000 0.999 0.00 1.00
#> TCGA.BR.6709.01 1 0.000 0.996 1.00 0.00
#> TCGA.FP.7916.01 2 0.000 0.999 0.00 1.00
#> TCGA.R5.A7ZR.01 1 0.000 0.996 1.00 0.00
#> TCGA.B7.5816.01 2 0.000 0.999 0.00 1.00
#> TCGA.CG.5721.01 1 0.760 0.718 0.78 0.22
#> TCGA.SW.A7EA.01 2 0.000 0.999 0.00 1.00
#> TCGA.RD.A8NB.01 2 0.141 0.979 0.02 0.98
#> TCGA.BR.6801.01 1 0.000 0.996 1.00 0.00
#> TCGA.IN.AB1X.01 2 0.000 0.999 0.00 1.00
#> TCGA.D7.5579.01 1 0.000 0.996 1.00 0.00
#> TCGA.CG.5728.01 2 0.000 0.999 0.00 1.00
#> TCGA.R5.A7ZI.01 1 0.000 0.996 1.00 0.00
#> TCGA.IN.A7NU.01 2 0.000 0.999 0.00 1.00
#> TCGA.CG.5732.01 1 0.000 0.996 1.00 0.00
#> TCGA.ZQ.A9CR.01 1 0.000 0.996 1.00 0.00
#> TCGA.D7.5578.01 2 0.000 0.999 0.00 1.00
#> TCGA.BR.6803.01 1 0.000 0.996 1.00 0.00
#> TCGA.BR.8368.01 2 0.000 0.999 0.00 1.00
#> TCGA.SW.A7EB.01 1 0.000 0.996 1.00 0.00
#> TCGA.BR.8081.01 2 0.000 0.999 0.00 1.00
#> TCGA.VQ.A8P5.01 2 0.141 0.979 0.02 0.98
#> TCGA.CD.8535.01 2 0.000 0.999 0.00 1.00
#> TCGA.CG.5724.01 2 0.000 0.999 0.00 1.00
#> TCGA.D7.8574.01 1 0.000 0.996 1.00 0.00
#> TCGA.HJ.7597.01 1 0.000 0.996 1.00 0.00
#> TCGA.HF.A5NB.01 2 0.000 0.999 0.00 1.00
#> TCGA.VQ.A8PB.01 2 0.000 0.999 0.00 1.00
#> TCGA.R5.A7ZE.01 1 0.000 0.996 1.00 0.00
#> TCGA.CD.5803.01 1 0.000 0.996 1.00 0.00
#> TCGA.CG.5725.01 1 0.000 0.996 1.00 0.00
#> TCGA.D7.6820.01 1 0.000 0.996 1.00 0.00
#> TCGA.CD.5802.01 1 0.000 0.996 1.00 0.00
#> TCGA.R5.A7ZF.01 1 0.000 0.996 1.00 0.00
#> TCGA.D7.A6F0.01 1 0.000 0.996 1.00 0.00
#> TCGA.CG.5727.01 1 0.000 0.996 1.00 0.00
#> TCGA.VQ.A8PC.01 1 0.000 0.996 1.00 0.00
#> TCGA.CD.A486.01 1 0.000 0.996 1.00 0.00
#> TCGA.RD.A8N2.01 1 0.000 0.996 1.00 0.00
#> TCGA.IN.A6RI.01 1 0.000 0.996 1.00 0.00
#> TCGA.HU.8243.01 2 0.529 0.863 0.12 0.88
#> TCGA.CD.A48C.01 2 0.000 0.999 0.00 1.00
#> TCGA.RD.A8N5.01 1 0.000 0.996 1.00 0.00
#> TCGA.RD.A8N1.01 1 0.000 0.996 1.00 0.00
#> TCGA.HU.A4GF.01 1 0.000 0.996 1.00 0.00
#> TCGA.BR.8362.01 2 0.000 0.999 0.00 1.00
#> TCGA.BR.8285.01 2 0.000 0.999 0.00 1.00
#> TCGA.CD.8532.01 1 0.000 0.996 1.00 0.00
#> TCGA.VQ.A8E2.01 1 0.000 0.996 1.00 0.00
#> TCGA.BR.8373.01 1 0.000 0.996 1.00 0.00
#> TCGA.BR.8361.01 2 0.000 0.999 0.00 1.00
#> TCGA.BR.8058.01 1 0.000 0.996 1.00 0.00
#> TCGA.IN.8462.01 2 0.000 0.999 0.00 1.00
#> TCGA.HU.A4G9.01 2 0.000 0.999 0.00 1.00
#> TCGA.CD.8524.01 2 0.000 0.999 0.00 1.00
#> TCGA.D7.A748.01 1 0.000 0.996 1.00 0.00
#> TCGA.CD.8527.01 1 0.000 0.996 1.00 0.00
#> TCGA.VQ.A8DV.01 1 0.000 0.996 1.00 0.00
#> TCGA.CD.8528.01 2 0.000 0.999 0.00 1.00
#> TCGA.BR.A453.01 1 0.000 0.996 1.00 0.00
#> TCGA.RD.A8N6.01 1 0.000 0.996 1.00 0.00
#> TCGA.HU.8245.01 1 0.000 0.996 1.00 0.00
#> TCGA.ZA.A8F6.01 1 0.000 0.996 1.00 0.00
#> TCGA.BR.8367.01 2 0.000 0.999 0.00 1.00
#> TCGA.BR.8380.01 2 0.000 0.999 0.00 1.00
#> TCGA.FP.A4BE.01 2 0.000 0.999 0.00 1.00
#> TCGA.HU.8238.01 2 0.000 0.999 0.00 1.00
#> TCGA.BR.8078.01 2 0.000 0.999 0.00 1.00
#> TCGA.HU.8249.01 1 0.000 0.996 1.00 0.00
#> TCGA.RD.A8N0.01 1 0.000 0.996 1.00 0.00
#> TCGA.BR.8365.01 1 0.000 0.996 1.00 0.00
#> TCGA.FP.8211.01 1 0.000 0.996 1.00 0.00
#> TCGA.RD.A8N4.01 1 0.000 0.996 1.00 0.00
#> TCGA.VQ.A8DU.01 1 0.000 0.996 1.00 0.00
#> TCGA.VQ.A8DL.01 1 0.000 0.996 1.00 0.00
#> TCGA.VQ.A8DZ.01 1 0.000 0.996 1.00 0.00
#> TCGA.D7.8572.01 1 0.000 0.996 1.00 0.00
#> TCGA.RD.A7BW.01 1 0.000 0.996 1.00 0.00
#> TCGA.R5.A804.01 2 0.000 0.999 0.00 1.00
#> TCGA.BR.A4CS.01 2 0.000 0.999 0.00 1.00
#> TCGA.CD.8531.01 2 0.000 0.999 0.00 1.00
#> TCGA.CD.A487.01 1 0.000 0.996 1.00 0.00
#> TCGA.BR.8371.01 1 0.000 0.996 1.00 0.00
#> TCGA.BR.8059.01 1 0.000 0.996 1.00 0.00
#> TCGA.D7.A6ET.01 1 0.000 0.996 1.00 0.00
#> TCGA.FP.8099.01 2 0.000 0.999 0.00 1.00
#> TCGA.D7.8579.01 1 0.995 0.150 0.54 0.46
#> TCGA.BR.8297.01 2 0.000 0.999 0.00 1.00
#> TCGA.D7.8576.01 1 0.000 0.996 1.00 0.00
#> TCGA.VQ.A8DT.01 2 0.000 0.999 0.00 1.00
#> TCGA.FP.A8CX.01 1 0.000 0.996 1.00 0.00
#> TCGA.HU.A4GH.01 1 0.000 0.996 1.00 0.00
#> TCGA.CD.8526.01 1 0.000 0.996 1.00 0.00
#> TCGA.HU.A4G6.01 2 0.000 0.999 0.00 1.00
#> TCGA.D7.8578.01 1 0.000 0.996 1.00 0.00
#> TCGA.HU.A4G3.01 2 0.000 0.999 0.00 1.00
#> TCGA.D7.A74A.01 2 0.000 0.999 0.00 1.00
#> TCGA.RD.A7C1.01 2 0.000 0.999 0.00 1.00
#> TCGA.F1.A448.01 2 0.000 0.999 0.00 1.00
#> TCGA.D7.8575.01 1 0.000 0.996 1.00 0.00
#> TCGA.BR.8372.01 2 0.000 0.999 0.00 1.00
#> TCGA.VQ.A8P3.01 2 0.000 0.999 0.00 1.00
#> TCGA.RD.A8MW.01 1 0.000 0.996 1.00 0.00
#> TCGA.BR.8286.01 2 0.000 0.999 0.00 1.00
#> TCGA.BR.8369.01 2 0.000 0.999 0.00 1.00
#> TCGA.BR.8364.01 1 0.000 0.996 1.00 0.00
#> TCGA.HU.8244.01 2 0.000 0.999 0.00 1.00
#> TCGA.KB.A6F7.01 1 0.000 0.996 1.00 0.00
#> TCGA.FP.A4BF.01 2 0.000 0.999 0.00 1.00
#> TCGA.R5.A805.01 2 0.000 0.999 0.00 1.00
#> TCGA.IN.A6RL.01 1 0.000 0.996 1.00 0.00
#> TCGA.IN.A6RR.01 2 0.000 0.999 0.00 1.00
#> TCGA.BR.A4CR.01 1 0.000 0.996 1.00 0.00
#> TCGA.CD.A489.01 1 0.000 0.996 1.00 0.00
#> TCGA.HU.A4GY.01 1 0.000 0.996 1.00 0.00
#> TCGA.BR.8289.01 1 0.000 0.996 1.00 0.00
#> TCGA.FP.8209.01 1 0.000 0.996 1.00 0.00
#> TCGA.BR.8296.01 2 0.000 0.999 0.00 1.00
#> TCGA.CD.A48A.01 2 0.000 0.999 0.00 1.00
#> TCGA.BR.8060.01 1 0.000 0.996 1.00 0.00
#> TCGA.BR.8077.01 1 0.000 0.996 1.00 0.00
#> TCGA.CD.8534.01 2 0.000 0.999 0.00 1.00
#> TCGA.BR.7959.01 2 0.000 0.999 0.00 1.00
#> TCGA.VQ.A8P2.01 2 0.000 0.999 0.00 1.00
#> TCGA.EQ.8122.01 1 0.000 0.996 1.00 0.00
#> TCGA.D7.8573.01 2 0.000 0.999 0.00 1.00
#> TCGA.BR.A44T.01 1 0.000 0.996 1.00 0.00
#> TCGA.RD.A8MV.01 1 0.000 0.996 1.00 0.00
#> TCGA.CD.8536.01 2 0.000 0.999 0.00 1.00
#> TCGA.BR.8360.01 2 0.000 0.999 0.00 1.00
#> TCGA.BR.8291.01 1 0.000 0.996 1.00 0.00
#> TCGA.FP.8210.01 1 0.000 0.996 1.00 0.00
#> TCGA.RD.A7BS.01 1 0.000 0.996 1.00 0.00
#> TCGA.BR.A44U.01 2 0.000 0.999 0.00 1.00
#> TCGA.CD.8529.01 1 0.000 0.996 1.00 0.00
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.VQ.A94P.01 1 0.0000 0.9940 1.00 0.00 0.00
#> TCGA.D7.6521.01 1 0.0000 0.9940 1.00 0.00 0.00
#> TCGA.VQ.A8PE.01 1 0.0000 0.9940 1.00 0.00 0.00
#> TCGA.D7.6519.01 1 0.0000 0.9940 1.00 0.00 0.00
#> TCGA.BR.6452.01 2 0.0000 0.9813 0.00 1.00 0.00
#> TCGA.BR.8485.01 1 0.0000 0.9940 1.00 0.00 0.00
#> TCGA.VQ.A8PO.01 2 0.0000 0.9813 0.00 1.00 0.00
#> TCGA.VQ.AA69.01 2 0.0000 0.9813 0.00 1.00 0.00
#> TCGA.BR.8683.01 3 0.0000 0.9602 0.00 0.00 1.00
#> TCGA.BR.8486.01 1 0.0000 0.9940 1.00 0.00 0.00
#> TCGA.D7.6522.01 1 0.0000 0.9940 1.00 0.00 0.00
#> TCGA.CG.5716.01 3 0.0000 0.9602 0.00 0.00 1.00
#> TCGA.BR.8589.01 2 0.0000 0.9813 0.00 1.00 0.00
#> TCGA.BR.8382.01 2 0.0000 0.9813 0.00 1.00 0.00
#> TCGA.VQ.AA68.01 3 0.2066 0.9094 0.00 0.06 0.94
#> TCGA.VQ.A8PJ.01 1 0.0000 0.9940 1.00 0.00 0.00
#> TCGA.VQ.A8PH.01 1 0.0000 0.9940 1.00 0.00 0.00
#> TCGA.HU.8604.01 2 0.0000 0.9813 0.00 1.00 0.00
#> TCGA.BR.8676.01 2 0.0000 0.9813 0.00 1.00 0.00
#> TCGA.CG.4441.01 3 0.0000 0.9602 0.00 0.00 1.00
#> TCGA.D7.6520.01 1 0.0000 0.9940 1.00 0.00 0.00
#> TCGA.VQ.AA64.01 1 0.0000 0.9940 1.00 0.00 0.00
#> TCGA.D7.6527.01 1 0.0000 0.9940 1.00 0.00 0.00
#> TCGA.VQ.A8PM.01 1 0.0000 0.9940 1.00 0.00 0.00
#> TCGA.VQ.A923.01 2 0.0000 0.9813 0.00 1.00 0.00
#> TCGA.BR.8384.01 3 0.0000 0.9602 0.00 0.00 1.00
#> TCGA.BR.6453.01 3 0.0000 0.9602 0.00 0.00 1.00
#> TCGA.VQ.A928.01 1 0.0000 0.9940 1.00 0.00 0.00
#> TCGA.VQ.A8E0.01 1 0.0000 0.9940 1.00 0.00 0.00
#> TCGA.BR.8679.01 2 0.0000 0.9813 0.00 1.00 0.00
#> TCGA.VQ.A91S.01 3 0.0000 0.9602 0.00 0.00 1.00
#> TCGA.BR.8678.01 1 0.0000 0.9940 1.00 0.00 0.00
#> TCGA.D7.6528.01 3 0.0000 0.9602 0.00 0.00 1.00
#> TCGA.VQ.A8E7.01 3 0.0000 0.9602 0.00 0.00 1.00
#> TCGA.BR.8680.01 3 0.0000 0.9602 0.00 0.00 1.00
#> TCGA.BR.8483.01 3 0.0000 0.9602 0.00 0.00 1.00
#> TCGA.BR.6566.01 3 0.0000 0.9602 0.00 0.00 1.00
#> TCGA.VQ.A91X.01 3 0.0000 0.9602 0.00 0.00 1.00
#> TCGA.VQ.A91Q.01 1 0.0000 0.9940 1.00 0.00 0.00
#> TCGA.VQ.A92D.01 2 0.0000 0.9813 0.00 1.00 0.00
#> TCGA.VQ.A91Z.01 1 0.2066 0.9346 0.94 0.00 0.06
#> TCGA.BR.6455.01 2 0.0000 0.9813 0.00 1.00 0.00
#> TCGA.BR.8591.01 2 0.0000 0.9813 0.00 1.00 0.00
#> TCGA.HU.8608.01 2 0.0000 0.9813 0.00 1.00 0.00
#> TCGA.VQ.A94U.01 3 0.0000 0.9602 0.00 0.00 1.00
#> TCGA.VQ.A94T.01 1 0.0892 0.9750 0.98 0.00 0.02
#> TCGA.VQ.A91A.01 3 0.0000 0.9602 0.00 0.00 1.00
#> TCGA.VQ.A91D.01 2 0.0000 0.9813 0.00 1.00 0.00
#> TCGA.D7.6518.01 3 0.0000 0.9602 0.00 0.00 1.00
#> TCGA.BR.8484.01 1 0.0000 0.9940 1.00 0.00 0.00
#> TCGA.VQ.A91N.01 1 0.0000 0.9940 1.00 0.00 0.00
#> TCGA.VQ.A91E.01 3 0.5835 0.4894 0.00 0.34 0.66
#> TCGA.VQ.A8PY.01 3 0.4291 0.7720 0.00 0.18 0.82
#> TCGA.HU.8602.01 2 0.0000 0.9813 0.00 1.00 0.00
#> TCGA.BR.8381.01 2 0.0000 0.9813 0.00 1.00 0.00
#> TCGA.BR.6452.11 3 0.6309 -0.0149 0.50 0.00 0.50
#> TCGA.IN.8663.01 2 0.0000 0.9813 0.00 1.00 0.00
#> TCGA.VQ.A8PS.01 1 0.0000 0.9940 1.00 0.00 0.00
#> TCGA.VQ.A91W.01 2 0.0000 0.9813 0.00 1.00 0.00
#> TCGA.BR.6454.01 1 0.0000 0.9940 1.00 0.00 0.00
#> TCGA.BR.8682.01 3 0.0000 0.9602 0.00 0.00 1.00
#> TCGA.VQ.A91V.01 3 0.0000 0.9602 0.00 0.00 1.00
#> TCGA.VQ.A8PZ.01 3 0.0000 0.9602 0.00 0.00 1.00
#> TCGA.BR.8590.01 1 0.0000 0.9940 1.00 0.00 0.00
#> TCGA.F1.6177.01 2 0.0000 0.9813 0.00 1.00 0.00
#> TCGA.VQ.A8PQ.01 1 0.0000 0.9940 1.00 0.00 0.00
#> TCGA.VQ.A91U.01 1 0.0000 0.9940 1.00 0.00 0.00
#> TCGA.VQ.AA6I.01 2 0.0000 0.9813 0.00 1.00 0.00
#> TCGA.CG.4437.01 2 0.0000 0.9813 0.00 1.00 0.00
#> TCGA.VQ.A8PP.01 2 0.0000 0.9813 0.00 1.00 0.00
#> TCGA.BR.6565.01 1 0.0000 0.9940 1.00 0.00 0.00
#> TCGA.VQ.A91Y.01 1 0.0000 0.9940 1.00 0.00 0.00
#> TCGA.VQ.A8PF.01 2 0.0000 0.9813 0.00 1.00 0.00
#> TCGA.BR.6456.01 1 0.0000 0.9940 1.00 0.00 0.00
#> TCGA.BR.6458.01 3 0.0000 0.9602 0.00 0.00 1.00
#> TCGA.VQ.A925.01 1 0.0000 0.9940 1.00 0.00 0.00
#> TCGA.VQ.A927.01 1 0.0000 0.9940 1.00 0.00 0.00
#> TCGA.BR.8592.01 3 0.0000 0.9602 0.00 0.00 1.00
#> TCGA.BR.6566.11 1 0.0000 0.9940 1.00 0.00 0.00
#> TCGA.IN.AB1V.01 1 0.0000 0.9940 1.00 0.00 0.00
#> TCGA.VQ.AA6F.01 1 0.0000 0.9940 1.00 0.00 0.00
#> TCGA.VQ.AA6J.01 1 0.0000 0.9940 1.00 0.00 0.00
#> TCGA.BR.8487.01 2 0.0000 0.9813 0.00 1.00 0.00
#> TCGA.D7.6525.01 3 0.3686 0.8232 0.00 0.14 0.86
#> TCGA.VQ.A94O.01 1 0.0000 0.9940 1.00 0.00 0.00
#> TCGA.BR.8588.01 3 0.0000 0.9602 0.00 0.00 1.00
#> TCGA.HU.8610.01 3 0.0000 0.9602 0.00 0.00 1.00
#> TCGA.D7.6526.01 1 0.0000 0.9940 1.00 0.00 0.00
#> TCGA.VQ.A8PD.01 3 0.0000 0.9602 0.00 0.00 1.00
#> TCGA.D7.6524.01 3 0.0000 0.9602 0.00 0.00 1.00
#> TCGA.3M.AB46.01 1 0.0000 0.9940 1.00 0.00 0.00
#> TCGA.3M.AB47.01 3 0.0000 0.9602 0.00 0.00 1.00
#> TCGA.BR.8677.01 1 0.3686 0.8398 0.86 0.00 0.14
#> TCGA.BR.6457.01 3 0.0000 0.9602 0.00 0.00 1.00
#> TCGA.BR.8687.01 1 0.0000 0.9940 1.00 0.00 0.00
#> TCGA.VQ.A91K.01 2 0.0000 0.9813 0.00 1.00 0.00
#> TCGA.BR.8690.01 1 0.0000 0.9940 1.00 0.00 0.00
#> TCGA.BR.8686.01 2 0.0000 0.9813 0.00 1.00 0.00
#> TCGA.FP.8631.01 1 0.0000 0.9940 1.00 0.00 0.00
#> TCGA.VQ.A922.01 1 0.0000 0.9940 1.00 0.00 0.00
#> TCGA.BR.A452.01 1 0.0000 0.9940 1.00 0.00 0.00
#> TCGA.IN.A6RO.01 2 0.0000 0.9813 0.00 1.00 0.00
#> TCGA.BR.A4QI.01 2 0.0000 0.9813 0.00 1.00 0.00
#> TCGA.D7.A6EV.01 3 0.0000 0.9602 0.00 0.00 1.00
#> TCGA.HU.A4G2.01 2 0.0000 0.9813 0.00 1.00 0.00
#> TCGA.BR.A4IY.01 2 0.0000 0.9813 0.00 1.00 0.00
#> TCGA.VQ.A8PU.01 1 0.4002 0.8127 0.84 0.00 0.16
#> TCGA.BR.A4J4.01 2 0.0000 0.9813 0.00 1.00 0.00
#> TCGA.VQ.A94R.01 2 0.0000 0.9813 0.00 1.00 0.00
#> TCGA.HU.A4H4.01 3 0.1529 0.9274 0.00 0.04 0.96
#> TCGA.BR.7707.01 2 0.0000 0.9813 0.00 1.00 0.00
#> TCGA.FP.7829.01 2 0.0000 0.9813 0.00 1.00 0.00
#> TCGA.BR.A4J5.01 3 0.0000 0.9602 0.00 0.00 1.00
#> TCGA.HU.A4H0.01 2 0.0000 0.9813 0.00 1.00 0.00
#> TCGA.HU.A4HD.01 1 0.0000 0.9940 1.00 0.00 0.00
#> TCGA.KB.A6F5.01 1 0.0000 0.9940 1.00 0.00 0.00
#> TCGA.VQ.AA6K.01 1 0.0000 0.9940 1.00 0.00 0.00
#> TCGA.HF.7133.01 1 0.0000 0.9940 1.00 0.00 0.00
#> TCGA.F1.6875.01 1 0.0000 0.9940 1.00 0.00 0.00
#> TCGA.MX.A666.01 1 0.0000 0.9940 1.00 0.00 0.00
#> TCGA.BR.7717.01 3 0.0000 0.9602 0.00 0.00 1.00
#> TCGA.BR.A4PF.01 2 0.3340 0.8482 0.00 0.88 0.12
#> TCGA.BR.A4IU.01 3 0.0000 0.9602 0.00 0.00 1.00
#> TCGA.VQ.A8PX.01 1 0.0000 0.9940 1.00 0.00 0.00
#> TCGA.BR.A4IV.01 1 0.0000 0.9940 1.00 0.00 0.00
#> TCGA.D7.A6EX.01 1 0.0000 0.9940 1.00 0.00 0.00
#> TCGA.BR.A4IZ.01 1 0.0000 0.9940 1.00 0.00 0.00
#> TCGA.BR.A4J9.01 1 0.0000 0.9940 1.00 0.00 0.00
#> TCGA.CD.A4MJ.01 2 0.0000 0.9813 0.00 1.00 0.00
#> TCGA.B7.A5TN.01 1 0.0000 0.9940 1.00 0.00 0.00
#> TCGA.BR.7715.01 3 0.0000 0.9602 0.00 0.00 1.00
#> TCGA.BR.7704.01 1 0.0000 0.9940 1.00 0.00 0.00
#> TCGA.BR.A4J1.01 1 0.0000 0.9940 1.00 0.00 0.00
#> TCGA.HU.A4GP.01 2 0.0000 0.9813 0.00 1.00 0.00
#> TCGA.D7.A4YY.01 2 0.0000 0.9813 0.00 1.00 0.00
#> TCGA.VQ.AA6G.01 2 0.0000 0.9813 0.00 1.00 0.00
#> TCGA.HU.A4GJ.01 3 0.0000 0.9602 0.00 0.00 1.00
#> TCGA.CD.A4MI.01 2 0.0000 0.9813 0.00 1.00 0.00
#> TCGA.BR.7196.01 3 0.0000 0.9602 0.00 0.00 1.00
#> TCGA.BR.6563.01 3 0.4796 0.7048 0.22 0.00 0.78
#> TCGA.VQ.A924.01 2 0.0000 0.9813 0.00 1.00 0.00
#> TCGA.BR.7716.01 1 0.0000 0.9940 1.00 0.00 0.00
#> TCGA.FP.7735.01 1 0.0000 0.9940 1.00 0.00 0.00
#> TCGA.BR.7723.01 1 0.0000 0.9940 1.00 0.00 0.00
#> TCGA.HU.A4H8.01 2 0.0000 0.9813 0.00 1.00 0.00
#> TCGA.IN.A6RJ.01 3 0.0000 0.9602 0.00 0.00 1.00
#> TCGA.HU.A4H3.01 2 0.0000 0.9813 0.00 1.00 0.00
#> TCGA.EQ.A4SO.01 1 0.0000 0.9940 1.00 0.00 0.00
#> TCGA.CD.A4MH.01 1 0.0000 0.9940 1.00 0.00 0.00
#> TCGA.BR.A4J7.01 1 0.0000 0.9940 1.00 0.00 0.00
#> TCGA.HF.7131.01 1 0.0000 0.9940 1.00 0.00 0.00
#> TCGA.D7.A74B.01 1 0.0000 0.9940 1.00 0.00 0.00
#> TCGA.BR.A4PE.01 2 0.0000 0.9813 0.00 1.00 0.00
#> TCGA.BR.A4J8.01 2 0.0000 0.9813 0.00 1.00 0.00
#> TCGA.HU.A4GX.01 3 0.0000 0.9602 0.00 0.00 1.00
#> TCGA.HU.A4G8.01 3 0.1529 0.9276 0.00 0.04 0.96
#> TCGA.HU.A4GT.01 2 0.0000 0.9813 0.00 1.00 0.00
#> TCGA.HU.A4GC.01 3 0.0000 0.9602 0.00 0.00 1.00
#> TCGA.BR.A4CQ.01 2 0.0000 0.9813 0.00 1.00 0.00
#> TCGA.D7.A6F2.01 1 0.0000 0.9940 1.00 0.00 0.00
#> TCGA.RD.A7BT.01 1 0.0000 0.9940 1.00 0.00 0.00
#> TCGA.BR.A4J6.01 1 0.0000 0.9940 1.00 0.00 0.00
#> TCGA.HU.A4GQ.01 2 0.0000 0.9813 0.00 1.00 0.00
#> TCGA.HF.7136.01 1 0.0000 0.9940 1.00 0.00 0.00
#> TCGA.BR.A4QM.01 2 0.0000 0.9813 0.00 1.00 0.00
#> TCGA.BR.A4PD.01 1 0.0000 0.9940 1.00 0.00 0.00
#> TCGA.VQ.A8PK.01 1 0.0000 0.9940 1.00 0.00 0.00
#> TCGA.B7.A5TK.01 3 0.0000 0.9602 0.00 0.00 1.00
#> TCGA.D7.A4YX.01 2 0.0000 0.9813 0.00 1.00 0.00
#> TCGA.D7.A4Z0.01 3 0.0000 0.9602 0.00 0.00 1.00
#> TCGA.VQ.A8PT.01 2 0.0000 0.9813 0.00 1.00 0.00
#> TCGA.IN.A6RN.01 1 0.0000 0.9940 1.00 0.00 0.00
#> TCGA.CD.A4MG.01 2 0.0000 0.9813 0.00 1.00 0.00
#> TCGA.D7.A747.01 1 0.0000 0.9940 1.00 0.00 0.00
#> TCGA.R5.A7O7.01 3 0.0000 0.9602 0.00 0.00 1.00
#> TCGA.F1.A72C.01 1 0.0000 0.9940 1.00 0.00 0.00
#> TCGA.BR.A4J2.01 3 0.0000 0.9602 0.00 0.00 1.00
#> TCGA.MX.A663.01 1 0.0000 0.9940 1.00 0.00 0.00
#> TCGA.D7.A4YV.01 2 0.0000 0.9813 0.00 1.00 0.00
#> TCGA.HU.A4GD.01 3 0.0000 0.9602 0.00 0.00 1.00
#> TCGA.BR.A4QL.01 2 0.0000 0.9813 0.00 1.00 0.00
#> TCGA.BR.7703.01 2 0.0000 0.9813 0.00 1.00 0.00
#> TCGA.VQ.AA6B.01 3 0.0000 0.9602 0.00 0.00 1.00
#> TCGA.VQ.AA6D.01 1 0.0000 0.9940 1.00 0.00 0.00
#> TCGA.D7.A6EZ.01 2 0.0000 0.9813 0.00 1.00 0.00
#> TCGA.D7.A4YU.01 2 0.0000 0.9813 0.00 1.00 0.00
#> TCGA.VQ.AA6A.01 1 0.0000 0.9940 1.00 0.00 0.00
#> TCGA.IN.7806.01 1 0.0000 0.9940 1.00 0.00 0.00
#> TCGA.HU.A4HB.01 3 0.0000 0.9602 0.00 0.00 1.00
#> TCGA.HU.A4H2.01 3 0.0000 0.9602 0.00 0.00 1.00
#> TCGA.IN.A6RP.01 2 0.0000 0.9813 0.00 1.00 0.00
#> TCGA.HU.A4H5.01 1 0.0000 0.9940 1.00 0.00 0.00
#> TCGA.HU.A4GU.01 2 0.0000 0.9813 0.00 1.00 0.00
#> TCGA.MX.A5UJ.01 2 0.0000 0.9813 0.00 1.00 0.00
#> TCGA.HU.A4GN.01 2 0.0000 0.9813 0.00 1.00 0.00
#> TCGA.CD.5804.01 1 0.0000 0.9940 1.00 0.00 0.00
#> TCGA.HU.A4H6.01 2 0.0000 0.9813 0.00 1.00 0.00
#> TCGA.HF.7132.01 2 0.6302 0.0521 0.00 0.52 0.48
#> TCGA.D7.A4YT.01 1 0.0000 0.9940 1.00 0.00 0.00
#> TCGA.HF.7134.01 2 0.0000 0.9813 0.00 1.00 0.00
#> TCGA.BR.6852.01 3 0.6280 0.1584 0.00 0.46 0.54
#> TCGA.BR.8370.01 2 0.0000 0.9813 0.00 1.00 0.00
#> TCGA.EQ.5647.01 1 0.0000 0.9940 1.00 0.00 0.00
#> TCGA.IN.A7NT.01 3 0.0000 0.9602 0.00 0.00 1.00
#> TCGA.RD.A8N9.01 1 0.0000 0.9940 1.00 0.00 0.00
#> TCGA.D7.5577.01 2 0.0000 0.9813 0.00 1.00 0.00
#> TCGA.CG.5717.01 1 0.0000 0.9940 1.00 0.00 0.00
#> TCGA.D7.6818.01 1 0.0000 0.9940 1.00 0.00 0.00
#> TCGA.CG.5734.01 3 0.0000 0.9602 0.00 0.00 1.00
#> TCGA.VQ.A8P8.01 3 0.0000 0.9602 0.00 0.00 1.00
#> TCGA.BR.6707.01 2 0.0000 0.9813 0.00 1.00 0.00
#> TCGA.B7.5818.01 2 0.0000 0.9813 0.00 1.00 0.00
#> TCGA.CD.8525.01 1 0.0000 0.9940 1.00 0.00 0.00
#> TCGA.BR.6705.01 3 0.0000 0.9602 0.00 0.00 1.00
#> TCGA.BR.4288.01 1 0.0000 0.9940 1.00 0.00 0.00
#> TCGA.CD.5813.01 1 0.0000 0.9940 1.00 0.00 0.00
#> TCGA.CG.5723.01 1 0.0000 0.9940 1.00 0.00 0.00
#> TCGA.CD.5800.01 1 0.0000 0.9940 1.00 0.00 0.00
#> TCGA.CG.5718.01 1 0.0000 0.9940 1.00 0.00 0.00
#> TCGA.BR.8080.01 1 0.5016 0.6899 0.76 0.00 0.24
#> TCGA.CG.5733.01 2 0.0000 0.9813 0.00 1.00 0.00
#> TCGA.D7.6817.01 1 0.0000 0.9940 1.00 0.00 0.00
#> TCGA.KB.A93G.01 1 0.0000 0.9940 1.00 0.00 0.00
#> TCGA.CD.5799.01 1 0.0000 0.9940 1.00 0.00 0.00
#> TCGA.BR.7851.01 2 0.0000 0.9813 0.00 1.00 0.00
#> TCGA.BR.7722.01 1 0.0000 0.9940 1.00 0.00 0.00
#> TCGA.MX.A5UG.01 3 0.0000 0.9602 0.00 0.00 1.00
#> TCGA.CD.8533.01 3 0.0000 0.9602 0.00 0.00 1.00
#> TCGA.BR.7957.01 3 0.0000 0.9602 0.00 0.00 1.00
#> TCGA.CG.5722.01 3 0.0000 0.9602 0.00 0.00 1.00
#> TCGA.F1.6874.01 3 0.0000 0.9602 0.00 0.00 1.00
#> TCGA.CG.5730.01 3 0.3340 0.8318 0.12 0.00 0.88
#> TCGA.CG.5726.01 2 0.0000 0.9813 0.00 1.00 0.00
#> TCGA.IP.7968.01 3 0.0000 0.9602 0.00 0.00 1.00
#> TCGA.BR.8363.01 2 0.0000 0.9813 0.00 1.00 0.00
#> TCGA.BR.7901.01 1 0.0000 0.9940 1.00 0.00 0.00
#> TCGA.D7.6822.01 3 0.0000 0.9602 0.00 0.00 1.00
#> TCGA.BR.6710.01 1 0.0000 0.9940 1.00 0.00 0.00
#> TCGA.CG.5720.01 2 0.6045 0.3697 0.00 0.62 0.38
#> TCGA.D7.8570.01 2 0.0000 0.9813 0.00 1.00 0.00
#> TCGA.B7.A5TI.01 1 0.0000 0.9940 1.00 0.00 0.00
#> TCGA.D7.6815.01 1 0.0000 0.9940 1.00 0.00 0.00
#> TCGA.BR.8284.01 2 0.6045 0.3697 0.00 0.62 0.38
#> TCGA.BR.8295.01 1 0.0000 0.9940 1.00 0.00 0.00
#> TCGA.BR.7197.01 1 0.0000 0.9940 1.00 0.00 0.00
#> TCGA.B7.A5TJ.01 2 0.0000 0.9813 0.00 1.00 0.00
#> TCGA.D7.A6EY.01 3 0.0000 0.9602 0.00 0.00 1.00
#> TCGA.BR.8366.01 2 0.0000 0.9813 0.00 1.00 0.00
#> TCGA.IN.A7NR.01 1 0.0000 0.9940 1.00 0.00 0.00
#> TCGA.BR.6706.01 3 0.0000 0.9602 0.00 0.00 1.00
#> TCGA.IN.7808.01 3 0.0000 0.9602 0.00 0.00 1.00
#> TCGA.BR.6564.01 1 0.0000 0.9940 1.00 0.00 0.00
#> TCGA.KB.A93H.01 3 0.6280 0.1371 0.46 0.00 0.54
#> TCGA.KB.A93J.01 1 0.0000 0.9940 1.00 0.00 0.00
#> TCGA.CD.5798.01 1 0.0000 0.9940 1.00 0.00 0.00
#> TCGA.CD.8530.01 1 0.0000 0.9940 1.00 0.00 0.00
#> TCGA.BR.6802.01 3 0.0000 0.9602 0.00 0.00 1.00
#> TCGA.CG.5719.01 1 0.0000 0.9940 1.00 0.00 0.00
#> TCGA.VQ.A8E3.01 2 0.0000 0.9813 0.00 1.00 0.00
#> TCGA.CD.5801.01 2 0.0000 0.9813 0.00 1.00 0.00
#> TCGA.FP.A9TM.01 3 0.6126 0.3415 0.00 0.40 0.60
#> TCGA.BR.7958.01 2 0.0000 0.9813 0.00 1.00 0.00
#> TCGA.FP.7998.01 3 0.0000 0.9602 0.00 0.00 1.00
#> TCGA.IN.A6RS.01 3 0.0000 0.9602 0.00 0.00 1.00
#> TCGA.BR.6709.01 1 0.0000 0.9940 1.00 0.00 0.00
#> TCGA.FP.7916.01 2 0.0000 0.9813 0.00 1.00 0.00
#> TCGA.R5.A7ZR.01 1 0.0000 0.9940 1.00 0.00 0.00
#> TCGA.B7.5816.01 3 0.0000 0.9602 0.00 0.00 1.00
#> TCGA.CG.5721.01 3 0.0000 0.9602 0.00 0.00 1.00
#> TCGA.SW.A7EA.01 2 0.0000 0.9813 0.00 1.00 0.00
#> TCGA.RD.A8NB.01 3 0.0000 0.9602 0.00 0.00 1.00
#> TCGA.BR.6801.01 1 0.0000 0.9940 1.00 0.00 0.00
#> TCGA.IN.AB1X.01 3 0.0000 0.9602 0.00 0.00 1.00
#> TCGA.D7.5579.01 1 0.0000 0.9940 1.00 0.00 0.00
#> TCGA.CG.5728.01 3 0.0000 0.9602 0.00 0.00 1.00
#> TCGA.R5.A7ZI.01 1 0.0000 0.9940 1.00 0.00 0.00
#> TCGA.IN.A7NU.01 3 0.0000 0.9602 0.00 0.00 1.00
#> TCGA.CG.5732.01 1 0.0000 0.9940 1.00 0.00 0.00
#> TCGA.ZQ.A9CR.01 1 0.0000 0.9940 1.00 0.00 0.00
#> TCGA.D7.5578.01 3 0.0000 0.9602 0.00 0.00 1.00
#> TCGA.BR.6803.01 1 0.0000 0.9940 1.00 0.00 0.00
#> TCGA.BR.8368.01 2 0.0000 0.9813 0.00 1.00 0.00
#> TCGA.SW.A7EB.01 1 0.0000 0.9940 1.00 0.00 0.00
#> TCGA.BR.8081.01 2 0.0000 0.9813 0.00 1.00 0.00
#> TCGA.VQ.A8P5.01 3 0.0000 0.9602 0.00 0.00 1.00
#> TCGA.CD.8535.01 2 0.0892 0.9616 0.00 0.98 0.02
#> TCGA.CG.5724.01 3 0.2066 0.9094 0.00 0.06 0.94
#> TCGA.D7.8574.01 1 0.0000 0.9940 1.00 0.00 0.00
#> TCGA.HJ.7597.01 1 0.0000 0.9940 1.00 0.00 0.00
#> TCGA.HF.A5NB.01 2 0.0000 0.9813 0.00 1.00 0.00
#> TCGA.VQ.A8PB.01 3 0.0000 0.9602 0.00 0.00 1.00
#> TCGA.R5.A7ZE.01 1 0.0000 0.9940 1.00 0.00 0.00
#> TCGA.CD.5803.01 1 0.0000 0.9940 1.00 0.00 0.00
#> TCGA.CG.5725.01 1 0.0000 0.9940 1.00 0.00 0.00
#> TCGA.D7.6820.01 1 0.0000 0.9940 1.00 0.00 0.00
#> TCGA.CD.5802.01 1 0.0000 0.9940 1.00 0.00 0.00
#> TCGA.R5.A7ZF.01 1 0.0000 0.9940 1.00 0.00 0.00
#> TCGA.D7.A6F0.01 1 0.0000 0.9940 1.00 0.00 0.00
#> TCGA.CG.5727.01 3 0.0000 0.9602 0.00 0.00 1.00
#> TCGA.VQ.A8PC.01 3 0.0000 0.9602 0.00 0.00 1.00
#> TCGA.CD.A486.01 1 0.0000 0.9940 1.00 0.00 0.00
#> TCGA.RD.A8N2.01 1 0.0000 0.9940 1.00 0.00 0.00
#> TCGA.IN.A6RI.01 1 0.0000 0.9940 1.00 0.00 0.00
#> TCGA.HU.8243.01 3 0.0000 0.9602 0.00 0.00 1.00
#> TCGA.CD.A48C.01 2 0.0000 0.9813 0.00 1.00 0.00
#> TCGA.RD.A8N5.01 1 0.0000 0.9940 1.00 0.00 0.00
#> TCGA.RD.A8N1.01 1 0.0000 0.9940 1.00 0.00 0.00
#> TCGA.HU.A4GF.01 1 0.0000 0.9940 1.00 0.00 0.00
#> TCGA.BR.8362.01 3 0.0000 0.9602 0.00 0.00 1.00
#> TCGA.BR.8285.01 2 0.0000 0.9813 0.00 1.00 0.00
#> TCGA.CD.8532.01 1 0.0000 0.9940 1.00 0.00 0.00
#> TCGA.VQ.A8E2.01 1 0.0000 0.9940 1.00 0.00 0.00
#> TCGA.BR.8373.01 1 0.0000 0.9940 1.00 0.00 0.00
#> TCGA.BR.8361.01 2 0.0000 0.9813 0.00 1.00 0.00
#> TCGA.BR.8058.01 1 0.0000 0.9940 1.00 0.00 0.00
#> TCGA.IN.8462.01 3 0.3686 0.8232 0.00 0.14 0.86
#> TCGA.HU.A4G9.01 2 0.0000 0.9813 0.00 1.00 0.00
#> TCGA.CD.8524.01 3 0.0000 0.9602 0.00 0.00 1.00
#> TCGA.D7.A748.01 1 0.0000 0.9940 1.00 0.00 0.00
#> TCGA.CD.8527.01 1 0.5216 0.6545 0.74 0.00 0.26
#> TCGA.VQ.A8DV.01 1 0.0000 0.9940 1.00 0.00 0.00
#> TCGA.CD.8528.01 2 0.0000 0.9813 0.00 1.00 0.00
#> TCGA.BR.A453.01 3 0.0000 0.9602 0.00 0.00 1.00
#> TCGA.RD.A8N6.01 1 0.0000 0.9940 1.00 0.00 0.00
#> TCGA.HU.8245.01 1 0.0000 0.9940 1.00 0.00 0.00
#> TCGA.ZA.A8F6.01 1 0.0000 0.9940 1.00 0.00 0.00
#> TCGA.BR.8367.01 3 0.0000 0.9602 0.00 0.00 1.00
#> TCGA.BR.8380.01 3 0.0000 0.9602 0.00 0.00 1.00
#> TCGA.FP.A4BE.01 2 0.0000 0.9813 0.00 1.00 0.00
#> TCGA.HU.8238.01 3 0.2066 0.9095 0.00 0.06 0.94
#> TCGA.BR.8078.01 2 0.0000 0.9813 0.00 1.00 0.00
#> TCGA.HU.8249.01 3 0.0000 0.9602 0.00 0.00 1.00
#> TCGA.RD.A8N0.01 1 0.0000 0.9940 1.00 0.00 0.00
#> TCGA.BR.8365.01 1 0.0000 0.9940 1.00 0.00 0.00
#> TCGA.FP.8211.01 1 0.0000 0.9940 1.00 0.00 0.00
#> TCGA.RD.A8N4.01 1 0.0000 0.9940 1.00 0.00 0.00
#> TCGA.VQ.A8DU.01 1 0.0000 0.9940 1.00 0.00 0.00
#> TCGA.VQ.A8DL.01 1 0.0000 0.9940 1.00 0.00 0.00
#> TCGA.VQ.A8DZ.01 1 0.0000 0.9940 1.00 0.00 0.00
#> TCGA.D7.8572.01 1 0.0000 0.9940 1.00 0.00 0.00
#> TCGA.RD.A7BW.01 1 0.0000 0.9940 1.00 0.00 0.00
#> TCGA.R5.A804.01 3 0.0000 0.9602 0.00 0.00 1.00
#> TCGA.BR.A4CS.01 3 0.0000 0.9602 0.00 0.00 1.00
#> TCGA.CD.8531.01 2 0.0000 0.9813 0.00 1.00 0.00
#> TCGA.CD.A487.01 1 0.0000 0.9940 1.00 0.00 0.00
#> TCGA.BR.8371.01 1 0.0000 0.9940 1.00 0.00 0.00
#> TCGA.BR.8059.01 1 0.0000 0.9940 1.00 0.00 0.00
#> TCGA.D7.A6ET.01 3 0.0000 0.9602 0.00 0.00 1.00
#> TCGA.FP.8099.01 3 0.0000 0.9602 0.00 0.00 1.00
#> TCGA.D7.8579.01 3 0.0000 0.9602 0.00 0.00 1.00
#> TCGA.BR.8297.01 3 0.0000 0.9602 0.00 0.00 1.00
#> TCGA.D7.8576.01 1 0.0000 0.9940 1.00 0.00 0.00
#> TCGA.VQ.A8DT.01 2 0.6302 0.0520 0.00 0.52 0.48
#> TCGA.FP.A8CX.01 1 0.0000 0.9940 1.00 0.00 0.00
#> TCGA.HU.A4GH.01 1 0.0000 0.9940 1.00 0.00 0.00
#> TCGA.CD.8526.01 1 0.0000 0.9940 1.00 0.00 0.00
#> TCGA.HU.A4G6.01 2 0.0000 0.9813 0.00 1.00 0.00
#> TCGA.D7.8578.01 1 0.0000 0.9940 1.00 0.00 0.00
#> TCGA.HU.A4G3.01 2 0.0000 0.9813 0.00 1.00 0.00
#> TCGA.D7.A74A.01 2 0.0000 0.9813 0.00 1.00 0.00
#> TCGA.RD.A7C1.01 3 0.0000 0.9602 0.00 0.00 1.00
#> TCGA.F1.A448.01 3 0.0000 0.9602 0.00 0.00 1.00
#> TCGA.D7.8575.01 3 0.0000 0.9602 0.00 0.00 1.00
#> TCGA.BR.8372.01 2 0.0000 0.9813 0.00 1.00 0.00
#> TCGA.VQ.A8P3.01 3 0.6302 0.0874 0.00 0.48 0.52
#> TCGA.RD.A8MW.01 1 0.0000 0.9940 1.00 0.00 0.00
#> TCGA.BR.8286.01 3 0.4291 0.7718 0.00 0.18 0.82
#> TCGA.BR.8369.01 3 0.0000 0.9602 0.00 0.00 1.00
#> TCGA.BR.8364.01 1 0.0000 0.9940 1.00 0.00 0.00
#> TCGA.HU.8244.01 2 0.0000 0.9813 0.00 1.00 0.00
#> TCGA.KB.A6F7.01 1 0.0000 0.9940 1.00 0.00 0.00
#> TCGA.FP.A4BF.01 3 0.4291 0.7721 0.00 0.18 0.82
#> TCGA.R5.A805.01 3 0.0000 0.9602 0.00 0.00 1.00
#> TCGA.IN.A6RL.01 3 0.0000 0.9602 0.00 0.00 1.00
#> TCGA.IN.A6RR.01 2 0.0000 0.9813 0.00 1.00 0.00
#> TCGA.BR.A4CR.01 1 0.0000 0.9940 1.00 0.00 0.00
#> TCGA.CD.A489.01 1 0.2959 0.8896 0.90 0.00 0.10
#> TCGA.HU.A4GY.01 1 0.2066 0.9346 0.94 0.00 0.06
#> TCGA.BR.8289.01 3 0.0000 0.9602 0.00 0.00 1.00
#> TCGA.FP.8209.01 1 0.0000 0.9940 1.00 0.00 0.00
#> TCGA.BR.8296.01 3 0.0000 0.9602 0.00 0.00 1.00
#> TCGA.CD.A48A.01 3 0.0000 0.9602 0.00 0.00 1.00
#> TCGA.BR.8060.01 1 0.0000 0.9940 1.00 0.00 0.00
#> TCGA.BR.8077.01 1 0.0000 0.9940 1.00 0.00 0.00
#> TCGA.CD.8534.01 3 0.0000 0.9602 0.00 0.00 1.00
#> TCGA.BR.7959.01 3 0.0000 0.9602 0.00 0.00 1.00
#> TCGA.VQ.A8P2.01 2 0.0000 0.9813 0.00 1.00 0.00
#> TCGA.EQ.8122.01 1 0.0000 0.9940 1.00 0.00 0.00
#> TCGA.D7.8573.01 2 0.0000 0.9813 0.00 1.00 0.00
#> TCGA.BR.A44T.01 1 0.0000 0.9940 1.00 0.00 0.00
#> TCGA.RD.A8MV.01 3 0.2066 0.8997 0.06 0.00 0.94
#> TCGA.CD.8536.01 3 0.0000 0.9602 0.00 0.00 1.00
#> TCGA.BR.8360.01 2 0.0000 0.9813 0.00 1.00 0.00
#> TCGA.BR.8291.01 1 0.0000 0.9940 1.00 0.00 0.00
#> TCGA.FP.8210.01 1 0.0000 0.9940 1.00 0.00 0.00
#> TCGA.RD.A7BS.01 1 0.0000 0.9940 1.00 0.00 0.00
#> TCGA.BR.A44U.01 3 0.2959 0.8689 0.00 0.10 0.90
#> TCGA.CD.8529.01 1 0.0000 0.9940 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.VQ.A94P.01 4 0.4277 0.694 0.28 0.00 0.00 0.72
#> TCGA.D7.6521.01 4 0.0000 0.784 0.00 0.00 0.00 1.00
#> TCGA.VQ.A8PE.01 1 0.0000 0.931 1.00 0.00 0.00 0.00
#> TCGA.D7.6519.01 1 0.0000 0.931 1.00 0.00 0.00 0.00
#> TCGA.BR.6452.01 2 0.3975 0.767 0.00 0.76 0.24 0.00
#> TCGA.BR.8485.01 1 0.0000 0.931 1.00 0.00 0.00 0.00
#> TCGA.VQ.A8PO.01 2 0.4277 0.729 0.00 0.72 0.28 0.00
#> TCGA.VQ.AA69.01 2 0.0000 0.922 0.00 1.00 0.00 0.00
#> TCGA.BR.8683.01 4 0.0000 0.784 0.00 0.00 0.00 1.00
#> TCGA.BR.8486.01 1 0.0000 0.931 1.00 0.00 0.00 0.00
#> TCGA.D7.6522.01 4 0.3801 0.730 0.22 0.00 0.00 0.78
#> TCGA.CG.5716.01 4 0.0000 0.784 0.00 0.00 0.00 1.00
#> TCGA.BR.8589.01 2 0.0000 0.922 0.00 1.00 0.00 0.00
#> TCGA.BR.8382.01 3 0.4522 0.387 0.00 0.32 0.68 0.00
#> TCGA.VQ.AA68.01 3 0.0000 0.880 0.00 0.00 1.00 0.00
#> TCGA.VQ.A8PJ.01 1 0.0000 0.931 1.00 0.00 0.00 0.00
#> TCGA.VQ.A8PH.01 1 0.0000 0.931 1.00 0.00 0.00 0.00
#> TCGA.HU.8604.01 2 0.4406 0.701 0.00 0.70 0.30 0.00
#> TCGA.BR.8676.01 2 0.0000 0.922 0.00 1.00 0.00 0.00
#> TCGA.CG.4441.01 4 0.3400 0.619 0.00 0.00 0.18 0.82
#> TCGA.D7.6520.01 1 0.0000 0.931 1.00 0.00 0.00 0.00
#> TCGA.VQ.AA64.01 4 0.4277 0.694 0.28 0.00 0.00 0.72
#> TCGA.D7.6527.01 1 0.0000 0.931 1.00 0.00 0.00 0.00
#> TCGA.VQ.A8PM.01 1 0.0000 0.931 1.00 0.00 0.00 0.00
#> TCGA.VQ.A923.01 2 0.0000 0.922 0.00 1.00 0.00 0.00
#> TCGA.BR.8384.01 4 0.0000 0.784 0.00 0.00 0.00 1.00
#> TCGA.BR.6453.01 3 0.4277 0.734 0.00 0.00 0.72 0.28
#> TCGA.VQ.A928.01 4 0.0000 0.784 0.00 0.00 0.00 1.00
#> TCGA.VQ.A8E0.01 1 0.2921 0.809 0.86 0.00 0.00 0.14
#> TCGA.BR.8679.01 2 0.4277 0.729 0.00 0.72 0.28 0.00
#> TCGA.VQ.A91S.01 4 0.3172 0.646 0.00 0.00 0.16 0.84
#> TCGA.BR.8678.01 1 0.0000 0.931 1.00 0.00 0.00 0.00
#> TCGA.D7.6528.01 4 0.3975 0.521 0.00 0.00 0.24 0.76
#> TCGA.VQ.A8E7.01 3 0.0000 0.880 0.00 0.00 1.00 0.00
#> TCGA.BR.8680.01 3 0.2011 0.858 0.00 0.00 0.92 0.08
#> TCGA.BR.8483.01 3 0.4406 0.708 0.00 0.00 0.70 0.30
#> TCGA.BR.6566.01 3 0.0000 0.880 0.00 0.00 1.00 0.00
#> TCGA.VQ.A91X.01 3 0.3975 0.765 0.00 0.00 0.76 0.24
#> TCGA.VQ.A91Q.01 4 0.4277 0.694 0.28 0.00 0.00 0.72
#> TCGA.VQ.A92D.01 2 0.0000 0.922 0.00 1.00 0.00 0.00
#> TCGA.VQ.A91Z.01 4 0.3400 0.692 0.18 0.00 0.00 0.82
#> TCGA.BR.6455.01 2 0.0000 0.922 0.00 1.00 0.00 0.00
#> TCGA.BR.8591.01 2 0.0000 0.922 0.00 1.00 0.00 0.00
#> TCGA.HU.8608.01 2 0.0707 0.912 0.00 0.98 0.02 0.00
#> TCGA.VQ.A94U.01 3 0.0707 0.877 0.00 0.00 0.98 0.02
#> TCGA.VQ.A94T.01 4 0.0000 0.784 0.00 0.00 0.00 1.00
#> TCGA.VQ.A91A.01 3 0.0000 0.880 0.00 0.00 1.00 0.00
#> TCGA.VQ.A91D.01 2 0.0000 0.922 0.00 1.00 0.00 0.00
#> TCGA.D7.6518.01 4 0.0000 0.784 0.00 0.00 0.00 1.00
#> TCGA.BR.8484.01 4 0.4277 0.694 0.28 0.00 0.00 0.72
#> TCGA.VQ.A91N.01 4 0.2647 0.755 0.12 0.00 0.00 0.88
#> TCGA.VQ.A91E.01 3 0.0000 0.880 0.00 0.00 1.00 0.00
#> TCGA.VQ.A8PY.01 3 0.0000 0.880 0.00 0.00 1.00 0.00
#> TCGA.HU.8602.01 2 0.0000 0.922 0.00 1.00 0.00 0.00
#> TCGA.BR.8381.01 2 0.4277 0.729 0.00 0.72 0.28 0.00
#> TCGA.BR.6452.11 4 0.0000 0.784 0.00 0.00 0.00 1.00
#> TCGA.IN.8663.01 2 0.0000 0.922 0.00 1.00 0.00 0.00
#> TCGA.VQ.A8PS.01 4 0.4277 0.694 0.28 0.00 0.00 0.72
#> TCGA.VQ.A91W.01 2 0.3172 0.828 0.00 0.84 0.16 0.00
#> TCGA.BR.6454.01 4 0.0000 0.784 0.00 0.00 0.00 1.00
#> TCGA.BR.8682.01 3 0.4277 0.734 0.00 0.00 0.72 0.28
#> TCGA.VQ.A91V.01 3 0.0000 0.880 0.00 0.00 1.00 0.00
#> TCGA.VQ.A8PZ.01 3 0.0000 0.880 0.00 0.00 1.00 0.00
#> TCGA.BR.8590.01 4 0.4277 0.694 0.28 0.00 0.00 0.72
#> TCGA.F1.6177.01 2 0.0000 0.922 0.00 1.00 0.00 0.00
#> TCGA.VQ.A8PQ.01 1 0.3172 0.785 0.84 0.00 0.00 0.16
#> TCGA.VQ.A91U.01 1 0.0000 0.931 1.00 0.00 0.00 0.00
#> TCGA.VQ.AA6I.01 3 0.3801 0.610 0.00 0.22 0.78 0.00
#> TCGA.CG.4437.01 3 0.3400 0.678 0.00 0.18 0.82 0.00
#> TCGA.VQ.A8PP.01 3 0.3610 0.646 0.00 0.20 0.80 0.00
#> TCGA.BR.6565.01 1 0.0000 0.931 1.00 0.00 0.00 0.00
#> TCGA.VQ.A91Y.01 1 0.0000 0.931 1.00 0.00 0.00 0.00
#> TCGA.VQ.A8PF.01 2 0.4277 0.729 0.00 0.72 0.28 0.00
#> TCGA.BR.6456.01 1 0.0000 0.931 1.00 0.00 0.00 0.00
#> TCGA.BR.6458.01 3 0.4277 0.734 0.00 0.00 0.72 0.28
#> TCGA.VQ.A925.01 1 0.0000 0.931 1.00 0.00 0.00 0.00
#> TCGA.VQ.A927.01 4 0.4134 0.709 0.26 0.00 0.00 0.74
#> TCGA.BR.8592.01 4 0.3610 0.590 0.00 0.00 0.20 0.80
#> TCGA.BR.6566.11 1 0.4624 0.440 0.66 0.00 0.00 0.34
#> TCGA.IN.AB1V.01 1 0.0000 0.931 1.00 0.00 0.00 0.00
#> TCGA.VQ.AA6F.01 4 0.4277 0.694 0.28 0.00 0.00 0.72
#> TCGA.VQ.AA6J.01 4 0.0000 0.784 0.00 0.00 0.00 1.00
#> TCGA.BR.8487.01 2 0.0000 0.922 0.00 1.00 0.00 0.00
#> TCGA.D7.6525.01 3 0.0000 0.880 0.00 0.00 1.00 0.00
#> TCGA.VQ.A94O.01 1 0.0000 0.931 1.00 0.00 0.00 0.00
#> TCGA.BR.8588.01 3 0.2011 0.858 0.00 0.00 0.92 0.08
#> TCGA.HU.8610.01 4 0.0000 0.784 0.00 0.00 0.00 1.00
#> TCGA.D7.6526.01 1 0.0000 0.931 1.00 0.00 0.00 0.00
#> TCGA.VQ.A8PD.01 3 0.4277 0.734 0.00 0.00 0.72 0.28
#> TCGA.D7.6524.01 3 0.3801 0.778 0.00 0.00 0.78 0.22
#> TCGA.3M.AB46.01 1 0.0000 0.931 1.00 0.00 0.00 0.00
#> TCGA.3M.AB47.01 3 0.4277 0.734 0.00 0.00 0.72 0.28
#> TCGA.BR.8677.01 4 0.0000 0.784 0.00 0.00 0.00 1.00
#> TCGA.BR.6457.01 4 0.3610 0.590 0.00 0.00 0.20 0.80
#> TCGA.BR.8687.01 1 0.0000 0.931 1.00 0.00 0.00 0.00
#> TCGA.VQ.A91K.01 2 0.0000 0.922 0.00 1.00 0.00 0.00
#> TCGA.BR.8690.01 1 0.0000 0.931 1.00 0.00 0.00 0.00
#> TCGA.BR.8686.01 2 0.0000 0.922 0.00 1.00 0.00 0.00
#> TCGA.FP.8631.01 1 0.0000 0.931 1.00 0.00 0.00 0.00
#> TCGA.VQ.A922.01 1 0.0000 0.931 1.00 0.00 0.00 0.00
#> TCGA.BR.A452.01 4 0.4277 0.694 0.28 0.00 0.00 0.72
#> TCGA.IN.A6RO.01 2 0.0000 0.922 0.00 1.00 0.00 0.00
#> TCGA.BR.A4QI.01 2 0.0000 0.922 0.00 1.00 0.00 0.00
#> TCGA.D7.A6EV.01 3 0.4277 0.734 0.00 0.00 0.72 0.28
#> TCGA.HU.A4G2.01 2 0.0000 0.922 0.00 1.00 0.00 0.00
#> TCGA.BR.A4IY.01 2 0.0000 0.922 0.00 1.00 0.00 0.00
#> TCGA.VQ.A8PU.01 4 0.0000 0.784 0.00 0.00 0.00 1.00
#> TCGA.BR.A4J4.01 2 0.0000 0.922 0.00 1.00 0.00 0.00
#> TCGA.VQ.A94R.01 3 0.1211 0.848 0.00 0.04 0.96 0.00
#> TCGA.HU.A4H4.01 3 0.0000 0.880 0.00 0.00 1.00 0.00
#> TCGA.BR.7707.01 2 0.3801 0.784 0.00 0.78 0.22 0.00
#> TCGA.FP.7829.01 2 0.0000 0.922 0.00 1.00 0.00 0.00
#> TCGA.BR.A4J5.01 3 0.0707 0.877 0.00 0.00 0.98 0.02
#> TCGA.HU.A4H0.01 2 0.0000 0.922 0.00 1.00 0.00 0.00
#> TCGA.HU.A4HD.01 1 0.0000 0.931 1.00 0.00 0.00 0.00
#> TCGA.KB.A6F5.01 1 0.0000 0.931 1.00 0.00 0.00 0.00
#> TCGA.VQ.AA6K.01 4 0.3975 0.720 0.24 0.00 0.00 0.76
#> TCGA.HF.7133.01 4 0.4277 0.694 0.28 0.00 0.00 0.72
#> TCGA.F1.6875.01 4 0.4907 0.495 0.42 0.00 0.00 0.58
#> TCGA.MX.A666.01 1 0.0000 0.931 1.00 0.00 0.00 0.00
#> TCGA.BR.7717.01 3 0.0000 0.880 0.00 0.00 1.00 0.00
#> TCGA.BR.A4PF.01 3 0.0000 0.880 0.00 0.00 1.00 0.00
#> TCGA.BR.A4IU.01 3 0.4277 0.734 0.00 0.00 0.72 0.28
#> TCGA.VQ.A8PX.01 1 0.3400 0.758 0.82 0.00 0.00 0.18
#> TCGA.BR.A4IV.01 4 0.4277 0.694 0.28 0.00 0.00 0.72
#> TCGA.D7.A6EX.01 4 0.4277 0.694 0.28 0.00 0.00 0.72
#> TCGA.BR.A4IZ.01 4 0.0000 0.784 0.00 0.00 0.00 1.00
#> TCGA.BR.A4J9.01 4 0.4277 0.694 0.28 0.00 0.00 0.72
#> TCGA.CD.A4MJ.01 2 0.0000 0.922 0.00 1.00 0.00 0.00
#> TCGA.B7.A5TN.01 1 0.0000 0.931 1.00 0.00 0.00 0.00
#> TCGA.BR.7715.01 3 0.4277 0.734 0.00 0.00 0.72 0.28
#> TCGA.BR.7704.01 1 0.0000 0.931 1.00 0.00 0.00 0.00
#> TCGA.BR.A4J1.01 1 0.0000 0.931 1.00 0.00 0.00 0.00
#> TCGA.HU.A4GP.01 2 0.4855 0.513 0.00 0.60 0.40 0.00
#> TCGA.D7.A4YY.01 2 0.0000 0.922 0.00 1.00 0.00 0.00
#> TCGA.VQ.AA6G.01 2 0.2647 0.855 0.00 0.88 0.12 0.00
#> TCGA.HU.A4GJ.01 3 0.4277 0.734 0.00 0.00 0.72 0.28
#> TCGA.CD.A4MI.01 2 0.4277 0.729 0.00 0.72 0.28 0.00
#> TCGA.BR.7196.01 3 0.0000 0.880 0.00 0.00 1.00 0.00
#> TCGA.BR.6563.01 4 0.0000 0.784 0.00 0.00 0.00 1.00
#> TCGA.VQ.A924.01 2 0.3801 0.784 0.00 0.78 0.22 0.00
#> TCGA.BR.7716.01 1 0.0000 0.931 1.00 0.00 0.00 0.00
#> TCGA.FP.7735.01 4 0.4277 0.694 0.28 0.00 0.00 0.72
#> TCGA.BR.7723.01 1 0.0000 0.931 1.00 0.00 0.00 0.00
#> TCGA.HU.A4H8.01 2 0.0000 0.922 0.00 1.00 0.00 0.00
#> TCGA.IN.A6RJ.01 3 0.4277 0.734 0.00 0.00 0.72 0.28
#> TCGA.HU.A4H3.01 2 0.0000 0.922 0.00 1.00 0.00 0.00
#> TCGA.EQ.A4SO.01 1 0.2921 0.809 0.86 0.00 0.00 0.14
#> TCGA.CD.A4MH.01 1 0.0000 0.931 1.00 0.00 0.00 0.00
#> TCGA.BR.A4J7.01 4 0.2011 0.781 0.08 0.00 0.00 0.92
#> TCGA.HF.7131.01 1 0.0000 0.931 1.00 0.00 0.00 0.00
#> TCGA.D7.A74B.01 1 0.2345 0.850 0.90 0.00 0.00 0.10
#> TCGA.BR.A4PE.01 2 0.0000 0.922 0.00 1.00 0.00 0.00
#> TCGA.BR.A4J8.01 2 0.4134 0.749 0.00 0.74 0.26 0.00
#> TCGA.HU.A4GX.01 4 0.0707 0.774 0.00 0.00 0.02 0.98
#> TCGA.HU.A4G8.01 3 0.0000 0.880 0.00 0.00 1.00 0.00
#> TCGA.HU.A4GT.01 2 0.0000 0.922 0.00 1.00 0.00 0.00
#> TCGA.HU.A4GC.01 3 0.0000 0.880 0.00 0.00 1.00 0.00
#> TCGA.BR.A4CQ.01 2 0.0000 0.922 0.00 1.00 0.00 0.00
#> TCGA.D7.A6F2.01 1 0.0000 0.931 1.00 0.00 0.00 0.00
#> TCGA.RD.A7BT.01 4 0.2345 0.754 0.10 0.00 0.00 0.90
#> TCGA.BR.A4J6.01 4 0.4277 0.694 0.28 0.00 0.00 0.72
#> TCGA.HU.A4GQ.01 2 0.0000 0.922 0.00 1.00 0.00 0.00
#> TCGA.HF.7136.01 1 0.0000 0.931 1.00 0.00 0.00 0.00
#> TCGA.BR.A4QM.01 2 0.0000 0.922 0.00 1.00 0.00 0.00
#> TCGA.BR.A4PD.01 4 0.0000 0.784 0.00 0.00 0.00 1.00
#> TCGA.VQ.A8PK.01 1 0.0000 0.931 1.00 0.00 0.00 0.00
#> TCGA.B7.A5TK.01 3 0.0000 0.880 0.00 0.00 1.00 0.00
#> TCGA.D7.A4YX.01 2 0.0000 0.922 0.00 1.00 0.00 0.00
#> TCGA.D7.A4Z0.01 3 0.0000 0.880 0.00 0.00 1.00 0.00
#> TCGA.VQ.A8PT.01 2 0.0000 0.922 0.00 1.00 0.00 0.00
#> TCGA.IN.A6RN.01 1 0.0000 0.931 1.00 0.00 0.00 0.00
#> TCGA.CD.A4MG.01 2 0.0000 0.922 0.00 1.00 0.00 0.00
#> TCGA.D7.A747.01 4 0.4277 0.694 0.28 0.00 0.00 0.72
#> TCGA.R5.A7O7.01 3 0.4277 0.734 0.00 0.00 0.72 0.28
#> TCGA.F1.A72C.01 4 0.4277 0.694 0.28 0.00 0.00 0.72
#> TCGA.BR.A4J2.01 4 0.4134 0.479 0.00 0.00 0.26 0.74
#> TCGA.MX.A663.01 1 0.0000 0.931 1.00 0.00 0.00 0.00
#> TCGA.D7.A4YV.01 2 0.0000 0.922 0.00 1.00 0.00 0.00
#> TCGA.HU.A4GD.01 4 0.1637 0.747 0.00 0.00 0.06 0.94
#> TCGA.BR.A4QL.01 2 0.0000 0.922 0.00 1.00 0.00 0.00
#> TCGA.BR.7703.01 2 0.0000 0.922 0.00 1.00 0.00 0.00
#> TCGA.VQ.AA6B.01 3 0.4277 0.734 0.00 0.00 0.72 0.28
#> TCGA.VQ.AA6D.01 1 0.0000 0.931 1.00 0.00 0.00 0.00
#> TCGA.D7.A6EZ.01 2 0.0000 0.922 0.00 1.00 0.00 0.00
#> TCGA.D7.A4YU.01 2 0.0000 0.922 0.00 1.00 0.00 0.00
#> TCGA.VQ.AA6A.01 1 0.4624 0.307 0.66 0.00 0.00 0.34
#> TCGA.IN.7806.01 4 0.4994 0.356 0.48 0.00 0.00 0.52
#> TCGA.HU.A4HB.01 4 0.1211 0.762 0.00 0.00 0.04 0.96
#> TCGA.HU.A4H2.01 3 0.4277 0.734 0.00 0.00 0.72 0.28
#> TCGA.IN.A6RP.01 3 0.2647 0.762 0.00 0.12 0.88 0.00
#> TCGA.HU.A4H5.01 1 0.0000 0.931 1.00 0.00 0.00 0.00
#> TCGA.HU.A4GU.01 2 0.0000 0.922 0.00 1.00 0.00 0.00
#> TCGA.MX.A5UJ.01 2 0.4277 0.729 0.00 0.72 0.28 0.00
#> TCGA.HU.A4GN.01 2 0.0000 0.922 0.00 1.00 0.00 0.00
#> TCGA.CD.5804.01 1 0.0000 0.931 1.00 0.00 0.00 0.00
#> TCGA.HU.A4H6.01 2 0.4277 0.729 0.00 0.72 0.28 0.00
#> TCGA.HF.7132.01 3 0.0000 0.880 0.00 0.00 1.00 0.00
#> TCGA.D7.A4YT.01 1 0.0000 0.931 1.00 0.00 0.00 0.00
#> TCGA.HF.7134.01 2 0.0000 0.922 0.00 1.00 0.00 0.00
#> TCGA.BR.6852.01 3 0.0000 0.880 0.00 0.00 1.00 0.00
#> TCGA.BR.8370.01 2 0.0000 0.922 0.00 1.00 0.00 0.00
#> TCGA.EQ.5647.01 4 0.4277 0.694 0.28 0.00 0.00 0.72
#> TCGA.IN.A7NT.01 4 0.3172 0.647 0.00 0.00 0.16 0.84
#> TCGA.RD.A8N9.01 1 0.1211 0.902 0.96 0.00 0.00 0.04
#> TCGA.D7.5577.01 2 0.0000 0.922 0.00 1.00 0.00 0.00
#> TCGA.CG.5717.01 4 0.4134 0.709 0.26 0.00 0.00 0.74
#> TCGA.D7.6818.01 1 0.0000 0.931 1.00 0.00 0.00 0.00
#> TCGA.CG.5734.01 4 0.0000 0.784 0.00 0.00 0.00 1.00
#> TCGA.VQ.A8P8.01 3 0.0000 0.880 0.00 0.00 1.00 0.00
#> TCGA.BR.6707.01 2 0.4277 0.729 0.00 0.72 0.28 0.00
#> TCGA.B7.5818.01 2 0.0000 0.922 0.00 1.00 0.00 0.00
#> TCGA.CD.8525.01 1 0.0000 0.931 1.00 0.00 0.00 0.00
#> TCGA.BR.6705.01 4 0.3801 0.557 0.00 0.00 0.22 0.78
#> TCGA.BR.4288.01 1 0.0000 0.931 1.00 0.00 0.00 0.00
#> TCGA.CD.5813.01 4 0.4277 0.694 0.28 0.00 0.00 0.72
#> TCGA.CG.5723.01 4 0.0000 0.784 0.00 0.00 0.00 1.00
#> TCGA.CD.5800.01 1 0.0000 0.931 1.00 0.00 0.00 0.00
#> TCGA.CG.5718.01 1 0.0000 0.931 1.00 0.00 0.00 0.00
#> TCGA.BR.8080.01 4 0.0000 0.784 0.00 0.00 0.00 1.00
#> TCGA.CG.5733.01 2 0.3801 0.784 0.00 0.78 0.22 0.00
#> TCGA.D7.6817.01 1 0.0000 0.931 1.00 0.00 0.00 0.00
#> TCGA.KB.A93G.01 4 0.4134 0.709 0.26 0.00 0.00 0.74
#> TCGA.CD.5799.01 1 0.0000 0.931 1.00 0.00 0.00 0.00
#> TCGA.BR.7851.01 2 0.0000 0.922 0.00 1.00 0.00 0.00
#> TCGA.BR.7722.01 4 0.4277 0.694 0.28 0.00 0.00 0.72
#> TCGA.MX.A5UG.01 4 0.0000 0.784 0.00 0.00 0.00 1.00
#> TCGA.CD.8533.01 3 0.0000 0.880 0.00 0.00 1.00 0.00
#> TCGA.BR.7957.01 4 0.4134 0.481 0.00 0.00 0.26 0.74
#> TCGA.CG.5722.01 3 0.0000 0.880 0.00 0.00 1.00 0.00
#> TCGA.F1.6874.01 4 0.3975 0.521 0.00 0.00 0.24 0.76
#> TCGA.CG.5730.01 4 0.3821 0.680 0.04 0.00 0.12 0.84
#> TCGA.CG.5726.01 2 0.0000 0.922 0.00 1.00 0.00 0.00
#> TCGA.IP.7968.01 4 0.3172 0.647 0.00 0.00 0.16 0.84
#> TCGA.BR.8363.01 3 0.3610 0.646 0.00 0.20 0.80 0.00
#> TCGA.BR.7901.01 1 0.0000 0.931 1.00 0.00 0.00 0.00
#> TCGA.D7.6822.01 3 0.3610 0.792 0.00 0.00 0.80 0.20
#> TCGA.BR.6710.01 1 0.2345 0.850 0.90 0.00 0.00 0.10
#> TCGA.CG.5720.01 3 0.0000 0.880 0.00 0.00 1.00 0.00
#> TCGA.D7.8570.01 2 0.4277 0.729 0.00 0.72 0.28 0.00
#> TCGA.B7.A5TI.01 1 0.4994 -0.066 0.52 0.00 0.00 0.48
#> TCGA.D7.6815.01 4 0.2647 0.755 0.12 0.00 0.00 0.88
#> TCGA.BR.8284.01 3 0.0000 0.880 0.00 0.00 1.00 0.00
#> TCGA.BR.8295.01 1 0.0000 0.931 1.00 0.00 0.00 0.00
#> TCGA.BR.7197.01 1 0.4522 0.368 0.68 0.00 0.00 0.32
#> TCGA.B7.A5TJ.01 2 0.0000 0.922 0.00 1.00 0.00 0.00
#> TCGA.D7.A6EY.01 3 0.4277 0.734 0.00 0.00 0.72 0.28
#> TCGA.BR.8366.01 2 0.4277 0.729 0.00 0.72 0.28 0.00
#> TCGA.IN.A7NR.01 1 0.2921 0.809 0.86 0.00 0.00 0.14
#> TCGA.BR.6706.01 3 0.0000 0.880 0.00 0.00 1.00 0.00
#> TCGA.IN.7808.01 3 0.1211 0.873 0.00 0.00 0.96 0.04
#> TCGA.BR.6564.01 1 0.3400 0.758 0.82 0.00 0.00 0.18
#> TCGA.KB.A93H.01 4 0.3853 0.701 0.16 0.00 0.02 0.82
#> TCGA.KB.A93J.01 1 0.1211 0.903 0.96 0.00 0.00 0.04
#> TCGA.CD.5798.01 4 0.4277 0.694 0.28 0.00 0.00 0.72
#> TCGA.CD.8530.01 4 0.4855 0.536 0.40 0.00 0.00 0.60
#> TCGA.BR.6802.01 3 0.1637 0.866 0.00 0.00 0.94 0.06
#> TCGA.CG.5719.01 4 0.4277 0.694 0.28 0.00 0.00 0.72
#> TCGA.VQ.A8E3.01 2 0.4277 0.729 0.00 0.72 0.28 0.00
#> TCGA.CD.5801.01 3 0.3400 0.678 0.00 0.18 0.82 0.00
#> TCGA.FP.A9TM.01 3 0.0000 0.880 0.00 0.00 1.00 0.00
#> TCGA.BR.7958.01 2 0.0000 0.922 0.00 1.00 0.00 0.00
#> TCGA.FP.7998.01 3 0.0000 0.880 0.00 0.00 1.00 0.00
#> TCGA.IN.A6RS.01 3 0.0000 0.880 0.00 0.00 1.00 0.00
#> TCGA.BR.6709.01 4 0.4277 0.694 0.28 0.00 0.00 0.72
#> TCGA.FP.7916.01 2 0.4277 0.729 0.00 0.72 0.28 0.00
#> TCGA.R5.A7ZR.01 1 0.4790 0.189 0.62 0.00 0.00 0.38
#> TCGA.B7.5816.01 3 0.0000 0.880 0.00 0.00 1.00 0.00
#> TCGA.CG.5721.01 3 0.4277 0.734 0.00 0.00 0.72 0.28
#> TCGA.SW.A7EA.01 2 0.0000 0.922 0.00 1.00 0.00 0.00
#> TCGA.RD.A8NB.01 3 0.4277 0.734 0.00 0.00 0.72 0.28
#> TCGA.BR.6801.01 4 0.1637 0.785 0.06 0.00 0.00 0.94
#> TCGA.IN.AB1X.01 3 0.0000 0.880 0.00 0.00 1.00 0.00
#> TCGA.D7.5579.01 4 0.4277 0.694 0.28 0.00 0.00 0.72
#> TCGA.CG.5728.01 3 0.1211 0.873 0.00 0.00 0.96 0.04
#> TCGA.R5.A7ZI.01 4 0.4713 0.552 0.36 0.00 0.00 0.64
#> TCGA.IN.A7NU.01 3 0.0000 0.880 0.00 0.00 1.00 0.00
#> TCGA.CG.5732.01 1 0.0000 0.931 1.00 0.00 0.00 0.00
#> TCGA.ZQ.A9CR.01 1 0.0000 0.931 1.00 0.00 0.00 0.00
#> TCGA.D7.5578.01 3 0.3610 0.791 0.00 0.00 0.80 0.20
#> TCGA.BR.6803.01 1 0.3400 0.758 0.82 0.00 0.00 0.18
#> TCGA.BR.8368.01 2 0.0000 0.922 0.00 1.00 0.00 0.00
#> TCGA.SW.A7EB.01 1 0.0000 0.931 1.00 0.00 0.00 0.00
#> TCGA.BR.8081.01 3 0.3610 0.646 0.00 0.20 0.80 0.00
#> TCGA.VQ.A8P5.01 3 0.4277 0.734 0.00 0.00 0.72 0.28
#> TCGA.CD.8535.01 3 0.0707 0.866 0.00 0.02 0.98 0.00
#> TCGA.CG.5724.01 3 0.0000 0.880 0.00 0.00 1.00 0.00
#> TCGA.D7.8574.01 4 0.2921 0.763 0.14 0.00 0.00 0.86
#> TCGA.HJ.7597.01 1 0.4790 0.325 0.62 0.00 0.00 0.38
#> TCGA.HF.A5NB.01 2 0.0000 0.922 0.00 1.00 0.00 0.00
#> TCGA.VQ.A8PB.01 3 0.0000 0.880 0.00 0.00 1.00 0.00
#> TCGA.R5.A7ZE.01 1 0.0000 0.931 1.00 0.00 0.00 0.00
#> TCGA.CD.5803.01 4 0.4277 0.694 0.28 0.00 0.00 0.72
#> TCGA.CG.5725.01 1 0.0000 0.931 1.00 0.00 0.00 0.00
#> TCGA.D7.6820.01 1 0.0000 0.931 1.00 0.00 0.00 0.00
#> TCGA.CD.5802.01 1 0.0000 0.931 1.00 0.00 0.00 0.00
#> TCGA.R5.A7ZF.01 1 0.3400 0.759 0.82 0.00 0.00 0.18
#> TCGA.D7.A6F0.01 1 0.0000 0.931 1.00 0.00 0.00 0.00
#> TCGA.CG.5727.01 4 0.2345 0.713 0.00 0.00 0.10 0.90
#> TCGA.VQ.A8PC.01 4 0.0707 0.774 0.00 0.00 0.02 0.98
#> TCGA.CD.A486.01 1 0.0000 0.931 1.00 0.00 0.00 0.00
#> TCGA.RD.A8N2.01 1 0.2647 0.830 0.88 0.00 0.00 0.12
#> TCGA.IN.A6RI.01 1 0.0000 0.931 1.00 0.00 0.00 0.00
#> TCGA.HU.8243.01 3 0.4277 0.734 0.00 0.00 0.72 0.28
#> TCGA.CD.A48C.01 2 0.4713 0.597 0.00 0.64 0.36 0.00
#> TCGA.RD.A8N5.01 4 0.4134 0.709 0.26 0.00 0.00 0.74
#> TCGA.RD.A8N1.01 1 0.0000 0.931 1.00 0.00 0.00 0.00
#> TCGA.HU.A4GF.01 1 0.0000 0.931 1.00 0.00 0.00 0.00
#> TCGA.BR.8362.01 3 0.2921 0.827 0.00 0.00 0.86 0.14
#> TCGA.BR.8285.01 2 0.4277 0.729 0.00 0.72 0.28 0.00
#> TCGA.CD.8532.01 4 0.4277 0.694 0.28 0.00 0.00 0.72
#> TCGA.VQ.A8E2.01 1 0.0000 0.931 1.00 0.00 0.00 0.00
#> TCGA.BR.8373.01 4 0.3975 0.644 0.24 0.00 0.00 0.76
#> TCGA.BR.8361.01 2 0.4277 0.729 0.00 0.72 0.28 0.00
#> TCGA.BR.8058.01 4 0.4277 0.694 0.28 0.00 0.00 0.72
#> TCGA.IN.8462.01 3 0.0000 0.880 0.00 0.00 1.00 0.00
#> TCGA.HU.A4G9.01 2 0.0000 0.922 0.00 1.00 0.00 0.00
#> TCGA.CD.8524.01 3 0.4277 0.734 0.00 0.00 0.72 0.28
#> TCGA.D7.A748.01 4 0.3975 0.720 0.24 0.00 0.00 0.76
#> TCGA.CD.8527.01 4 0.2011 0.764 0.08 0.00 0.00 0.92
#> TCGA.VQ.A8DV.01 1 0.0000 0.931 1.00 0.00 0.00 0.00
#> TCGA.CD.8528.01 2 0.0000 0.922 0.00 1.00 0.00 0.00
#> TCGA.BR.A453.01 4 0.0000 0.784 0.00 0.00 0.00 1.00
#> TCGA.RD.A8N6.01 1 0.0000 0.931 1.00 0.00 0.00 0.00
#> TCGA.HU.8245.01 1 0.0000 0.931 1.00 0.00 0.00 0.00
#> TCGA.ZA.A8F6.01 4 0.4277 0.694 0.28 0.00 0.00 0.72
#> TCGA.BR.8367.01 3 0.4277 0.734 0.00 0.00 0.72 0.28
#> TCGA.BR.8380.01 3 0.0000 0.880 0.00 0.00 1.00 0.00
#> TCGA.FP.A4BE.01 2 0.0000 0.922 0.00 1.00 0.00 0.00
#> TCGA.HU.8238.01 3 0.0000 0.880 0.00 0.00 1.00 0.00
#> TCGA.BR.8078.01 2 0.0000 0.922 0.00 1.00 0.00 0.00
#> TCGA.HU.8249.01 4 0.2345 0.713 0.00 0.00 0.10 0.90
#> TCGA.RD.A8N0.01 1 0.5000 -0.148 0.50 0.00 0.00 0.50
#> TCGA.BR.8365.01 1 0.3172 0.785 0.84 0.00 0.00 0.16
#> TCGA.FP.8211.01 4 0.4277 0.694 0.28 0.00 0.00 0.72
#> TCGA.RD.A8N4.01 1 0.3172 0.785 0.84 0.00 0.00 0.16
#> TCGA.VQ.A8DU.01 1 0.0000 0.931 1.00 0.00 0.00 0.00
#> TCGA.VQ.A8DL.01 1 0.0000 0.931 1.00 0.00 0.00 0.00
#> TCGA.VQ.A8DZ.01 1 0.0000 0.931 1.00 0.00 0.00 0.00
#> TCGA.D7.8572.01 1 0.0000 0.931 1.00 0.00 0.00 0.00
#> TCGA.RD.A7BW.01 1 0.2345 0.850 0.90 0.00 0.00 0.10
#> TCGA.R5.A804.01 3 0.0000 0.880 0.00 0.00 1.00 0.00
#> TCGA.BR.A4CS.01 3 0.0707 0.877 0.00 0.00 0.98 0.02
#> TCGA.CD.8531.01 2 0.0000 0.922 0.00 1.00 0.00 0.00
#> TCGA.CD.A487.01 4 0.1211 0.788 0.04 0.00 0.00 0.96
#> TCGA.BR.8371.01 4 0.4134 0.709 0.26 0.00 0.00 0.74
#> TCGA.BR.8059.01 4 0.0000 0.784 0.00 0.00 0.00 1.00
#> TCGA.D7.A6ET.01 4 0.0000 0.784 0.00 0.00 0.00 1.00
#> TCGA.FP.8099.01 3 0.0000 0.880 0.00 0.00 1.00 0.00
#> TCGA.D7.8579.01 3 0.4277 0.734 0.00 0.00 0.72 0.28
#> TCGA.BR.8297.01 3 0.4277 0.734 0.00 0.00 0.72 0.28
#> TCGA.D7.8576.01 4 0.4277 0.694 0.28 0.00 0.00 0.72
#> TCGA.VQ.A8DT.01 3 0.0000 0.880 0.00 0.00 1.00 0.00
#> TCGA.FP.A8CX.01 4 0.0000 0.784 0.00 0.00 0.00 1.00
#> TCGA.HU.A4GH.01 1 0.0000 0.931 1.00 0.00 0.00 0.00
#> TCGA.CD.8526.01 1 0.0000 0.931 1.00 0.00 0.00 0.00
#> TCGA.HU.A4G6.01 2 0.0000 0.922 0.00 1.00 0.00 0.00
#> TCGA.D7.8578.01 1 0.1211 0.902 0.96 0.00 0.00 0.04
#> TCGA.HU.A4G3.01 3 0.2921 0.736 0.00 0.14 0.86 0.00
#> TCGA.D7.A74A.01 2 0.4134 0.749 0.00 0.74 0.26 0.00
#> TCGA.RD.A7C1.01 3 0.0000 0.880 0.00 0.00 1.00 0.00
#> TCGA.F1.A448.01 3 0.0000 0.880 0.00 0.00 1.00 0.00
#> TCGA.D7.8575.01 4 0.2011 0.731 0.00 0.00 0.08 0.92
#> TCGA.BR.8372.01 2 0.0000 0.922 0.00 1.00 0.00 0.00
#> TCGA.VQ.A8P3.01 3 0.0000 0.880 0.00 0.00 1.00 0.00
#> TCGA.RD.A8MW.01 1 0.0000 0.931 1.00 0.00 0.00 0.00
#> TCGA.BR.8286.01 3 0.0000 0.880 0.00 0.00 1.00 0.00
#> TCGA.BR.8369.01 3 0.0707 0.877 0.00 0.00 0.98 0.02
#> TCGA.BR.8364.01 1 0.3172 0.785 0.84 0.00 0.00 0.16
#> TCGA.HU.8244.01 2 0.0000 0.922 0.00 1.00 0.00 0.00
#> TCGA.KB.A6F7.01 1 0.0000 0.931 1.00 0.00 0.00 0.00
#> TCGA.FP.A4BF.01 3 0.0000 0.880 0.00 0.00 1.00 0.00
#> TCGA.R5.A805.01 3 0.1211 0.873 0.00 0.00 0.96 0.04
#> TCGA.IN.A6RL.01 4 0.3400 0.619 0.00 0.00 0.18 0.82
#> TCGA.IN.A6RR.01 2 0.0707 0.912 0.00 0.98 0.02 0.00
#> TCGA.BR.A4CR.01 1 0.0000 0.931 1.00 0.00 0.00 0.00
#> TCGA.CD.A489.01 4 0.0000 0.784 0.00 0.00 0.00 1.00
#> TCGA.HU.A4GY.01 4 0.0000 0.784 0.00 0.00 0.00 1.00
#> TCGA.BR.8289.01 4 0.2011 0.731 0.00 0.00 0.08 0.92
#> TCGA.FP.8209.01 1 0.4713 0.385 0.64 0.00 0.00 0.36
#> TCGA.BR.8296.01 3 0.0000 0.880 0.00 0.00 1.00 0.00
#> TCGA.CD.A48A.01 3 0.3975 0.765 0.00 0.00 0.76 0.24
#> TCGA.BR.8060.01 1 0.0000 0.931 1.00 0.00 0.00 0.00
#> TCGA.BR.8077.01 1 0.0000 0.931 1.00 0.00 0.00 0.00
#> TCGA.CD.8534.01 3 0.4277 0.734 0.00 0.00 0.72 0.28
#> TCGA.BR.7959.01 3 0.1211 0.873 0.00 0.00 0.96 0.04
#> TCGA.VQ.A8P2.01 2 0.0000 0.922 0.00 1.00 0.00 0.00
#> TCGA.EQ.8122.01 1 0.0000 0.931 1.00 0.00 0.00 0.00
#> TCGA.D7.8573.01 2 0.0000 0.922 0.00 1.00 0.00 0.00
#> TCGA.BR.A44T.01 1 0.4948 0.109 0.56 0.00 0.00 0.44
#> TCGA.RD.A8MV.01 4 0.0000 0.784 0.00 0.00 0.00 1.00
#> TCGA.CD.8536.01 3 0.0000 0.880 0.00 0.00 1.00 0.00
#> TCGA.BR.8360.01 2 0.0000 0.922 0.00 1.00 0.00 0.00
#> TCGA.BR.8291.01 1 0.1637 0.886 0.94 0.00 0.00 0.06
#> TCGA.FP.8210.01 4 0.4134 0.709 0.26 0.00 0.00 0.74
#> TCGA.RD.A7BS.01 4 0.4277 0.694 0.28 0.00 0.00 0.72
#> TCGA.BR.A44U.01 3 0.0000 0.880 0.00 0.00 1.00 0.00
#> TCGA.CD.8529.01 4 0.4277 0.694 0.28 0.00 0.00 0.72
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> TCGA.VQ.A94P.01 4 0.1216 0.9154 0.02 0.00 0.00 0.96 0.02
#> TCGA.D7.6521.01 4 0.1732 0.8625 0.00 0.00 0.00 0.92 0.08
#> TCGA.VQ.A8PE.01 1 0.0000 0.9478 1.00 0.00 0.00 0.00 0.00
#> TCGA.D7.6519.01 1 0.3109 0.7332 0.80 0.00 0.00 0.20 0.00
#> TCGA.BR.6452.01 3 0.4287 0.2221 0.00 0.46 0.54 0.00 0.00
#> TCGA.BR.8485.01 1 0.0609 0.9390 0.98 0.00 0.00 0.02 0.00
#> TCGA.VQ.A8PO.01 3 0.4287 0.2221 0.00 0.46 0.54 0.00 0.00
#> TCGA.VQ.AA69.01 2 0.0609 0.9760 0.00 0.98 0.00 0.00 0.02
#> TCGA.BR.8683.01 5 0.3796 0.5416 0.00 0.00 0.00 0.30 0.70
#> TCGA.BR.8486.01 1 0.0609 0.9390 0.98 0.00 0.00 0.02 0.00
#> TCGA.D7.6522.01 4 0.1216 0.9154 0.02 0.00 0.00 0.96 0.02
#> TCGA.CG.5716.01 5 0.4126 0.4456 0.00 0.00 0.00 0.38 0.62
#> TCGA.BR.8589.01 2 0.0609 0.9760 0.00 0.98 0.00 0.00 0.02
#> TCGA.BR.8382.01 3 0.1216 0.6874 0.00 0.02 0.96 0.00 0.02
#> TCGA.VQ.AA68.01 3 0.0000 0.7018 0.00 0.00 1.00 0.00 0.00
#> TCGA.VQ.A8PJ.01 1 0.0000 0.9478 1.00 0.00 0.00 0.00 0.00
#> TCGA.VQ.A8PH.01 1 0.0000 0.9478 1.00 0.00 0.00 0.00 0.00
#> TCGA.HU.8604.01 3 0.4798 0.2309 0.00 0.44 0.54 0.00 0.02
#> TCGA.BR.8676.01 2 0.0609 0.9760 0.00 0.98 0.00 0.00 0.02
#> TCGA.CG.4441.01 5 0.1043 0.6482 0.00 0.00 0.00 0.04 0.96
#> TCGA.D7.6520.01 1 0.0000 0.9478 1.00 0.00 0.00 0.00 0.00
#> TCGA.VQ.AA64.01 4 0.1216 0.9154 0.02 0.00 0.00 0.96 0.02
#> TCGA.D7.6527.01 1 0.0000 0.9478 1.00 0.00 0.00 0.00 0.00
#> TCGA.VQ.A8PM.01 1 0.0000 0.9478 1.00 0.00 0.00 0.00 0.00
#> TCGA.VQ.A923.01 2 0.0609 0.9760 0.00 0.98 0.00 0.00 0.02
#> TCGA.BR.8384.01 5 0.4126 0.4456 0.00 0.00 0.00 0.38 0.62
#> TCGA.BR.6453.01 5 0.4287 0.4603 0.00 0.00 0.46 0.00 0.54
#> TCGA.VQ.A928.01 4 0.1732 0.8625 0.00 0.00 0.00 0.92 0.08
#> TCGA.VQ.A8E0.01 4 0.2929 0.7881 0.18 0.00 0.00 0.82 0.00
#> TCGA.BR.8679.01 3 0.4262 0.2663 0.00 0.44 0.56 0.00 0.00
#> TCGA.VQ.A91S.01 5 0.3521 0.6536 0.00 0.00 0.14 0.04 0.82
#> TCGA.BR.8678.01 1 0.3513 0.7706 0.80 0.00 0.00 0.02 0.18
#> TCGA.D7.6528.01 5 0.1043 0.6482 0.00 0.00 0.00 0.04 0.96
#> TCGA.VQ.A8E7.01 3 0.3983 0.0977 0.00 0.00 0.66 0.00 0.34
#> TCGA.BR.8680.01 5 0.4307 0.3715 0.00 0.00 0.50 0.00 0.50
#> TCGA.BR.8483.01 5 0.1648 0.6431 0.00 0.00 0.04 0.02 0.94
#> TCGA.BR.6566.01 3 0.0000 0.7018 0.00 0.00 1.00 0.00 0.00
#> TCGA.VQ.A91X.01 5 0.3106 0.6283 0.00 0.00 0.14 0.02 0.84
#> TCGA.VQ.A91Q.01 4 0.1216 0.9154 0.02 0.00 0.00 0.96 0.02
#> TCGA.VQ.A92D.01 2 0.0000 0.9818 0.00 1.00 0.00 0.00 0.00
#> TCGA.VQ.A91Z.01 5 0.2438 0.6182 0.06 0.00 0.00 0.04 0.90
#> TCGA.BR.6455.01 2 0.0609 0.9760 0.00 0.98 0.00 0.00 0.02
#> TCGA.BR.8591.01 2 0.0000 0.9818 0.00 1.00 0.00 0.00 0.00
#> TCGA.HU.8608.01 2 0.4456 0.4376 0.00 0.66 0.32 0.00 0.02
#> TCGA.VQ.A94U.01 3 0.4182 -0.0950 0.00 0.00 0.60 0.00 0.40
#> TCGA.VQ.A94T.01 4 0.4060 0.4305 0.00 0.00 0.00 0.64 0.36
#> TCGA.VQ.A91A.01 3 0.0000 0.7018 0.00 0.00 1.00 0.00 0.00
#> TCGA.VQ.A91D.01 2 0.0000 0.9818 0.00 1.00 0.00 0.00 0.00
#> TCGA.D7.6518.01 5 0.4262 0.3146 0.00 0.00 0.00 0.44 0.56
#> TCGA.BR.8484.01 4 0.1216 0.9154 0.02 0.00 0.00 0.96 0.02
#> TCGA.VQ.A91N.01 5 0.4982 0.4167 0.20 0.00 0.00 0.10 0.70
#> TCGA.VQ.A91E.01 3 0.0000 0.7018 0.00 0.00 1.00 0.00 0.00
#> TCGA.VQ.A8PY.01 3 0.0000 0.7018 0.00 0.00 1.00 0.00 0.00
#> TCGA.HU.8602.01 2 0.0609 0.9760 0.00 0.98 0.00 0.00 0.02
#> TCGA.BR.8381.01 3 0.4798 0.2309 0.00 0.44 0.54 0.00 0.02
#> TCGA.BR.6452.11 4 0.1043 0.9001 0.00 0.00 0.00 0.96 0.04
#> TCGA.IN.8663.01 2 0.0000 0.9818 0.00 1.00 0.00 0.00 0.00
#> TCGA.VQ.A8PS.01 4 0.1216 0.9154 0.02 0.00 0.00 0.96 0.02
#> TCGA.VQ.A91W.01 3 0.4818 0.1760 0.00 0.46 0.52 0.00 0.02
#> TCGA.BR.6454.01 4 0.1410 0.8784 0.00 0.00 0.00 0.94 0.06
#> TCGA.BR.8682.01 5 0.4287 0.4603 0.00 0.00 0.46 0.00 0.54
#> TCGA.VQ.A91V.01 3 0.0000 0.7018 0.00 0.00 1.00 0.00 0.00
#> TCGA.VQ.A8PZ.01 3 0.0609 0.6871 0.00 0.00 0.98 0.00 0.02
#> TCGA.BR.8590.01 4 0.1216 0.9154 0.02 0.00 0.00 0.96 0.02
#> TCGA.F1.6177.01 2 0.0000 0.9818 0.00 1.00 0.00 0.00 0.00
#> TCGA.VQ.A8PQ.01 4 0.1732 0.8757 0.08 0.00 0.00 0.92 0.00
#> TCGA.VQ.A91U.01 1 0.3106 0.8124 0.84 0.00 0.00 0.02 0.14
#> TCGA.VQ.AA6I.01 3 0.1410 0.6766 0.00 0.06 0.94 0.00 0.00
#> TCGA.CG.4437.01 3 0.0000 0.7018 0.00 0.00 1.00 0.00 0.00
#> TCGA.VQ.A8PP.01 3 0.0000 0.7018 0.00 0.00 1.00 0.00 0.00
#> TCGA.BR.6565.01 1 0.0000 0.9478 1.00 0.00 0.00 0.00 0.00
#> TCGA.VQ.A91Y.01 1 0.0000 0.9478 1.00 0.00 0.00 0.00 0.00
#> TCGA.VQ.A8PF.01 3 0.4798 0.2309 0.00 0.44 0.54 0.00 0.02
#> TCGA.BR.6456.01 1 0.0609 0.9390 0.98 0.00 0.00 0.02 0.00
#> TCGA.BR.6458.01 5 0.4182 0.5211 0.00 0.00 0.40 0.00 0.60
#> TCGA.VQ.A925.01 1 0.1410 0.8972 0.94 0.00 0.00 0.06 0.00
#> TCGA.VQ.A927.01 4 0.1216 0.9154 0.02 0.00 0.00 0.96 0.02
#> TCGA.BR.8592.01 5 0.5341 0.5895 0.00 0.00 0.30 0.08 0.62
#> TCGA.BR.6566.11 4 0.1043 0.9026 0.04 0.00 0.00 0.96 0.00
#> TCGA.IN.AB1V.01 1 0.0000 0.9478 1.00 0.00 0.00 0.00 0.00
#> TCGA.VQ.AA6F.01 4 0.1216 0.9154 0.02 0.00 0.00 0.96 0.02
#> TCGA.VQ.AA6J.01 4 0.1732 0.8625 0.00 0.00 0.00 0.92 0.08
#> TCGA.BR.8487.01 2 0.0000 0.9818 0.00 1.00 0.00 0.00 0.00
#> TCGA.D7.6525.01 3 0.0000 0.7018 0.00 0.00 1.00 0.00 0.00
#> TCGA.VQ.A94O.01 1 0.0000 0.9478 1.00 0.00 0.00 0.00 0.00
#> TCGA.BR.8588.01 3 0.4287 -0.2802 0.00 0.00 0.54 0.00 0.46
#> TCGA.HU.8610.01 5 0.3796 0.5416 0.00 0.00 0.00 0.30 0.70
#> TCGA.D7.6526.01 1 0.0000 0.9478 1.00 0.00 0.00 0.00 0.00
#> TCGA.VQ.A8PD.01 5 0.4227 0.5102 0.00 0.00 0.42 0.00 0.58
#> TCGA.D7.6524.01 5 0.4287 0.4603 0.00 0.00 0.46 0.00 0.54
#> TCGA.3M.AB46.01 1 0.0000 0.9478 1.00 0.00 0.00 0.00 0.00
#> TCGA.3M.AB47.01 5 0.4287 0.4603 0.00 0.00 0.46 0.00 0.54
#> TCGA.BR.8677.01 4 0.1732 0.8625 0.00 0.00 0.00 0.92 0.08
#> TCGA.BR.6457.01 5 0.5156 0.5830 0.00 0.00 0.32 0.06 0.62
#> TCGA.BR.8687.01 1 0.0609 0.9390 0.98 0.00 0.00 0.02 0.00
#> TCGA.VQ.A91K.01 2 0.0000 0.9818 0.00 1.00 0.00 0.00 0.00
#> TCGA.BR.8690.01 1 0.2516 0.8144 0.86 0.00 0.00 0.14 0.00
#> TCGA.BR.8686.01 2 0.0609 0.9760 0.00 0.98 0.00 0.00 0.02
#> TCGA.FP.8631.01 1 0.0000 0.9478 1.00 0.00 0.00 0.00 0.00
#> TCGA.VQ.A922.01 1 0.0000 0.9478 1.00 0.00 0.00 0.00 0.00
#> TCGA.BR.A452.01 4 0.0609 0.9023 0.00 0.00 0.00 0.98 0.02
#> TCGA.IN.A6RO.01 2 0.0000 0.9818 0.00 1.00 0.00 0.00 0.00
#> TCGA.BR.A4QI.01 2 0.0000 0.9818 0.00 1.00 0.00 0.00 0.00
#> TCGA.D7.A6EV.01 5 0.4060 0.5597 0.00 0.00 0.36 0.00 0.64
#> TCGA.HU.A4G2.01 2 0.0609 0.9760 0.00 0.98 0.00 0.00 0.02
#> TCGA.BR.A4IY.01 2 0.0609 0.9760 0.00 0.98 0.00 0.00 0.02
#> TCGA.VQ.A8PU.01 4 0.1732 0.8625 0.00 0.00 0.00 0.92 0.08
#> TCGA.BR.A4J4.01 2 0.0609 0.9760 0.00 0.98 0.00 0.00 0.02
#> TCGA.VQ.A94R.01 3 0.0609 0.6949 0.00 0.02 0.98 0.00 0.00
#> TCGA.HU.A4H4.01 3 0.0000 0.7018 0.00 0.00 1.00 0.00 0.00
#> TCGA.BR.7707.01 3 0.4287 0.2221 0.00 0.46 0.54 0.00 0.00
#> TCGA.FP.7829.01 2 0.0000 0.9818 0.00 1.00 0.00 0.00 0.00
#> TCGA.BR.A4J5.01 3 0.4126 -0.0293 0.00 0.00 0.62 0.00 0.38
#> TCGA.HU.A4H0.01 2 0.0609 0.9760 0.00 0.98 0.00 0.00 0.02
#> TCGA.HU.A4HD.01 1 0.0000 0.9478 1.00 0.00 0.00 0.00 0.00
#> TCGA.KB.A6F5.01 1 0.0000 0.9478 1.00 0.00 0.00 0.00 0.00
#> TCGA.VQ.AA6K.01 4 0.0609 0.9023 0.00 0.00 0.00 0.98 0.02
#> TCGA.HF.7133.01 4 0.0609 0.9120 0.02 0.00 0.00 0.98 0.00
#> TCGA.F1.6875.01 1 0.5689 0.3015 0.48 0.00 0.00 0.08 0.44
#> TCGA.MX.A666.01 1 0.0000 0.9478 1.00 0.00 0.00 0.00 0.00
#> TCGA.BR.7717.01 3 0.0000 0.7018 0.00 0.00 1.00 0.00 0.00
#> TCGA.BR.A4PF.01 3 0.0000 0.7018 0.00 0.00 1.00 0.00 0.00
#> TCGA.BR.A4IU.01 5 0.4262 0.4873 0.00 0.00 0.44 0.00 0.56
#> TCGA.VQ.A8PX.01 4 0.1410 0.8991 0.06 0.00 0.00 0.94 0.00
#> TCGA.BR.A4IV.01 4 0.1216 0.9154 0.02 0.00 0.00 0.96 0.02
#> TCGA.D7.A6EX.01 4 0.0609 0.9023 0.00 0.00 0.00 0.98 0.02
#> TCGA.BR.A4IZ.01 4 0.0609 0.9120 0.02 0.00 0.00 0.98 0.00
#> TCGA.BR.A4J9.01 4 0.1216 0.9154 0.02 0.00 0.00 0.96 0.02
#> TCGA.CD.A4MJ.01 2 0.0000 0.9818 0.00 1.00 0.00 0.00 0.00
#> TCGA.B7.A5TN.01 1 0.0000 0.9478 1.00 0.00 0.00 0.00 0.00
#> TCGA.BR.7715.01 5 0.2732 0.6275 0.00 0.00 0.16 0.00 0.84
#> TCGA.BR.7704.01 1 0.0609 0.9390 0.98 0.00 0.00 0.02 0.00
#> TCGA.BR.A4J1.01 1 0.0000 0.9478 1.00 0.00 0.00 0.00 0.00
#> TCGA.HU.A4GP.01 3 0.4262 0.2663 0.00 0.44 0.56 0.00 0.00
#> TCGA.D7.A4YY.01 2 0.0000 0.9818 0.00 1.00 0.00 0.00 0.00
#> TCGA.VQ.AA6G.01 3 0.4302 0.1663 0.00 0.48 0.52 0.00 0.00
#> TCGA.HU.A4GJ.01 5 0.4262 0.4873 0.00 0.00 0.44 0.00 0.56
#> TCGA.CD.A4MI.01 3 0.4798 0.2309 0.00 0.44 0.54 0.00 0.02
#> TCGA.BR.7196.01 3 0.3561 0.3058 0.00 0.00 0.74 0.00 0.26
#> TCGA.BR.6563.01 5 0.4126 0.4456 0.00 0.00 0.00 0.38 0.62
#> TCGA.VQ.A924.01 3 0.4798 0.2309 0.00 0.44 0.54 0.00 0.02
#> TCGA.BR.7716.01 1 0.0609 0.9390 0.98 0.00 0.00 0.02 0.00
#> TCGA.FP.7735.01 4 0.1216 0.9154 0.02 0.00 0.00 0.96 0.02
#> TCGA.BR.7723.01 1 0.0000 0.9478 1.00 0.00 0.00 0.00 0.00
#> TCGA.HU.A4H8.01 2 0.0000 0.9818 0.00 1.00 0.00 0.00 0.00
#> TCGA.IN.A6RJ.01 5 0.4182 0.5292 0.00 0.00 0.40 0.00 0.60
#> TCGA.HU.A4H3.01 2 0.0000 0.9818 0.00 1.00 0.00 0.00 0.00
#> TCGA.EQ.A4SO.01 4 0.3796 0.6207 0.30 0.00 0.00 0.70 0.00
#> TCGA.CD.A4MH.01 1 0.0609 0.9390 0.98 0.00 0.00 0.02 0.00
#> TCGA.BR.A4J7.01 4 0.0609 0.9023 0.00 0.00 0.00 0.98 0.02
#> TCGA.HF.7131.01 1 0.1732 0.8863 0.92 0.00 0.00 0.08 0.00
#> TCGA.D7.A74B.01 4 0.3983 0.5186 0.34 0.00 0.00 0.66 0.00
#> TCGA.BR.A4PE.01 2 0.0000 0.9818 0.00 1.00 0.00 0.00 0.00
#> TCGA.BR.A4J8.01 3 0.4798 0.2309 0.00 0.44 0.54 0.00 0.02
#> TCGA.HU.A4GX.01 5 0.3796 0.5416 0.00 0.00 0.00 0.30 0.70
#> TCGA.HU.A4G8.01 3 0.0000 0.7018 0.00 0.00 1.00 0.00 0.00
#> TCGA.HU.A4GT.01 2 0.0000 0.9818 0.00 1.00 0.00 0.00 0.00
#> TCGA.HU.A4GC.01 3 0.1043 0.6650 0.00 0.00 0.96 0.00 0.04
#> TCGA.BR.A4CQ.01 2 0.0000 0.9818 0.00 1.00 0.00 0.00 0.00
#> TCGA.D7.A6F2.01 1 0.0000 0.9478 1.00 0.00 0.00 0.00 0.00
#> TCGA.RD.A7BT.01 5 0.3110 0.6051 0.06 0.00 0.00 0.08 0.86
#> TCGA.BR.A4J6.01 4 0.0609 0.9120 0.02 0.00 0.00 0.98 0.00
#> TCGA.HU.A4GQ.01 2 0.0000 0.9818 0.00 1.00 0.00 0.00 0.00
#> TCGA.HF.7136.01 1 0.0000 0.9478 1.00 0.00 0.00 0.00 0.00
#> TCGA.BR.A4QM.01 2 0.0000 0.9818 0.00 1.00 0.00 0.00 0.00
#> TCGA.BR.A4PD.01 5 0.4287 -0.1383 0.00 0.00 0.00 0.46 0.54
#> TCGA.VQ.A8PK.01 1 0.0000 0.9478 1.00 0.00 0.00 0.00 0.00
#> TCGA.B7.A5TK.01 3 0.0609 0.6871 0.00 0.00 0.98 0.00 0.02
#> TCGA.D7.A4YX.01 2 0.0609 0.9760 0.00 0.98 0.00 0.00 0.02
#> TCGA.D7.A4Z0.01 3 0.0000 0.7018 0.00 0.00 1.00 0.00 0.00
#> TCGA.VQ.A8PT.01 2 0.0000 0.9818 0.00 1.00 0.00 0.00 0.00
#> TCGA.IN.A6RN.01 1 0.0000 0.9478 1.00 0.00 0.00 0.00 0.00
#> TCGA.CD.A4MG.01 2 0.0000 0.9818 0.00 1.00 0.00 0.00 0.00
#> TCGA.D7.A747.01 4 0.1216 0.9154 0.02 0.00 0.00 0.96 0.02
#> TCGA.R5.A7O7.01 5 0.4060 0.5586 0.00 0.00 0.36 0.00 0.64
#> TCGA.F1.A72C.01 4 0.1216 0.9154 0.02 0.00 0.00 0.96 0.02
#> TCGA.BR.A4J2.01 5 0.4748 0.5988 0.00 0.00 0.30 0.04 0.66
#> TCGA.MX.A663.01 1 0.0000 0.9478 1.00 0.00 0.00 0.00 0.00
#> TCGA.D7.A4YV.01 2 0.0000 0.9818 0.00 1.00 0.00 0.00 0.00
#> TCGA.HU.A4GD.01 5 0.1043 0.6482 0.00 0.00 0.00 0.04 0.96
#> TCGA.BR.A4QL.01 2 0.0000 0.9818 0.00 1.00 0.00 0.00 0.00
#> TCGA.BR.7703.01 2 0.0000 0.9818 0.00 1.00 0.00 0.00 0.00
#> TCGA.VQ.AA6B.01 5 0.3424 0.6130 0.00 0.00 0.24 0.00 0.76
#> TCGA.VQ.AA6D.01 1 0.0000 0.9478 1.00 0.00 0.00 0.00 0.00
#> TCGA.D7.A6EZ.01 2 0.0609 0.9760 0.00 0.98 0.00 0.00 0.02
#> TCGA.D7.A4YU.01 2 0.0000 0.9818 0.00 1.00 0.00 0.00 0.00
#> TCGA.VQ.AA6A.01 1 0.5048 0.4690 0.58 0.00 0.00 0.04 0.38
#> TCGA.IN.7806.01 1 0.5157 0.3601 0.52 0.00 0.00 0.04 0.44
#> TCGA.HU.A4HB.01 5 0.3796 0.5416 0.00 0.00 0.00 0.30 0.70
#> TCGA.HU.A4H2.01 5 0.2732 0.6275 0.00 0.00 0.16 0.00 0.84
#> TCGA.IN.A6RP.01 3 0.0609 0.6949 0.00 0.02 0.98 0.00 0.00
#> TCGA.HU.A4H5.01 1 0.0000 0.9478 1.00 0.00 0.00 0.00 0.00
#> TCGA.HU.A4GU.01 2 0.0000 0.9818 0.00 1.00 0.00 0.00 0.00
#> TCGA.MX.A5UJ.01 3 0.4262 0.2663 0.00 0.44 0.56 0.00 0.00
#> TCGA.HU.A4GN.01 2 0.0000 0.9818 0.00 1.00 0.00 0.00 0.00
#> TCGA.CD.5804.01 1 0.0000 0.9478 1.00 0.00 0.00 0.00 0.00
#> TCGA.HU.A4H6.01 3 0.4798 0.2309 0.00 0.44 0.54 0.00 0.02
#> TCGA.HF.7132.01 3 0.0000 0.7018 0.00 0.00 1.00 0.00 0.00
#> TCGA.D7.A4YT.01 1 0.0000 0.9478 1.00 0.00 0.00 0.00 0.00
#> TCGA.HF.7134.01 2 0.0000 0.9818 0.00 1.00 0.00 0.00 0.00
#> TCGA.BR.6852.01 3 0.0000 0.7018 0.00 0.00 1.00 0.00 0.00
#> TCGA.BR.8370.01 2 0.0609 0.9760 0.00 0.98 0.00 0.00 0.02
#> TCGA.EQ.5647.01 4 0.0609 0.9120 0.02 0.00 0.00 0.98 0.00
#> TCGA.IN.A7NT.01 5 0.1043 0.6482 0.00 0.00 0.00 0.04 0.96
#> TCGA.RD.A8N9.01 4 0.4262 0.2642 0.44 0.00 0.00 0.56 0.00
#> TCGA.D7.5577.01 2 0.0609 0.9760 0.00 0.98 0.00 0.00 0.02
#> TCGA.CG.5717.01 4 0.1216 0.9154 0.02 0.00 0.00 0.96 0.02
#> TCGA.D7.6818.01 1 0.0000 0.9478 1.00 0.00 0.00 0.00 0.00
#> TCGA.CG.5734.01 5 0.3895 0.5329 0.00 0.00 0.00 0.32 0.68
#> TCGA.VQ.A8P8.01 3 0.0000 0.7018 0.00 0.00 1.00 0.00 0.00
#> TCGA.BR.6707.01 3 0.4798 0.2309 0.00 0.44 0.54 0.00 0.02
#> TCGA.B7.5818.01 2 0.0609 0.9760 0.00 0.98 0.00 0.00 0.02
#> TCGA.CD.8525.01 1 0.0609 0.9390 0.98 0.00 0.00 0.02 0.00
#> TCGA.BR.6705.01 5 0.5156 0.5830 0.00 0.00 0.32 0.06 0.62
#> TCGA.BR.4288.01 1 0.0000 0.9478 1.00 0.00 0.00 0.00 0.00
#> TCGA.CD.5813.01 4 0.1216 0.9154 0.02 0.00 0.00 0.96 0.02
#> TCGA.CG.5723.01 4 0.1732 0.8625 0.00 0.00 0.00 0.92 0.08
#> TCGA.CD.5800.01 1 0.0609 0.9390 0.98 0.00 0.00 0.02 0.00
#> TCGA.CG.5718.01 1 0.0609 0.9390 0.98 0.00 0.00 0.02 0.00
#> TCGA.BR.8080.01 5 0.2020 0.6393 0.00 0.00 0.00 0.10 0.90
#> TCGA.CG.5733.01 3 0.4287 0.2221 0.00 0.46 0.54 0.00 0.00
#> TCGA.D7.6817.01 1 0.0000 0.9478 1.00 0.00 0.00 0.00 0.00
#> TCGA.KB.A93G.01 4 0.1216 0.9154 0.02 0.00 0.00 0.96 0.02
#> TCGA.CD.5799.01 1 0.0000 0.9478 1.00 0.00 0.00 0.00 0.00
#> TCGA.BR.7851.01 2 0.0609 0.9760 0.00 0.98 0.00 0.00 0.02
#> TCGA.BR.7722.01 4 0.1216 0.9154 0.02 0.00 0.00 0.96 0.02
#> TCGA.MX.A5UG.01 5 0.4126 0.4456 0.00 0.00 0.00 0.38 0.62
#> TCGA.CD.8533.01 3 0.0000 0.7018 0.00 0.00 1.00 0.00 0.00
#> TCGA.BR.7957.01 5 0.5156 0.5830 0.00 0.00 0.32 0.06 0.62
#> TCGA.CG.5722.01 3 0.0609 0.6871 0.00 0.00 0.98 0.00 0.02
#> TCGA.F1.6874.01 5 0.3319 0.6478 0.00 0.00 0.16 0.02 0.82
#> TCGA.CG.5730.01 5 0.1043 0.6482 0.00 0.00 0.00 0.04 0.96
#> TCGA.CG.5726.01 2 0.0609 0.9649 0.00 0.98 0.02 0.00 0.00
#> TCGA.IP.7968.01 5 0.1043 0.6482 0.00 0.00 0.00 0.04 0.96
#> TCGA.BR.8363.01 3 0.0609 0.6950 0.00 0.00 0.98 0.00 0.02
#> TCGA.BR.7901.01 1 0.0000 0.9478 1.00 0.00 0.00 0.00 0.00
#> TCGA.D7.6822.01 5 0.4287 0.4603 0.00 0.00 0.46 0.00 0.54
#> TCGA.BR.6710.01 4 0.4060 0.5005 0.36 0.00 0.00 0.64 0.00
#> TCGA.CG.5720.01 3 0.0000 0.7018 0.00 0.00 1.00 0.00 0.00
#> TCGA.D7.8570.01 3 0.4798 0.2309 0.00 0.44 0.54 0.00 0.02
#> TCGA.B7.A5TI.01 4 0.1043 0.9098 0.04 0.00 0.00 0.96 0.00
#> TCGA.D7.6815.01 5 0.5599 0.2675 0.12 0.00 0.00 0.26 0.62
#> TCGA.BR.8284.01 3 0.0000 0.7018 0.00 0.00 1.00 0.00 0.00
#> TCGA.BR.8295.01 1 0.0000 0.9478 1.00 0.00 0.00 0.00 0.00
#> TCGA.BR.7197.01 1 0.5048 0.4690 0.58 0.00 0.00 0.04 0.38
#> TCGA.B7.A5TJ.01 2 0.0000 0.9818 0.00 1.00 0.00 0.00 0.00
#> TCGA.D7.A6EY.01 5 0.4060 0.5560 0.00 0.00 0.36 0.00 0.64
#> TCGA.BR.8366.01 3 0.4798 0.2309 0.00 0.44 0.54 0.00 0.02
#> TCGA.IN.A7NR.01 4 0.2732 0.7965 0.16 0.00 0.00 0.84 0.00
#> TCGA.BR.6706.01 3 0.4126 -0.0293 0.00 0.00 0.62 0.00 0.38
#> TCGA.IN.7808.01 3 0.4182 -0.0950 0.00 0.00 0.60 0.00 0.40
#> TCGA.BR.6564.01 4 0.1410 0.8907 0.06 0.00 0.00 0.94 0.00
#> TCGA.KB.A93H.01 5 0.1043 0.6482 0.00 0.00 0.00 0.04 0.96
#> TCGA.KB.A93J.01 1 0.4182 0.2546 0.60 0.00 0.00 0.40 0.00
#> TCGA.CD.5798.01 4 0.1216 0.9154 0.02 0.00 0.00 0.96 0.02
#> TCGA.CD.8530.01 1 0.5232 0.5146 0.60 0.00 0.00 0.06 0.34
#> TCGA.BR.6802.01 3 0.4262 -0.2222 0.00 0.00 0.56 0.00 0.44
#> TCGA.CG.5719.01 4 0.0609 0.9120 0.02 0.00 0.00 0.98 0.00
#> TCGA.VQ.A8E3.01 3 0.4262 0.2663 0.00 0.44 0.56 0.00 0.00
#> TCGA.CD.5801.01 3 0.0609 0.6950 0.00 0.00 0.98 0.00 0.02
#> TCGA.FP.A9TM.01 3 0.0000 0.7018 0.00 0.00 1.00 0.00 0.00
#> TCGA.BR.7958.01 2 0.0609 0.9760 0.00 0.98 0.00 0.00 0.02
#> TCGA.FP.7998.01 3 0.0609 0.6871 0.00 0.00 0.98 0.00 0.02
#> TCGA.IN.A6RS.01 3 0.4060 0.0366 0.00 0.00 0.64 0.00 0.36
#> TCGA.BR.6709.01 4 0.0609 0.9120 0.02 0.00 0.00 0.98 0.00
#> TCGA.FP.7916.01 3 0.4798 0.2309 0.00 0.44 0.54 0.00 0.02
#> TCGA.R5.A7ZR.01 1 0.5095 0.4387 0.56 0.00 0.00 0.04 0.40
#> TCGA.B7.5816.01 3 0.0000 0.7018 0.00 0.00 1.00 0.00 0.00
#> TCGA.CG.5721.01 5 0.4227 0.5097 0.00 0.00 0.42 0.00 0.58
#> TCGA.SW.A7EA.01 2 0.0000 0.9818 0.00 1.00 0.00 0.00 0.00
#> TCGA.RD.A8NB.01 5 0.4287 0.4603 0.00 0.00 0.46 0.00 0.54
#> TCGA.BR.6801.01 4 0.1732 0.8625 0.00 0.00 0.00 0.92 0.08
#> TCGA.IN.AB1X.01 3 0.0000 0.7018 0.00 0.00 1.00 0.00 0.00
#> TCGA.D7.5579.01 4 0.1410 0.8784 0.00 0.00 0.00 0.94 0.06
#> TCGA.CG.5728.01 3 0.4262 -0.2222 0.00 0.00 0.56 0.00 0.44
#> TCGA.R5.A7ZI.01 4 0.0609 0.9120 0.02 0.00 0.00 0.98 0.00
#> TCGA.IN.A7NU.01 3 0.0000 0.7018 0.00 0.00 1.00 0.00 0.00
#> TCGA.CG.5732.01 1 0.0000 0.9478 1.00 0.00 0.00 0.00 0.00
#> TCGA.ZQ.A9CR.01 1 0.0609 0.9390 0.98 0.00 0.00 0.02 0.00
#> TCGA.D7.5578.01 5 0.4182 0.5211 0.00 0.00 0.40 0.00 0.60
#> TCGA.BR.6803.01 4 0.1410 0.8907 0.06 0.00 0.00 0.94 0.00
#> TCGA.BR.8368.01 2 0.0000 0.9818 0.00 1.00 0.00 0.00 0.00
#> TCGA.SW.A7EB.01 1 0.0000 0.9478 1.00 0.00 0.00 0.00 0.00
#> TCGA.BR.8081.01 3 0.0609 0.6950 0.00 0.00 0.98 0.00 0.02
#> TCGA.VQ.A8P5.01 5 0.4287 0.4603 0.00 0.00 0.46 0.00 0.54
#> TCGA.CD.8535.01 3 0.1410 0.6768 0.00 0.06 0.94 0.00 0.00
#> TCGA.CG.5724.01 3 0.0000 0.7018 0.00 0.00 1.00 0.00 0.00
#> TCGA.D7.8574.01 4 0.1216 0.9154 0.02 0.00 0.00 0.96 0.02
#> TCGA.HJ.7597.01 4 0.1043 0.9026 0.04 0.00 0.00 0.96 0.00
#> TCGA.HF.A5NB.01 2 0.0000 0.9818 0.00 1.00 0.00 0.00 0.00
#> TCGA.VQ.A8PB.01 3 0.0000 0.7018 0.00 0.00 1.00 0.00 0.00
#> TCGA.R5.A7ZE.01 1 0.0000 0.9478 1.00 0.00 0.00 0.00 0.00
#> TCGA.CD.5803.01 4 0.0609 0.9120 0.02 0.00 0.00 0.98 0.00
#> TCGA.CG.5725.01 1 0.0000 0.9478 1.00 0.00 0.00 0.00 0.00
#> TCGA.D7.6820.01 1 0.0000 0.9478 1.00 0.00 0.00 0.00 0.00
#> TCGA.CD.5802.01 1 0.0609 0.9339 0.98 0.00 0.00 0.02 0.00
#> TCGA.R5.A7ZF.01 4 0.1732 0.8757 0.08 0.00 0.00 0.92 0.00
#> TCGA.D7.A6F0.01 1 0.0000 0.9478 1.00 0.00 0.00 0.00 0.00
#> TCGA.CG.5727.01 5 0.1043 0.6482 0.00 0.00 0.00 0.04 0.96
#> TCGA.VQ.A8PC.01 5 0.4126 0.4456 0.00 0.00 0.00 0.38 0.62
#> TCGA.CD.A486.01 1 0.0000 0.9478 1.00 0.00 0.00 0.00 0.00
#> TCGA.RD.A8N2.01 4 0.3424 0.7005 0.24 0.00 0.00 0.76 0.00
#> TCGA.IN.A6RI.01 1 0.0000 0.9478 1.00 0.00 0.00 0.00 0.00
#> TCGA.HU.8243.01 5 0.1648 0.6431 0.00 0.00 0.04 0.02 0.94
#> TCGA.CD.A48C.01 3 0.4262 0.2663 0.00 0.44 0.56 0.00 0.00
#> TCGA.RD.A8N5.01 4 0.1216 0.9154 0.02 0.00 0.00 0.96 0.02
#> TCGA.RD.A8N1.01 1 0.0000 0.9478 1.00 0.00 0.00 0.00 0.00
#> TCGA.HU.A4GF.01 1 0.0000 0.9478 1.00 0.00 0.00 0.00 0.00
#> TCGA.BR.8362.01 5 0.4287 0.4603 0.00 0.00 0.46 0.00 0.54
#> TCGA.BR.8285.01 3 0.4767 0.2723 0.00 0.42 0.56 0.00 0.02
#> TCGA.CD.8532.01 4 0.1216 0.9154 0.02 0.00 0.00 0.96 0.02
#> TCGA.VQ.A8E2.01 1 0.0000 0.9478 1.00 0.00 0.00 0.00 0.00
#> TCGA.BR.8373.01 5 0.5095 -0.0530 0.40 0.00 0.00 0.04 0.56
#> TCGA.BR.8361.01 3 0.4287 0.2221 0.00 0.46 0.54 0.00 0.00
#> TCGA.BR.8058.01 4 0.0609 0.9120 0.02 0.00 0.00 0.98 0.00
#> TCGA.IN.8462.01 3 0.0000 0.7018 0.00 0.00 1.00 0.00 0.00
#> TCGA.HU.A4G9.01 2 0.0000 0.9818 0.00 1.00 0.00 0.00 0.00
#> TCGA.CD.8524.01 5 0.4182 0.5211 0.00 0.00 0.40 0.00 0.60
#> TCGA.D7.A748.01 4 0.0609 0.9120 0.02 0.00 0.00 0.98 0.00
#> TCGA.CD.8527.01 5 0.1043 0.6482 0.00 0.00 0.00 0.04 0.96
#> TCGA.VQ.A8DV.01 1 0.0000 0.9478 1.00 0.00 0.00 0.00 0.00
#> TCGA.CD.8528.01 2 0.0000 0.9818 0.00 1.00 0.00 0.00 0.00
#> TCGA.BR.A453.01 5 0.4126 0.4456 0.00 0.00 0.00 0.38 0.62
#> TCGA.RD.A8N6.01 1 0.0000 0.9478 1.00 0.00 0.00 0.00 0.00
#> TCGA.HU.8245.01 1 0.0000 0.9478 1.00 0.00 0.00 0.00 0.00
#> TCGA.ZA.A8F6.01 4 0.1732 0.8625 0.00 0.00 0.00 0.92 0.08
#> TCGA.BR.8367.01 5 0.4287 0.4603 0.00 0.00 0.46 0.00 0.54
#> TCGA.BR.8380.01 3 0.0609 0.6871 0.00 0.00 0.98 0.00 0.02
#> TCGA.FP.A4BE.01 2 0.0000 0.9818 0.00 1.00 0.00 0.00 0.00
#> TCGA.HU.8238.01 3 0.0000 0.7018 0.00 0.00 1.00 0.00 0.00
#> TCGA.BR.8078.01 2 0.0000 0.9818 0.00 1.00 0.00 0.00 0.00
#> TCGA.HU.8249.01 5 0.1043 0.6482 0.00 0.00 0.00 0.04 0.96
#> TCGA.RD.A8N0.01 4 0.1043 0.9026 0.04 0.00 0.00 0.96 0.00
#> TCGA.BR.8365.01 4 0.1732 0.8757 0.08 0.00 0.00 0.92 0.00
#> TCGA.FP.8211.01 4 0.1216 0.9154 0.02 0.00 0.00 0.96 0.02
#> TCGA.RD.A8N4.01 4 0.1732 0.8757 0.08 0.00 0.00 0.92 0.00
#> TCGA.VQ.A8DU.01 1 0.0000 0.9478 1.00 0.00 0.00 0.00 0.00
#> TCGA.VQ.A8DL.01 1 0.0609 0.9390 0.98 0.00 0.00 0.02 0.00
#> TCGA.VQ.A8DZ.01 1 0.0000 0.9478 1.00 0.00 0.00 0.00 0.00
#> TCGA.D7.8572.01 1 0.0000 0.9478 1.00 0.00 0.00 0.00 0.00
#> TCGA.RD.A7BW.01 4 0.3983 0.5186 0.34 0.00 0.00 0.66 0.00
#> TCGA.R5.A804.01 3 0.3895 0.1548 0.00 0.00 0.68 0.00 0.32
#> TCGA.BR.A4CS.01 3 0.4262 -0.2227 0.00 0.00 0.56 0.00 0.44
#> TCGA.CD.8531.01 2 0.0609 0.9760 0.00 0.98 0.00 0.00 0.02
#> TCGA.CD.A487.01 5 0.4262 -0.0779 0.00 0.00 0.00 0.44 0.56
#> TCGA.BR.8371.01 4 0.1216 0.9154 0.02 0.00 0.00 0.96 0.02
#> TCGA.BR.8059.01 5 0.3796 0.3300 0.00 0.00 0.00 0.30 0.70
#> TCGA.D7.A6ET.01 5 0.4126 0.4456 0.00 0.00 0.00 0.38 0.62
#> TCGA.FP.8099.01 3 0.2280 0.5617 0.00 0.00 0.88 0.00 0.12
#> TCGA.D7.8579.01 5 0.4262 0.4873 0.00 0.00 0.44 0.00 0.56
#> TCGA.BR.8297.01 5 0.4287 0.4603 0.00 0.00 0.46 0.00 0.54
#> TCGA.D7.8576.01 4 0.0609 0.9120 0.02 0.00 0.00 0.98 0.00
#> TCGA.VQ.A8DT.01 3 0.0000 0.7018 0.00 0.00 1.00 0.00 0.00
#> TCGA.FP.A8CX.01 5 0.1732 0.6370 0.00 0.00 0.00 0.08 0.92
#> TCGA.HU.A4GH.01 1 0.0000 0.9478 1.00 0.00 0.00 0.00 0.00
#> TCGA.CD.8526.01 1 0.0609 0.9390 0.98 0.00 0.00 0.02 0.00
#> TCGA.HU.A4G6.01 2 0.0609 0.9760 0.00 0.98 0.00 0.00 0.02
#> TCGA.D7.8578.01 1 0.3274 0.6764 0.78 0.00 0.00 0.22 0.00
#> TCGA.HU.A4G3.01 3 0.0000 0.7018 0.00 0.00 1.00 0.00 0.00
#> TCGA.D7.A74A.01 3 0.4287 0.2221 0.00 0.46 0.54 0.00 0.00
#> TCGA.RD.A7C1.01 3 0.0000 0.7018 0.00 0.00 1.00 0.00 0.00
#> TCGA.F1.A448.01 3 0.0000 0.7018 0.00 0.00 1.00 0.00 0.00
#> TCGA.D7.8575.01 5 0.3796 0.5416 0.00 0.00 0.00 0.30 0.70
#> TCGA.BR.8372.01 2 0.0000 0.9818 0.00 1.00 0.00 0.00 0.00
#> TCGA.VQ.A8P3.01 3 0.0000 0.7018 0.00 0.00 1.00 0.00 0.00
#> TCGA.RD.A8MW.01 1 0.0000 0.9478 1.00 0.00 0.00 0.00 0.00
#> TCGA.BR.8286.01 3 0.0000 0.7018 0.00 0.00 1.00 0.00 0.00
#> TCGA.BR.8369.01 3 0.4182 -0.0950 0.00 0.00 0.60 0.00 0.40
#> TCGA.BR.8364.01 4 0.1732 0.8757 0.08 0.00 0.00 0.92 0.00
#> TCGA.HU.8244.01 2 0.0609 0.9649 0.00 0.98 0.02 0.00 0.00
#> TCGA.KB.A6F7.01 1 0.0000 0.9478 1.00 0.00 0.00 0.00 0.00
#> TCGA.FP.A4BF.01 3 0.0000 0.7018 0.00 0.00 1.00 0.00 0.00
#> TCGA.R5.A805.01 3 0.4182 -0.0950 0.00 0.00 0.60 0.00 0.40
#> TCGA.IN.A6RL.01 5 0.1043 0.6482 0.00 0.00 0.00 0.04 0.96
#> TCGA.IN.A6RR.01 2 0.3424 0.6273 0.00 0.76 0.24 0.00 0.00
#> TCGA.BR.A4CR.01 1 0.0000 0.9478 1.00 0.00 0.00 0.00 0.00
#> TCGA.CD.A489.01 4 0.3274 0.6597 0.00 0.00 0.00 0.78 0.22
#> TCGA.HU.A4GY.01 4 0.1043 0.8921 0.00 0.00 0.00 0.96 0.04
#> TCGA.BR.8289.01 5 0.1043 0.6482 0.00 0.00 0.00 0.04 0.96
#> TCGA.FP.8209.01 4 0.1043 0.9026 0.04 0.00 0.00 0.96 0.00
#> TCGA.BR.8296.01 3 0.0000 0.7018 0.00 0.00 1.00 0.00 0.00
#> TCGA.CD.A48A.01 5 0.4287 0.4603 0.00 0.00 0.46 0.00 0.54
#> TCGA.BR.8060.01 1 0.0000 0.9478 1.00 0.00 0.00 0.00 0.00
#> TCGA.BR.8077.01 1 0.2077 0.8974 0.92 0.00 0.00 0.04 0.04
#> TCGA.CD.8534.01 5 0.4182 0.5292 0.00 0.00 0.40 0.00 0.60
#> TCGA.BR.7959.01 3 0.4182 -0.0950 0.00 0.00 0.60 0.00 0.40
#> TCGA.VQ.A8P2.01 2 0.0000 0.9818 0.00 1.00 0.00 0.00 0.00
#> TCGA.EQ.8122.01 1 0.0609 0.9390 0.98 0.00 0.00 0.02 0.00
#> TCGA.D7.8573.01 2 0.0609 0.9760 0.00 0.98 0.00 0.00 0.02
#> TCGA.BR.A44T.01 4 0.1043 0.9026 0.04 0.00 0.00 0.96 0.00
#> TCGA.RD.A8MV.01 5 0.3895 0.5329 0.00 0.00 0.00 0.32 0.68
#> TCGA.CD.8536.01 3 0.0000 0.7018 0.00 0.00 1.00 0.00 0.00
#> TCGA.BR.8360.01 2 0.0000 0.9818 0.00 1.00 0.00 0.00 0.00
#> TCGA.BR.8291.01 4 0.4227 0.3560 0.42 0.00 0.00 0.58 0.00
#> TCGA.FP.8210.01 4 0.1216 0.9154 0.02 0.00 0.00 0.96 0.02
#> TCGA.RD.A7BS.01 4 0.1216 0.9154 0.02 0.00 0.00 0.96 0.02
#> TCGA.BR.A44U.01 3 0.0000 0.7018 0.00 0.00 1.00 0.00 0.00
#> TCGA.CD.8529.01 4 0.3731 0.7790 0.16 0.00 0.00 0.80 0.04
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> TCGA.VQ.A94P.01 4 0.1092 0.8892 0.02 0.00 0.00 0.96 0.02 0.00
#> TCGA.D7.6521.01 4 0.2190 0.8587 0.00 0.00 0.00 0.90 0.04 0.06
#> TCGA.VQ.A8PE.01 1 0.0000 0.9419 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D7.6519.01 1 0.5331 0.5413 0.62 0.00 0.00 0.26 0.10 0.02
#> TCGA.BR.6452.01 3 0.4002 0.5028 0.00 0.32 0.66 0.00 0.02 0.00
#> TCGA.BR.8485.01 1 0.2403 0.8885 0.90 0.00 0.00 0.04 0.04 0.02
#> TCGA.VQ.A8PO.01 3 0.4360 0.5846 0.00 0.26 0.68 0.00 0.06 0.00
#> TCGA.VQ.AA69.01 2 0.1480 0.9327 0.00 0.94 0.00 0.00 0.04 0.02
#> TCGA.BR.8683.01 5 0.5608 0.5237 0.00 0.00 0.00 0.20 0.54 0.26
#> TCGA.BR.8486.01 1 0.3258 0.8383 0.84 0.00 0.00 0.04 0.10 0.02
#> TCGA.D7.6522.01 4 0.1807 0.8829 0.02 0.00 0.00 0.92 0.06 0.00
#> TCGA.CG.5716.01 5 0.5628 0.5312 0.00 0.00 0.00 0.22 0.54 0.24
#> TCGA.BR.8589.01 2 0.1480 0.9327 0.00 0.94 0.00 0.00 0.04 0.02
#> TCGA.BR.8382.01 3 0.1480 0.6766 0.00 0.02 0.94 0.00 0.04 0.00
#> TCGA.VQ.AA68.01 3 0.3309 0.6403 0.00 0.00 0.72 0.00 0.28 0.00
#> TCGA.VQ.A8PJ.01 1 0.0000 0.9419 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.VQ.A8PH.01 1 0.0000 0.9419 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HU.8604.01 3 0.3351 0.6403 0.00 0.16 0.80 0.00 0.04 0.00
#> TCGA.BR.8676.01 2 0.1480 0.9327 0.00 0.94 0.00 0.00 0.04 0.02
#> TCGA.CG.4441.01 6 0.0937 0.7171 0.00 0.00 0.00 0.00 0.04 0.96
#> TCGA.D7.6520.01 1 0.0000 0.9419 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.VQ.AA64.01 4 0.1092 0.8880 0.02 0.00 0.00 0.96 0.00 0.02
#> TCGA.D7.6527.01 1 0.0000 0.9419 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.VQ.A8PM.01 1 0.0000 0.9419 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.VQ.A923.01 2 0.2020 0.9204 0.00 0.92 0.02 0.00 0.04 0.02
#> TCGA.BR.8384.01 5 0.5628 0.5312 0.00 0.00 0.00 0.22 0.54 0.24
#> TCGA.BR.6453.01 5 0.5684 0.6716 0.00 0.00 0.28 0.00 0.52 0.20
#> TCGA.VQ.A928.01 4 0.2728 0.8259 0.00 0.00 0.00 0.86 0.04 0.10
#> TCGA.VQ.A8E0.01 4 0.2631 0.7886 0.18 0.00 0.00 0.82 0.00 0.00
#> TCGA.BR.8679.01 3 0.4360 0.5846 0.00 0.26 0.68 0.00 0.06 0.00
#> TCGA.VQ.A91S.01 5 0.5058 0.4729 0.00 0.00 0.02 0.04 0.54 0.40
#> TCGA.BR.8678.01 1 0.2454 0.7845 0.84 0.00 0.00 0.00 0.00 0.16
#> TCGA.D7.6528.01 6 0.1556 0.6897 0.00 0.00 0.00 0.00 0.08 0.92
#> TCGA.VQ.A8E7.01 5 0.4172 0.3703 0.00 0.00 0.28 0.00 0.68 0.04
#> TCGA.BR.8680.01 5 0.5173 0.6355 0.00 0.00 0.20 0.00 0.62 0.18
#> TCGA.BR.8483.01 6 0.2048 0.6820 0.00 0.00 0.00 0.00 0.12 0.88
#> TCGA.BR.6566.01 3 0.0000 0.6777 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.VQ.A91X.01 6 0.2350 0.6626 0.00 0.00 0.02 0.00 0.10 0.88
#> TCGA.VQ.A91Q.01 4 0.1092 0.8880 0.02 0.00 0.00 0.96 0.00 0.02
#> TCGA.VQ.A92D.01 2 0.0000 0.9526 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.VQ.A91Z.01 6 0.1480 0.7143 0.04 0.00 0.00 0.00 0.02 0.94
#> TCGA.BR.6455.01 2 0.1480 0.9327 0.00 0.94 0.00 0.00 0.04 0.02
#> TCGA.BR.8591.01 2 0.0000 0.9526 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.HU.8608.01 3 0.5115 0.0110 0.00 0.46 0.48 0.00 0.04 0.02
#> TCGA.VQ.A94U.01 5 0.4265 0.3198 0.00 0.00 0.30 0.00 0.66 0.04
#> TCGA.VQ.A94T.01 6 0.4609 0.2050 0.00 0.00 0.00 0.42 0.04 0.54
#> TCGA.VQ.A91A.01 3 0.3309 0.6403 0.00 0.00 0.72 0.00 0.28 0.00
#> TCGA.VQ.A91D.01 2 0.0000 0.9526 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.D7.6518.01 5 0.5712 0.4894 0.00 0.00 0.00 0.26 0.52 0.22
#> TCGA.BR.8484.01 4 0.1635 0.8841 0.02 0.00 0.00 0.94 0.02 0.02
#> TCGA.VQ.A91N.01 6 0.1267 0.7021 0.06 0.00 0.00 0.00 0.00 0.94
#> TCGA.VQ.A91E.01 3 0.0000 0.6777 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.VQ.A8PY.01 3 0.0000 0.6777 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.HU.8602.01 2 0.3007 0.8672 0.00 0.86 0.08 0.00 0.04 0.02
#> TCGA.BR.8381.01 3 0.4574 0.5095 0.00 0.26 0.68 0.00 0.04 0.02
#> TCGA.BR.6452.11 4 0.3829 0.7949 0.00 0.00 0.00 0.76 0.18 0.06
#> TCGA.IN.8663.01 2 0.0000 0.9526 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.VQ.A8PS.01 4 0.1092 0.8880 0.02 0.00 0.00 0.96 0.00 0.02
#> TCGA.VQ.A91W.01 3 0.4675 0.4837 0.00 0.28 0.66 0.00 0.04 0.02
#> TCGA.BR.6454.01 4 0.2190 0.8587 0.00 0.00 0.00 0.90 0.04 0.06
#> TCGA.BR.8682.01 5 0.5520 0.6554 0.00 0.00 0.20 0.00 0.56 0.24
#> TCGA.VQ.A91V.01 3 0.4265 0.5902 0.00 0.00 0.66 0.00 0.30 0.04
#> TCGA.VQ.A8PZ.01 3 0.3756 -0.1437 0.00 0.00 0.60 0.00 0.40 0.00
#> TCGA.BR.8590.01 4 0.1092 0.8880 0.02 0.00 0.00 0.96 0.00 0.02
#> TCGA.F1.6177.01 2 0.0000 0.9526 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.VQ.A8PQ.01 4 0.2581 0.8588 0.00 0.00 0.00 0.86 0.12 0.02
#> TCGA.VQ.A91U.01 1 0.2631 0.7666 0.82 0.00 0.00 0.00 0.00 0.18
#> TCGA.VQ.AA6I.01 3 0.3315 0.6746 0.00 0.02 0.78 0.00 0.20 0.00
#> TCGA.CG.4437.01 3 0.0547 0.6817 0.00 0.00 0.98 0.00 0.02 0.00
#> TCGA.VQ.A8PP.01 3 0.2260 0.6813 0.00 0.00 0.86 0.00 0.14 0.00
#> TCGA.BR.6565.01 1 0.0000 0.9419 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.VQ.A91Y.01 1 0.0000 0.9419 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.VQ.A8PF.01 3 0.4460 0.5415 0.00 0.24 0.70 0.00 0.04 0.02
#> TCGA.BR.6456.01 1 0.3572 0.8204 0.82 0.00 0.00 0.06 0.10 0.02
#> TCGA.BR.6458.01 6 0.5575 -0.4357 0.00 0.00 0.14 0.00 0.40 0.46
#> TCGA.VQ.A925.01 1 0.3460 0.6810 0.76 0.00 0.00 0.22 0.00 0.02
#> TCGA.VQ.A927.01 4 0.1807 0.8829 0.02 0.00 0.00 0.92 0.06 0.00
#> TCGA.BR.8592.01 5 0.6433 0.6503 0.00 0.00 0.14 0.08 0.54 0.24
#> TCGA.BR.6566.11 4 0.2581 0.8588 0.00 0.00 0.00 0.86 0.12 0.02
#> TCGA.IN.AB1V.01 1 0.0547 0.9287 0.98 0.00 0.00 0.02 0.00 0.00
#> TCGA.VQ.AA6F.01 4 0.1092 0.8880 0.02 0.00 0.00 0.96 0.00 0.02
#> TCGA.VQ.AA6J.01 4 0.2474 0.8456 0.00 0.00 0.00 0.88 0.04 0.08
#> TCGA.BR.8487.01 2 0.0000 0.9526 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.D7.6525.01 3 0.3309 0.6403 0.00 0.00 0.72 0.00 0.28 0.00
#> TCGA.VQ.A94O.01 1 0.0000 0.9419 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BR.8588.01 5 0.5692 0.6531 0.00 0.00 0.32 0.00 0.50 0.18
#> TCGA.HU.8610.01 5 0.5712 0.5300 0.00 0.00 0.00 0.22 0.52 0.26
#> TCGA.D7.6526.01 1 0.0547 0.9333 0.98 0.00 0.00 0.02 0.00 0.00
#> TCGA.VQ.A8PD.01 5 0.6002 0.6752 0.00 0.00 0.20 0.02 0.54 0.24
#> TCGA.D7.6524.01 5 0.5684 0.6716 0.00 0.00 0.28 0.00 0.52 0.20
#> TCGA.3M.AB46.01 1 0.0547 0.9295 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.3M.AB47.01 5 0.5712 0.6647 0.00 0.00 0.22 0.00 0.52 0.26
#> TCGA.BR.8677.01 4 0.3660 0.8171 0.00 0.00 0.00 0.78 0.16 0.06
#> TCGA.BR.6457.01 5 0.6431 0.5907 0.00 0.00 0.06 0.16 0.52 0.26
#> TCGA.BR.8687.01 1 0.3846 0.8002 0.80 0.00 0.00 0.08 0.10 0.02
#> TCGA.VQ.A91K.01 2 0.0000 0.9526 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.BR.8690.01 1 0.5457 0.5879 0.64 0.00 0.00 0.22 0.10 0.04
#> TCGA.BR.8686.01 2 0.3688 0.7971 0.00 0.80 0.14 0.00 0.04 0.02
#> TCGA.FP.8631.01 1 0.0000 0.9419 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.VQ.A922.01 1 0.0000 0.9419 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BR.A452.01 4 0.2020 0.8780 0.02 0.00 0.00 0.92 0.02 0.04
#> TCGA.IN.A6RO.01 2 0.0000 0.9526 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.BR.A4QI.01 2 0.0000 0.9526 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.D7.A6EV.01 5 0.5371 0.5574 0.00 0.00 0.12 0.00 0.52 0.36
#> TCGA.HU.A4G2.01 2 0.1480 0.9327 0.00 0.94 0.00 0.00 0.04 0.02
#> TCGA.BR.A4IY.01 2 0.4042 0.7408 0.00 0.76 0.18 0.00 0.04 0.02
#> TCGA.VQ.A8PU.01 4 0.2190 0.8587 0.00 0.00 0.00 0.90 0.04 0.06
#> TCGA.BR.A4J4.01 2 0.1480 0.9327 0.00 0.94 0.00 0.00 0.04 0.02
#> TCGA.VQ.A94R.01 3 0.3819 0.6432 0.00 0.02 0.70 0.00 0.28 0.00
#> TCGA.HU.A4H4.01 3 0.0937 0.6754 0.00 0.00 0.96 0.00 0.04 0.00
#> TCGA.BR.7707.01 3 0.3647 0.4349 0.00 0.36 0.64 0.00 0.00 0.00
#> TCGA.FP.7829.01 2 0.0000 0.9526 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.BR.A4J5.01 5 0.5371 0.6212 0.00 0.00 0.36 0.00 0.52 0.12
#> TCGA.HU.A4H0.01 2 0.1480 0.9327 0.00 0.94 0.00 0.00 0.04 0.02
#> TCGA.HU.A4HD.01 1 0.0000 0.9419 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.KB.A6F5.01 1 0.0000 0.9419 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.VQ.AA6K.01 4 0.1635 0.8841 0.02 0.00 0.00 0.94 0.02 0.02
#> TCGA.HF.7133.01 4 0.2350 0.8600 0.00 0.00 0.00 0.88 0.10 0.02
#> TCGA.F1.6875.01 6 0.4613 0.5316 0.26 0.00 0.00 0.08 0.00 0.66
#> TCGA.MX.A666.01 1 0.0000 0.9419 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BR.7717.01 3 0.4265 0.5902 0.00 0.00 0.66 0.00 0.30 0.04
#> TCGA.BR.A4PF.01 3 0.2941 0.6602 0.00 0.00 0.78 0.00 0.22 0.00
#> TCGA.BR.A4IU.01 5 0.5628 0.6765 0.00 0.00 0.22 0.00 0.54 0.24
#> TCGA.VQ.A8PX.01 4 0.1092 0.8881 0.02 0.00 0.00 0.96 0.02 0.00
#> TCGA.BR.A4IV.01 4 0.2020 0.8857 0.02 0.00 0.00 0.92 0.04 0.02
#> TCGA.D7.A6EX.01 4 0.1480 0.8852 0.00 0.00 0.00 0.94 0.02 0.04
#> TCGA.BR.A4IZ.01 4 0.2350 0.8772 0.00 0.00 0.00 0.88 0.10 0.02
#> TCGA.BR.A4J9.01 4 0.1635 0.8841 0.02 0.00 0.00 0.94 0.02 0.02
#> TCGA.CD.A4MJ.01 2 0.0000 0.9526 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.B7.A5TN.01 1 0.0000 0.9419 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BR.7715.01 6 0.3351 0.5830 0.00 0.00 0.04 0.00 0.16 0.80
#> TCGA.BR.7704.01 1 0.2403 0.8885 0.90 0.00 0.00 0.04 0.04 0.02
#> TCGA.BR.A4J1.01 1 0.0000 0.9419 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HU.A4GP.01 3 0.5569 0.6173 0.00 0.18 0.54 0.00 0.28 0.00
#> TCGA.D7.A4YY.01 2 0.0000 0.9526 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.VQ.AA6G.01 3 0.5882 0.3864 0.00 0.38 0.42 0.00 0.20 0.00
#> TCGA.HU.A4GJ.01 5 0.5569 0.6668 0.00 0.00 0.28 0.00 0.54 0.18
#> TCGA.CD.A4MI.01 3 0.3351 0.6403 0.00 0.16 0.80 0.00 0.04 0.00
#> TCGA.BR.7196.01 3 0.3851 -0.3426 0.00 0.00 0.54 0.00 0.46 0.00
#> TCGA.BR.6563.01 5 0.5721 0.5098 0.00 0.00 0.00 0.24 0.52 0.24
#> TCGA.VQ.A924.01 3 0.4420 0.4193 0.00 0.34 0.62 0.00 0.04 0.00
#> TCGA.BR.7716.01 1 0.2725 0.8737 0.88 0.00 0.00 0.04 0.06 0.02
#> TCGA.FP.7735.01 4 0.1092 0.8880 0.02 0.00 0.00 0.96 0.00 0.02
#> TCGA.BR.7723.01 1 0.0000 0.9419 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HU.A4H8.01 2 0.0000 0.9526 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.IN.A6RJ.01 5 0.5840 0.6676 0.00 0.00 0.16 0.02 0.56 0.26
#> TCGA.HU.A4H3.01 2 0.0000 0.9526 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.EQ.A4SO.01 4 0.2941 0.7412 0.22 0.00 0.00 0.78 0.00 0.00
#> TCGA.CD.A4MH.01 1 0.2403 0.8885 0.90 0.00 0.00 0.04 0.04 0.02
#> TCGA.BR.A4J7.01 4 0.1635 0.8841 0.02 0.00 0.00 0.94 0.02 0.02
#> TCGA.HF.7131.01 1 0.4502 0.7313 0.74 0.00 0.00 0.14 0.10 0.02
#> TCGA.D7.A74B.01 4 0.4713 0.7247 0.14 0.00 0.00 0.72 0.12 0.02
#> TCGA.BR.A4PE.01 2 0.0000 0.9526 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.BR.A4J8.01 3 0.4172 0.5101 0.00 0.28 0.68 0.00 0.04 0.00
#> TCGA.HU.A4GX.01 5 0.5438 0.5355 0.00 0.00 0.00 0.16 0.56 0.28
#> TCGA.HU.A4G8.01 3 0.0000 0.6777 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.HU.A4GT.01 2 0.0000 0.9526 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.HU.A4GC.01 3 0.4482 0.5262 0.00 0.00 0.60 0.00 0.36 0.04
#> TCGA.BR.A4CQ.01 2 0.0000 0.9526 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.D7.A6F2.01 1 0.0000 0.9419 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.RD.A7BT.01 6 0.2020 0.7066 0.04 0.00 0.00 0.02 0.02 0.92
#> TCGA.BR.A4J6.01 4 0.2350 0.8600 0.00 0.00 0.00 0.88 0.10 0.02
#> TCGA.HU.A4GQ.01 2 0.0937 0.9389 0.00 0.96 0.00 0.00 0.04 0.00
#> TCGA.HF.7136.01 1 0.0000 0.9419 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BR.A4QM.01 2 0.0547 0.9392 0.00 0.98 0.02 0.00 0.00 0.00
#> TCGA.BR.A4PD.01 6 0.2981 0.5921 0.00 0.00 0.00 0.16 0.02 0.82
#> TCGA.VQ.A8PK.01 1 0.0000 0.9419 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.B7.A5TK.01 3 0.3756 -0.1677 0.00 0.00 0.60 0.00 0.40 0.00
#> TCGA.D7.A4YX.01 2 0.1480 0.9327 0.00 0.94 0.00 0.00 0.04 0.02
#> TCGA.D7.A4Z0.01 3 0.1556 0.6713 0.00 0.00 0.92 0.00 0.08 0.00
#> TCGA.VQ.A8PT.01 2 0.0000 0.9526 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.IN.A6RN.01 1 0.0547 0.9333 0.98 0.00 0.00 0.02 0.00 0.00
#> TCGA.CD.A4MG.01 2 0.0000 0.9526 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.D7.A747.01 4 0.2020 0.8857 0.02 0.00 0.00 0.92 0.04 0.02
#> TCGA.R5.A7O7.01 5 0.5371 0.5999 0.00 0.00 0.12 0.00 0.52 0.36
#> TCGA.F1.A72C.01 4 0.1092 0.8880 0.02 0.00 0.00 0.96 0.00 0.02
#> TCGA.BR.A4J2.01 5 0.5973 0.6297 0.00 0.00 0.08 0.08 0.58 0.26
#> TCGA.MX.A663.01 1 0.0000 0.9419 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D7.A4YV.01 2 0.0000 0.9526 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.HU.A4GD.01 6 0.1556 0.7068 0.00 0.00 0.00 0.00 0.08 0.92
#> TCGA.BR.A4QL.01 2 0.0000 0.9526 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.BR.7703.01 2 0.0000 0.9526 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.VQ.AA6B.01 5 0.5285 0.4626 0.00 0.00 0.10 0.00 0.48 0.42
#> TCGA.VQ.AA6D.01 1 0.0547 0.9333 0.98 0.00 0.00 0.02 0.00 0.00
#> TCGA.D7.A6EZ.01 2 0.1480 0.9327 0.00 0.94 0.00 0.00 0.04 0.02
#> TCGA.D7.A4YU.01 2 0.0000 0.9526 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.VQ.AA6A.01 6 0.3499 0.4685 0.32 0.00 0.00 0.00 0.00 0.68
#> TCGA.IN.7806.01 6 0.3916 0.4911 0.30 0.00 0.00 0.02 0.00 0.68
#> TCGA.HU.A4HB.01 5 0.5608 0.5384 0.00 0.00 0.00 0.20 0.54 0.26
#> TCGA.HU.A4H2.01 6 0.3163 0.5809 0.00 0.00 0.04 0.00 0.14 0.82
#> TCGA.IN.A6RP.01 3 0.3309 0.6403 0.00 0.00 0.72 0.00 0.28 0.00
#> TCGA.HU.A4H5.01 1 0.0000 0.9419 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HU.A4GU.01 2 0.0000 0.9526 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.MX.A5UJ.01 3 0.3950 0.6097 0.00 0.24 0.72 0.00 0.04 0.00
#> TCGA.HU.A4GN.01 2 0.0000 0.9526 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.CD.5804.01 1 0.0000 0.9419 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HU.A4H6.01 3 0.3351 0.6403 0.00 0.16 0.80 0.00 0.04 0.00
#> TCGA.HF.7132.01 3 0.0000 0.6777 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.D7.A4YT.01 1 0.0000 0.9419 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HF.7134.01 2 0.0547 0.9397 0.00 0.98 0.00 0.00 0.02 0.00
#> TCGA.BR.6852.01 3 0.0000 0.6777 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.BR.8370.01 2 0.1480 0.9327 0.00 0.94 0.00 0.00 0.04 0.02
#> TCGA.EQ.5647.01 4 0.2350 0.8600 0.00 0.00 0.00 0.88 0.10 0.02
#> TCGA.IN.A7NT.01 6 0.1267 0.7057 0.00 0.00 0.00 0.00 0.06 0.94
#> TCGA.RD.A8N9.01 4 0.4982 0.6569 0.20 0.00 0.00 0.68 0.10 0.02
#> TCGA.D7.5577.01 2 0.3688 0.7971 0.00 0.80 0.14 0.00 0.04 0.02
#> TCGA.CG.5717.01 4 0.1807 0.8829 0.02 0.00 0.00 0.92 0.06 0.00
#> TCGA.D7.6818.01 1 0.0000 0.9419 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CG.5734.01 5 0.5921 0.4584 0.00 0.00 0.00 0.24 0.46 0.30
#> TCGA.VQ.A8P8.01 3 0.0937 0.6524 0.00 0.00 0.96 0.00 0.04 0.00
#> TCGA.BR.6707.01 3 0.4574 0.5095 0.00 0.26 0.68 0.00 0.04 0.02
#> TCGA.B7.5818.01 2 0.1480 0.9327 0.00 0.94 0.00 0.00 0.04 0.02
#> TCGA.CD.8525.01 1 0.3007 0.8570 0.86 0.00 0.00 0.04 0.08 0.02
#> TCGA.BR.6705.01 5 0.6347 0.6556 0.00 0.00 0.16 0.06 0.54 0.24
#> TCGA.BR.4288.01 1 0.0000 0.9419 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CD.5813.01 4 0.1635 0.8841 0.02 0.00 0.00 0.94 0.02 0.02
#> TCGA.CG.5723.01 4 0.2474 0.8456 0.00 0.00 0.00 0.88 0.04 0.08
#> TCGA.CD.5800.01 1 0.2020 0.9012 0.92 0.00 0.00 0.02 0.04 0.02
#> TCGA.CG.5718.01 1 0.2403 0.8885 0.90 0.00 0.00 0.04 0.04 0.02
#> TCGA.BR.8080.01 6 0.1814 0.6778 0.00 0.00 0.00 0.00 0.10 0.90
#> TCGA.CG.5733.01 3 0.3647 0.4349 0.00 0.36 0.64 0.00 0.00 0.00
#> TCGA.D7.6817.01 1 0.0000 0.9419 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.KB.A93G.01 4 0.1807 0.8829 0.02 0.00 0.00 0.92 0.06 0.00
#> TCGA.CD.5799.01 1 0.0000 0.9419 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BR.7851.01 2 0.0547 0.9464 0.00 0.98 0.00 0.00 0.02 0.00
#> TCGA.BR.7722.01 4 0.1092 0.8880 0.02 0.00 0.00 0.96 0.00 0.02
#> TCGA.MX.A5UG.01 5 0.5628 0.5312 0.00 0.00 0.00 0.22 0.54 0.24
#> TCGA.CD.8533.01 3 0.4420 0.5565 0.00 0.00 0.62 0.00 0.34 0.04
#> TCGA.BR.7957.01 5 0.6210 0.6645 0.00 0.00 0.18 0.04 0.54 0.24
#> TCGA.CG.5722.01 3 0.3647 -0.0404 0.00 0.00 0.64 0.00 0.36 0.00
#> TCGA.F1.6874.01 5 0.5302 0.5467 0.00 0.00 0.04 0.04 0.56 0.36
#> TCGA.CG.5730.01 6 0.0937 0.7171 0.00 0.00 0.00 0.00 0.04 0.96
#> TCGA.CG.5726.01 2 0.3660 0.6763 0.00 0.78 0.16 0.00 0.06 0.00
#> TCGA.IP.7968.01 6 0.0937 0.7171 0.00 0.00 0.00 0.00 0.04 0.96
#> TCGA.BR.8363.01 3 0.0937 0.6766 0.00 0.00 0.96 0.00 0.04 0.00
#> TCGA.BR.7901.01 1 0.0000 0.9419 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D7.6822.01 5 0.4247 0.4795 0.00 0.00 0.24 0.00 0.70 0.06
#> TCGA.BR.6710.01 4 0.3950 0.7115 0.24 0.00 0.00 0.72 0.04 0.00
#> TCGA.CG.5720.01 3 0.0000 0.6777 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.D7.8570.01 3 0.4460 0.5415 0.00 0.24 0.70 0.00 0.04 0.02
#> TCGA.B7.A5TI.01 4 0.1092 0.8880 0.02 0.00 0.00 0.96 0.00 0.02
#> TCGA.D7.6815.01 6 0.1807 0.6976 0.06 0.00 0.00 0.02 0.00 0.92
#> TCGA.BR.8284.01 3 0.0000 0.6777 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.BR.8295.01 1 0.0547 0.9333 0.98 0.00 0.00 0.02 0.00 0.00
#> TCGA.BR.7197.01 6 0.3499 0.4685 0.32 0.00 0.00 0.00 0.00 0.68
#> TCGA.B7.A5TJ.01 2 0.0000 0.9526 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.D7.A6EY.01 6 0.5586 -0.5140 0.00 0.00 0.14 0.00 0.42 0.44
#> TCGA.BR.8366.01 3 0.4574 0.5095 0.00 0.26 0.68 0.00 0.04 0.02
#> TCGA.IN.A7NR.01 4 0.3111 0.8466 0.02 0.00 0.00 0.84 0.12 0.02
#> TCGA.BR.6706.01 3 0.3851 -0.3426 0.00 0.00 0.54 0.00 0.46 0.00
#> TCGA.IN.7808.01 5 0.4462 0.4517 0.00 0.00 0.28 0.00 0.66 0.06
#> TCGA.BR.6564.01 4 0.2581 0.8588 0.00 0.00 0.00 0.86 0.12 0.02
#> TCGA.KB.A93H.01 6 0.0937 0.7171 0.00 0.00 0.00 0.00 0.04 0.96
#> TCGA.KB.A93J.01 4 0.4078 0.5254 0.34 0.00 0.00 0.64 0.00 0.02
#> TCGA.CD.5798.01 4 0.1635 0.8841 0.02 0.00 0.00 0.94 0.02 0.02
#> TCGA.CD.8530.01 6 0.4646 0.0913 0.46 0.00 0.00 0.04 0.00 0.50
#> TCGA.BR.6802.01 5 0.5569 0.6576 0.00 0.00 0.32 0.00 0.52 0.16
#> TCGA.CG.5719.01 4 0.2094 0.8684 0.00 0.00 0.00 0.90 0.08 0.02
#> TCGA.VQ.A8E3.01 3 0.4810 0.6308 0.00 0.22 0.66 0.00 0.12 0.00
#> TCGA.CD.5801.01 3 0.1480 0.6725 0.00 0.00 0.94 0.00 0.04 0.02
#> TCGA.FP.A9TM.01 3 0.2260 0.6812 0.00 0.00 0.86 0.00 0.14 0.00
#> TCGA.BR.7958.01 2 0.4042 0.7408 0.00 0.76 0.18 0.00 0.04 0.02
#> TCGA.FP.7998.01 3 0.3756 -0.1677 0.00 0.00 0.60 0.00 0.40 0.00
#> TCGA.IN.A6RS.01 5 0.4420 0.2505 0.00 0.00 0.34 0.00 0.62 0.04
#> TCGA.BR.6709.01 4 0.2581 0.8588 0.00 0.00 0.00 0.86 0.12 0.02
#> TCGA.FP.7916.01 3 0.4460 0.5415 0.00 0.24 0.70 0.00 0.04 0.02
#> TCGA.R5.A7ZR.01 6 0.3309 0.5220 0.28 0.00 0.00 0.00 0.00 0.72
#> TCGA.B7.5816.01 3 0.0000 0.6777 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.CG.5721.01 5 0.5684 0.6682 0.00 0.00 0.20 0.00 0.52 0.28
#> TCGA.SW.A7EA.01 2 0.0000 0.9526 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.RD.A8NB.01 5 0.5684 0.6716 0.00 0.00 0.28 0.00 0.52 0.20
#> TCGA.BR.6801.01 4 0.1807 0.8719 0.00 0.00 0.00 0.92 0.02 0.06
#> TCGA.IN.AB1X.01 3 0.0000 0.6777 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.D7.5579.01 4 0.2020 0.8780 0.02 0.00 0.00 0.92 0.02 0.04
#> TCGA.CG.5728.01 5 0.5618 0.6427 0.00 0.00 0.34 0.00 0.50 0.16
#> TCGA.R5.A7ZI.01 4 0.2581 0.8588 0.00 0.00 0.00 0.86 0.12 0.02
#> TCGA.IN.A7NU.01 3 0.3409 0.6229 0.00 0.00 0.70 0.00 0.30 0.00
#> TCGA.CG.5732.01 1 0.0000 0.9419 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.ZQ.A9CR.01 1 0.2403 0.8885 0.90 0.00 0.00 0.04 0.04 0.02
#> TCGA.D7.5578.01 6 0.5523 -0.3386 0.00 0.00 0.14 0.00 0.36 0.50
#> TCGA.BR.6803.01 4 0.2581 0.8588 0.00 0.00 0.00 0.86 0.12 0.02
#> TCGA.BR.8368.01 2 0.0000 0.9526 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.SW.A7EB.01 1 0.0000 0.9419 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BR.8081.01 3 0.0547 0.6781 0.00 0.00 0.98 0.00 0.02 0.00
#> TCGA.VQ.A8P5.01 5 0.5520 0.6633 0.00 0.00 0.20 0.00 0.56 0.24
#> TCGA.CD.8535.01 3 0.3819 0.6432 0.00 0.02 0.70 0.00 0.28 0.00
#> TCGA.CG.5724.01 3 0.3309 0.6403 0.00 0.00 0.72 0.00 0.28 0.00
#> TCGA.D7.8574.01 4 0.1807 0.8829 0.02 0.00 0.00 0.92 0.06 0.00
#> TCGA.HJ.7597.01 4 0.2581 0.8588 0.00 0.00 0.00 0.86 0.12 0.02
#> TCGA.HF.A5NB.01 2 0.0000 0.9526 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.VQ.A8PB.01 3 0.3309 0.6403 0.00 0.00 0.72 0.00 0.28 0.00
#> TCGA.R5.A7ZE.01 1 0.0547 0.9333 0.98 0.00 0.00 0.02 0.00 0.00
#> TCGA.CD.5803.01 4 0.2581 0.8588 0.00 0.00 0.00 0.86 0.12 0.02
#> TCGA.CG.5725.01 1 0.0000 0.9419 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D7.6820.01 1 0.0000 0.9419 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CD.5802.01 1 0.1814 0.8503 0.90 0.00 0.00 0.10 0.00 0.00
#> TCGA.R5.A7ZF.01 4 0.2581 0.8588 0.00 0.00 0.00 0.86 0.12 0.02
#> TCGA.D7.A6F0.01 1 0.0547 0.9333 0.98 0.00 0.00 0.02 0.00 0.00
#> TCGA.CG.5727.01 6 0.0937 0.7171 0.00 0.00 0.00 0.00 0.04 0.96
#> TCGA.VQ.A8PC.01 5 0.5712 0.5300 0.00 0.00 0.00 0.22 0.52 0.26
#> TCGA.CD.A486.01 1 0.0000 0.9419 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.RD.A8N2.01 4 0.3795 0.8126 0.06 0.00 0.00 0.80 0.12 0.02
#> TCGA.IN.A6RI.01 1 0.0000 0.9419 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HU.8243.01 6 0.2350 0.6626 0.00 0.00 0.02 0.00 0.10 0.88
#> TCGA.CD.A48C.01 3 0.5569 0.6173 0.00 0.18 0.54 0.00 0.28 0.00
#> TCGA.RD.A8N5.01 4 0.1807 0.8829 0.02 0.00 0.00 0.92 0.06 0.00
#> TCGA.RD.A8N1.01 1 0.0000 0.9419 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HU.A4GF.01 1 0.0000 0.9419 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BR.8362.01 5 0.5628 0.6604 0.00 0.00 0.22 0.00 0.54 0.24
#> TCGA.BR.8285.01 3 0.4334 0.5683 0.00 0.22 0.72 0.00 0.04 0.02
#> TCGA.CD.8532.01 4 0.1092 0.8880 0.02 0.00 0.00 0.96 0.00 0.02
#> TCGA.VQ.A8E2.01 1 0.0000 0.9419 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BR.8373.01 6 0.2260 0.6505 0.14 0.00 0.00 0.00 0.00 0.86
#> TCGA.BR.8361.01 3 0.4360 0.5846 0.00 0.26 0.68 0.00 0.06 0.00
#> TCGA.BR.8058.01 4 0.2581 0.8588 0.00 0.00 0.00 0.86 0.12 0.02
#> TCGA.IN.8462.01 3 0.3309 0.6403 0.00 0.00 0.72 0.00 0.28 0.00
#> TCGA.HU.A4G9.01 2 0.0000 0.9526 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.CD.8524.01 6 0.5481 -0.2873 0.00 0.00 0.14 0.00 0.34 0.52
#> TCGA.D7.A748.01 4 0.2581 0.8588 0.00 0.00 0.00 0.86 0.12 0.02
#> TCGA.CD.8527.01 6 0.0937 0.7171 0.00 0.00 0.00 0.00 0.04 0.96
#> TCGA.VQ.A8DV.01 1 0.0000 0.9419 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CD.8528.01 2 0.0000 0.9526 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.BR.A453.01 5 0.5628 0.5312 0.00 0.00 0.00 0.22 0.54 0.24
#> TCGA.RD.A8N6.01 1 0.0547 0.9333 0.98 0.00 0.00 0.02 0.00 0.00
#> TCGA.HU.8245.01 1 0.0000 0.9419 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.ZA.A8F6.01 4 0.1807 0.8719 0.00 0.00 0.00 0.92 0.02 0.06
#> TCGA.BR.8367.01 5 0.5419 0.6658 0.00 0.00 0.20 0.00 0.58 0.22
#> TCGA.BR.8380.01 3 0.3499 0.1121 0.00 0.00 0.68 0.00 0.32 0.00
#> TCGA.FP.A4BE.01 2 0.0000 0.9526 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.HU.8238.01 3 0.3499 0.6217 0.00 0.00 0.68 0.00 0.32 0.00
#> TCGA.BR.8078.01 2 0.0000 0.9526 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.HU.8249.01 6 0.1556 0.7054 0.00 0.00 0.00 0.00 0.08 0.92
#> TCGA.RD.A8N0.01 4 0.2581 0.8588 0.00 0.00 0.00 0.86 0.12 0.02
#> TCGA.BR.8365.01 4 0.2581 0.8588 0.00 0.00 0.00 0.86 0.12 0.02
#> TCGA.FP.8211.01 4 0.1092 0.8880 0.02 0.00 0.00 0.96 0.00 0.02
#> TCGA.RD.A8N4.01 4 0.2581 0.8588 0.00 0.00 0.00 0.86 0.12 0.02
#> TCGA.VQ.A8DU.01 1 0.0000 0.9419 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.VQ.A8DL.01 1 0.3572 0.8204 0.82 0.00 0.00 0.06 0.10 0.02
#> TCGA.VQ.A8DZ.01 1 0.0000 0.9419 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D7.8572.01 1 0.0000 0.9419 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.RD.A7BW.01 4 0.4713 0.7247 0.14 0.00 0.00 0.72 0.12 0.02
#> TCGA.R5.A804.01 5 0.5037 0.5697 0.00 0.00 0.38 0.00 0.54 0.08
#> TCGA.BR.A4CS.01 5 0.4360 0.4712 0.00 0.00 0.26 0.00 0.68 0.06
#> TCGA.CD.8531.01 2 0.2725 0.8873 0.00 0.88 0.06 0.00 0.04 0.02
#> TCGA.CD.A487.01 6 0.2981 0.6147 0.00 0.00 0.00 0.16 0.02 0.82
#> TCGA.BR.8371.01 4 0.1807 0.8829 0.02 0.00 0.00 0.92 0.06 0.00
#> TCGA.BR.8059.01 6 0.2094 0.6803 0.00 0.00 0.00 0.08 0.02 0.90
#> TCGA.D7.A6ET.01 5 0.5628 0.5312 0.00 0.00 0.00 0.22 0.54 0.24
#> TCGA.FP.8099.01 3 0.4420 0.5336 0.00 0.00 0.62 0.00 0.34 0.04
#> TCGA.D7.8579.01 5 0.5608 0.6689 0.00 0.00 0.20 0.00 0.54 0.26
#> TCGA.BR.8297.01 5 0.5608 0.6530 0.00 0.00 0.20 0.00 0.54 0.26
#> TCGA.D7.8576.01 4 0.1807 0.8744 0.00 0.00 0.00 0.92 0.06 0.02
#> TCGA.VQ.A8DT.01 3 0.3309 0.6403 0.00 0.00 0.72 0.00 0.28 0.00
#> TCGA.FP.A8CX.01 6 0.1865 0.7013 0.00 0.00 0.00 0.04 0.04 0.92
#> TCGA.HU.A4GH.01 1 0.0000 0.9419 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CD.8526.01 1 0.3007 0.8570 0.86 0.00 0.00 0.04 0.08 0.02
#> TCGA.HU.A4G6.01 2 0.1480 0.9327 0.00 0.94 0.00 0.00 0.04 0.02
#> TCGA.D7.8578.01 1 0.3647 0.3847 0.64 0.00 0.00 0.36 0.00 0.00
#> TCGA.HU.A4G3.01 3 0.3198 0.6503 0.00 0.00 0.74 0.00 0.26 0.00
#> TCGA.D7.A74A.01 3 0.5608 0.5741 0.00 0.26 0.54 0.00 0.20 0.00
#> TCGA.RD.A7C1.01 3 0.2631 0.6674 0.00 0.00 0.82 0.00 0.18 0.00
#> TCGA.F1.A448.01 3 0.0937 0.6754 0.00 0.00 0.96 0.00 0.04 0.00
#> TCGA.D7.8575.01 5 0.5530 0.5415 0.00 0.00 0.00 0.22 0.56 0.22
#> TCGA.BR.8372.01 2 0.0000 0.9526 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.VQ.A8P3.01 3 0.3309 0.6403 0.00 0.00 0.72 0.00 0.28 0.00
#> TCGA.RD.A8MW.01 1 0.0000 0.9419 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BR.8286.01 3 0.3309 0.6403 0.00 0.00 0.72 0.00 0.28 0.00
#> TCGA.BR.8369.01 5 0.5747 0.6297 0.00 0.00 0.30 0.00 0.50 0.20
#> TCGA.BR.8364.01 4 0.2581 0.8588 0.00 0.00 0.00 0.86 0.12 0.02
#> TCGA.HU.8244.01 2 0.2094 0.8574 0.00 0.90 0.08 0.00 0.02 0.00
#> TCGA.KB.A6F7.01 1 0.0547 0.9333 0.98 0.00 0.00 0.02 0.00 0.00
#> TCGA.FP.A4BF.01 3 0.3309 0.6403 0.00 0.00 0.72 0.00 0.28 0.00
#> TCGA.R5.A805.01 5 0.3711 0.4479 0.00 0.00 0.26 0.00 0.72 0.02
#> TCGA.IN.A6RL.01 6 0.0937 0.7171 0.00 0.00 0.00 0.00 0.04 0.96
#> TCGA.IN.A6RR.01 2 0.5364 0.1295 0.00 0.56 0.30 0.00 0.14 0.00
#> TCGA.BR.A4CR.01 1 0.0000 0.9419 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CD.A489.01 4 0.3351 0.7483 0.00 0.00 0.00 0.80 0.04 0.16
#> TCGA.HU.A4GY.01 4 0.2956 0.8606 0.00 0.00 0.00 0.84 0.12 0.04
#> TCGA.BR.8289.01 6 0.0937 0.7171 0.00 0.00 0.00 0.00 0.04 0.96
#> TCGA.FP.8209.01 4 0.1480 0.8877 0.02 0.00 0.00 0.94 0.04 0.00
#> TCGA.BR.8296.01 3 0.1267 0.6350 0.00 0.00 0.94 0.00 0.06 0.00
#> TCGA.CD.A48A.01 5 0.4834 0.4686 0.00 0.00 0.26 0.00 0.64 0.10
#> TCGA.BR.8060.01 1 0.0547 0.9333 0.98 0.00 0.00 0.02 0.00 0.00
#> TCGA.BR.8077.01 1 0.3631 0.8255 0.82 0.00 0.00 0.04 0.04 0.10
#> TCGA.CD.8534.01 5 0.5102 0.6694 0.00 0.00 0.14 0.00 0.62 0.24
#> TCGA.BR.7959.01 5 0.4265 0.3595 0.00 0.00 0.30 0.00 0.66 0.04
#> TCGA.VQ.A8P2.01 2 0.0000 0.9526 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.EQ.8122.01 1 0.2020 0.9012 0.92 0.00 0.00 0.02 0.04 0.02
#> TCGA.D7.8573.01 2 0.1480 0.9327 0.00 0.94 0.00 0.00 0.04 0.02
#> TCGA.BR.A44T.01 4 0.2581 0.8588 0.00 0.00 0.00 0.86 0.12 0.02
#> TCGA.RD.A8MV.01 6 0.5530 0.1723 0.00 0.00 0.00 0.22 0.22 0.56
#> TCGA.CD.8536.01 3 0.3309 0.6403 0.00 0.00 0.72 0.00 0.28 0.00
#> TCGA.BR.8360.01 2 0.0000 0.9526 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.BR.8291.01 4 0.3499 0.6110 0.32 0.00 0.00 0.68 0.00 0.00
#> TCGA.FP.8210.01 4 0.1807 0.8829 0.02 0.00 0.00 0.92 0.06 0.00
#> TCGA.RD.A7BS.01 4 0.1635 0.8841 0.02 0.00 0.00 0.94 0.02 0.02
#> TCGA.BR.A44U.01 3 0.3309 0.6403 0.00 0.00 0.72 0.00 0.28 0.00
#> TCGA.CD.8529.01 4 0.2728 0.8311 0.10 0.00 0.00 0.86 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.VQ.A94P.01 4 0.3745 0.803904 0.00 0.00 0.00 0.70 0.04 0.00 0.26
#> TCGA.D7.6521.01 4 0.4832 0.796664 0.00 0.00 0.00 0.58 0.04 0.04 0.34
#> TCGA.VQ.A8PE.01 1 0.0000 0.918155 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D7.6519.01 1 0.3985 0.345853 0.52 0.00 0.00 0.46 0.02 0.00 0.00
#> TCGA.BR.6452.01 3 0.2163 0.636004 0.00 0.10 0.88 0.00 0.00 0.02 0.00
#> TCGA.BR.8485.01 1 0.2864 0.836427 0.84 0.00 0.00 0.12 0.02 0.02 0.00
#> TCGA.VQ.A8PO.01 3 0.3541 0.620818 0.00 0.08 0.80 0.00 0.00 0.02 0.10
#> TCGA.VQ.AA69.01 2 0.1718 0.895257 0.00 0.92 0.00 0.00 0.00 0.04 0.04
#> TCGA.BR.8683.01 5 0.3661 0.690420 0.00 0.00 0.00 0.02 0.74 0.02 0.22
#> TCGA.BR.8486.01 1 0.3307 0.744318 0.74 0.00 0.00 0.24 0.02 0.00 0.00
#> TCGA.D7.6522.01 4 0.4211 0.804864 0.00 0.00 0.00 0.68 0.04 0.02 0.26
#> TCGA.CG.5716.01 5 0.3208 0.725123 0.00 0.00 0.00 0.04 0.82 0.02 0.12
#> TCGA.BR.8589.01 2 0.2857 0.865088 0.00 0.86 0.06 0.00 0.00 0.04 0.04
#> TCGA.BR.8382.01 3 0.1166 0.632013 0.00 0.00 0.94 0.00 0.06 0.00 0.00
#> TCGA.VQ.AA68.01 3 0.3546 -0.237416 0.00 0.00 0.54 0.00 0.00 0.00 0.46
#> TCGA.VQ.A8PJ.01 1 0.0000 0.918155 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.VQ.A8PH.01 1 0.0000 0.918155 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HU.8604.01 3 0.2278 0.640053 0.00 0.08 0.88 0.00 0.04 0.00 0.00
#> TCGA.BR.8676.01 2 0.2857 0.865088 0.00 0.86 0.06 0.00 0.00 0.04 0.04
#> TCGA.CG.4441.01 6 0.2421 0.820764 0.00 0.00 0.00 0.02 0.08 0.88 0.02
#> TCGA.D7.6520.01 1 0.0000 0.918155 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.VQ.AA64.01 4 0.4146 0.805376 0.00 0.00 0.00 0.64 0.02 0.02 0.32
#> TCGA.D7.6527.01 1 0.0000 0.918155 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.VQ.A8PM.01 1 0.0000 0.918155 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.VQ.A923.01 2 0.2857 0.865088 0.00 0.86 0.06 0.00 0.00 0.04 0.04
#> TCGA.BR.8384.01 5 0.3208 0.725123 0.00 0.00 0.00 0.04 0.82 0.02 0.12
#> TCGA.BR.6453.01 5 0.1928 0.768055 0.00 0.00 0.08 0.00 0.90 0.00 0.02
#> TCGA.VQ.A928.01 4 0.5083 0.773596 0.00 0.00 0.00 0.56 0.04 0.06 0.34
#> TCGA.VQ.A8E0.01 4 0.4993 0.759166 0.12 0.00 0.00 0.62 0.00 0.02 0.24
#> TCGA.BR.8679.01 3 0.3315 0.625991 0.00 0.08 0.82 0.00 0.00 0.02 0.08
#> TCGA.VQ.A91S.01 5 0.2016 0.771998 0.00 0.00 0.00 0.00 0.90 0.04 0.06
#> TCGA.BR.8678.01 1 0.3294 0.481389 0.66 0.00 0.00 0.00 0.00 0.34 0.00
#> TCGA.D7.6528.01 6 0.3199 0.764832 0.00 0.00 0.00 0.00 0.14 0.80 0.06
#> TCGA.VQ.A8E7.01 7 0.4742 0.651111 0.00 0.00 0.16 0.00 0.22 0.00 0.62
#> TCGA.BR.8680.01 5 0.3186 0.667742 0.00 0.00 0.02 0.00 0.76 0.00 0.22
#> TCGA.BR.8483.01 6 0.4478 0.638970 0.00 0.00 0.00 0.00 0.14 0.66 0.20
#> TCGA.BR.6566.01 3 0.2313 0.628119 0.00 0.00 0.88 0.00 0.06 0.00 0.06
#> TCGA.VQ.A91X.01 6 0.3517 0.603596 0.00 0.00 0.00 0.00 0.02 0.70 0.28
#> TCGA.VQ.A91Q.01 4 0.4524 0.796172 0.00 0.00 0.00 0.60 0.02 0.04 0.34
#> TCGA.VQ.A92D.01 2 0.1718 0.897629 0.00 0.92 0.04 0.00 0.00 0.04 0.00
#> TCGA.VQ.A91Z.01 6 0.1860 0.829616 0.00 0.00 0.00 0.02 0.04 0.92 0.02
#> TCGA.BR.6455.01 2 0.2857 0.865088 0.00 0.86 0.06 0.00 0.00 0.04 0.04
#> TCGA.BR.8591.01 2 0.0000 0.913271 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HU.8608.01 3 0.4193 0.501626 0.00 0.20 0.72 0.00 0.00 0.04 0.04
#> TCGA.VQ.A94U.01 7 0.4742 0.651111 0.00 0.00 0.16 0.00 0.22 0.00 0.62
#> TCGA.VQ.A94T.01 6 0.5870 0.239202 0.00 0.00 0.00 0.12 0.06 0.48 0.34
#> TCGA.VQ.A91A.01 3 0.3525 -0.160863 0.00 0.00 0.56 0.00 0.00 0.00 0.44
#> TCGA.VQ.A91D.01 2 0.0000 0.913271 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D7.6518.01 5 0.4139 0.633976 0.00 0.00 0.00 0.06 0.72 0.02 0.20
#> TCGA.BR.8484.01 4 0.4524 0.796172 0.00 0.00 0.00 0.60 0.02 0.04 0.34
#> TCGA.VQ.A91N.01 6 0.1664 0.827428 0.00 0.00 0.00 0.02 0.06 0.92 0.00
#> TCGA.VQ.A91E.01 3 0.2313 0.628119 0.00 0.00 0.88 0.00 0.06 0.00 0.06
#> TCGA.VQ.A8PY.01 3 0.2313 0.628119 0.00 0.00 0.88 0.00 0.06 0.00 0.06
#> TCGA.HU.8602.01 2 0.4772 0.525041 0.00 0.60 0.32 0.00 0.00 0.04 0.04
#> TCGA.BR.8381.01 3 0.3208 0.608138 0.00 0.12 0.82 0.00 0.02 0.00 0.04
#> TCGA.BR.6452.11 4 0.5016 0.100438 0.00 0.00 0.00 0.46 0.42 0.00 0.12
#> TCGA.IN.8663.01 2 0.0504 0.908422 0.00 0.98 0.00 0.00 0.00 0.02 0.00
#> TCGA.VQ.A8PS.01 4 0.4146 0.805376 0.00 0.00 0.00 0.64 0.02 0.02 0.32
#> TCGA.VQ.A91W.01 3 0.3734 0.569067 0.00 0.14 0.78 0.00 0.00 0.04 0.04
#> TCGA.BR.6454.01 4 0.4524 0.796172 0.00 0.00 0.00 0.60 0.02 0.04 0.34
#> TCGA.BR.8682.01 5 0.3052 0.690211 0.00 0.00 0.02 0.00 0.78 0.00 0.20
#> TCGA.VQ.A91V.01 7 0.4175 0.599828 0.00 0.00 0.38 0.00 0.04 0.00 0.58
#> TCGA.VQ.A8PZ.01 5 0.3546 0.223687 0.00 0.00 0.46 0.00 0.54 0.00 0.00
#> TCGA.BR.8590.01 4 0.4212 0.802126 0.00 0.00 0.00 0.62 0.02 0.02 0.34
#> TCGA.F1.6177.01 2 0.0000 0.913271 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.VQ.A8PQ.01 4 0.0863 0.709965 0.04 0.00 0.00 0.96 0.00 0.00 0.00
#> TCGA.VQ.A91U.01 1 0.3755 0.438477 0.64 0.00 0.00 0.02 0.00 0.34 0.00
#> TCGA.VQ.AA6I.01 3 0.3186 0.446927 0.00 0.00 0.76 0.00 0.00 0.02 0.22
#> TCGA.CG.4437.01 3 0.1166 0.625922 0.00 0.00 0.94 0.00 0.00 0.00 0.06
#> TCGA.VQ.A8PP.01 3 0.2745 0.534993 0.00 0.00 0.82 0.00 0.00 0.02 0.16
#> TCGA.BR.6565.01 1 0.0000 0.918155 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.VQ.A91Y.01 1 0.0000 0.918155 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.VQ.A8PF.01 3 0.3208 0.608138 0.00 0.12 0.82 0.00 0.02 0.00 0.04
#> TCGA.BR.6456.01 1 0.3417 0.724405 0.72 0.00 0.00 0.26 0.02 0.00 0.00
#> TCGA.BR.6458.01 6 0.6277 -0.020633 0.00 0.00 0.04 0.00 0.32 0.34 0.30
#> TCGA.VQ.A925.01 1 0.5723 -0.064000 0.48 0.00 0.00 0.30 0.00 0.02 0.20
#> TCGA.VQ.A927.01 4 0.4211 0.804864 0.00 0.00 0.00 0.68 0.04 0.02 0.26
#> TCGA.BR.8592.01 5 0.0863 0.778191 0.00 0.00 0.00 0.04 0.96 0.00 0.00
#> TCGA.BR.6566.11 4 0.1006 0.715789 0.02 0.00 0.00 0.96 0.02 0.00 0.00
#> TCGA.IN.AB1V.01 1 0.0504 0.907344 0.98 0.00 0.00 0.00 0.00 0.00 0.02
#> TCGA.VQ.AA6F.01 4 0.4212 0.802126 0.00 0.00 0.00 0.62 0.02 0.02 0.34
#> TCGA.VQ.AA6J.01 4 0.5295 0.771035 0.00 0.00 0.00 0.54 0.08 0.04 0.34
#> TCGA.BR.8487.01 2 0.0000 0.913271 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D7.6525.01 3 0.3525 -0.160863 0.00 0.00 0.56 0.00 0.00 0.00 0.44
#> TCGA.VQ.A94O.01 1 0.0000 0.918155 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BR.8588.01 5 0.2278 0.761937 0.00 0.00 0.08 0.00 0.88 0.00 0.04
#> TCGA.HU.8610.01 5 0.3307 0.644451 0.00 0.00 0.00 0.00 0.74 0.02 0.24
#> TCGA.D7.6526.01 1 0.0863 0.904699 0.96 0.00 0.00 0.04 0.00 0.00 0.00
#> TCGA.VQ.A8PD.01 5 0.1166 0.778788 0.00 0.00 0.06 0.00 0.94 0.00 0.00
#> TCGA.D7.6524.01 5 0.2016 0.769010 0.00 0.00 0.06 0.00 0.90 0.00 0.04
#> TCGA.3M.AB46.01 1 0.0504 0.906846 0.98 0.00 0.00 0.00 0.00 0.00 0.02
#> TCGA.3M.AB47.01 5 0.2572 0.757702 0.00 0.00 0.06 0.00 0.86 0.00 0.08
#> TCGA.BR.8677.01 4 0.4162 0.726101 0.00 0.00 0.00 0.74 0.12 0.02 0.12
#> TCGA.BR.6457.01 5 0.1860 0.783684 0.00 0.00 0.04 0.00 0.92 0.02 0.02
#> TCGA.BR.8687.01 1 0.3517 0.700591 0.70 0.00 0.00 0.28 0.02 0.00 0.00
#> TCGA.VQ.A91K.01 2 0.0000 0.913271 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BR.8690.01 4 0.4386 -0.140813 0.42 0.00 0.00 0.54 0.02 0.02 0.00
#> TCGA.BR.8686.01 2 0.4832 0.494317 0.00 0.58 0.34 0.00 0.00 0.04 0.04
#> TCGA.FP.8631.01 1 0.0000 0.918155 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.VQ.A922.01 1 0.0000 0.918155 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BR.A452.01 4 0.4994 0.774184 0.00 0.00 0.00 0.56 0.02 0.08 0.34
#> TCGA.IN.A6RO.01 2 0.0000 0.913271 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BR.A4QI.01 2 0.0504 0.910748 0.00 0.98 0.00 0.00 0.00 0.02 0.00
#> TCGA.D7.A6EV.01 5 0.4978 0.195674 0.00 0.00 0.00 0.00 0.50 0.12 0.38
#> TCGA.HU.A4G2.01 2 0.1718 0.895257 0.00 0.92 0.00 0.00 0.00 0.04 0.04
#> TCGA.BR.A4IY.01 2 0.4882 0.456265 0.00 0.56 0.36 0.00 0.00 0.04 0.04
#> TCGA.VQ.A8PU.01 4 0.4832 0.786383 0.00 0.00 0.00 0.58 0.04 0.04 0.34
#> TCGA.BR.A4J4.01 2 0.2857 0.865088 0.00 0.86 0.06 0.00 0.00 0.04 0.04
#> TCGA.VQ.A94R.01 3 0.3943 -0.130547 0.00 0.00 0.56 0.00 0.00 0.02 0.42
#> TCGA.HU.A4H4.01 3 0.1664 0.629878 0.00 0.00 0.92 0.00 0.02 0.00 0.06
#> TCGA.BR.7707.01 3 0.1886 0.630013 0.00 0.12 0.88 0.00 0.00 0.00 0.00
#> TCGA.FP.7829.01 2 0.0504 0.908422 0.00 0.98 0.00 0.00 0.00 0.02 0.00
#> TCGA.BR.A4J5.01 5 0.2572 0.746317 0.00 0.00 0.06 0.00 0.86 0.00 0.08
#> TCGA.HU.A4H0.01 2 0.1718 0.895257 0.00 0.92 0.00 0.00 0.00 0.04 0.04
#> TCGA.HU.A4HD.01 1 0.0000 0.918155 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.KB.A6F5.01 1 0.0000 0.918155 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.VQ.AA6K.01 4 0.4524 0.796172 0.00 0.00 0.00 0.60 0.02 0.04 0.34
#> TCGA.HF.7133.01 4 0.2864 0.761527 0.00 0.00 0.00 0.84 0.02 0.02 0.12
#> TCGA.F1.6875.01 6 0.3000 0.771916 0.04 0.00 0.00 0.02 0.00 0.84 0.10
#> TCGA.MX.A666.01 1 0.0000 0.918155 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BR.7717.01 7 0.4328 0.631240 0.00 0.00 0.34 0.00 0.06 0.00 0.60
#> TCGA.BR.A4PF.01 3 0.2832 0.430881 0.00 0.00 0.76 0.00 0.00 0.00 0.24
#> TCGA.BR.A4IU.01 5 0.1006 0.783974 0.00 0.00 0.02 0.00 0.96 0.00 0.02
#> TCGA.VQ.A8PX.01 4 0.3927 0.801077 0.04 0.00 0.00 0.66 0.00 0.00 0.30
#> TCGA.BR.A4IV.01 4 0.4211 0.804864 0.00 0.00 0.00 0.68 0.04 0.02 0.26
#> TCGA.D7.A6EX.01 4 0.4718 0.793130 0.00 0.00 0.00 0.60 0.02 0.06 0.32
#> TCGA.BR.A4IZ.01 4 0.2803 0.759190 0.00 0.00 0.00 0.84 0.06 0.00 0.10
#> TCGA.BR.A4J9.01 4 0.4212 0.802126 0.00 0.00 0.00 0.62 0.02 0.02 0.34
#> TCGA.CD.A4MJ.01 2 0.0863 0.907083 0.00 0.96 0.00 0.00 0.00 0.04 0.00
#> TCGA.B7.A5TN.01 1 0.0000 0.918155 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BR.7715.01 6 0.4597 0.445662 0.00 0.00 0.00 0.00 0.08 0.56 0.36
#> TCGA.BR.7704.01 1 0.2864 0.836427 0.84 0.00 0.00 0.12 0.02 0.02 0.00
#> TCGA.BR.A4J1.01 1 0.0000 0.918155 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HU.A4GP.01 3 0.5105 -0.075107 0.00 0.08 0.50 0.00 0.00 0.02 0.40
#> TCGA.D7.A4YY.01 2 0.0000 0.913271 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.VQ.AA6G.01 3 0.5844 0.125901 0.00 0.32 0.44 0.00 0.00 0.02 0.22
#> TCGA.HU.A4GJ.01 5 0.0504 0.784483 0.00 0.00 0.02 0.00 0.98 0.00 0.00
#> TCGA.CD.A4MI.01 3 0.1671 0.638760 0.00 0.10 0.90 0.00 0.00 0.00 0.00
#> TCGA.BR.7196.01 5 0.2422 0.690919 0.00 0.00 0.18 0.00 0.82 0.00 0.00
#> TCGA.BR.6563.01 5 0.3991 0.631500 0.00 0.00 0.00 0.04 0.72 0.02 0.22
#> TCGA.VQ.A924.01 3 0.1886 0.630013 0.00 0.12 0.88 0.00 0.00 0.00 0.00
#> TCGA.BR.7716.01 1 0.2906 0.799906 0.80 0.00 0.00 0.18 0.02 0.00 0.00
#> TCGA.FP.7735.01 4 0.4146 0.805376 0.00 0.00 0.00 0.64 0.02 0.02 0.32
#> TCGA.BR.7723.01 1 0.0000 0.918155 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HU.A4H8.01 2 0.0000 0.913271 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.IN.A6RJ.01 5 0.2016 0.777989 0.00 0.00 0.06 0.00 0.90 0.00 0.04
#> TCGA.HU.A4H3.01 2 0.0000 0.913271 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EQ.A4SO.01 4 0.4742 0.734039 0.16 0.00 0.00 0.62 0.00 0.00 0.22
#> TCGA.CD.A4MH.01 1 0.2864 0.836427 0.84 0.00 0.00 0.12 0.02 0.02 0.00
#> TCGA.BR.A4J7.01 4 0.4524 0.796172 0.00 0.00 0.00 0.60 0.02 0.04 0.34
#> TCGA.HF.7131.01 1 0.3606 0.675385 0.68 0.00 0.00 0.30 0.02 0.00 0.00
#> TCGA.D7.A74B.01 4 0.1166 0.694077 0.06 0.00 0.00 0.94 0.00 0.00 0.00
#> TCGA.BR.A4PE.01 2 0.0000 0.913271 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BR.A4J8.01 3 0.1671 0.638760 0.00 0.10 0.90 0.00 0.00 0.00 0.00
#> TCGA.HU.A4GX.01 5 0.2213 0.773095 0.00 0.00 0.00 0.04 0.90 0.02 0.04
#> TCGA.HU.A4G8.01 3 0.2016 0.629338 0.00 0.00 0.90 0.00 0.04 0.00 0.06
#> TCGA.HU.A4GT.01 2 0.0504 0.908422 0.00 0.98 0.00 0.00 0.00 0.02 0.00
#> TCGA.HU.A4GC.01 7 0.4615 0.625890 0.00 0.00 0.30 0.00 0.10 0.00 0.60
#> TCGA.BR.A4CQ.01 2 0.0000 0.913271 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D7.A6F2.01 1 0.0504 0.909198 0.98 0.00 0.00 0.00 0.00 0.02 0.00
#> TCGA.RD.A7BT.01 6 0.1363 0.829204 0.00 0.00 0.00 0.02 0.04 0.94 0.00
#> TCGA.BR.A4J6.01 4 0.1363 0.749754 0.00 0.00 0.00 0.94 0.02 0.00 0.04
#> TCGA.HU.A4GQ.01 2 0.0863 0.907083 0.00 0.96 0.00 0.00 0.00 0.04 0.00
#> TCGA.HF.7136.01 1 0.0000 0.918155 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BR.A4QM.01 2 0.2016 0.886614 0.00 0.90 0.06 0.00 0.00 0.04 0.00
#> TCGA.BR.A4PD.01 6 0.1664 0.827428 0.00 0.00 0.00 0.02 0.06 0.92 0.00
#> TCGA.VQ.A8PK.01 1 0.0000 0.918155 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.B7.A5TK.01 3 0.3546 -0.000521 0.00 0.00 0.54 0.00 0.46 0.00 0.00
#> TCGA.D7.A4YX.01 2 0.1718 0.895257 0.00 0.92 0.00 0.00 0.00 0.04 0.04
#> TCGA.D7.A4Z0.01 3 0.3835 0.496113 0.00 0.00 0.74 0.00 0.10 0.00 0.16
#> TCGA.VQ.A8PT.01 2 0.0000 0.913271 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.IN.A6RN.01 1 0.0863 0.904699 0.96 0.00 0.00 0.04 0.00 0.00 0.00
#> TCGA.CD.A4MG.01 2 0.0000 0.913271 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D7.A747.01 4 0.4211 0.804864 0.00 0.00 0.00 0.68 0.04 0.02 0.26
#> TCGA.R5.A7O7.01 5 0.2563 0.772273 0.00 0.00 0.04 0.00 0.88 0.04 0.04
#> TCGA.F1.A72C.01 4 0.4146 0.805376 0.00 0.00 0.00 0.64 0.02 0.02 0.32
#> TCGA.BR.A4J2.01 5 0.0863 0.779852 0.00 0.00 0.00 0.00 0.96 0.04 0.00
#> TCGA.MX.A663.01 1 0.0000 0.918155 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D7.A4YV.01 2 0.0504 0.908422 0.00 0.98 0.00 0.00 0.00 0.02 0.00
#> TCGA.HU.A4GD.01 6 0.2654 0.809911 0.00 0.00 0.00 0.02 0.10 0.86 0.02
#> TCGA.BR.A4QL.01 2 0.0000 0.913271 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BR.7703.01 2 0.0504 0.908422 0.00 0.98 0.00 0.00 0.00 0.02 0.00
#> TCGA.VQ.AA6B.01 5 0.4478 0.567322 0.00 0.00 0.00 0.00 0.66 0.14 0.20
#> TCGA.VQ.AA6D.01 1 0.1860 0.888376 0.92 0.00 0.00 0.04 0.02 0.02 0.00
#> TCGA.D7.A6EZ.01 2 0.1718 0.895257 0.00 0.92 0.00 0.00 0.00 0.04 0.04
#> TCGA.D7.A4YU.01 2 0.1006 0.908262 0.00 0.96 0.02 0.00 0.00 0.02 0.00
#> TCGA.VQ.AA6A.01 6 0.2159 0.798219 0.06 0.00 0.00 0.02 0.02 0.90 0.00
#> TCGA.IN.7806.01 6 0.1363 0.815168 0.04 0.00 0.00 0.02 0.00 0.94 0.00
#> TCGA.HU.A4HB.01 5 0.2376 0.734559 0.00 0.00 0.00 0.00 0.86 0.02 0.12
#> TCGA.HU.A4H2.01 6 0.4451 0.551247 0.00 0.00 0.00 0.00 0.10 0.64 0.26
#> TCGA.IN.A6RP.01 3 0.3867 0.018175 0.00 0.00 0.60 0.00 0.00 0.02 0.38
#> TCGA.HU.A4H5.01 1 0.0000 0.918155 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HU.A4GU.01 2 0.0000 0.913271 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.MX.A5UJ.01 3 0.3315 0.630831 0.00 0.08 0.82 0.00 0.00 0.02 0.08
#> TCGA.HU.A4GN.01 2 0.0000 0.913271 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CD.5804.01 1 0.0000 0.918155 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HU.A4H6.01 3 0.1671 0.638760 0.00 0.10 0.90 0.00 0.00 0.00 0.00
#> TCGA.HF.7132.01 3 0.1166 0.625922 0.00 0.00 0.94 0.00 0.00 0.00 0.06
#> TCGA.D7.A4YT.01 1 0.0000 0.918155 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HF.7134.01 2 0.2159 0.849232 0.00 0.90 0.06 0.00 0.00 0.02 0.02
#> TCGA.BR.6852.01 3 0.1166 0.632013 0.00 0.00 0.94 0.00 0.06 0.00 0.00
#> TCGA.BR.8370.01 2 0.0863 0.907083 0.00 0.96 0.00 0.00 0.00 0.04 0.00
#> TCGA.EQ.5647.01 4 0.2864 0.761527 0.00 0.00 0.00 0.84 0.02 0.02 0.12
#> TCGA.IN.A7NT.01 6 0.1928 0.810461 0.00 0.00 0.00 0.00 0.08 0.90 0.02
#> TCGA.RD.A8N9.01 4 0.2569 0.636458 0.14 0.00 0.00 0.84 0.02 0.00 0.00
#> TCGA.D7.5577.01 2 0.4882 0.452215 0.00 0.56 0.36 0.00 0.00 0.04 0.04
#> TCGA.CG.5717.01 4 0.4305 0.805762 0.00 0.00 0.00 0.66 0.04 0.02 0.28
#> TCGA.D7.6818.01 1 0.0000 0.918155 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CG.5734.01 5 0.4461 0.484939 0.00 0.00 0.00 0.04 0.62 0.02 0.32
#> TCGA.VQ.A8P8.01 3 0.2708 0.480531 0.00 0.00 0.78 0.00 0.22 0.00 0.00
#> TCGA.BR.6707.01 3 0.3691 0.594834 0.00 0.12 0.80 0.00 0.02 0.02 0.04
#> TCGA.B7.5818.01 2 0.2857 0.865088 0.00 0.86 0.06 0.00 0.00 0.04 0.04
#> TCGA.CD.8525.01 1 0.3052 0.782077 0.78 0.00 0.00 0.20 0.02 0.00 0.00
#> TCGA.BR.6705.01 5 0.1363 0.779921 0.00 0.00 0.02 0.04 0.94 0.00 0.00
#> TCGA.BR.4288.01 1 0.0000 0.918155 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CD.5813.01 4 0.4524 0.796172 0.00 0.00 0.00 0.60 0.02 0.04 0.34
#> TCGA.CG.5723.01 4 0.4832 0.786383 0.00 0.00 0.00 0.58 0.04 0.04 0.34
#> TCGA.CD.5800.01 1 0.1664 0.885730 0.92 0.00 0.00 0.06 0.02 0.00 0.00
#> TCGA.CG.5718.01 1 0.2376 0.846145 0.86 0.00 0.00 0.12 0.02 0.00 0.00
#> TCGA.BR.8080.01 6 0.2572 0.798270 0.00 0.00 0.00 0.06 0.08 0.86 0.00
#> TCGA.CG.5733.01 3 0.1886 0.630013 0.00 0.12 0.88 0.00 0.00 0.00 0.00
#> TCGA.D7.6817.01 1 0.0000 0.918155 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.KB.A93G.01 4 0.4211 0.804864 0.00 0.00 0.00 0.68 0.04 0.02 0.26
#> TCGA.CD.5799.01 1 0.0000 0.918155 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BR.7851.01 2 0.1363 0.903512 0.00 0.94 0.02 0.00 0.00 0.04 0.00
#> TCGA.BR.7722.01 4 0.4146 0.805376 0.00 0.00 0.00 0.64 0.02 0.02 0.32
#> TCGA.MX.A5UG.01 5 0.3208 0.725123 0.00 0.00 0.00 0.04 0.82 0.02 0.12
#> TCGA.CD.8533.01 7 0.4487 0.608580 0.00 0.00 0.32 0.00 0.08 0.00 0.60
#> TCGA.BR.7957.01 5 0.1363 0.779921 0.00 0.00 0.02 0.04 0.94 0.00 0.00
#> TCGA.CG.5722.01 3 0.3525 0.068884 0.00 0.00 0.56 0.00 0.44 0.00 0.00
#> TCGA.F1.6874.01 5 0.1860 0.781443 0.00 0.00 0.02 0.00 0.92 0.02 0.04
#> TCGA.CG.5730.01 6 0.1860 0.829616 0.00 0.00 0.00 0.02 0.04 0.92 0.02
#> TCGA.CG.5726.01 2 0.3848 0.666314 0.00 0.76 0.16 0.00 0.00 0.02 0.06
#> TCGA.IP.7968.01 6 0.1860 0.829616 0.00 0.00 0.00 0.02 0.04 0.92 0.02
#> TCGA.BR.8363.01 3 0.1166 0.632013 0.00 0.00 0.94 0.00 0.06 0.00 0.00
#> TCGA.BR.7901.01 1 0.0000 0.918155 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D7.6822.01 7 0.4787 0.525921 0.00 0.00 0.12 0.00 0.30 0.00 0.58
#> TCGA.BR.6710.01 4 0.3052 0.668945 0.20 0.00 0.00 0.78 0.00 0.00 0.02
#> TCGA.CG.5720.01 3 0.1166 0.625922 0.00 0.00 0.94 0.00 0.00 0.00 0.06
#> TCGA.D7.8570.01 3 0.3208 0.608138 0.00 0.12 0.82 0.00 0.02 0.00 0.04
#> TCGA.B7.A5TI.01 4 0.4146 0.802493 0.02 0.00 0.00 0.64 0.00 0.02 0.32
#> TCGA.D7.6815.01 6 0.1664 0.827428 0.00 0.00 0.00 0.02 0.06 0.92 0.00
#> TCGA.BR.8284.01 3 0.1166 0.625922 0.00 0.00 0.94 0.00 0.00 0.00 0.06
#> TCGA.BR.8295.01 1 0.0863 0.904699 0.96 0.00 0.00 0.04 0.00 0.00 0.00
#> TCGA.BR.7197.01 6 0.2159 0.798219 0.06 0.00 0.00 0.02 0.02 0.90 0.00
#> TCGA.B7.A5TJ.01 2 0.0000 0.913271 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D7.A6EY.01 5 0.3902 0.689243 0.00 0.00 0.04 0.00 0.76 0.16 0.04
#> TCGA.BR.8366.01 3 0.3208 0.608138 0.00 0.12 0.82 0.00 0.02 0.00 0.04
#> TCGA.IN.A7NR.01 4 0.1363 0.704184 0.04 0.00 0.00 0.94 0.02 0.00 0.00
#> TCGA.BR.6706.01 5 0.2422 0.690919 0.00 0.00 0.18 0.00 0.82 0.00 0.00
#> TCGA.IN.7808.01 7 0.4692 0.296312 0.00 0.00 0.08 0.00 0.42 0.00 0.50
#> TCGA.BR.6564.01 4 0.0863 0.709965 0.04 0.00 0.00 0.96 0.00 0.00 0.00
#> TCGA.KB.A93H.01 6 0.1860 0.829616 0.00 0.00 0.00 0.02 0.04 0.92 0.02
#> TCGA.KB.A93J.01 4 0.5196 0.720620 0.16 0.00 0.00 0.60 0.00 0.02 0.22
#> TCGA.CD.5798.01 4 0.4524 0.803065 0.00 0.00 0.00 0.60 0.04 0.02 0.34
#> TCGA.CD.8530.01 6 0.5347 0.582135 0.12 0.00 0.00 0.02 0.02 0.62 0.22
#> TCGA.BR.6802.01 5 0.2313 0.760448 0.00 0.00 0.06 0.00 0.88 0.00 0.06
#> TCGA.CG.5719.01 4 0.2163 0.772566 0.00 0.00 0.00 0.88 0.02 0.00 0.10
#> TCGA.VQ.A8E3.01 3 0.4001 0.541953 0.00 0.06 0.74 0.00 0.00 0.02 0.18
#> TCGA.CD.5801.01 3 0.2016 0.620748 0.00 0.00 0.90 0.00 0.06 0.00 0.04
#> TCGA.FP.A9TM.01 3 0.2708 0.463277 0.00 0.00 0.78 0.00 0.00 0.00 0.22
#> TCGA.BR.7958.01 2 0.4954 0.366832 0.00 0.52 0.40 0.00 0.00 0.04 0.04
#> TCGA.FP.7998.01 3 0.3546 -0.000521 0.00 0.00 0.54 0.00 0.46 0.00 0.00
#> TCGA.IN.A6RS.01 7 0.4698 0.632291 0.00 0.00 0.14 0.00 0.24 0.00 0.62
#> TCGA.BR.6709.01 4 0.0504 0.723206 0.00 0.00 0.00 0.98 0.02 0.00 0.00
#> TCGA.FP.7916.01 3 0.3208 0.608138 0.00 0.12 0.82 0.00 0.02 0.00 0.04
#> TCGA.R5.A7ZR.01 6 0.2159 0.798219 0.06 0.00 0.00 0.02 0.02 0.90 0.00
#> TCGA.B7.5816.01 3 0.2313 0.628119 0.00 0.00 0.88 0.00 0.06 0.00 0.06
#> TCGA.CG.5721.01 5 0.2313 0.767829 0.00 0.00 0.06 0.00 0.88 0.00 0.06
#> TCGA.SW.A7EA.01 2 0.0000 0.913271 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.RD.A8NB.01 5 0.1433 0.771330 0.00 0.00 0.08 0.00 0.92 0.00 0.00
#> TCGA.BR.6801.01 4 0.4524 0.796172 0.00 0.00 0.00 0.60 0.02 0.04 0.34
#> TCGA.IN.AB1X.01 3 0.2313 0.628119 0.00 0.00 0.88 0.00 0.06 0.00 0.06
#> TCGA.D7.5579.01 4 0.5083 0.787964 0.00 0.00 0.00 0.56 0.04 0.06 0.34
#> TCGA.CG.5728.01 5 0.2278 0.761937 0.00 0.00 0.08 0.00 0.88 0.00 0.04
#> TCGA.R5.A7ZI.01 4 0.0000 0.725206 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.IN.A7NU.01 7 0.4638 0.584666 0.00 0.00 0.38 0.00 0.08 0.00 0.54
#> TCGA.CG.5732.01 1 0.0000 0.918155 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.ZQ.A9CR.01 1 0.2864 0.836427 0.84 0.00 0.00 0.12 0.02 0.02 0.00
#> TCGA.D7.5578.01 6 0.5957 0.206442 0.00 0.00 0.04 0.00 0.18 0.46 0.32
#> TCGA.BR.6803.01 4 0.0863 0.709965 0.04 0.00 0.00 0.96 0.00 0.00 0.00
#> TCGA.BR.8368.01 2 0.0504 0.908422 0.00 0.98 0.00 0.00 0.00 0.02 0.00
#> TCGA.SW.A7EB.01 1 0.0000 0.918155 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BR.8081.01 3 0.1166 0.632013 0.00 0.00 0.94 0.00 0.06 0.00 0.00
#> TCGA.VQ.A8P5.01 5 0.4108 0.534842 0.00 0.00 0.06 0.00 0.66 0.00 0.28
#> TCGA.CD.8535.01 7 0.3562 0.340475 0.00 0.00 0.50 0.00 0.00 0.00 0.50
#> TCGA.CG.5724.01 7 0.3558 0.406154 0.00 0.00 0.48 0.00 0.00 0.00 0.52
#> TCGA.D7.8574.01 4 0.4461 0.805570 0.00 0.00 0.00 0.62 0.04 0.02 0.32
#> TCGA.HJ.7597.01 4 0.0504 0.718154 0.02 0.00 0.00 0.98 0.00 0.00 0.00
#> TCGA.HF.A5NB.01 2 0.0504 0.908422 0.00 0.98 0.00 0.00 0.00 0.02 0.00
#> TCGA.VQ.A8PB.01 7 0.3994 0.410401 0.00 0.00 0.48 0.00 0.02 0.00 0.50
#> TCGA.R5.A7ZE.01 1 0.1860 0.888376 0.92 0.00 0.00 0.04 0.02 0.02 0.00
#> TCGA.CD.5803.01 4 0.0504 0.723206 0.00 0.00 0.00 0.98 0.02 0.00 0.00
#> TCGA.CG.5725.01 1 0.0000 0.918155 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D7.6820.01 1 0.0000 0.918155 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CD.5802.01 1 0.0504 0.906427 0.98 0.00 0.00 0.02 0.00 0.00 0.00
#> TCGA.R5.A7ZF.01 4 0.1363 0.704184 0.04 0.00 0.00 0.94 0.02 0.00 0.00
#> TCGA.D7.A6F0.01 1 0.0863 0.904699 0.96 0.00 0.00 0.04 0.00 0.00 0.00
#> TCGA.CG.5727.01 6 0.2421 0.820764 0.00 0.00 0.00 0.02 0.08 0.88 0.02
#> TCGA.VQ.A8PC.01 5 0.2745 0.717983 0.00 0.00 0.00 0.00 0.82 0.02 0.16
#> TCGA.CD.A486.01 1 0.0000 0.918155 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.RD.A8N2.01 4 0.0863 0.709965 0.04 0.00 0.00 0.96 0.00 0.00 0.00
#> TCGA.IN.A6RI.01 1 0.0000 0.918155 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HU.8243.01 6 0.3186 0.678419 0.00 0.00 0.00 0.00 0.02 0.76 0.22
#> TCGA.CD.A48C.01 3 0.5123 -0.073243 0.00 0.08 0.48 0.00 0.00 0.02 0.42
#> TCGA.RD.A8N5.01 4 0.4388 0.805317 0.00 0.00 0.00 0.64 0.04 0.02 0.30
#> TCGA.RD.A8N1.01 1 0.0000 0.918155 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HU.A4GF.01 1 0.1006 0.902818 0.96 0.00 0.00 0.00 0.02 0.02 0.00
#> TCGA.BR.8362.01 5 0.3186 0.667742 0.00 0.00 0.02 0.00 0.76 0.00 0.22
#> TCGA.BR.8285.01 3 0.3208 0.608138 0.00 0.12 0.82 0.00 0.02 0.00 0.04
#> TCGA.CD.8532.01 4 0.4146 0.805376 0.00 0.00 0.00 0.64 0.02 0.02 0.32
#> TCGA.VQ.A8E2.01 1 0.0000 0.918155 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BR.8373.01 6 0.1860 0.810008 0.04 0.00 0.00 0.02 0.02 0.92 0.00
#> TCGA.BR.8361.01 3 0.3541 0.620818 0.00 0.08 0.80 0.00 0.00 0.02 0.10
#> TCGA.BR.8058.01 4 0.0504 0.723206 0.00 0.00 0.00 0.98 0.02 0.00 0.00
#> TCGA.IN.8462.01 3 0.3525 -0.160863 0.00 0.00 0.56 0.00 0.00 0.00 0.44
#> TCGA.HU.A4G9.01 2 0.0000 0.913271 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CD.8524.01 6 0.6196 0.027182 0.00 0.00 0.04 0.00 0.24 0.38 0.34
#> TCGA.D7.A748.01 4 0.0863 0.732318 0.00 0.00 0.00 0.96 0.04 0.00 0.00
#> TCGA.CD.8527.01 6 0.1363 0.829204 0.00 0.00 0.00 0.02 0.04 0.94 0.00
#> TCGA.VQ.A8DV.01 1 0.0000 0.918155 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CD.8528.01 2 0.0504 0.908422 0.00 0.98 0.00 0.00 0.00 0.02 0.00
#> TCGA.BR.A453.01 5 0.3208 0.725123 0.00 0.00 0.00 0.04 0.82 0.02 0.12
#> TCGA.RD.A8N6.01 1 0.0504 0.911949 0.98 0.00 0.00 0.02 0.00 0.00 0.00
#> TCGA.HU.8245.01 1 0.0000 0.918155 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.ZA.A8F6.01 4 0.4832 0.796664 0.00 0.00 0.00 0.58 0.04 0.04 0.34
#> TCGA.BR.8367.01 5 0.2745 0.726209 0.00 0.00 0.02 0.00 0.82 0.00 0.16
#> TCGA.BR.8380.01 5 0.3525 0.280277 0.00 0.00 0.44 0.00 0.56 0.00 0.00
#> TCGA.FP.A4BE.01 2 0.0000 0.913271 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HU.8238.01 7 0.3459 0.559057 0.00 0.00 0.40 0.00 0.00 0.00 0.60
#> TCGA.BR.8078.01 2 0.0863 0.907083 0.00 0.96 0.00 0.00 0.00 0.04 0.00
#> TCGA.HU.8249.01 6 0.3541 0.781238 0.00 0.00 0.00 0.02 0.10 0.80 0.08
#> TCGA.RD.A8N0.01 4 0.1006 0.715789 0.02 0.00 0.00 0.96 0.02 0.00 0.00
#> TCGA.BR.8365.01 4 0.0863 0.709965 0.04 0.00 0.00 0.96 0.00 0.00 0.00
#> TCGA.FP.8211.01 4 0.4212 0.802126 0.00 0.00 0.00 0.62 0.02 0.02 0.34
#> TCGA.RD.A8N4.01 4 0.0863 0.709965 0.04 0.00 0.00 0.96 0.00 0.00 0.00
#> TCGA.VQ.A8DU.01 1 0.0000 0.918155 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.VQ.A8DL.01 1 0.3517 0.702659 0.70 0.00 0.00 0.28 0.02 0.00 0.00
#> TCGA.VQ.A8DZ.01 1 0.0000 0.918155 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D7.8572.01 1 0.0000 0.918155 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.RD.A7BW.01 4 0.1166 0.694077 0.06 0.00 0.00 0.94 0.00 0.00 0.00
#> TCGA.R5.A804.01 5 0.2572 0.746317 0.00 0.00 0.06 0.00 0.86 0.00 0.08
#> TCGA.BR.A4CS.01 7 0.4669 0.302318 0.00 0.00 0.08 0.00 0.40 0.00 0.52
#> TCGA.CD.8531.01 2 0.4623 0.602208 0.00 0.64 0.28 0.00 0.00 0.04 0.04
#> TCGA.CD.A487.01 6 0.3396 0.748985 0.00 0.00 0.00 0.02 0.04 0.80 0.14
#> TCGA.BR.8371.01 4 0.4211 0.804864 0.00 0.00 0.00 0.68 0.04 0.02 0.26
#> TCGA.BR.8059.01 6 0.3991 0.675068 0.00 0.00 0.00 0.02 0.04 0.72 0.22
#> TCGA.D7.A6ET.01 5 0.2722 0.730468 0.00 0.00 0.00 0.04 0.84 0.00 0.12
#> TCGA.FP.8099.01 7 0.4718 0.629875 0.00 0.00 0.32 0.00 0.06 0.02 0.60
#> TCGA.D7.8579.01 5 0.1363 0.783434 0.00 0.00 0.04 0.00 0.94 0.00 0.02
#> TCGA.BR.8297.01 5 0.4388 0.501805 0.00 0.00 0.04 0.00 0.64 0.02 0.30
#> TCGA.D7.8576.01 4 0.3780 0.804936 0.00 0.00 0.00 0.72 0.02 0.02 0.24
#> TCGA.VQ.A8DT.01 3 0.3546 -0.237416 0.00 0.00 0.54 0.00 0.00 0.00 0.46
#> TCGA.FP.A8CX.01 6 0.1363 0.829204 0.00 0.00 0.00 0.02 0.04 0.94 0.00
#> TCGA.HU.A4GH.01 1 0.0000 0.918155 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CD.8526.01 1 0.3052 0.782077 0.78 0.00 0.00 0.20 0.02 0.00 0.00
#> TCGA.HU.A4G6.01 2 0.1718 0.895257 0.00 0.92 0.00 0.00 0.00 0.04 0.04
#> TCGA.D7.8578.01 1 0.5665 -0.353441 0.42 0.00 0.00 0.40 0.00 0.02 0.16
#> TCGA.HU.A4G3.01 3 0.3459 -0.017149 0.00 0.00 0.60 0.00 0.00 0.00 0.40
#> TCGA.D7.A74A.01 3 0.4587 0.509675 0.00 0.10 0.68 0.00 0.00 0.02 0.20
#> TCGA.RD.A7C1.01 3 0.3358 0.102668 0.00 0.00 0.64 0.00 0.00 0.00 0.36
#> TCGA.F1.A448.01 3 0.2278 0.620951 0.00 0.00 0.88 0.00 0.04 0.00 0.08
#> TCGA.D7.8575.01 5 0.3530 0.706615 0.00 0.00 0.00 0.02 0.76 0.02 0.20
#> TCGA.BR.8372.01 2 0.0000 0.913271 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.VQ.A8P3.01 3 0.3525 -0.160863 0.00 0.00 0.56 0.00 0.00 0.00 0.44
#> TCGA.RD.A8MW.01 1 0.0000 0.918155 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BR.8286.01 3 0.3546 -0.236577 0.00 0.00 0.54 0.00 0.00 0.00 0.46
#> TCGA.BR.8369.01 5 0.4638 0.207847 0.00 0.00 0.08 0.00 0.54 0.00 0.38
#> TCGA.BR.8364.01 4 0.0863 0.709965 0.04 0.00 0.00 0.96 0.00 0.00 0.00
#> TCGA.HU.8244.01 2 0.3000 0.781302 0.00 0.84 0.10 0.00 0.00 0.02 0.04
#> TCGA.KB.A6F7.01 1 0.0863 0.904699 0.96 0.00 0.00 0.04 0.00 0.00 0.00
#> TCGA.FP.A4BF.01 3 0.3525 -0.160863 0.00 0.00 0.56 0.00 0.00 0.00 0.44
#> TCGA.R5.A805.01 7 0.4737 0.459807 0.00 0.00 0.10 0.00 0.34 0.00 0.56
#> TCGA.IN.A6RL.01 6 0.1860 0.829616 0.00 0.00 0.00 0.02 0.04 0.92 0.02
#> TCGA.IN.A6RR.01 2 0.5798 -0.146370 0.00 0.44 0.34 0.00 0.00 0.02 0.20
#> TCGA.BR.A4CR.01 1 0.0863 0.904699 0.96 0.00 0.00 0.04 0.00 0.00 0.00
#> TCGA.CD.A489.01 4 0.5330 0.755841 0.00 0.00 0.00 0.54 0.06 0.06 0.34
#> TCGA.HU.A4GY.01 4 0.3744 0.756215 0.00 0.00 0.00 0.78 0.08 0.02 0.12
#> TCGA.BR.8289.01 6 0.1363 0.829204 0.00 0.00 0.00 0.02 0.04 0.94 0.00
#> TCGA.FP.8209.01 4 0.3566 0.785925 0.02 0.00 0.00 0.78 0.04 0.00 0.16
#> TCGA.BR.8296.01 3 0.2708 0.481161 0.00 0.00 0.78 0.00 0.22 0.00 0.00
#> TCGA.CD.A48A.01 7 0.4908 0.608989 0.00 0.00 0.10 0.00 0.26 0.02 0.62
#> TCGA.BR.8060.01 1 0.0863 0.904699 0.96 0.00 0.00 0.04 0.00 0.00 0.00
#> TCGA.BR.8077.01 1 0.4378 0.676716 0.70 0.00 0.00 0.08 0.02 0.20 0.00
#> TCGA.CD.8534.01 5 0.2864 0.747017 0.00 0.00 0.02 0.00 0.84 0.02 0.12
#> TCGA.BR.7959.01 7 0.4630 0.591841 0.00 0.00 0.12 0.00 0.26 0.00 0.62
#> TCGA.VQ.A8P2.01 2 0.0000 0.913271 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EQ.8122.01 1 0.2163 0.860069 0.88 0.00 0.00 0.10 0.02 0.00 0.00
#> TCGA.D7.8573.01 2 0.1718 0.895257 0.00 0.92 0.00 0.00 0.00 0.04 0.04
#> TCGA.BR.A44T.01 4 0.1006 0.715789 0.02 0.00 0.00 0.96 0.02 0.00 0.00
#> TCGA.RD.A8MV.01 5 0.5604 0.270242 0.00 0.00 0.00 0.02 0.48 0.16 0.34
#> TCGA.CD.8536.01 7 0.3562 0.347781 0.00 0.00 0.50 0.00 0.00 0.00 0.50
#> TCGA.BR.8360.01 2 0.0000 0.913271 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BR.8291.01 4 0.3815 0.484971 0.36 0.00 0.00 0.62 0.00 0.00 0.02
#> TCGA.FP.8210.01 4 0.4211 0.804864 0.00 0.00 0.00 0.68 0.04 0.02 0.26
#> TCGA.RD.A7BS.01 4 0.4524 0.803065 0.00 0.00 0.00 0.60 0.04 0.02 0.34
#> TCGA.BR.A44U.01 7 0.3496 0.531448 0.00 0.00 0.42 0.00 0.00 0.00 0.58
#> TCGA.CD.8529.01 4 0.5330 0.757696 0.06 0.00 0.00 0.54 0.00 0.06 0.34
cbind(get_classes(res, k = 8), get_membership(res, k = 8))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7 p8
#> TCGA.VQ.A94P.01 4 0.2591 0.6785 0.00 0.00 0.04 0.86 0.02 0.00 0.00 0.08
#> TCGA.D7.6521.01 4 0.2204 0.7226 0.00 0.00 0.04 0.90 0.02 0.02 0.00 0.02
#> TCGA.VQ.A8PE.01 1 0.0000 0.9125 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D7.6519.01 1 0.5231 0.3153 0.52 0.00 0.04 0.12 0.00 0.00 0.00 0.32
#> TCGA.BR.6452.01 3 0.4004 0.5895 0.00 0.00 0.50 0.00 0.00 0.00 0.46 0.04
#> TCGA.BR.8485.01 1 0.3337 0.7971 0.78 0.00 0.04 0.00 0.00 0.02 0.00 0.16
#> TCGA.VQ.A8PO.01 7 0.4004 -0.5815 0.00 0.00 0.46 0.00 0.00 0.00 0.50 0.04
#> TCGA.VQ.AA69.01 2 0.2132 0.8666 0.00 0.88 0.04 0.00 0.00 0.00 0.00 0.08
#> TCGA.BR.8683.01 5 0.6374 0.5038 0.00 0.00 0.10 0.16 0.52 0.06 0.00 0.16
#> TCGA.BR.8486.01 1 0.4174 0.5808 0.62 0.00 0.04 0.02 0.00 0.00 0.00 0.32
#> TCGA.D7.6522.01 4 0.2591 0.6785 0.00 0.00 0.04 0.86 0.02 0.00 0.00 0.08
#> TCGA.CG.5716.01 5 0.1741 0.7436 0.00 0.00 0.04 0.02 0.92 0.00 0.00 0.02
#> TCGA.BR.8589.01 2 0.2648 0.8474 0.00 0.84 0.08 0.00 0.00 0.00 0.00 0.08
#> TCGA.BR.8382.01 3 0.3272 0.7690 0.00 0.00 0.58 0.00 0.00 0.00 0.42 0.00
#> TCGA.VQ.AA68.01 7 0.0000 0.5547 0.00 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.VQ.A8PJ.01 1 0.0471 0.9034 0.98 0.00 0.00 0.00 0.00 0.00 0.00 0.02
#> TCGA.VQ.A8PH.01 1 0.0000 0.9125 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HU.8604.01 3 0.3193 0.7716 0.00 0.00 0.62 0.00 0.00 0.00 0.38 0.00
#> TCGA.BR.8676.01 2 0.2862 0.8391 0.00 0.82 0.10 0.00 0.00 0.00 0.00 0.08
#> TCGA.CG.4441.01 6 0.3128 0.7699 0.00 0.00 0.04 0.00 0.04 0.82 0.00 0.10
#> TCGA.D7.6520.01 1 0.0000 0.9125 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.VQ.AA64.01 4 0.0471 0.7192 0.00 0.00 0.00 0.98 0.00 0.00 0.00 0.02
#> TCGA.D7.6527.01 1 0.0000 0.9125 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.VQ.A8PM.01 1 0.0000 0.9125 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.VQ.A923.01 2 0.3385 0.7896 0.00 0.76 0.16 0.00 0.00 0.00 0.00 0.08
#> TCGA.BR.8384.01 5 0.1741 0.7436 0.00 0.00 0.04 0.02 0.92 0.00 0.00 0.02
#> TCGA.BR.6453.01 5 0.0808 0.7532 0.00 0.00 0.04 0.00 0.96 0.00 0.00 0.00
#> TCGA.VQ.A928.01 4 0.2020 0.6973 0.00 0.00 0.02 0.90 0.00 0.02 0.00 0.06
#> TCGA.VQ.A8E0.01 4 0.0471 0.7192 0.00 0.00 0.00 0.98 0.00 0.00 0.00 0.02
#> TCGA.BR.8679.01 7 0.3907 -0.2859 0.00 0.00 0.38 0.00 0.00 0.00 0.58 0.04
#> TCGA.VQ.A91S.01 5 0.4590 0.6097 0.00 0.00 0.10 0.00 0.68 0.06 0.00 0.16
#> TCGA.BR.8678.01 1 0.4004 0.0702 0.50 0.00 0.00 0.00 0.00 0.46 0.00 0.04
#> TCGA.D7.6528.01 6 0.4394 0.7039 0.00 0.00 0.06 0.00 0.08 0.70 0.00 0.16
#> TCGA.VQ.A8E7.01 7 0.6614 0.2532 0.00 0.00 0.22 0.00 0.20 0.04 0.44 0.10
#> TCGA.BR.8680.01 5 0.6417 0.3913 0.00 0.00 0.24 0.00 0.44 0.04 0.06 0.22
#> TCGA.BR.8483.01 6 0.6219 0.4404 0.00 0.00 0.24 0.00 0.06 0.44 0.02 0.24
#> TCGA.BR.6566.01 3 0.3299 0.7562 0.00 0.00 0.56 0.00 0.00 0.00 0.44 0.00
#> TCGA.VQ.A91X.01 6 0.5488 0.6503 0.00 0.00 0.08 0.00 0.10 0.64 0.06 0.12
#> TCGA.VQ.A91Q.01 4 0.2020 0.7102 0.00 0.00 0.02 0.90 0.00 0.02 0.00 0.06
#> TCGA.VQ.A92D.01 2 0.2864 0.8201 0.00 0.84 0.06 0.00 0.00 0.00 0.08 0.02
#> TCGA.VQ.A91Z.01 6 0.1887 0.8018 0.00 0.00 0.00 0.00 0.06 0.90 0.00 0.04
#> TCGA.BR.6455.01 2 0.2862 0.8391 0.00 0.82 0.10 0.00 0.00 0.00 0.00 0.08
#> TCGA.BR.8591.01 2 0.0000 0.9007 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HU.8608.01 3 0.5245 0.5598 0.00 0.10 0.58 0.00 0.00 0.00 0.24 0.08
#> TCGA.VQ.A94U.01 7 0.6184 0.3224 0.00 0.00 0.22 0.00 0.18 0.04 0.50 0.06
#> TCGA.VQ.A94T.01 4 0.4294 0.4129 0.00 0.00 0.04 0.68 0.00 0.22 0.00 0.06
#> TCGA.VQ.A91A.01 7 0.0471 0.5473 0.00 0.00 0.02 0.00 0.00 0.00 0.98 0.00
#> TCGA.VQ.A91D.01 2 0.0000 0.9007 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D7.6518.01 5 0.3924 0.5991 0.00 0.00 0.04 0.20 0.72 0.00 0.00 0.04
#> TCGA.BR.8484.01 4 0.0471 0.7330 0.00 0.00 0.00 0.98 0.02 0.00 0.00 0.00
#> TCGA.VQ.A91N.01 6 0.2020 0.7987 0.02 0.00 0.00 0.00 0.02 0.90 0.00 0.06
#> TCGA.VQ.A91E.01 3 0.3299 0.7562 0.00 0.00 0.56 0.00 0.00 0.00 0.44 0.00
#> TCGA.VQ.A8PY.01 3 0.3299 0.7562 0.00 0.00 0.56 0.00 0.00 0.00 0.44 0.00
#> TCGA.HU.8602.01 2 0.4370 0.3836 0.00 0.52 0.40 0.00 0.00 0.00 0.00 0.08
#> TCGA.BR.8381.01 3 0.3083 0.7670 0.00 0.00 0.66 0.00 0.00 0.00 0.34 0.00
#> TCGA.BR.6452.11 5 0.5363 0.1883 0.00 0.00 0.04 0.14 0.50 0.00 0.00 0.32
#> TCGA.IN.8663.01 2 0.0000 0.9007 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.VQ.A8PS.01 4 0.0471 0.7192 0.00 0.00 0.00 0.98 0.00 0.00 0.00 0.02
#> TCGA.VQ.A91W.01 3 0.4255 0.6919 0.00 0.00 0.58 0.00 0.00 0.00 0.34 0.08
#> TCGA.BR.6454.01 4 0.1874 0.7216 0.00 0.00 0.02 0.92 0.02 0.02 0.00 0.02
#> TCGA.BR.8682.01 5 0.5960 0.4771 0.00 0.00 0.22 0.00 0.52 0.04 0.04 0.18
#> TCGA.VQ.A91V.01 7 0.3303 0.5544 0.00 0.00 0.20 0.00 0.00 0.02 0.76 0.02
#> TCGA.VQ.A8PZ.01 5 0.4511 0.1198 0.00 0.00 0.38 0.00 0.52 0.00 0.10 0.00
#> TCGA.BR.8590.01 4 0.1607 0.7161 0.00 0.00 0.04 0.92 0.00 0.00 0.00 0.04
#> TCGA.F1.6177.01 2 0.0000 0.9007 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.VQ.A8PQ.01 8 0.3729 0.8843 0.02 0.00 0.00 0.46 0.00 0.00 0.00 0.52
#> TCGA.VQ.A91U.01 1 0.3862 0.3705 0.60 0.00 0.00 0.00 0.00 0.36 0.00 0.04
#> TCGA.VQ.AA6I.01 7 0.2350 0.4058 0.00 0.00 0.10 0.00 0.00 0.00 0.86 0.04
#> TCGA.CG.4437.01 3 0.3318 0.7416 0.00 0.00 0.54 0.00 0.00 0.00 0.46 0.00
#> TCGA.VQ.A8PP.01 7 0.2725 0.3299 0.00 0.00 0.14 0.00 0.00 0.00 0.82 0.04
#> TCGA.BR.6565.01 1 0.0000 0.9125 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.VQ.A91Y.01 1 0.0000 0.9125 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.VQ.A8PF.01 3 0.3083 0.7670 0.00 0.00 0.66 0.00 0.00 0.00 0.34 0.00
#> TCGA.BR.6456.01 1 0.4325 0.4546 0.56 0.00 0.04 0.02 0.00 0.00 0.00 0.38
#> TCGA.BR.6458.01 5 0.7037 0.0150 0.00 0.00 0.12 0.00 0.38 0.28 0.12 0.10
#> TCGA.VQ.A925.01 4 0.3514 0.2532 0.34 0.00 0.00 0.64 0.00 0.00 0.00 0.02
#> TCGA.VQ.A927.01 4 0.2591 0.6785 0.00 0.00 0.04 0.86 0.02 0.00 0.00 0.08
#> TCGA.BR.8592.01 5 0.0941 0.7552 0.00 0.00 0.00 0.02 0.96 0.00 0.00 0.02
#> TCGA.BR.6566.11 8 0.3318 0.8743 0.00 0.00 0.00 0.46 0.00 0.00 0.00 0.54
#> TCGA.IN.AB1V.01 1 0.0471 0.9006 0.98 0.00 0.00 0.02 0.00 0.00 0.00 0.00
#> TCGA.VQ.AA6F.01 4 0.0471 0.7192 0.00 0.00 0.00 0.98 0.00 0.00 0.00 0.02
#> TCGA.VQ.AA6J.01 4 0.2532 0.7197 0.00 0.00 0.04 0.88 0.02 0.02 0.00 0.04
#> TCGA.BR.8487.01 2 0.0000 0.9007 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D7.6525.01 7 0.0000 0.5547 0.00 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.VQ.A94O.01 1 0.0000 0.9125 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BR.8588.01 5 0.2020 0.7409 0.00 0.00 0.02 0.00 0.90 0.00 0.06 0.02
#> TCGA.HU.8610.01 5 0.4110 0.6561 0.00 0.00 0.06 0.10 0.76 0.02 0.00 0.06
#> TCGA.D7.6526.01 1 0.1275 0.8923 0.94 0.00 0.04 0.00 0.00 0.00 0.00 0.02
#> TCGA.VQ.A8PD.01 5 0.0941 0.7552 0.00 0.00 0.00 0.02 0.96 0.00 0.00 0.02
#> TCGA.D7.6524.01 5 0.1275 0.7512 0.00 0.00 0.04 0.00 0.94 0.00 0.02 0.00
#> TCGA.3M.AB46.01 1 0.0941 0.8924 0.96 0.00 0.00 0.02 0.00 0.00 0.00 0.02
#> TCGA.3M.AB47.01 5 0.1275 0.7392 0.00 0.00 0.00 0.00 0.94 0.00 0.02 0.04
#> TCGA.BR.8677.01 8 0.5347 0.5637 0.00 0.00 0.04 0.42 0.12 0.00 0.00 0.42
#> TCGA.BR.6457.01 5 0.1408 0.7505 0.00 0.00 0.02 0.02 0.94 0.00 0.00 0.02
#> TCGA.BR.8687.01 1 0.4466 0.5257 0.60 0.00 0.04 0.04 0.00 0.00 0.00 0.32
#> TCGA.VQ.A91K.01 2 0.0000 0.9007 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BR.8690.01 8 0.6055 0.3989 0.22 0.00 0.04 0.20 0.00 0.04 0.00 0.50
#> TCGA.BR.8686.01 2 0.4391 0.3303 0.00 0.50 0.42 0.00 0.00 0.00 0.00 0.08
#> TCGA.FP.8631.01 1 0.0000 0.9125 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.VQ.A922.01 1 0.0000 0.9125 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BR.A452.01 4 0.2132 0.6752 0.00 0.00 0.00 0.88 0.00 0.08 0.00 0.04
#> TCGA.IN.A6RO.01 2 0.0000 0.9007 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BR.A4QI.01 2 0.0000 0.9007 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D7.A6EV.01 5 0.7421 0.1747 0.00 0.00 0.22 0.00 0.32 0.16 0.10 0.20
#> TCGA.HU.A4G2.01 2 0.2132 0.8666 0.00 0.88 0.04 0.00 0.00 0.00 0.00 0.08
#> TCGA.BR.A4IY.01 3 0.4403 -0.1906 0.00 0.44 0.48 0.00 0.00 0.00 0.00 0.08
#> TCGA.VQ.A8PU.01 4 0.2020 0.6973 0.00 0.00 0.02 0.90 0.00 0.02 0.00 0.06
#> TCGA.BR.A4J4.01 2 0.2648 0.8474 0.00 0.84 0.08 0.00 0.00 0.00 0.00 0.08
#> TCGA.VQ.A94R.01 7 0.1275 0.5423 0.00 0.00 0.02 0.00 0.00 0.00 0.94 0.04
#> TCGA.HU.A4H4.01 7 0.3329 -0.6516 0.00 0.00 0.48 0.00 0.00 0.00 0.52 0.00
#> TCGA.BR.7707.01 3 0.3690 0.7269 0.00 0.00 0.56 0.00 0.00 0.00 0.42 0.02
#> TCGA.FP.7829.01 2 0.2591 0.8203 0.00 0.86 0.02 0.00 0.00 0.00 0.08 0.04
#> TCGA.BR.A4J5.01 5 0.1275 0.7512 0.00 0.00 0.02 0.00 0.94 0.00 0.04 0.00
#> TCGA.HU.A4H0.01 2 0.2132 0.8666 0.00 0.88 0.04 0.00 0.00 0.00 0.00 0.08
#> TCGA.HU.A4HD.01 1 0.0000 0.9125 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.KB.A6F5.01 1 0.0000 0.9125 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.VQ.AA6K.01 4 0.1408 0.7297 0.00 0.00 0.00 0.94 0.02 0.02 0.00 0.02
#> TCGA.HF.7133.01 4 0.2756 -0.0172 0.00 0.00 0.00 0.74 0.00 0.00 0.00 0.26
#> TCGA.F1.6875.01 6 0.3178 0.7382 0.02 0.00 0.00 0.14 0.00 0.80 0.00 0.04
#> TCGA.MX.A666.01 1 0.0000 0.9125 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BR.7717.01 7 0.4309 0.5384 0.00 0.00 0.18 0.00 0.06 0.00 0.70 0.06
#> TCGA.BR.A4PF.01 7 0.2534 0.2357 0.00 0.00 0.22 0.00 0.00 0.00 0.78 0.00
#> TCGA.BR.A4IU.01 5 0.0471 0.7558 0.00 0.00 0.02 0.00 0.98 0.00 0.00 0.00
#> TCGA.VQ.A8PX.01 4 0.1091 0.6900 0.00 0.00 0.00 0.94 0.00 0.00 0.00 0.06
#> TCGA.BR.A4IV.01 4 0.2591 0.6785 0.00 0.00 0.04 0.86 0.02 0.00 0.00 0.08
#> TCGA.D7.A6EX.01 4 0.2165 0.6817 0.00 0.00 0.00 0.88 0.00 0.06 0.00 0.06
#> TCGA.BR.A4IZ.01 8 0.4886 0.6860 0.00 0.00 0.04 0.44 0.06 0.00 0.00 0.46
#> TCGA.BR.A4J9.01 4 0.1741 0.7229 0.00 0.00 0.04 0.92 0.02 0.00 0.00 0.02
#> TCGA.CD.A4MJ.01 2 0.0000 0.9007 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.B7.A5TN.01 1 0.0471 0.9034 0.98 0.00 0.00 0.00 0.00 0.00 0.00 0.02
#> TCGA.BR.7715.01 6 0.6669 0.4360 0.00 0.00 0.20 0.00 0.06 0.46 0.10 0.18
#> TCGA.BR.7704.01 1 0.3337 0.7971 0.78 0.00 0.04 0.00 0.00 0.02 0.00 0.16
#> TCGA.BR.A4J1.01 1 0.0000 0.9125 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HU.A4GP.01 7 0.1607 0.5368 0.00 0.00 0.04 0.00 0.00 0.00 0.92 0.04
#> TCGA.D7.A4YY.01 2 0.0000 0.9007 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.VQ.AA6G.01 7 0.3178 0.4213 0.00 0.14 0.02 0.00 0.00 0.00 0.80 0.04
#> TCGA.HU.A4GJ.01 5 0.0808 0.7532 0.00 0.00 0.04 0.00 0.96 0.00 0.00 0.00
#> TCGA.CD.A4MI.01 3 0.3237 0.7646 0.00 0.00 0.60 0.00 0.00 0.00 0.40 0.00
#> TCGA.BR.7196.01 5 0.2888 0.6709 0.00 0.00 0.16 0.00 0.80 0.00 0.04 0.00
#> TCGA.BR.6563.01 5 0.2348 0.7197 0.00 0.00 0.04 0.06 0.88 0.00 0.00 0.02
#> TCGA.VQ.A924.01 3 0.3272 0.7460 0.00 0.00 0.58 0.00 0.00 0.00 0.42 0.00
#> TCGA.BR.7716.01 1 0.3036 0.7821 0.78 0.00 0.04 0.00 0.00 0.00 0.00 0.18
#> TCGA.FP.7735.01 4 0.0471 0.7192 0.00 0.00 0.00 0.98 0.00 0.00 0.00 0.02
#> TCGA.BR.7723.01 1 0.0000 0.9125 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HU.A4H8.01 2 0.0000 0.9007 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.IN.A6RJ.01 5 0.0471 0.7567 0.00 0.00 0.00 0.02 0.98 0.00 0.00 0.00
#> TCGA.HU.A4H3.01 2 0.0000 0.9007 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EQ.A4SO.01 4 0.0471 0.7192 0.00 0.00 0.00 0.98 0.00 0.00 0.00 0.02
#> TCGA.CD.A4MH.01 1 0.3337 0.7971 0.78 0.00 0.04 0.00 0.00 0.02 0.00 0.16
#> TCGA.BR.A4J7.01 4 0.1874 0.7216 0.00 0.00 0.02 0.92 0.02 0.02 0.00 0.02
#> TCGA.HF.7131.01 1 0.5080 0.3801 0.54 0.00 0.04 0.10 0.00 0.00 0.00 0.32
#> TCGA.D7.A74B.01 8 0.3729 0.8843 0.02 0.00 0.00 0.46 0.00 0.00 0.00 0.52
#> TCGA.BR.A4PE.01 2 0.0000 0.9007 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BR.A4J8.01 3 0.3237 0.7646 0.00 0.00 0.60 0.00 0.00 0.00 0.40 0.00
#> TCGA.HU.A4GX.01 5 0.4914 0.6273 0.00 0.00 0.06 0.06 0.68 0.04 0.00 0.16
#> TCGA.HU.A4G8.01 3 0.3329 0.7151 0.00 0.00 0.52 0.00 0.00 0.00 0.48 0.00
#> TCGA.HU.A4GT.01 2 0.1275 0.8770 0.00 0.94 0.02 0.00 0.00 0.00 0.00 0.04
#> TCGA.HU.A4GC.01 7 0.5422 0.5078 0.00 0.00 0.22 0.00 0.04 0.04 0.60 0.10
#> TCGA.BR.A4CQ.01 2 0.0000 0.9007 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D7.A6F2.01 1 0.1607 0.8647 0.92 0.00 0.00 0.00 0.00 0.04 0.00 0.04
#> TCGA.RD.A7BT.01 6 0.2071 0.7990 0.00 0.00 0.00 0.04 0.02 0.90 0.00 0.04
#> TCGA.BR.A4J6.01 4 0.3318 -0.7618 0.00 0.00 0.00 0.54 0.00 0.00 0.00 0.46
#> TCGA.HU.A4GQ.01 2 0.1341 0.8810 0.00 0.92 0.00 0.00 0.00 0.00 0.00 0.08
#> TCGA.HF.7136.01 1 0.0000 0.9125 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BR.A4QM.01 2 0.3185 0.8091 0.00 0.82 0.08 0.00 0.00 0.00 0.06 0.04
#> TCGA.BR.A4PD.01 6 0.2020 0.7985 0.00 0.00 0.00 0.02 0.02 0.90 0.00 0.06
#> TCGA.VQ.A8PK.01 1 0.0000 0.9125 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.B7.A5TK.01 3 0.4340 0.2968 0.00 0.00 0.54 0.00 0.38 0.00 0.08 0.00
#> TCGA.D7.A4YX.01 2 0.2132 0.8666 0.00 0.88 0.04 0.00 0.00 0.00 0.00 0.08
#> TCGA.D7.A4Z0.01 7 0.4556 -0.3925 0.00 0.00 0.38 0.00 0.06 0.00 0.54 0.02
#> TCGA.VQ.A8PT.01 2 0.0000 0.9007 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.IN.A6RN.01 1 0.1275 0.8923 0.94 0.00 0.04 0.00 0.00 0.00 0.00 0.02
#> TCGA.CD.A4MG.01 2 0.0000 0.9007 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D7.A747.01 4 0.2591 0.6785 0.00 0.00 0.04 0.86 0.02 0.00 0.00 0.08
#> TCGA.R5.A7O7.01 5 0.0471 0.7500 0.00 0.00 0.00 0.00 0.98 0.00 0.02 0.00
#> TCGA.F1.A72C.01 4 0.0471 0.7192 0.00 0.00 0.00 0.98 0.00 0.00 0.00 0.02
#> TCGA.BR.A4J2.01 5 0.0471 0.7567 0.00 0.00 0.00 0.02 0.98 0.00 0.00 0.00
#> TCGA.MX.A663.01 1 0.0000 0.9125 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D7.A4YV.01 2 0.1275 0.8827 0.00 0.94 0.04 0.00 0.00 0.00 0.00 0.02
#> TCGA.HU.A4GD.01 6 0.3873 0.7136 0.00 0.00 0.06 0.00 0.02 0.72 0.00 0.20
#> TCGA.BR.A4QL.01 2 0.0471 0.8943 0.00 0.98 0.02 0.00 0.00 0.00 0.00 0.00
#> TCGA.BR.7703.01 2 0.0941 0.8904 0.00 0.96 0.02 0.00 0.00 0.00 0.00 0.02
#> TCGA.VQ.AA6B.01 5 0.7148 0.2127 0.00 0.00 0.24 0.00 0.34 0.14 0.06 0.22
#> TCGA.VQ.AA6D.01 1 0.2348 0.8639 0.88 0.00 0.04 0.00 0.00 0.02 0.00 0.06
#> TCGA.D7.A6EZ.01 2 0.2132 0.8666 0.00 0.88 0.04 0.00 0.00 0.00 0.00 0.08
#> TCGA.D7.A4YU.01 2 0.1091 0.8844 0.00 0.94 0.06 0.00 0.00 0.00 0.00 0.00
#> TCGA.VQ.AA6A.01 6 0.1887 0.7855 0.06 0.00 0.00 0.00 0.00 0.90 0.00 0.04
#> TCGA.IN.7806.01 6 0.2071 0.7946 0.02 0.00 0.00 0.04 0.00 0.90 0.00 0.04
#> TCGA.HU.A4HB.01 5 0.2624 0.7234 0.00 0.00 0.06 0.02 0.86 0.00 0.00 0.06
#> TCGA.HU.A4H2.01 6 0.5936 0.5830 0.00 0.00 0.08 0.00 0.16 0.58 0.06 0.12
#> TCGA.IN.A6RP.01 7 0.0808 0.5396 0.00 0.00 0.00 0.00 0.00 0.00 0.96 0.04
#> TCGA.HU.A4H5.01 1 0.0000 0.9125 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HU.A4GU.01 2 0.0000 0.9007 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.MX.A5UJ.01 7 0.3971 -0.4544 0.00 0.00 0.42 0.00 0.00 0.00 0.54 0.04
#> TCGA.HU.A4GN.01 2 0.0000 0.9007 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CD.5804.01 1 0.0000 0.9125 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HU.A4H6.01 3 0.3237 0.7646 0.00 0.00 0.60 0.00 0.00 0.00 0.40 0.00
#> TCGA.HF.7132.01 3 0.3299 0.7562 0.00 0.00 0.56 0.00 0.00 0.00 0.44 0.00
#> TCGA.D7.A4YT.01 1 0.0000 0.9125 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HF.7134.01 2 0.3794 0.6922 0.00 0.74 0.04 0.00 0.00 0.00 0.18 0.04
#> TCGA.BR.6852.01 3 0.3272 0.7690 0.00 0.00 0.58 0.00 0.00 0.00 0.42 0.00
#> TCGA.BR.8370.01 2 0.2132 0.8666 0.00 0.88 0.04 0.00 0.00 0.00 0.00 0.08
#> TCGA.EQ.5647.01 4 0.2756 -0.0172 0.00 0.00 0.00 0.74 0.00 0.00 0.00 0.26
#> TCGA.IN.A7NT.01 6 0.1887 0.8018 0.00 0.00 0.00 0.00 0.06 0.90 0.00 0.04
#> TCGA.RD.A8N9.01 8 0.5550 0.5636 0.16 0.00 0.04 0.38 0.00 0.00 0.00 0.42
#> TCGA.D7.5577.01 2 0.4403 0.2726 0.00 0.48 0.44 0.00 0.00 0.00 0.00 0.08
#> TCGA.CG.5717.01 4 0.2591 0.6785 0.00 0.00 0.04 0.86 0.02 0.00 0.00 0.08
#> TCGA.D7.6818.01 1 0.0000 0.9125 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CG.5734.01 5 0.5364 0.4841 0.00 0.00 0.06 0.24 0.60 0.04 0.00 0.06
#> TCGA.VQ.A8P8.01 3 0.4686 0.6056 0.00 0.00 0.56 0.00 0.16 0.00 0.28 0.00
#> TCGA.BR.6707.01 3 0.4050 0.7143 0.00 0.00 0.60 0.00 0.00 0.00 0.34 0.06
#> TCGA.B7.5818.01 2 0.2648 0.8474 0.00 0.84 0.08 0.00 0.00 0.00 0.00 0.08
#> TCGA.CD.8525.01 1 0.3170 0.7608 0.76 0.00 0.04 0.00 0.00 0.00 0.00 0.20
#> TCGA.BR.6705.01 5 0.0941 0.7552 0.00 0.00 0.00 0.02 0.96 0.00 0.00 0.02
#> TCGA.BR.4288.01 1 0.0000 0.9125 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CD.5813.01 4 0.1408 0.7297 0.00 0.00 0.00 0.94 0.02 0.02 0.00 0.02
#> TCGA.CG.5723.01 4 0.1874 0.7216 0.00 0.00 0.02 0.92 0.02 0.02 0.00 0.02
#> TCGA.CD.5800.01 1 0.2132 0.8602 0.88 0.00 0.04 0.00 0.00 0.00 0.00 0.08
#> TCGA.CG.5718.01 1 0.2725 0.8157 0.82 0.00 0.04 0.00 0.00 0.00 0.00 0.14
#> TCGA.BR.8080.01 6 0.3319 0.7708 0.00 0.00 0.02 0.02 0.08 0.82 0.00 0.06
#> TCGA.CG.5733.01 3 0.3690 0.7269 0.00 0.00 0.56 0.00 0.00 0.00 0.42 0.02
#> TCGA.D7.6817.01 1 0.0000 0.9125 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.KB.A93G.01 4 0.2591 0.6785 0.00 0.00 0.04 0.86 0.02 0.00 0.00 0.08
#> TCGA.CD.5799.01 1 0.0000 0.9125 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BR.7851.01 2 0.1275 0.8925 0.00 0.94 0.02 0.00 0.00 0.00 0.00 0.04
#> TCGA.BR.7722.01 4 0.0471 0.7192 0.00 0.00 0.00 0.98 0.00 0.00 0.00 0.02
#> TCGA.MX.A5UG.01 5 0.1741 0.7436 0.00 0.00 0.04 0.02 0.92 0.00 0.00 0.02
#> TCGA.CD.8533.01 7 0.5960 0.4513 0.00 0.00 0.22 0.00 0.04 0.04 0.52 0.18
#> TCGA.BR.7957.01 5 0.0941 0.7552 0.00 0.00 0.00 0.02 0.96 0.00 0.00 0.02
#> TCGA.CG.5722.01 3 0.4433 0.3743 0.00 0.00 0.56 0.00 0.34 0.00 0.10 0.00
#> TCGA.F1.6874.01 5 0.0471 0.7567 0.00 0.00 0.00 0.02 0.98 0.00 0.00 0.00
#> TCGA.CG.5730.01 6 0.1887 0.8018 0.00 0.00 0.00 0.00 0.06 0.90 0.00 0.04
#> TCGA.CG.5726.01 2 0.4636 0.1999 0.00 0.52 0.04 0.00 0.00 0.00 0.40 0.04
#> TCGA.IP.7968.01 6 0.1887 0.8018 0.00 0.00 0.00 0.00 0.06 0.90 0.00 0.04
#> TCGA.BR.8363.01 3 0.3272 0.7690 0.00 0.00 0.58 0.00 0.00 0.00 0.42 0.00
#> TCGA.BR.7901.01 1 0.0000 0.9125 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D7.6822.01 7 0.6795 0.1573 0.00 0.00 0.22 0.00 0.24 0.06 0.40 0.08
#> TCGA.BR.6710.01 4 0.4799 -0.4860 0.16 0.00 0.00 0.52 0.00 0.00 0.00 0.32
#> TCGA.CG.5720.01 3 0.3299 0.7562 0.00 0.00 0.56 0.00 0.00 0.00 0.44 0.00
#> TCGA.D7.8570.01 3 0.3083 0.7670 0.00 0.00 0.66 0.00 0.00 0.00 0.34 0.00
#> TCGA.B7.A5TI.01 4 0.0471 0.7192 0.00 0.00 0.00 0.98 0.00 0.00 0.00 0.02
#> TCGA.D7.6815.01 6 0.2020 0.7957 0.02 0.00 0.00 0.02 0.00 0.90 0.00 0.06
#> TCGA.BR.8284.01 3 0.3318 0.7416 0.00 0.00 0.54 0.00 0.00 0.00 0.46 0.00
#> TCGA.BR.8295.01 1 0.1275 0.8923 0.94 0.00 0.04 0.00 0.00 0.00 0.00 0.02
#> TCGA.BR.7197.01 6 0.2165 0.7853 0.06 0.00 0.00 0.00 0.00 0.88 0.00 0.06
#> TCGA.B7.A5TJ.01 2 0.0000 0.9007 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D7.A6EY.01 5 0.4834 0.4809 0.00 0.00 0.04 0.00 0.66 0.20 0.02 0.08
#> TCGA.BR.8366.01 3 0.3083 0.7670 0.00 0.00 0.66 0.00 0.00 0.00 0.34 0.00
#> TCGA.IN.A7NR.01 8 0.4125 0.8444 0.02 0.00 0.02 0.44 0.00 0.00 0.00 0.52
#> TCGA.BR.6706.01 5 0.2888 0.6709 0.00 0.00 0.16 0.00 0.80 0.00 0.04 0.00
#> TCGA.IN.7808.01 5 0.5363 0.2870 0.00 0.00 0.14 0.00 0.50 0.00 0.32 0.04
#> TCGA.BR.6564.01 8 0.3729 0.8843 0.02 0.00 0.00 0.46 0.00 0.00 0.00 0.52
#> TCGA.KB.A93H.01 6 0.1887 0.8018 0.00 0.00 0.00 0.00 0.06 0.90 0.00 0.04
#> TCGA.KB.A93J.01 4 0.2350 0.6085 0.10 0.00 0.00 0.86 0.00 0.00 0.00 0.04
#> TCGA.CD.5798.01 4 0.1741 0.7229 0.00 0.00 0.04 0.92 0.02 0.00 0.00 0.02
#> TCGA.CD.8530.01 6 0.5080 0.4044 0.10 0.00 0.00 0.32 0.00 0.54 0.00 0.04
#> TCGA.BR.6802.01 5 0.1887 0.7411 0.00 0.00 0.04 0.00 0.90 0.00 0.06 0.00
#> TCGA.CG.5719.01 4 0.3142 -0.4491 0.00 0.00 0.00 0.64 0.00 0.00 0.00 0.36
#> TCGA.VQ.A8E3.01 7 0.3404 0.1358 0.00 0.00 0.24 0.00 0.00 0.00 0.72 0.04
#> TCGA.CD.5801.01 3 0.3083 0.7670 0.00 0.00 0.66 0.00 0.00 0.00 0.34 0.00
#> TCGA.FP.A9TM.01 7 0.2534 0.1854 0.00 0.00 0.22 0.00 0.00 0.00 0.78 0.00
#> TCGA.BR.7958.01 3 0.4370 -0.0610 0.00 0.40 0.52 0.00 0.00 0.00 0.00 0.08
#> TCGA.FP.7998.01 3 0.4340 0.2968 0.00 0.00 0.54 0.00 0.38 0.00 0.08 0.00
#> TCGA.IN.A6RS.01 7 0.5800 0.3856 0.00 0.00 0.22 0.00 0.16 0.02 0.54 0.06
#> TCGA.BR.6709.01 8 0.3318 0.8743 0.00 0.00 0.00 0.46 0.00 0.00 0.00 0.54
#> TCGA.FP.7916.01 3 0.3083 0.7670 0.00 0.00 0.66 0.00 0.00 0.00 0.34 0.00
#> TCGA.R5.A7ZR.01 6 0.2132 0.7900 0.04 0.00 0.00 0.00 0.00 0.88 0.00 0.08
#> TCGA.B7.5816.01 3 0.3299 0.7562 0.00 0.00 0.56 0.00 0.00 0.00 0.44 0.00
#> TCGA.CG.5721.01 5 0.0471 0.7500 0.00 0.00 0.00 0.00 0.98 0.00 0.02 0.00
#> TCGA.SW.A7EA.01 2 0.0000 0.9007 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.RD.A8NB.01 5 0.0808 0.7532 0.00 0.00 0.04 0.00 0.96 0.00 0.00 0.00
#> TCGA.BR.6801.01 4 0.1874 0.7216 0.00 0.00 0.02 0.92 0.02 0.02 0.00 0.02
#> TCGA.IN.AB1X.01 3 0.3690 0.7486 0.00 0.00 0.56 0.00 0.02 0.00 0.42 0.00
#> TCGA.D7.5579.01 4 0.2858 0.7038 0.00 0.00 0.04 0.86 0.02 0.04 0.00 0.04
#> TCGA.CG.5728.01 5 0.2348 0.7388 0.00 0.00 0.04 0.00 0.88 0.00 0.06 0.02
#> TCGA.R5.A7ZI.01 8 0.3329 0.8633 0.00 0.00 0.00 0.48 0.00 0.00 0.00 0.52
#> TCGA.IN.A7NU.01 7 0.3314 0.5511 0.00 0.00 0.08 0.00 0.10 0.00 0.80 0.02
#> TCGA.CG.5732.01 1 0.0000 0.9125 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.ZQ.A9CR.01 1 0.3337 0.7971 0.78 0.00 0.04 0.00 0.00 0.02 0.00 0.16
#> TCGA.D7.5578.01 6 0.7037 0.2570 0.00 0.00 0.12 0.00 0.28 0.38 0.12 0.10
#> TCGA.BR.6803.01 8 0.3729 0.8843 0.02 0.00 0.00 0.46 0.00 0.00 0.00 0.52
#> TCGA.BR.8368.01 2 0.1607 0.8717 0.00 0.92 0.04 0.00 0.00 0.00 0.00 0.04
#> TCGA.SW.A7EB.01 1 0.0000 0.9125 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BR.8081.01 3 0.3272 0.7690 0.00 0.00 0.58 0.00 0.00 0.00 0.42 0.00
#> TCGA.VQ.A8P5.01 5 0.4963 0.5758 0.00 0.00 0.18 0.00 0.66 0.02 0.08 0.06
#> TCGA.CD.8535.01 7 0.2025 0.5752 0.00 0.00 0.10 0.00 0.00 0.00 0.88 0.02
#> TCGA.CG.5724.01 7 0.1341 0.5745 0.00 0.00 0.08 0.00 0.00 0.00 0.92 0.00
#> TCGA.D7.8574.01 4 0.1741 0.7229 0.00 0.00 0.04 0.92 0.02 0.00 0.00 0.02
#> TCGA.HJ.7597.01 8 0.3329 0.8633 0.00 0.00 0.00 0.48 0.00 0.00 0.00 0.52
#> TCGA.HF.A5NB.01 2 0.0941 0.8867 0.00 0.96 0.02 0.00 0.00 0.00 0.00 0.02
#> TCGA.VQ.A8PB.01 7 0.2020 0.5700 0.00 0.00 0.06 0.00 0.02 0.00 0.90 0.02
#> TCGA.R5.A7ZE.01 1 0.2348 0.8639 0.88 0.00 0.04 0.00 0.00 0.02 0.00 0.06
#> TCGA.CD.5803.01 8 0.3318 0.8743 0.00 0.00 0.00 0.46 0.00 0.00 0.00 0.54
#> TCGA.CG.5725.01 1 0.0000 0.9125 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D7.6820.01 1 0.0000 0.9125 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CD.5802.01 1 0.0000 0.9125 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.R5.A7ZF.01 8 0.3714 0.8652 0.02 0.00 0.00 0.44 0.00 0.00 0.00 0.54
#> TCGA.D7.A6F0.01 1 0.1275 0.8923 0.94 0.00 0.04 0.00 0.00 0.00 0.00 0.02
#> TCGA.CG.5727.01 6 0.3002 0.7679 0.00 0.00 0.02 0.00 0.04 0.82 0.00 0.12
#> TCGA.VQ.A8PC.01 5 0.1741 0.7436 0.00 0.00 0.04 0.02 0.92 0.00 0.00 0.02
#> TCGA.CD.A486.01 1 0.0000 0.9125 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.RD.A8N2.01 8 0.3729 0.8843 0.02 0.00 0.00 0.46 0.00 0.00 0.00 0.52
#> TCGA.IN.A6RI.01 1 0.0000 0.9125 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HU.8243.01 6 0.4846 0.7017 0.00 0.00 0.06 0.00 0.10 0.70 0.04 0.10
#> TCGA.CD.A48C.01 7 0.1607 0.5368 0.00 0.00 0.04 0.00 0.00 0.00 0.92 0.04
#> TCGA.RD.A8N5.01 4 0.2071 0.7128 0.00 0.00 0.04 0.90 0.02 0.00 0.00 0.04
#> TCGA.RD.A8N1.01 1 0.0000 0.9125 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HU.A4GF.01 1 0.1607 0.8647 0.92 0.00 0.00 0.00 0.00 0.04 0.00 0.04
#> TCGA.BR.8362.01 5 0.6371 0.4284 0.00 0.00 0.22 0.00 0.48 0.04 0.08 0.18
#> TCGA.BR.8285.01 3 0.3083 0.7670 0.00 0.00 0.66 0.00 0.00 0.00 0.34 0.00
#> TCGA.CD.8532.01 4 0.0471 0.7192 0.00 0.00 0.00 0.98 0.00 0.00 0.00 0.02
#> TCGA.VQ.A8E2.01 1 0.0000 0.9125 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BR.8373.01 6 0.2265 0.7985 0.02 0.00 0.00 0.00 0.02 0.88 0.00 0.08
#> TCGA.BR.8361.01 7 0.3862 -0.2680 0.00 0.00 0.36 0.00 0.00 0.00 0.60 0.04
#> TCGA.BR.8058.01 8 0.3318 0.8743 0.00 0.00 0.00 0.46 0.00 0.00 0.00 0.54
#> TCGA.IN.8462.01 7 0.0000 0.5547 0.00 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.HU.A4G9.01 2 0.0000 0.9007 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CD.8524.01 6 0.7107 0.2865 0.00 0.00 0.10 0.00 0.26 0.38 0.14 0.12
#> TCGA.D7.A748.01 8 0.4004 0.8153 0.00 0.00 0.04 0.46 0.00 0.00 0.00 0.50
#> TCGA.CD.8527.01 6 0.1557 0.8020 0.00 0.00 0.00 0.00 0.06 0.92 0.00 0.02
#> TCGA.VQ.A8DV.01 1 0.0000 0.9125 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CD.8528.01 2 0.1607 0.8717 0.00 0.92 0.04 0.00 0.00 0.00 0.00 0.04
#> TCGA.BR.A453.01 5 0.1741 0.7436 0.00 0.00 0.04 0.02 0.92 0.00 0.00 0.02
#> TCGA.RD.A8N6.01 1 0.1275 0.8923 0.94 0.00 0.04 0.00 0.00 0.00 0.00 0.02
#> TCGA.HU.8245.01 1 0.0000 0.9125 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.ZA.A8F6.01 4 0.3131 0.6854 0.00 0.00 0.04 0.84 0.02 0.04 0.00 0.06
#> TCGA.BR.8367.01 5 0.4096 0.6528 0.00 0.00 0.16 0.00 0.74 0.04 0.02 0.04
#> TCGA.BR.8380.01 5 0.4588 0.2239 0.00 0.00 0.34 0.00 0.54 0.00 0.12 0.00
#> TCGA.FP.A4BE.01 2 0.0000 0.9007 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HU.8238.01 7 0.3991 0.5395 0.00 0.00 0.22 0.00 0.00 0.02 0.70 0.06
#> TCGA.BR.8078.01 2 0.0471 0.8975 0.00 0.98 0.00 0.00 0.00 0.00 0.00 0.02
#> TCGA.HU.8249.01 6 0.4503 0.6493 0.00 0.00 0.14 0.00 0.02 0.66 0.00 0.18
#> TCGA.RD.A8N0.01 8 0.3318 0.8743 0.00 0.00 0.00 0.46 0.00 0.00 0.00 0.54
#> TCGA.BR.8365.01 8 0.3729 0.8843 0.02 0.00 0.00 0.46 0.00 0.00 0.00 0.52
#> TCGA.FP.8211.01 4 0.0808 0.7200 0.00 0.00 0.00 0.96 0.00 0.00 0.00 0.04
#> TCGA.RD.A8N4.01 8 0.3729 0.8843 0.02 0.00 0.00 0.46 0.00 0.00 0.00 0.52
#> TCGA.VQ.A8DU.01 1 0.0000 0.9125 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.VQ.A8DL.01 1 0.4233 0.5293 0.60 0.00 0.04 0.02 0.00 0.00 0.00 0.34
#> TCGA.VQ.A8DZ.01 1 0.0000 0.9125 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D7.8572.01 1 0.0000 0.9125 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.RD.A7BW.01 8 0.3714 0.8652 0.02 0.00 0.00 0.44 0.00 0.00 0.00 0.54
#> TCGA.R5.A804.01 5 0.2165 0.7342 0.00 0.00 0.06 0.00 0.88 0.00 0.06 0.00
#> TCGA.BR.A4CS.01 7 0.6561 -0.0553 0.00 0.00 0.22 0.00 0.34 0.04 0.34 0.06
#> TCGA.CD.8531.01 2 0.4518 0.4679 0.00 0.56 0.36 0.00 0.00 0.02 0.00 0.06
#> TCGA.CD.A487.01 6 0.3615 0.6777 0.00 0.00 0.02 0.20 0.00 0.74 0.00 0.04
#> TCGA.BR.8371.01 4 0.2591 0.6785 0.00 0.00 0.04 0.86 0.02 0.00 0.00 0.08
#> TCGA.BR.8059.01 6 0.4280 0.6246 0.00 0.00 0.02 0.24 0.02 0.68 0.00 0.04
#> TCGA.D7.A6ET.01 5 0.1741 0.7436 0.00 0.00 0.04 0.02 0.92 0.00 0.00 0.02
#> TCGA.FP.8099.01 7 0.5376 0.5048 0.00 0.00 0.20 0.00 0.04 0.06 0.62 0.08
#> TCGA.D7.8579.01 5 0.0000 0.7544 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.BR.8297.01 5 0.4590 0.5792 0.00 0.00 0.16 0.00 0.68 0.00 0.10 0.06
#> TCGA.D7.8576.01 4 0.2406 0.2896 0.00 0.00 0.00 0.80 0.00 0.00 0.00 0.20
#> TCGA.VQ.A8DT.01 7 0.0941 0.5617 0.00 0.00 0.02 0.00 0.00 0.00 0.96 0.02
#> TCGA.FP.A8CX.01 6 0.1887 0.7993 0.00 0.00 0.00 0.00 0.06 0.90 0.00 0.04
#> TCGA.HU.A4GH.01 1 0.0000 0.9125 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CD.8526.01 1 0.3293 0.7388 0.74 0.00 0.04 0.00 0.00 0.00 0.00 0.22
#> TCGA.HU.A4G6.01 2 0.2132 0.8666 0.00 0.88 0.04 0.00 0.00 0.00 0.00 0.08
#> TCGA.D7.8578.01 4 0.3237 0.1845 0.40 0.00 0.00 0.60 0.00 0.00 0.00 0.00
#> TCGA.HU.A4G3.01 7 0.0471 0.5486 0.00 0.00 0.00 0.00 0.00 0.00 0.98 0.02
#> TCGA.D7.A74A.01 7 0.3293 0.2646 0.00 0.00 0.22 0.00 0.00 0.00 0.74 0.04
#> TCGA.RD.A7C1.01 7 0.2650 0.1616 0.00 0.00 0.24 0.00 0.00 0.00 0.76 0.00
#> TCGA.F1.A448.01 7 0.3329 -0.6359 0.00 0.00 0.48 0.00 0.00 0.00 0.52 0.00
#> TCGA.D7.8575.01 5 0.6269 0.5283 0.00 0.00 0.12 0.12 0.54 0.06 0.00 0.16
#> TCGA.BR.8372.01 2 0.0000 0.9007 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.VQ.A8P3.01 7 0.0471 0.5486 0.00 0.00 0.00 0.00 0.00 0.00 0.98 0.02
#> TCGA.RD.A8MW.01 1 0.0000 0.9125 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BR.8286.01 7 0.0471 0.5636 0.00 0.00 0.02 0.00 0.00 0.00 0.98 0.00
#> TCGA.BR.8369.01 5 0.5266 0.5025 0.00 0.00 0.16 0.00 0.60 0.00 0.16 0.08
#> TCGA.BR.8364.01 8 0.3729 0.8843 0.02 0.00 0.00 0.46 0.00 0.00 0.00 0.52
#> TCGA.HU.8244.01 2 0.4041 0.6282 0.00 0.70 0.04 0.00 0.00 0.00 0.22 0.04
#> TCGA.KB.A6F7.01 1 0.1275 0.8923 0.94 0.00 0.04 0.00 0.00 0.00 0.00 0.02
#> TCGA.FP.A4BF.01 7 0.0471 0.5390 0.00 0.00 0.02 0.00 0.00 0.00 0.98 0.00
#> TCGA.R5.A805.01 7 0.5386 -0.0913 0.00 0.00 0.18 0.00 0.40 0.00 0.40 0.02
#> TCGA.IN.A6RL.01 6 0.1887 0.8018 0.00 0.00 0.00 0.00 0.06 0.90 0.00 0.04
#> TCGA.IN.A6RR.01 7 0.3924 0.3731 0.00 0.20 0.04 0.00 0.00 0.00 0.72 0.04
#> TCGA.BR.A4CR.01 1 0.1275 0.8923 0.94 0.00 0.04 0.00 0.00 0.00 0.00 0.02
#> TCGA.CD.A489.01 4 0.2532 0.6881 0.00 0.00 0.02 0.88 0.04 0.02 0.00 0.04
#> TCGA.HU.A4GY.01 4 0.5456 -0.6038 0.00 0.00 0.04 0.44 0.08 0.02 0.00 0.42
#> TCGA.BR.8289.01 6 0.1741 0.8016 0.00 0.00 0.02 0.00 0.04 0.92 0.00 0.02
#> TCGA.FP.8209.01 4 0.2981 0.3750 0.00 0.00 0.02 0.76 0.00 0.00 0.00 0.22
#> TCGA.BR.8296.01 3 0.4622 0.6302 0.00 0.00 0.56 0.00 0.14 0.00 0.30 0.00
#> TCGA.CD.A48A.01 7 0.7304 0.0826 0.00 0.00 0.24 0.00 0.18 0.06 0.28 0.24
#> TCGA.BR.8060.01 1 0.1275 0.8923 0.94 0.00 0.04 0.00 0.00 0.00 0.00 0.02
#> TCGA.BR.8077.01 1 0.5257 0.4283 0.54 0.00 0.04 0.00 0.00 0.28 0.00 0.14
#> TCGA.CD.8534.01 5 0.4939 0.5645 0.00 0.00 0.18 0.00 0.62 0.04 0.00 0.16
#> TCGA.BR.7959.01 7 0.6353 0.2457 0.00 0.00 0.22 0.00 0.22 0.04 0.46 0.06
#> TCGA.VQ.A8P2.01 2 0.0000 0.9007 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EQ.8122.01 1 0.1887 0.8726 0.90 0.00 0.04 0.00 0.00 0.00 0.00 0.06
#> TCGA.D7.8573.01 2 0.2132 0.8666 0.00 0.88 0.04 0.00 0.00 0.00 0.00 0.08
#> TCGA.BR.A44T.01 8 0.3318 0.8743 0.00 0.00 0.00 0.46 0.00 0.00 0.00 0.54
#> TCGA.RD.A8MV.01 5 0.5747 0.0844 0.00 0.00 0.06 0.42 0.42 0.04 0.00 0.06
#> TCGA.CD.8536.01 7 0.2348 0.5701 0.00 0.00 0.06 0.00 0.02 0.00 0.88 0.04
#> TCGA.BR.8360.01 2 0.0000 0.9007 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BR.8291.01 4 0.4693 -0.1566 0.42 0.00 0.00 0.46 0.00 0.00 0.00 0.12
#> TCGA.FP.8210.01 4 0.2591 0.6785 0.00 0.00 0.04 0.86 0.02 0.00 0.00 0.08
#> TCGA.RD.A7BS.01 4 0.1741 0.7229 0.00 0.00 0.04 0.92 0.02 0.00 0.00 0.02
#> TCGA.BR.A44U.01 7 0.3744 0.5510 0.00 0.00 0.18 0.00 0.00 0.02 0.74 0.06
#> TCGA.CD.8529.01 4 0.3452 0.6436 0.06 0.00 0.04 0.82 0.00 0.04 0.00 0.04
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
consensus_heatmap(res, k = 7)
consensus_heatmap(res, k = 8)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
membership_heatmap(res, k = 7)
membership_heatmap(res, k = 8)
As soon as the classes for columns are determined, the signatures that are significantly different between subgroups can be looked for. Following are the heatmaps for signatures.
get_signatures(res, k = 2)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
get_signatures(res, k = 7)
get_signatures(res, k = 8)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. To get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows (which is done by automatically selecting number of clusters).If there are too many signatures, top_signatures = ... can be set to only show the
signatures with the highest FDRs:
# code only for demonstration
# e.g. to show the top 500 most significant rows
tb = get_signature(res, k = ..., top_signatures = 500)
If the signatures are defined as these which are uniquely high in current group, diff_method argument
can be set to "uniquely_high_in_one_group":
# code only for demonstration
tb = get_signature(res, k = ..., diff_method = "uniquely_high_in_one_group")
UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
dimension_reduction(res, k = 7, method = "UMAP")
dimension_reduction(res, k = 8, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
If matrix rows can be associated to genes, consider to use functional_enrichment(res,
...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.
Parent node: Node0. Child nodes: Node011 , Node012 , Node013 , Node021 , Node022 , Node023 , Node031 , Node032-leaf , Node033 , Node034 .
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 176 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 0.5023 0.498 0.498
#> 3 3 1.000 0.982 0.992 0.3270 0.763 0.557
#> 4 4 0.804 0.846 0.883 0.1178 0.854 0.602
#> 5 5 0.868 0.852 0.876 0.0605 0.920 0.699
#> 6 6 0.800 0.734 0.831 0.0299 0.970 0.858
#> 7 7 0.841 0.807 0.848 0.0252 0.965 0.819
#> 8 8 0.884 0.822 0.863 0.0144 0.982 0.893
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.VQ.A94P.01 1 0.000 1.00 1.00 0.00
#> TCGA.D7.6521.01 1 0.000 1.00 1.00 0.00
#> TCGA.VQ.A8PE.01 2 0.000 1.00 0.00 1.00
#> TCGA.D7.6519.01 2 0.000 1.00 0.00 1.00
#> TCGA.BR.8485.01 2 0.000 1.00 0.00 1.00
#> TCGA.BR.8486.01 2 0.000 1.00 0.00 1.00
#> TCGA.D7.6522.01 1 0.000 1.00 1.00 0.00
#> TCGA.VQ.A8PJ.01 2 0.000 1.00 0.00 1.00
#> TCGA.VQ.A8PH.01 2 0.000 1.00 0.00 1.00
#> TCGA.D7.6520.01 2 0.000 1.00 0.00 1.00
#> TCGA.VQ.AA64.01 1 0.000 1.00 1.00 0.00
#> TCGA.D7.6527.01 2 0.000 1.00 0.00 1.00
#> TCGA.VQ.A8PM.01 1 0.000 1.00 1.00 0.00
#> TCGA.VQ.A928.01 1 0.000 1.00 1.00 0.00
#> TCGA.VQ.A8E0.01 1 0.000 1.00 1.00 0.00
#> TCGA.BR.8678.01 2 0.000 1.00 0.00 1.00
#> TCGA.VQ.A91Q.01 1 0.000 1.00 1.00 0.00
#> TCGA.VQ.A91Z.01 2 0.000 1.00 0.00 1.00
#> TCGA.VQ.A94T.01 1 0.000 1.00 1.00 0.00
#> TCGA.BR.8484.01 1 0.000 1.00 1.00 0.00
#> TCGA.VQ.A91N.01 2 0.000 1.00 0.00 1.00
#> TCGA.VQ.A8PS.01 1 0.000 1.00 1.00 0.00
#> TCGA.BR.6454.01 1 0.000 1.00 1.00 0.00
#> TCGA.BR.8590.01 1 0.000 1.00 1.00 0.00
#> TCGA.VQ.A8PQ.01 1 0.000 1.00 1.00 0.00
#> TCGA.VQ.A91U.01 2 0.000 1.00 0.00 1.00
#> TCGA.BR.6565.01 2 0.000 1.00 0.00 1.00
#> TCGA.VQ.A91Y.01 2 0.000 1.00 0.00 1.00
#> TCGA.BR.6456.01 2 0.000 1.00 0.00 1.00
#> TCGA.VQ.A925.01 2 0.000 1.00 0.00 1.00
#> TCGA.VQ.A927.01 1 0.000 1.00 1.00 0.00
#> TCGA.BR.6566.11 1 0.000 1.00 1.00 0.00
#> TCGA.IN.AB1V.01 2 0.000 1.00 0.00 1.00
#> TCGA.VQ.AA6F.01 1 0.000 1.00 1.00 0.00
#> TCGA.VQ.AA6J.01 1 0.000 1.00 1.00 0.00
#> TCGA.VQ.A94O.01 2 0.000 1.00 0.00 1.00
#> TCGA.D7.6526.01 2 0.000 1.00 0.00 1.00
#> TCGA.3M.AB46.01 2 0.000 1.00 0.00 1.00
#> TCGA.BR.8677.01 1 0.000 1.00 1.00 0.00
#> TCGA.BR.8687.01 2 0.000 1.00 0.00 1.00
#> TCGA.BR.8690.01 2 0.000 1.00 0.00 1.00
#> TCGA.FP.8631.01 2 0.000 1.00 0.00 1.00
#> TCGA.VQ.A922.01 2 0.000 1.00 0.00 1.00
#> TCGA.BR.A452.01 1 0.000 1.00 1.00 0.00
#> TCGA.VQ.A8PU.01 1 0.000 1.00 1.00 0.00
#> TCGA.HU.A4HD.01 2 0.000 1.00 0.00 1.00
#> TCGA.KB.A6F5.01 2 0.000 1.00 0.00 1.00
#> TCGA.VQ.AA6K.01 1 0.000 1.00 1.00 0.00
#> TCGA.HF.7133.01 2 0.000 1.00 0.00 1.00
#> TCGA.F1.6875.01 2 0.000 1.00 0.00 1.00
#> TCGA.MX.A666.01 2 0.000 1.00 0.00 1.00
#> TCGA.VQ.A8PX.01 1 0.000 1.00 1.00 0.00
#> TCGA.BR.A4IV.01 1 0.000 1.00 1.00 0.00
#> TCGA.D7.A6EX.01 1 0.000 1.00 1.00 0.00
#> TCGA.BR.A4IZ.01 1 0.000 1.00 1.00 0.00
#> TCGA.BR.A4J9.01 1 0.000 1.00 1.00 0.00
#> TCGA.B7.A5TN.01 2 0.000 1.00 0.00 1.00
#> TCGA.BR.7704.01 2 0.000 1.00 0.00 1.00
#> TCGA.BR.A4J1.01 2 0.000 1.00 0.00 1.00
#> TCGA.BR.7716.01 2 0.000 1.00 0.00 1.00
#> TCGA.FP.7735.01 1 0.000 1.00 1.00 0.00
#> TCGA.BR.7723.01 2 0.000 1.00 0.00 1.00
#> TCGA.EQ.A4SO.01 1 0.000 1.00 1.00 0.00
#> TCGA.CD.A4MH.01 2 0.000 1.00 0.00 1.00
#> TCGA.BR.A4J7.01 1 0.000 1.00 1.00 0.00
#> TCGA.HF.7131.01 2 0.000 1.00 0.00 1.00
#> TCGA.D7.A74B.01 1 0.000 1.00 1.00 0.00
#> TCGA.D7.A6F2.01 2 0.000 1.00 0.00 1.00
#> TCGA.RD.A7BT.01 2 0.000 1.00 0.00 1.00
#> TCGA.BR.A4J6.01 1 0.000 1.00 1.00 0.00
#> TCGA.HF.7136.01 2 0.000 1.00 0.00 1.00
#> TCGA.BR.A4PD.01 2 0.000 1.00 0.00 1.00
#> TCGA.VQ.A8PK.01 2 0.000 1.00 0.00 1.00
#> TCGA.IN.A6RN.01 2 0.000 1.00 0.00 1.00
#> TCGA.D7.A747.01 1 0.000 1.00 1.00 0.00
#> TCGA.F1.A72C.01 1 0.000 1.00 1.00 0.00
#> TCGA.MX.A663.01 2 0.000 1.00 0.00 1.00
#> TCGA.VQ.AA6D.01 2 0.000 1.00 0.00 1.00
#> TCGA.VQ.AA6A.01 2 0.000 1.00 0.00 1.00
#> TCGA.IN.7806.01 2 0.000 1.00 0.00 1.00
#> TCGA.HU.A4H5.01 2 0.000 1.00 0.00 1.00
#> TCGA.CD.5804.01 1 0.000 1.00 1.00 0.00
#> TCGA.D7.A4YT.01 2 0.000 1.00 0.00 1.00
#> TCGA.EQ.5647.01 2 0.000 1.00 0.00 1.00
#> TCGA.RD.A8N9.01 1 0.000 1.00 1.00 0.00
#> TCGA.CG.5717.01 1 0.000 1.00 1.00 0.00
#> TCGA.D7.6818.01 2 0.000 1.00 0.00 1.00
#> TCGA.CD.8525.01 2 0.000 1.00 0.00 1.00
#> TCGA.BR.4288.01 1 0.000 1.00 1.00 0.00
#> TCGA.CD.5813.01 1 0.000 1.00 1.00 0.00
#> TCGA.CG.5723.01 1 0.000 1.00 1.00 0.00
#> TCGA.CD.5800.01 1 0.141 0.98 0.98 0.02
#> TCGA.CG.5718.01 2 0.000 1.00 0.00 1.00
#> TCGA.BR.8080.01 1 0.000 1.00 1.00 0.00
#> TCGA.D7.6817.01 2 0.000 1.00 0.00 1.00
#> TCGA.KB.A93G.01 1 0.000 1.00 1.00 0.00
#> TCGA.CD.5799.01 2 0.000 1.00 0.00 1.00
#> TCGA.BR.7722.01 1 0.000 1.00 1.00 0.00
#> TCGA.BR.7901.01 2 0.000 1.00 0.00 1.00
#> TCGA.BR.6710.01 1 0.000 1.00 1.00 0.00
#> TCGA.B7.A5TI.01 1 0.000 1.00 1.00 0.00
#> TCGA.D7.6815.01 2 0.000 1.00 0.00 1.00
#> TCGA.BR.8295.01 2 0.000 1.00 0.00 1.00
#> TCGA.BR.7197.01 2 0.000 1.00 0.00 1.00
#> TCGA.IN.A7NR.01 1 0.000 1.00 1.00 0.00
#> TCGA.BR.6564.01 1 0.000 1.00 1.00 0.00
#> TCGA.KB.A93J.01 2 0.000 1.00 0.00 1.00
#> TCGA.CD.5798.01 1 0.000 1.00 1.00 0.00
#> TCGA.CD.8530.01 2 0.000 1.00 0.00 1.00
#> TCGA.CG.5719.01 1 0.000 1.00 1.00 0.00
#> TCGA.BR.6709.01 1 0.000 1.00 1.00 0.00
#> TCGA.R5.A7ZR.01 2 0.000 1.00 0.00 1.00
#> TCGA.BR.6801.01 1 0.000 1.00 1.00 0.00
#> TCGA.D7.5579.01 1 0.000 1.00 1.00 0.00
#> TCGA.R5.A7ZI.01 1 0.000 1.00 1.00 0.00
#> TCGA.CG.5732.01 2 0.000 1.00 0.00 1.00
#> TCGA.ZQ.A9CR.01 2 0.000 1.00 0.00 1.00
#> TCGA.BR.6803.01 1 0.000 1.00 1.00 0.00
#> TCGA.SW.A7EB.01 1 0.000 1.00 1.00 0.00
#> TCGA.D7.8574.01 1 0.000 1.00 1.00 0.00
#> TCGA.HJ.7597.01 1 0.000 1.00 1.00 0.00
#> TCGA.R5.A7ZE.01 2 0.000 1.00 0.00 1.00
#> TCGA.CD.5803.01 1 0.000 1.00 1.00 0.00
#> TCGA.CG.5725.01 2 0.000 1.00 0.00 1.00
#> TCGA.D7.6820.01 2 0.000 1.00 0.00 1.00
#> TCGA.CD.5802.01 1 0.000 1.00 1.00 0.00
#> TCGA.R5.A7ZF.01 1 0.000 1.00 1.00 0.00
#> TCGA.D7.A6F0.01 2 0.000 1.00 0.00 1.00
#> TCGA.CD.A486.01 2 0.000 1.00 0.00 1.00
#> TCGA.RD.A8N2.01 1 0.000 1.00 1.00 0.00
#> TCGA.IN.A6RI.01 2 0.000 1.00 0.00 1.00
#> TCGA.RD.A8N5.01 1 0.000 1.00 1.00 0.00
#> TCGA.RD.A8N1.01 1 0.000 1.00 1.00 0.00
#> TCGA.HU.A4GF.01 2 0.000 1.00 0.00 1.00
#> TCGA.CD.8532.01 1 0.000 1.00 1.00 0.00
#> TCGA.VQ.A8E2.01 2 0.000 1.00 0.00 1.00
#> TCGA.BR.8373.01 2 0.000 1.00 0.00 1.00
#> TCGA.BR.8058.01 1 0.000 1.00 1.00 0.00
#> TCGA.D7.A748.01 1 0.000 1.00 1.00 0.00
#> TCGA.CD.8527.01 2 0.000 1.00 0.00 1.00
#> TCGA.VQ.A8DV.01 2 0.000 1.00 0.00 1.00
#> TCGA.RD.A8N6.01 2 0.000 1.00 0.00 1.00
#> TCGA.HU.8245.01 2 0.000 1.00 0.00 1.00
#> TCGA.ZA.A8F6.01 2 0.000 1.00 0.00 1.00
#> TCGA.RD.A8N0.01 1 0.000 1.00 1.00 0.00
#> TCGA.BR.8365.01 1 0.000 1.00 1.00 0.00
#> TCGA.FP.8211.01 1 0.000 1.00 1.00 0.00
#> TCGA.RD.A8N4.01 1 0.000 1.00 1.00 0.00
#> TCGA.VQ.A8DU.01 2 0.000 1.00 0.00 1.00
#> TCGA.VQ.A8DL.01 2 0.000 1.00 0.00 1.00
#> TCGA.VQ.A8DZ.01 2 0.000 1.00 0.00 1.00
#> TCGA.D7.8572.01 2 0.000 1.00 0.00 1.00
#> TCGA.RD.A7BW.01 1 0.000 1.00 1.00 0.00
#> TCGA.CD.A487.01 2 0.000 1.00 0.00 1.00
#> TCGA.BR.8371.01 1 0.000 1.00 1.00 0.00
#> TCGA.BR.8059.01 2 0.000 1.00 0.00 1.00
#> TCGA.D7.8576.01 1 0.000 1.00 1.00 0.00
#> TCGA.FP.A8CX.01 2 0.000 1.00 0.00 1.00
#> TCGA.HU.A4GH.01 2 0.000 1.00 0.00 1.00
#> TCGA.CD.8526.01 2 0.000 1.00 0.00 1.00
#> TCGA.D7.8578.01 1 0.000 1.00 1.00 0.00
#> TCGA.RD.A8MW.01 2 0.000 1.00 0.00 1.00
#> TCGA.BR.8364.01 1 0.000 1.00 1.00 0.00
#> TCGA.KB.A6F7.01 2 0.000 1.00 0.00 1.00
#> TCGA.BR.A4CR.01 2 0.000 1.00 0.00 1.00
#> TCGA.CD.A489.01 1 0.000 1.00 1.00 0.00
#> TCGA.HU.A4GY.01 1 0.000 1.00 1.00 0.00
#> TCGA.FP.8209.01 1 0.000 1.00 1.00 0.00
#> TCGA.BR.8060.01 2 0.000 1.00 0.00 1.00
#> TCGA.BR.8077.01 2 0.000 1.00 0.00 1.00
#> TCGA.EQ.8122.01 2 0.000 1.00 0.00 1.00
#> TCGA.BR.A44T.01 1 0.000 1.00 1.00 0.00
#> TCGA.BR.8291.01 1 0.000 1.00 1.00 0.00
#> TCGA.FP.8210.01 1 0.000 1.00 1.00 0.00
#> TCGA.RD.A7BS.01 1 0.000 1.00 1.00 0.00
#> TCGA.CD.8529.01 1 0.000 1.00 1.00 0.00
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.VQ.A94P.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.D7.6521.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.VQ.A8PE.01 2 0.0000 0.997 0.00 1.00 0.00
#> TCGA.D7.6519.01 3 0.0000 0.993 0.00 0.00 1.00
#> TCGA.BR.8485.01 2 0.0000 0.997 0.00 1.00 0.00
#> TCGA.BR.8486.01 2 0.0000 0.997 0.00 1.00 0.00
#> TCGA.D7.6522.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.VQ.A8PJ.01 2 0.0000 0.997 0.00 1.00 0.00
#> TCGA.VQ.A8PH.01 2 0.0000 0.997 0.00 1.00 0.00
#> TCGA.D7.6520.01 2 0.0000 0.997 0.00 1.00 0.00
#> TCGA.VQ.AA64.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.D7.6527.01 2 0.0000 0.997 0.00 1.00 0.00
#> TCGA.VQ.A8PM.01 3 0.0000 0.993 0.00 0.00 1.00
#> TCGA.VQ.A928.01 1 0.0892 0.975 0.98 0.00 0.02
#> TCGA.VQ.A8E0.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.BR.8678.01 2 0.0000 0.997 0.00 1.00 0.00
#> TCGA.VQ.A91Q.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.VQ.A91Z.01 2 0.0000 0.997 0.00 1.00 0.00
#> TCGA.VQ.A94T.01 1 0.0892 0.975 0.98 0.00 0.02
#> TCGA.BR.8484.01 3 0.0000 0.993 0.00 0.00 1.00
#> TCGA.VQ.A91N.01 2 0.0000 0.997 0.00 1.00 0.00
#> TCGA.VQ.A8PS.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.BR.6454.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.BR.8590.01 1 0.0892 0.975 0.98 0.00 0.02
#> TCGA.VQ.A8PQ.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.VQ.A91U.01 2 0.0000 0.997 0.00 1.00 0.00
#> TCGA.BR.6565.01 2 0.0000 0.997 0.00 1.00 0.00
#> TCGA.VQ.A91Y.01 3 0.0000 0.993 0.00 0.00 1.00
#> TCGA.BR.6456.01 3 0.0000 0.993 0.00 0.00 1.00
#> TCGA.VQ.A925.01 3 0.0000 0.993 0.00 0.00 1.00
#> TCGA.VQ.A927.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.BR.6566.11 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.IN.AB1V.01 3 0.0000 0.993 0.00 0.00 1.00
#> TCGA.VQ.AA6F.01 1 0.0892 0.975 0.98 0.00 0.02
#> TCGA.VQ.AA6J.01 1 0.0892 0.975 0.98 0.00 0.02
#> TCGA.VQ.A94O.01 2 0.0000 0.997 0.00 1.00 0.00
#> TCGA.D7.6526.01 2 0.0000 0.997 0.00 1.00 0.00
#> TCGA.3M.AB46.01 2 0.2959 0.891 0.00 0.90 0.10
#> TCGA.BR.8677.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.BR.8687.01 3 0.0892 0.975 0.00 0.02 0.98
#> TCGA.BR.8690.01 3 0.0000 0.993 0.00 0.00 1.00
#> TCGA.FP.8631.01 2 0.0000 0.997 0.00 1.00 0.00
#> TCGA.VQ.A922.01 2 0.0000 0.997 0.00 1.00 0.00
#> TCGA.BR.A452.01 1 0.0892 0.975 0.98 0.00 0.02
#> TCGA.VQ.A8PU.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.HU.A4HD.01 2 0.0000 0.997 0.00 1.00 0.00
#> TCGA.KB.A6F5.01 3 0.0892 0.975 0.00 0.02 0.98
#> TCGA.VQ.AA6K.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.HF.7133.01 3 0.0000 0.993 0.00 0.00 1.00
#> TCGA.F1.6875.01 2 0.0000 0.997 0.00 1.00 0.00
#> TCGA.MX.A666.01 2 0.0000 0.997 0.00 1.00 0.00
#> TCGA.VQ.A8PX.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.BR.A4IV.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.D7.A6EX.01 3 0.0000 0.993 0.00 0.00 1.00
#> TCGA.BR.A4IZ.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.BR.A4J9.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.B7.A5TN.01 2 0.1529 0.959 0.00 0.96 0.04
#> TCGA.BR.7704.01 2 0.0000 0.997 0.00 1.00 0.00
#> TCGA.BR.A4J1.01 2 0.0000 0.997 0.00 1.00 0.00
#> TCGA.BR.7716.01 3 0.0000 0.993 0.00 0.00 1.00
#> TCGA.FP.7735.01 3 0.5016 0.675 0.24 0.00 0.76
#> TCGA.BR.7723.01 3 0.0000 0.993 0.00 0.00 1.00
#> TCGA.EQ.A4SO.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.CD.A4MH.01 2 0.0000 0.997 0.00 1.00 0.00
#> TCGA.BR.A4J7.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.HF.7131.01 2 0.1529 0.959 0.00 0.96 0.04
#> TCGA.D7.A74B.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.D7.A6F2.01 2 0.0000 0.997 0.00 1.00 0.00
#> TCGA.RD.A7BT.01 2 0.0000 0.997 0.00 1.00 0.00
#> TCGA.BR.A4J6.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.HF.7136.01 3 0.0000 0.993 0.00 0.00 1.00
#> TCGA.BR.A4PD.01 2 0.0000 0.997 0.00 1.00 0.00
#> TCGA.VQ.A8PK.01 2 0.0000 0.997 0.00 1.00 0.00
#> TCGA.IN.A6RN.01 2 0.0000 0.997 0.00 1.00 0.00
#> TCGA.D7.A747.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.F1.A72C.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.MX.A663.01 3 0.0000 0.993 0.00 0.00 1.00
#> TCGA.VQ.AA6D.01 2 0.0000 0.997 0.00 1.00 0.00
#> TCGA.VQ.AA6A.01 2 0.0000 0.997 0.00 1.00 0.00
#> TCGA.IN.7806.01 2 0.0000 0.997 0.00 1.00 0.00
#> TCGA.HU.A4H5.01 2 0.0000 0.997 0.00 1.00 0.00
#> TCGA.CD.5804.01 3 0.0000 0.993 0.00 0.00 1.00
#> TCGA.D7.A4YT.01 3 0.0000 0.993 0.00 0.00 1.00
#> TCGA.EQ.5647.01 3 0.0000 0.993 0.00 0.00 1.00
#> TCGA.RD.A8N9.01 1 0.4291 0.785 0.82 0.00 0.18
#> TCGA.CG.5717.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.D7.6818.01 3 0.0000 0.993 0.00 0.00 1.00
#> TCGA.CD.8525.01 3 0.0000 0.993 0.00 0.00 1.00
#> TCGA.BR.4288.01 3 0.0000 0.993 0.00 0.00 1.00
#> TCGA.CD.5813.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.CG.5723.01 1 0.6244 0.226 0.56 0.00 0.44
#> TCGA.CD.5800.01 3 0.0000 0.993 0.00 0.00 1.00
#> TCGA.CG.5718.01 2 0.0000 0.997 0.00 1.00 0.00
#> TCGA.BR.8080.01 1 0.0892 0.975 0.98 0.00 0.02
#> TCGA.D7.6817.01 2 0.0000 0.997 0.00 1.00 0.00
#> TCGA.KB.A93G.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.CD.5799.01 3 0.0000 0.993 0.00 0.00 1.00
#> TCGA.BR.7722.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.BR.7901.01 2 0.0000 0.997 0.00 1.00 0.00
#> TCGA.BR.6710.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.B7.A5TI.01 3 0.0000 0.993 0.00 0.00 1.00
#> TCGA.D7.6815.01 2 0.0000 0.997 0.00 1.00 0.00
#> TCGA.BR.8295.01 2 0.0000 0.997 0.00 1.00 0.00
#> TCGA.BR.7197.01 2 0.0000 0.997 0.00 1.00 0.00
#> TCGA.IN.A7NR.01 1 0.0892 0.975 0.98 0.00 0.02
#> TCGA.BR.6564.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.KB.A93J.01 2 0.0000 0.997 0.00 1.00 0.00
#> TCGA.CD.5798.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.CD.8530.01 3 0.0000 0.993 0.00 0.00 1.00
#> TCGA.CG.5719.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.BR.6709.01 1 0.0892 0.975 0.98 0.00 0.02
#> TCGA.R5.A7ZR.01 2 0.0000 0.997 0.00 1.00 0.00
#> TCGA.BR.6801.01 3 0.0000 0.993 0.00 0.00 1.00
#> TCGA.D7.5579.01 3 0.0000 0.993 0.00 0.00 1.00
#> TCGA.R5.A7ZI.01 3 0.0000 0.993 0.00 0.00 1.00
#> TCGA.CG.5732.01 3 0.0892 0.975 0.00 0.02 0.98
#> TCGA.ZQ.A9CR.01 3 0.0892 0.975 0.00 0.02 0.98
#> TCGA.BR.6803.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.SW.A7EB.01 1 0.0892 0.975 0.98 0.00 0.02
#> TCGA.D7.8574.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.HJ.7597.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.R5.A7ZE.01 2 0.0000 0.997 0.00 1.00 0.00
#> TCGA.CD.5803.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.CG.5725.01 2 0.0000 0.997 0.00 1.00 0.00
#> TCGA.D7.6820.01 2 0.0000 0.997 0.00 1.00 0.00
#> TCGA.CD.5802.01 3 0.0000 0.993 0.00 0.00 1.00
#> TCGA.R5.A7ZF.01 3 0.0000 0.993 0.00 0.00 1.00
#> TCGA.D7.A6F0.01 2 0.0000 0.997 0.00 1.00 0.00
#> TCGA.CD.A486.01 2 0.0000 0.997 0.00 1.00 0.00
#> TCGA.RD.A8N2.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.IN.A6RI.01 2 0.0000 0.997 0.00 1.00 0.00
#> TCGA.RD.A8N5.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.RD.A8N1.01 3 0.0000 0.993 0.00 0.00 1.00
#> TCGA.HU.A4GF.01 2 0.0000 0.997 0.00 1.00 0.00
#> TCGA.CD.8532.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.VQ.A8E2.01 3 0.0000 0.993 0.00 0.00 1.00
#> TCGA.BR.8373.01 2 0.0000 0.997 0.00 1.00 0.00
#> TCGA.BR.8058.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.D7.A748.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.CD.8527.01 3 0.0000 0.993 0.00 0.00 1.00
#> TCGA.VQ.A8DV.01 2 0.0000 0.997 0.00 1.00 0.00
#> TCGA.RD.A8N6.01 3 0.0000 0.993 0.00 0.00 1.00
#> TCGA.HU.8245.01 2 0.0000 0.997 0.00 1.00 0.00
#> TCGA.ZA.A8F6.01 3 0.0000 0.993 0.00 0.00 1.00
#> TCGA.RD.A8N0.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.BR.8365.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.FP.8211.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.RD.A8N4.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.VQ.A8DU.01 2 0.0000 0.997 0.00 1.00 0.00
#> TCGA.VQ.A8DL.01 3 0.0000 0.993 0.00 0.00 1.00
#> TCGA.VQ.A8DZ.01 2 0.0000 0.997 0.00 1.00 0.00
#> TCGA.D7.8572.01 3 0.0000 0.993 0.00 0.00 1.00
#> TCGA.RD.A7BW.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.CD.A487.01 3 0.0000 0.993 0.00 0.00 1.00
#> TCGA.BR.8371.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.BR.8059.01 3 0.0000 0.993 0.00 0.00 1.00
#> TCGA.D7.8576.01 1 0.0892 0.975 0.98 0.00 0.02
#> TCGA.FP.A8CX.01 3 0.0000 0.993 0.00 0.00 1.00
#> TCGA.HU.A4GH.01 2 0.0000 0.997 0.00 1.00 0.00
#> TCGA.CD.8526.01 3 0.0000 0.993 0.00 0.00 1.00
#> TCGA.D7.8578.01 3 0.0000 0.993 0.00 0.00 1.00
#> TCGA.RD.A8MW.01 3 0.0000 0.993 0.00 0.00 1.00
#> TCGA.BR.8364.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.KB.A6F7.01 2 0.0000 0.997 0.00 1.00 0.00
#> TCGA.BR.A4CR.01 3 0.0000 0.993 0.00 0.00 1.00
#> TCGA.CD.A489.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.HU.A4GY.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.FP.8209.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.BR.8060.01 2 0.0000 0.997 0.00 1.00 0.00
#> TCGA.BR.8077.01 2 0.0000 0.997 0.00 1.00 0.00
#> TCGA.EQ.8122.01 2 0.0000 0.997 0.00 1.00 0.00
#> TCGA.BR.A44T.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.BR.8291.01 3 0.0000 0.993 0.00 0.00 1.00
#> TCGA.FP.8210.01 1 0.0000 0.987 1.00 0.00 0.00
#> TCGA.RD.A7BS.01 1 0.0892 0.975 0.98 0.00 0.02
#> TCGA.CD.8529.01 3 0.0000 0.993 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.VQ.A94P.01 1 0.0000 0.989 1.00 0.00 0.00 0.00
#> TCGA.D7.6521.01 1 0.0000 0.989 1.00 0.00 0.00 0.00
#> TCGA.VQ.A8PE.01 2 0.4624 0.786 0.00 0.66 0.34 0.00
#> TCGA.D7.6519.01 3 0.4624 0.814 0.00 0.00 0.66 0.34
#> TCGA.BR.8485.01 2 0.4624 0.786 0.00 0.66 0.34 0.00
#> TCGA.BR.8486.01 2 0.4624 0.786 0.00 0.66 0.34 0.00
#> TCGA.D7.6522.01 1 0.0000 0.989 1.00 0.00 0.00 0.00
#> TCGA.VQ.A8PJ.01 2 0.0000 0.856 0.00 1.00 0.00 0.00
#> TCGA.VQ.A8PH.01 2 0.0000 0.856 0.00 1.00 0.00 0.00
#> TCGA.D7.6520.01 2 0.0000 0.856 0.00 1.00 0.00 0.00
#> TCGA.VQ.AA64.01 4 0.4624 0.601 0.34 0.00 0.00 0.66
#> TCGA.D7.6527.01 2 0.0000 0.856 0.00 1.00 0.00 0.00
#> TCGA.VQ.A8PM.01 4 0.0000 0.820 0.00 0.00 0.00 1.00
#> TCGA.VQ.A928.01 4 0.3975 0.751 0.24 0.00 0.00 0.76
#> TCGA.VQ.A8E0.01 1 0.4790 0.235 0.62 0.00 0.00 0.38
#> TCGA.BR.8678.01 2 0.0000 0.856 0.00 1.00 0.00 0.00
#> TCGA.VQ.A91Q.01 1 0.0000 0.989 1.00 0.00 0.00 0.00
#> TCGA.VQ.A91Z.01 3 0.1637 0.641 0.00 0.06 0.94 0.00
#> TCGA.VQ.A94T.01 4 0.3610 0.781 0.20 0.00 0.00 0.80
#> TCGA.BR.8484.01 4 0.0000 0.820 0.00 0.00 0.00 1.00
#> TCGA.VQ.A91N.01 2 0.0000 0.856 0.00 1.00 0.00 0.00
#> TCGA.VQ.A8PS.01 1 0.0000 0.989 1.00 0.00 0.00 0.00
#> TCGA.BR.6454.01 1 0.0000 0.989 1.00 0.00 0.00 0.00
#> TCGA.BR.8590.01 4 0.1637 0.819 0.06 0.00 0.00 0.94
#> TCGA.VQ.A8PQ.01 1 0.0000 0.989 1.00 0.00 0.00 0.00
#> TCGA.VQ.A91U.01 2 0.0000 0.856 0.00 1.00 0.00 0.00
#> TCGA.BR.6565.01 2 0.4406 0.799 0.00 0.70 0.30 0.00
#> TCGA.VQ.A91Y.01 3 0.0000 0.719 0.00 0.00 1.00 0.00
#> TCGA.BR.6456.01 3 0.4522 0.827 0.00 0.00 0.68 0.32
#> TCGA.VQ.A925.01 3 0.0000 0.719 0.00 0.00 1.00 0.00
#> TCGA.VQ.A927.01 1 0.0000 0.989 1.00 0.00 0.00 0.00
#> TCGA.BR.6566.11 1 0.0000 0.989 1.00 0.00 0.00 0.00
#> TCGA.IN.AB1V.01 3 0.4624 0.814 0.00 0.00 0.66 0.34
#> TCGA.VQ.AA6F.01 4 0.3975 0.751 0.24 0.00 0.00 0.76
#> TCGA.VQ.AA6J.01 4 0.3801 0.771 0.22 0.00 0.00 0.78
#> TCGA.VQ.A94O.01 2 0.0000 0.856 0.00 1.00 0.00 0.00
#> TCGA.D7.6526.01 2 0.0000 0.856 0.00 1.00 0.00 0.00
#> TCGA.3M.AB46.01 3 0.0000 0.719 0.00 0.00 1.00 0.00
#> TCGA.BR.8677.01 1 0.0000 0.989 1.00 0.00 0.00 0.00
#> TCGA.BR.8687.01 3 0.0000 0.719 0.00 0.00 1.00 0.00
#> TCGA.BR.8690.01 3 0.4522 0.827 0.00 0.00 0.68 0.32
#> TCGA.FP.8631.01 2 0.0000 0.856 0.00 1.00 0.00 0.00
#> TCGA.VQ.A922.01 2 0.4624 0.786 0.00 0.66 0.34 0.00
#> TCGA.BR.A452.01 4 0.3610 0.781 0.20 0.00 0.00 0.80
#> TCGA.VQ.A8PU.01 4 0.4624 0.601 0.34 0.00 0.00 0.66
#> TCGA.HU.A4HD.01 2 0.4624 0.786 0.00 0.66 0.34 0.00
#> TCGA.KB.A6F5.01 3 0.0000 0.719 0.00 0.00 1.00 0.00
#> TCGA.VQ.AA6K.01 1 0.0000 0.989 1.00 0.00 0.00 0.00
#> TCGA.HF.7133.01 3 0.4624 0.814 0.00 0.00 0.66 0.34
#> TCGA.F1.6875.01 2 0.4624 0.786 0.00 0.66 0.34 0.00
#> TCGA.MX.A666.01 2 0.4624 0.786 0.00 0.66 0.34 0.00
#> TCGA.VQ.A8PX.01 4 0.3975 0.751 0.24 0.00 0.00 0.76
#> TCGA.BR.A4IV.01 1 0.0000 0.989 1.00 0.00 0.00 0.00
#> TCGA.D7.A6EX.01 4 0.0000 0.820 0.00 0.00 0.00 1.00
#> TCGA.BR.A4IZ.01 1 0.0000 0.989 1.00 0.00 0.00 0.00
#> TCGA.BR.A4J9.01 1 0.0000 0.989 1.00 0.00 0.00 0.00
#> TCGA.B7.A5TN.01 3 0.0000 0.719 0.00 0.00 1.00 0.00
#> TCGA.BR.7704.01 2 0.0000 0.856 0.00 1.00 0.00 0.00
#> TCGA.BR.A4J1.01 2 0.0000 0.856 0.00 1.00 0.00 0.00
#> TCGA.BR.7716.01 3 0.3975 0.819 0.00 0.00 0.76 0.24
#> TCGA.FP.7735.01 4 0.0000 0.820 0.00 0.00 0.00 1.00
#> TCGA.BR.7723.01 3 0.3975 0.819 0.00 0.00 0.76 0.24
#> TCGA.EQ.A4SO.01 4 0.4406 0.667 0.30 0.00 0.00 0.70
#> TCGA.CD.A4MH.01 2 0.3610 0.820 0.00 0.80 0.20 0.00
#> TCGA.BR.A4J7.01 1 0.0000 0.989 1.00 0.00 0.00 0.00
#> TCGA.HF.7131.01 3 0.0000 0.719 0.00 0.00 1.00 0.00
#> TCGA.D7.A74B.01 1 0.0000 0.989 1.00 0.00 0.00 0.00
#> TCGA.D7.A6F2.01 2 0.4277 0.804 0.00 0.72 0.28 0.00
#> TCGA.RD.A7BT.01 2 0.4624 0.786 0.00 0.66 0.34 0.00
#> TCGA.BR.A4J6.01 1 0.0000 0.989 1.00 0.00 0.00 0.00
#> TCGA.HF.7136.01 3 0.0000 0.719 0.00 0.00 1.00 0.00
#> TCGA.BR.A4PD.01 2 0.4624 0.786 0.00 0.66 0.34 0.00
#> TCGA.VQ.A8PK.01 2 0.4624 0.786 0.00 0.66 0.34 0.00
#> TCGA.IN.A6RN.01 2 0.0000 0.856 0.00 1.00 0.00 0.00
#> TCGA.D7.A747.01 1 0.0000 0.989 1.00 0.00 0.00 0.00
#> TCGA.F1.A72C.01 1 0.0000 0.989 1.00 0.00 0.00 0.00
#> TCGA.MX.A663.01 3 0.4624 0.814 0.00 0.00 0.66 0.34
#> TCGA.VQ.AA6D.01 2 0.0000 0.856 0.00 1.00 0.00 0.00
#> TCGA.VQ.AA6A.01 2 0.0000 0.856 0.00 1.00 0.00 0.00
#> TCGA.IN.7806.01 2 0.4624 0.786 0.00 0.66 0.34 0.00
#> TCGA.HU.A4H5.01 2 0.0000 0.856 0.00 1.00 0.00 0.00
#> TCGA.CD.5804.01 4 0.0000 0.820 0.00 0.00 0.00 1.00
#> TCGA.D7.A4YT.01 3 0.4624 0.814 0.00 0.00 0.66 0.34
#> TCGA.EQ.5647.01 3 0.4624 0.814 0.00 0.00 0.66 0.34
#> TCGA.RD.A8N9.01 4 0.0000 0.820 0.00 0.00 0.00 1.00
#> TCGA.CG.5717.01 1 0.0000 0.989 1.00 0.00 0.00 0.00
#> TCGA.D7.6818.01 3 0.4522 0.827 0.00 0.00 0.68 0.32
#> TCGA.CD.8525.01 3 0.4134 0.822 0.00 0.00 0.74 0.26
#> TCGA.BR.4288.01 4 0.0000 0.820 0.00 0.00 0.00 1.00
#> TCGA.CD.5813.01 1 0.0000 0.989 1.00 0.00 0.00 0.00
#> TCGA.CG.5723.01 4 0.0000 0.820 0.00 0.00 0.00 1.00
#> TCGA.CD.5800.01 3 0.4624 0.814 0.00 0.00 0.66 0.34
#> TCGA.CG.5718.01 2 0.4624 0.786 0.00 0.66 0.34 0.00
#> TCGA.BR.8080.01 4 0.1637 0.819 0.06 0.00 0.00 0.94
#> TCGA.D7.6817.01 3 0.0707 0.696 0.00 0.02 0.98 0.00
#> TCGA.KB.A93G.01 4 0.4624 0.601 0.34 0.00 0.00 0.66
#> TCGA.CD.5799.01 3 0.3975 0.819 0.00 0.00 0.76 0.24
#> TCGA.BR.7722.01 1 0.0000 0.989 1.00 0.00 0.00 0.00
#> TCGA.BR.7901.01 2 0.4624 0.786 0.00 0.66 0.34 0.00
#> TCGA.BR.6710.01 1 0.0000 0.989 1.00 0.00 0.00 0.00
#> TCGA.B7.A5TI.01 4 0.0707 0.798 0.00 0.00 0.02 0.98
#> TCGA.D7.6815.01 2 0.4624 0.786 0.00 0.66 0.34 0.00
#> TCGA.BR.8295.01 2 0.0000 0.856 0.00 1.00 0.00 0.00
#> TCGA.BR.7197.01 2 0.0000 0.856 0.00 1.00 0.00 0.00
#> TCGA.IN.A7NR.01 4 0.2011 0.816 0.08 0.00 0.00 0.92
#> TCGA.BR.6564.01 1 0.0000 0.989 1.00 0.00 0.00 0.00
#> TCGA.KB.A93J.01 2 0.4522 0.793 0.00 0.68 0.32 0.00
#> TCGA.CD.5798.01 1 0.0000 0.989 1.00 0.00 0.00 0.00
#> TCGA.CD.8530.01 3 0.4522 0.827 0.00 0.00 0.68 0.32
#> TCGA.CG.5719.01 1 0.0000 0.989 1.00 0.00 0.00 0.00
#> TCGA.BR.6709.01 4 0.0707 0.821 0.02 0.00 0.00 0.98
#> TCGA.R5.A7ZR.01 2 0.0000 0.856 0.00 1.00 0.00 0.00
#> TCGA.BR.6801.01 4 0.0000 0.820 0.00 0.00 0.00 1.00
#> TCGA.D7.5579.01 4 0.0000 0.820 0.00 0.00 0.00 1.00
#> TCGA.R5.A7ZI.01 4 0.0000 0.820 0.00 0.00 0.00 1.00
#> TCGA.CG.5732.01 3 0.0000 0.719 0.00 0.00 1.00 0.00
#> TCGA.ZQ.A9CR.01 3 0.0000 0.719 0.00 0.00 1.00 0.00
#> TCGA.BR.6803.01 1 0.0000 0.989 1.00 0.00 0.00 0.00
#> TCGA.SW.A7EB.01 4 0.3172 0.794 0.16 0.00 0.00 0.84
#> TCGA.D7.8574.01 1 0.0000 0.989 1.00 0.00 0.00 0.00
#> TCGA.HJ.7597.01 1 0.0000 0.989 1.00 0.00 0.00 0.00
#> TCGA.R5.A7ZE.01 2 0.4522 0.793 0.00 0.68 0.32 0.00
#> TCGA.CD.5803.01 1 0.0000 0.989 1.00 0.00 0.00 0.00
#> TCGA.CG.5725.01 2 0.0000 0.856 0.00 1.00 0.00 0.00
#> TCGA.D7.6820.01 2 0.4624 0.786 0.00 0.66 0.34 0.00
#> TCGA.CD.5802.01 4 0.0000 0.820 0.00 0.00 0.00 1.00
#> TCGA.R5.A7ZF.01 4 0.0000 0.820 0.00 0.00 0.00 1.00
#> TCGA.D7.A6F0.01 2 0.0000 0.856 0.00 1.00 0.00 0.00
#> TCGA.CD.A486.01 2 0.4624 0.786 0.00 0.66 0.34 0.00
#> TCGA.RD.A8N2.01 1 0.0000 0.989 1.00 0.00 0.00 0.00
#> TCGA.IN.A6RI.01 2 0.0000 0.856 0.00 1.00 0.00 0.00
#> TCGA.RD.A8N5.01 1 0.0000 0.989 1.00 0.00 0.00 0.00
#> TCGA.RD.A8N1.01 4 0.0000 0.820 0.00 0.00 0.00 1.00
#> TCGA.HU.A4GF.01 2 0.0000 0.856 0.00 1.00 0.00 0.00
#> TCGA.CD.8532.01 1 0.0000 0.989 1.00 0.00 0.00 0.00
#> TCGA.VQ.A8E2.01 3 0.4522 0.827 0.00 0.00 0.68 0.32
#> TCGA.BR.8373.01 2 0.0000 0.856 0.00 1.00 0.00 0.00
#> TCGA.BR.8058.01 1 0.0000 0.989 1.00 0.00 0.00 0.00
#> TCGA.D7.A748.01 1 0.0000 0.989 1.00 0.00 0.00 0.00
#> TCGA.CD.8527.01 3 0.4624 0.814 0.00 0.00 0.66 0.34
#> TCGA.VQ.A8DV.01 2 0.0000 0.856 0.00 1.00 0.00 0.00
#> TCGA.RD.A8N6.01 3 0.3975 0.819 0.00 0.00 0.76 0.24
#> TCGA.HU.8245.01 2 0.4624 0.786 0.00 0.66 0.34 0.00
#> TCGA.ZA.A8F6.01 3 0.4522 0.827 0.00 0.00 0.68 0.32
#> TCGA.RD.A8N0.01 1 0.0000 0.989 1.00 0.00 0.00 0.00
#> TCGA.BR.8365.01 1 0.0000 0.989 1.00 0.00 0.00 0.00
#> TCGA.FP.8211.01 1 0.1211 0.943 0.96 0.00 0.00 0.04
#> TCGA.RD.A8N4.01 1 0.0000 0.989 1.00 0.00 0.00 0.00
#> TCGA.VQ.A8DU.01 2 0.0000 0.856 0.00 1.00 0.00 0.00
#> TCGA.VQ.A8DL.01 3 0.4624 0.814 0.00 0.00 0.66 0.34
#> TCGA.VQ.A8DZ.01 2 0.0000 0.856 0.00 1.00 0.00 0.00
#> TCGA.D7.8572.01 3 0.4522 0.827 0.00 0.00 0.68 0.32
#> TCGA.RD.A7BW.01 1 0.0000 0.989 1.00 0.00 0.00 0.00
#> TCGA.CD.A487.01 3 0.4624 0.814 0.00 0.00 0.66 0.34
#> TCGA.BR.8371.01 1 0.0000 0.989 1.00 0.00 0.00 0.00
#> TCGA.BR.8059.01 3 0.4624 0.814 0.00 0.00 0.66 0.34
#> TCGA.D7.8576.01 4 0.3975 0.751 0.24 0.00 0.00 0.76
#> TCGA.FP.A8CX.01 3 0.4522 0.827 0.00 0.00 0.68 0.32
#> TCGA.HU.A4GH.01 2 0.0000 0.856 0.00 1.00 0.00 0.00
#> TCGA.CD.8526.01 3 0.4522 0.827 0.00 0.00 0.68 0.32
#> TCGA.D7.8578.01 4 0.0000 0.820 0.00 0.00 0.00 1.00
#> TCGA.RD.A8MW.01 3 0.3975 0.819 0.00 0.00 0.76 0.24
#> TCGA.BR.8364.01 1 0.0000 0.989 1.00 0.00 0.00 0.00
#> TCGA.KB.A6F7.01 2 0.4624 0.786 0.00 0.66 0.34 0.00
#> TCGA.BR.A4CR.01 3 0.4522 0.827 0.00 0.00 0.68 0.32
#> TCGA.CD.A489.01 4 0.4624 0.601 0.34 0.00 0.00 0.66
#> TCGA.HU.A4GY.01 1 0.0000 0.989 1.00 0.00 0.00 0.00
#> TCGA.FP.8209.01 1 0.0000 0.989 1.00 0.00 0.00 0.00
#> TCGA.BR.8060.01 2 0.0000 0.856 0.00 1.00 0.00 0.00
#> TCGA.BR.8077.01 2 0.0000 0.856 0.00 1.00 0.00 0.00
#> TCGA.EQ.8122.01 2 0.4522 0.793 0.00 0.68 0.32 0.00
#> TCGA.BR.A44T.01 1 0.0000 0.989 1.00 0.00 0.00 0.00
#> TCGA.BR.8291.01 4 0.0000 0.820 0.00 0.00 0.00 1.00
#> TCGA.FP.8210.01 1 0.0000 0.989 1.00 0.00 0.00 0.00
#> TCGA.RD.A7BS.01 4 0.3801 0.771 0.22 0.00 0.00 0.78
#> TCGA.CD.8529.01 4 0.0000 0.820 0.00 0.00 0.00 1.00
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> TCGA.VQ.A94P.01 1 0.000 0.972 1.00 0.00 0.00 0.00 0.00
#> TCGA.D7.6521.01 1 0.141 0.955 0.94 0.06 0.00 0.00 0.00
#> TCGA.VQ.A8PE.01 5 0.000 0.769 0.00 0.00 0.00 0.00 1.00
#> TCGA.D7.6519.01 3 0.293 0.858 0.00 0.18 0.82 0.00 0.00
#> TCGA.BR.8485.01 5 0.000 0.769 0.00 0.00 0.00 0.00 1.00
#> TCGA.BR.8486.01 5 0.000 0.769 0.00 0.00 0.00 0.00 1.00
#> TCGA.D7.6522.01 1 0.000 0.972 1.00 0.00 0.00 0.00 0.00
#> TCGA.VQ.A8PJ.01 2 0.413 1.000 0.00 0.62 0.00 0.00 0.38
#> TCGA.VQ.A8PH.01 2 0.413 1.000 0.00 0.62 0.00 0.00 0.38
#> TCGA.D7.6520.01 2 0.413 1.000 0.00 0.62 0.00 0.00 0.38
#> TCGA.VQ.AA64.01 4 0.311 0.879 0.00 0.20 0.00 0.80 0.00
#> TCGA.D7.6527.01 2 0.413 1.000 0.00 0.62 0.00 0.00 0.38
#> TCGA.VQ.A8PM.01 4 0.000 0.913 0.00 0.00 0.00 1.00 0.00
#> TCGA.VQ.A928.01 4 0.252 0.904 0.00 0.14 0.00 0.86 0.00
#> TCGA.VQ.A8E0.01 4 0.560 0.669 0.20 0.16 0.00 0.64 0.00
#> TCGA.BR.8678.01 2 0.413 1.000 0.00 0.62 0.00 0.00 0.38
#> TCGA.VQ.A91Q.01 1 0.141 0.955 0.94 0.06 0.00 0.00 0.00
#> TCGA.VQ.A91Z.01 5 0.475 0.468 0.00 0.04 0.30 0.00 0.66
#> TCGA.VQ.A94T.01 4 0.252 0.904 0.00 0.14 0.00 0.86 0.00
#> TCGA.BR.8484.01 4 0.244 0.865 0.00 0.04 0.06 0.90 0.00
#> TCGA.VQ.A91N.01 2 0.413 1.000 0.00 0.62 0.00 0.00 0.38
#> TCGA.VQ.A8PS.01 1 0.000 0.972 1.00 0.00 0.00 0.00 0.00
#> TCGA.BR.6454.01 1 0.141 0.955 0.94 0.06 0.00 0.00 0.00
#> TCGA.BR.8590.01 4 0.000 0.913 0.00 0.00 0.00 1.00 0.00
#> TCGA.VQ.A8PQ.01 1 0.000 0.972 1.00 0.00 0.00 0.00 0.00
#> TCGA.VQ.A91U.01 5 0.406 -0.369 0.00 0.36 0.00 0.00 0.64
#> TCGA.BR.6565.01 5 0.000 0.769 0.00 0.00 0.00 0.00 1.00
#> TCGA.VQ.A91Y.01 3 0.141 0.863 0.00 0.00 0.94 0.00 0.06
#> TCGA.BR.6456.01 3 0.000 0.909 0.00 0.00 1.00 0.00 0.00
#> TCGA.VQ.A925.01 3 0.351 0.852 0.00 0.18 0.80 0.00 0.02
#> TCGA.VQ.A927.01 1 0.141 0.955 0.94 0.06 0.00 0.00 0.00
#> TCGA.BR.6566.11 1 0.000 0.972 1.00 0.00 0.00 0.00 0.00
#> TCGA.IN.AB1V.01 3 0.000 0.909 0.00 0.00 1.00 0.00 0.00
#> TCGA.VQ.AA6F.01 4 0.252 0.904 0.00 0.14 0.00 0.86 0.00
#> TCGA.VQ.AA6J.01 4 0.252 0.904 0.00 0.14 0.00 0.86 0.00
#> TCGA.VQ.A94O.01 2 0.413 1.000 0.00 0.62 0.00 0.00 0.38
#> TCGA.D7.6526.01 2 0.413 1.000 0.00 0.62 0.00 0.00 0.38
#> TCGA.3M.AB46.01 5 0.549 0.388 0.00 0.10 0.28 0.00 0.62
#> TCGA.BR.8677.01 1 0.141 0.955 0.94 0.06 0.00 0.00 0.00
#> TCGA.BR.8687.01 3 0.444 0.771 0.00 0.10 0.76 0.00 0.14
#> TCGA.BR.8690.01 3 0.000 0.909 0.00 0.00 1.00 0.00 0.00
#> TCGA.FP.8631.01 2 0.413 1.000 0.00 0.62 0.00 0.00 0.38
#> TCGA.VQ.A922.01 5 0.000 0.769 0.00 0.00 0.00 0.00 1.00
#> TCGA.BR.A452.01 4 0.252 0.904 0.00 0.14 0.00 0.86 0.00
#> TCGA.VQ.A8PU.01 4 0.311 0.879 0.00 0.20 0.00 0.80 0.00
#> TCGA.HU.A4HD.01 5 0.202 0.729 0.00 0.00 0.10 0.00 0.90
#> TCGA.KB.A6F5.01 5 0.426 0.222 0.00 0.00 0.44 0.00 0.56
#> TCGA.VQ.AA6K.01 1 0.000 0.972 1.00 0.00 0.00 0.00 0.00
#> TCGA.HF.7133.01 3 0.293 0.858 0.00 0.18 0.82 0.00 0.00
#> TCGA.F1.6875.01 5 0.000 0.769 0.00 0.00 0.00 0.00 1.00
#> TCGA.MX.A666.01 5 0.202 0.729 0.00 0.00 0.10 0.00 0.90
#> TCGA.VQ.A8PX.01 4 0.252 0.904 0.00 0.14 0.00 0.86 0.00
#> TCGA.BR.A4IV.01 1 0.000 0.972 1.00 0.00 0.00 0.00 0.00
#> TCGA.D7.A6EX.01 4 0.293 0.891 0.00 0.18 0.00 0.82 0.00
#> TCGA.BR.A4IZ.01 1 0.000 0.972 1.00 0.00 0.00 0.00 0.00
#> TCGA.BR.A4J9.01 1 0.000 0.972 1.00 0.00 0.00 0.00 0.00
#> TCGA.B7.A5TN.01 5 0.492 0.378 0.00 0.04 0.34 0.00 0.62
#> TCGA.BR.7704.01 2 0.413 1.000 0.00 0.62 0.00 0.00 0.38
#> TCGA.BR.A4J1.01 2 0.413 1.000 0.00 0.62 0.00 0.00 0.38
#> TCGA.BR.7716.01 3 0.000 0.909 0.00 0.00 1.00 0.00 0.00
#> TCGA.FP.7735.01 4 0.252 0.904 0.00 0.14 0.00 0.86 0.00
#> TCGA.BR.7723.01 3 0.000 0.909 0.00 0.00 1.00 0.00 0.00
#> TCGA.EQ.A4SO.01 4 0.311 0.879 0.00 0.20 0.00 0.80 0.00
#> TCGA.CD.A4MH.01 5 0.000 0.769 0.00 0.00 0.00 0.00 1.00
#> TCGA.BR.A4J7.01 1 0.000 0.972 1.00 0.00 0.00 0.00 0.00
#> TCGA.HF.7131.01 5 0.413 0.366 0.00 0.00 0.38 0.00 0.62
#> TCGA.D7.A74B.01 1 0.141 0.955 0.94 0.06 0.00 0.00 0.00
#> TCGA.D7.A6F2.01 5 0.000 0.769 0.00 0.00 0.00 0.00 1.00
#> TCGA.RD.A7BT.01 5 0.000 0.769 0.00 0.00 0.00 0.00 1.00
#> TCGA.BR.A4J6.01 1 0.000 0.972 1.00 0.00 0.00 0.00 0.00
#> TCGA.HF.7136.01 3 0.252 0.872 0.00 0.14 0.86 0.00 0.00
#> TCGA.BR.A4PD.01 5 0.202 0.729 0.00 0.00 0.10 0.00 0.90
#> TCGA.VQ.A8PK.01 5 0.202 0.729 0.00 0.00 0.10 0.00 0.90
#> TCGA.IN.A6RN.01 2 0.413 1.000 0.00 0.62 0.00 0.00 0.38
#> TCGA.D7.A747.01 1 0.141 0.955 0.94 0.06 0.00 0.00 0.00
#> TCGA.F1.A72C.01 1 0.000 0.972 1.00 0.00 0.00 0.00 0.00
#> TCGA.MX.A663.01 3 0.000 0.909 0.00 0.00 1.00 0.00 0.00
#> TCGA.VQ.AA6D.01 2 0.413 1.000 0.00 0.62 0.00 0.00 0.38
#> TCGA.VQ.AA6A.01 2 0.413 1.000 0.00 0.62 0.00 0.00 0.38
#> TCGA.IN.7806.01 5 0.000 0.769 0.00 0.00 0.00 0.00 1.00
#> TCGA.HU.A4H5.01 2 0.413 1.000 0.00 0.62 0.00 0.00 0.38
#> TCGA.CD.5804.01 4 0.141 0.885 0.00 0.00 0.06 0.94 0.00
#> TCGA.D7.A4YT.01 3 0.293 0.858 0.00 0.18 0.82 0.00 0.00
#> TCGA.EQ.5647.01 3 0.293 0.858 0.00 0.18 0.82 0.00 0.00
#> TCGA.RD.A8N9.01 4 0.252 0.904 0.00 0.14 0.00 0.86 0.00
#> TCGA.CG.5717.01 1 0.141 0.955 0.94 0.06 0.00 0.00 0.00
#> TCGA.D7.6818.01 3 0.000 0.909 0.00 0.00 1.00 0.00 0.00
#> TCGA.CD.8525.01 3 0.000 0.909 0.00 0.00 1.00 0.00 0.00
#> TCGA.BR.4288.01 4 0.141 0.885 0.00 0.00 0.06 0.94 0.00
#> TCGA.CD.5813.01 1 0.141 0.955 0.94 0.06 0.00 0.00 0.00
#> TCGA.CG.5723.01 4 0.000 0.913 0.00 0.00 0.00 1.00 0.00
#> TCGA.CD.5800.01 3 0.351 0.847 0.00 0.18 0.80 0.02 0.00
#> TCGA.CG.5718.01 5 0.000 0.769 0.00 0.00 0.00 0.00 1.00
#> TCGA.BR.8080.01 4 0.000 0.913 0.00 0.00 0.00 1.00 0.00
#> TCGA.D7.6817.01 5 0.413 0.366 0.00 0.00 0.38 0.00 0.62
#> TCGA.KB.A93G.01 4 0.141 0.896 0.00 0.06 0.00 0.94 0.00
#> TCGA.CD.5799.01 3 0.104 0.899 0.00 0.04 0.96 0.00 0.00
#> TCGA.BR.7722.01 1 0.141 0.955 0.94 0.06 0.00 0.00 0.00
#> TCGA.BR.7901.01 5 0.000 0.769 0.00 0.00 0.00 0.00 1.00
#> TCGA.BR.6710.01 1 0.000 0.972 1.00 0.00 0.00 0.00 0.00
#> TCGA.B7.A5TI.01 3 0.650 0.284 0.00 0.20 0.46 0.34 0.00
#> TCGA.D7.6815.01 5 0.000 0.769 0.00 0.00 0.00 0.00 1.00
#> TCGA.BR.8295.01 2 0.413 1.000 0.00 0.62 0.00 0.00 0.38
#> TCGA.BR.7197.01 2 0.413 1.000 0.00 0.62 0.00 0.00 0.38
#> TCGA.IN.A7NR.01 4 0.000 0.913 0.00 0.00 0.00 1.00 0.00
#> TCGA.BR.6564.01 1 0.000 0.972 1.00 0.00 0.00 0.00 0.00
#> TCGA.KB.A93J.01 5 0.000 0.769 0.00 0.00 0.00 0.00 1.00
#> TCGA.CD.5798.01 1 0.000 0.972 1.00 0.00 0.00 0.00 0.00
#> TCGA.CD.8530.01 3 0.000 0.909 0.00 0.00 1.00 0.00 0.00
#> TCGA.CG.5719.01 1 0.141 0.955 0.94 0.06 0.00 0.00 0.00
#> TCGA.BR.6709.01 4 0.000 0.913 0.00 0.00 0.00 1.00 0.00
#> TCGA.R5.A7ZR.01 2 0.413 1.000 0.00 0.62 0.00 0.00 0.38
#> TCGA.BR.6801.01 4 0.228 0.907 0.00 0.12 0.00 0.88 0.00
#> TCGA.D7.5579.01 4 0.000 0.913 0.00 0.00 0.00 1.00 0.00
#> TCGA.R5.A7ZI.01 4 0.000 0.913 0.00 0.00 0.00 1.00 0.00
#> TCGA.CG.5732.01 3 0.342 0.628 0.00 0.00 0.76 0.00 0.24
#> TCGA.ZQ.A9CR.01 3 0.389 0.467 0.00 0.00 0.68 0.00 0.32
#> TCGA.BR.6803.01 1 0.000 0.972 1.00 0.00 0.00 0.00 0.00
#> TCGA.SW.A7EB.01 4 0.000 0.913 0.00 0.00 0.00 1.00 0.00
#> TCGA.D7.8574.01 1 0.000 0.972 1.00 0.00 0.00 0.00 0.00
#> TCGA.HJ.7597.01 1 0.141 0.955 0.94 0.06 0.00 0.00 0.00
#> TCGA.R5.A7ZE.01 5 0.000 0.769 0.00 0.00 0.00 0.00 1.00
#> TCGA.CD.5803.01 1 0.141 0.955 0.94 0.06 0.00 0.00 0.00
#> TCGA.CG.5725.01 2 0.413 1.000 0.00 0.62 0.00 0.00 0.38
#> TCGA.D7.6820.01 5 0.000 0.769 0.00 0.00 0.00 0.00 1.00
#> TCGA.CD.5802.01 4 0.311 0.730 0.00 0.00 0.20 0.80 0.00
#> TCGA.R5.A7ZF.01 4 0.141 0.885 0.00 0.00 0.06 0.94 0.00
#> TCGA.D7.A6F0.01 2 0.413 1.000 0.00 0.62 0.00 0.00 0.38
#> TCGA.CD.A486.01 5 0.000 0.769 0.00 0.00 0.00 0.00 1.00
#> TCGA.RD.A8N2.01 1 0.000 0.972 1.00 0.00 0.00 0.00 0.00
#> TCGA.IN.A6RI.01 2 0.413 1.000 0.00 0.62 0.00 0.00 0.38
#> TCGA.RD.A8N5.01 1 0.000 0.972 1.00 0.00 0.00 0.00 0.00
#> TCGA.RD.A8N1.01 4 0.000 0.913 0.00 0.00 0.00 1.00 0.00
#> TCGA.HU.A4GF.01 2 0.413 1.000 0.00 0.62 0.00 0.00 0.38
#> TCGA.CD.8532.01 1 0.000 0.972 1.00 0.00 0.00 0.00 0.00
#> TCGA.VQ.A8E2.01 3 0.293 0.858 0.00 0.18 0.82 0.00 0.00
#> TCGA.BR.8373.01 5 0.429 -0.673 0.00 0.46 0.00 0.00 0.54
#> TCGA.BR.8058.01 1 0.000 0.972 1.00 0.00 0.00 0.00 0.00
#> TCGA.D7.A748.01 1 0.000 0.972 1.00 0.00 0.00 0.00 0.00
#> TCGA.CD.8527.01 3 0.293 0.858 0.00 0.18 0.82 0.00 0.00
#> TCGA.VQ.A8DV.01 2 0.413 1.000 0.00 0.62 0.00 0.00 0.38
#> TCGA.RD.A8N6.01 3 0.000 0.909 0.00 0.00 1.00 0.00 0.00
#> TCGA.HU.8245.01 5 0.252 0.700 0.00 0.00 0.14 0.00 0.86
#> TCGA.ZA.A8F6.01 3 0.000 0.909 0.00 0.00 1.00 0.00 0.00
#> TCGA.RD.A8N0.01 1 0.000 0.972 1.00 0.00 0.00 0.00 0.00
#> TCGA.BR.8365.01 1 0.141 0.955 0.94 0.06 0.00 0.00 0.00
#> TCGA.FP.8211.01 1 0.645 0.136 0.48 0.20 0.00 0.32 0.00
#> TCGA.RD.A8N4.01 1 0.000 0.972 1.00 0.00 0.00 0.00 0.00
#> TCGA.VQ.A8DU.01 5 0.426 -0.620 0.00 0.44 0.00 0.00 0.56
#> TCGA.VQ.A8DL.01 3 0.000 0.909 0.00 0.00 1.00 0.00 0.00
#> TCGA.VQ.A8DZ.01 2 0.413 1.000 0.00 0.62 0.00 0.00 0.38
#> TCGA.D7.8572.01 3 0.000 0.909 0.00 0.00 1.00 0.00 0.00
#> TCGA.RD.A7BW.01 1 0.141 0.955 0.94 0.06 0.00 0.00 0.00
#> TCGA.CD.A487.01 3 0.000 0.909 0.00 0.00 1.00 0.00 0.00
#> TCGA.BR.8371.01 1 0.000 0.972 1.00 0.00 0.00 0.00 0.00
#> TCGA.BR.8059.01 3 0.000 0.909 0.00 0.00 1.00 0.00 0.00
#> TCGA.D7.8576.01 4 0.252 0.904 0.00 0.14 0.00 0.86 0.00
#> TCGA.FP.A8CX.01 3 0.000 0.909 0.00 0.00 1.00 0.00 0.00
#> TCGA.HU.A4GH.01 2 0.413 1.000 0.00 0.62 0.00 0.00 0.38
#> TCGA.CD.8526.01 3 0.000 0.909 0.00 0.00 1.00 0.00 0.00
#> TCGA.D7.8578.01 4 0.141 0.885 0.00 0.00 0.06 0.94 0.00
#> TCGA.RD.A8MW.01 3 0.000 0.909 0.00 0.00 1.00 0.00 0.00
#> TCGA.BR.8364.01 1 0.000 0.972 1.00 0.00 0.00 0.00 0.00
#> TCGA.KB.A6F7.01 5 0.000 0.769 0.00 0.00 0.00 0.00 1.00
#> TCGA.BR.A4CR.01 3 0.293 0.858 0.00 0.18 0.82 0.00 0.00
#> TCGA.CD.A489.01 4 0.311 0.879 0.00 0.20 0.00 0.80 0.00
#> TCGA.HU.A4GY.01 1 0.000 0.972 1.00 0.00 0.00 0.00 0.00
#> TCGA.FP.8209.01 1 0.000 0.972 1.00 0.00 0.00 0.00 0.00
#> TCGA.BR.8060.01 2 0.413 1.000 0.00 0.62 0.00 0.00 0.38
#> TCGA.BR.8077.01 2 0.413 1.000 0.00 0.62 0.00 0.00 0.38
#> TCGA.EQ.8122.01 5 0.000 0.769 0.00 0.00 0.00 0.00 1.00
#> TCGA.BR.A44T.01 1 0.000 0.972 1.00 0.00 0.00 0.00 0.00
#> TCGA.BR.8291.01 4 0.000 0.913 0.00 0.00 0.00 1.00 0.00
#> TCGA.FP.8210.01 1 0.000 0.972 1.00 0.00 0.00 0.00 0.00
#> TCGA.RD.A7BS.01 4 0.000 0.913 0.00 0.00 0.00 1.00 0.00
#> TCGA.CD.8529.01 4 0.356 0.635 0.00 0.00 0.26 0.74 0.00
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> TCGA.VQ.A94P.01 1 0.0000 0.9446 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D7.6521.01 1 0.2454 0.8856 0.84 0.00 0.00 0.00 0.00 0.16
#> TCGA.VQ.A8PE.01 5 0.3309 0.8380 0.00 0.28 0.00 0.00 0.72 0.00
#> TCGA.D7.6519.01 3 0.3851 -0.6159 0.00 0.00 0.54 0.00 0.00 0.46
#> TCGA.BR.8485.01 5 0.3309 0.8380 0.00 0.28 0.00 0.00 0.72 0.00
#> TCGA.BR.8486.01 5 0.3309 0.8380 0.00 0.28 0.00 0.00 0.72 0.00
#> TCGA.D7.6522.01 1 0.0000 0.9446 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.VQ.A8PJ.01 2 0.0000 0.9600 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.VQ.A8PH.01 2 0.0937 0.9506 0.00 0.96 0.00 0.00 0.00 0.04
#> TCGA.D7.6520.01 2 0.0937 0.9506 0.00 0.96 0.00 0.00 0.00 0.04
#> TCGA.VQ.AA64.01 4 0.5520 0.6687 0.00 0.00 0.00 0.56 0.20 0.24
#> TCGA.D7.6527.01 2 0.0000 0.9600 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.VQ.A8PM.01 4 0.0937 0.7337 0.00 0.00 0.00 0.96 0.00 0.04
#> TCGA.VQ.A928.01 4 0.4929 0.7180 0.00 0.00 0.00 0.62 0.28 0.10
#> TCGA.VQ.A8E0.01 4 0.6629 0.5551 0.12 0.00 0.00 0.50 0.10 0.28
#> TCGA.BR.8678.01 2 0.0000 0.9600 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.VQ.A91Q.01 1 0.2631 0.8746 0.82 0.00 0.00 0.00 0.00 0.18
#> TCGA.VQ.A91Z.01 5 0.6392 0.5515 0.00 0.06 0.20 0.00 0.54 0.20
#> TCGA.VQ.A94T.01 4 0.4929 0.7180 0.00 0.00 0.00 0.62 0.28 0.10
#> TCGA.BR.8484.01 4 0.4328 0.4885 0.00 0.00 0.10 0.72 0.00 0.18
#> TCGA.VQ.A91N.01 2 0.0937 0.9506 0.00 0.96 0.00 0.00 0.00 0.04
#> TCGA.VQ.A8PS.01 1 0.0000 0.9446 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BR.6454.01 1 0.2454 0.8856 0.84 0.00 0.00 0.00 0.00 0.16
#> TCGA.BR.8590.01 4 0.0547 0.7500 0.00 0.00 0.00 0.98 0.02 0.00
#> TCGA.VQ.A8PQ.01 1 0.0000 0.9446 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.VQ.A91U.01 2 0.4067 0.4819 0.00 0.70 0.00 0.00 0.26 0.04
#> TCGA.BR.6565.01 5 0.4172 0.8128 0.00 0.28 0.00 0.00 0.68 0.04
#> TCGA.VQ.A91Y.01 3 0.1814 0.5424 0.00 0.00 0.90 0.00 0.10 0.00
#> TCGA.BR.6456.01 3 0.0000 0.6695 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.VQ.A925.01 6 0.3756 0.6116 0.00 0.00 0.40 0.00 0.00 0.60
#> TCGA.VQ.A927.01 1 0.2631 0.8746 0.82 0.00 0.00 0.00 0.00 0.18
#> TCGA.BR.6566.11 1 0.0000 0.9446 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.IN.AB1V.01 3 0.0000 0.6695 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.VQ.AA6F.01 4 0.4462 0.7301 0.00 0.00 0.00 0.66 0.28 0.06
#> TCGA.VQ.AA6J.01 4 0.4462 0.7301 0.00 0.00 0.00 0.66 0.28 0.06
#> TCGA.VQ.A94O.01 2 0.0000 0.9600 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.D7.6526.01 2 0.0000 0.9600 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.3M.AB46.01 5 0.5398 0.4572 0.00 0.00 0.18 0.00 0.58 0.24
#> TCGA.BR.8677.01 1 0.2631 0.8746 0.82 0.00 0.00 0.00 0.00 0.18
#> TCGA.BR.8687.01 3 0.5837 -0.2346 0.00 0.00 0.46 0.00 0.20 0.34
#> TCGA.BR.8690.01 3 0.0000 0.6695 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.FP.8631.01 2 0.0937 0.9506 0.00 0.96 0.00 0.00 0.00 0.04
#> TCGA.VQ.A922.01 5 0.3309 0.8380 0.00 0.28 0.00 0.00 0.72 0.00
#> TCGA.BR.A452.01 4 0.4929 0.7180 0.00 0.00 0.00 0.62 0.28 0.10
#> TCGA.VQ.A8PU.01 4 0.5438 0.6878 0.00 0.00 0.00 0.56 0.28 0.16
#> TCGA.HU.A4HD.01 5 0.4328 0.8122 0.00 0.18 0.10 0.00 0.72 0.00
#> TCGA.KB.A6F5.01 5 0.4758 0.3773 0.00 0.00 0.36 0.00 0.58 0.06
#> TCGA.VQ.AA6K.01 1 0.0000 0.9446 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HF.7133.01 3 0.3851 -0.6159 0.00 0.00 0.54 0.00 0.00 0.46
#> TCGA.F1.6875.01 5 0.5289 0.7722 0.00 0.28 0.00 0.00 0.58 0.14
#> TCGA.MX.A666.01 5 0.4328 0.8122 0.00 0.18 0.10 0.00 0.72 0.00
#> TCGA.VQ.A8PX.01 4 0.4929 0.7180 0.00 0.00 0.00 0.62 0.28 0.10
#> TCGA.BR.A4IV.01 1 0.0000 0.9446 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D7.A6EX.01 4 0.5867 0.5732 0.00 0.00 0.00 0.48 0.24 0.28
#> TCGA.BR.A4IZ.01 1 0.0000 0.9446 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BR.A4J9.01 1 0.0000 0.9446 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.B7.A5TN.01 5 0.5354 0.4730 0.00 0.00 0.26 0.00 0.58 0.16
#> TCGA.BR.7704.01 2 0.0937 0.9506 0.00 0.96 0.00 0.00 0.00 0.04
#> TCGA.BR.A4J1.01 2 0.0000 0.9600 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.BR.7716.01 3 0.0000 0.6695 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.FP.7735.01 4 0.4462 0.7301 0.00 0.00 0.00 0.66 0.28 0.06
#> TCGA.BR.7723.01 3 0.0937 0.6318 0.00 0.00 0.96 0.00 0.00 0.04
#> TCGA.EQ.A4SO.01 4 0.5438 0.6878 0.00 0.00 0.00 0.56 0.28 0.16
#> TCGA.CD.A4MH.01 5 0.4172 0.8128 0.00 0.28 0.00 0.00 0.68 0.04
#> TCGA.BR.A4J7.01 1 0.0000 0.9446 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HF.7131.01 5 0.3309 0.5799 0.00 0.00 0.28 0.00 0.72 0.00
#> TCGA.D7.A74B.01 1 0.2631 0.8746 0.82 0.00 0.00 0.00 0.00 0.18
#> TCGA.D7.A6F2.01 5 0.4711 0.7993 0.00 0.28 0.00 0.00 0.64 0.08
#> TCGA.RD.A7BT.01 5 0.4172 0.8257 0.00 0.28 0.00 0.00 0.68 0.04
#> TCGA.BR.A4J6.01 1 0.0000 0.9446 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HF.7136.01 3 0.3864 -0.4917 0.00 0.00 0.52 0.00 0.00 0.48
#> TCGA.BR.A4PD.01 5 0.4328 0.8122 0.00 0.18 0.10 0.00 0.72 0.00
#> TCGA.VQ.A8PK.01 5 0.4328 0.8122 0.00 0.18 0.10 0.00 0.72 0.00
#> TCGA.IN.A6RN.01 2 0.2190 0.8928 0.00 0.90 0.00 0.00 0.06 0.04
#> TCGA.D7.A747.01 1 0.3678 0.8396 0.78 0.00 0.00 0.02 0.02 0.18
#> TCGA.F1.A72C.01 1 0.0000 0.9446 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.MX.A663.01 3 0.0000 0.6695 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.VQ.AA6D.01 2 0.0000 0.9600 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.VQ.AA6A.01 2 0.0000 0.9600 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.IN.7806.01 5 0.3309 0.8380 0.00 0.28 0.00 0.00 0.72 0.00
#> TCGA.HU.A4H5.01 2 0.0000 0.9600 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.CD.5804.01 4 0.2190 0.6941 0.00 0.00 0.06 0.90 0.00 0.04
#> TCGA.D7.A4YT.01 6 0.3864 0.6451 0.00 0.00 0.48 0.00 0.00 0.52
#> TCGA.EQ.5647.01 3 0.3851 -0.6159 0.00 0.00 0.54 0.00 0.00 0.46
#> TCGA.RD.A8N9.01 4 0.4462 0.7301 0.00 0.00 0.00 0.66 0.28 0.06
#> TCGA.CG.5717.01 1 0.2454 0.8856 0.84 0.00 0.00 0.00 0.00 0.16
#> TCGA.D7.6818.01 3 0.0000 0.6695 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.CD.8525.01 3 0.0000 0.6695 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.BR.4288.01 4 0.3045 0.6464 0.00 0.00 0.10 0.84 0.00 0.06
#> TCGA.CD.5813.01 1 0.2454 0.8856 0.84 0.00 0.00 0.00 0.00 0.16
#> TCGA.CG.5723.01 4 0.0547 0.7408 0.00 0.00 0.00 0.98 0.00 0.02
#> TCGA.CD.5800.01 3 0.4993 -0.4424 0.00 0.00 0.56 0.08 0.00 0.36
#> TCGA.CG.5718.01 5 0.3309 0.8380 0.00 0.28 0.00 0.00 0.72 0.00
#> TCGA.BR.8080.01 4 0.0547 0.7500 0.00 0.00 0.00 0.98 0.02 0.00
#> TCGA.D7.6817.01 5 0.3309 0.5799 0.00 0.00 0.28 0.00 0.72 0.00
#> TCGA.KB.A93G.01 4 0.3156 0.6995 0.00 0.00 0.00 0.80 0.02 0.18
#> TCGA.CD.5799.01 3 0.2941 0.3370 0.00 0.00 0.78 0.00 0.00 0.22
#> TCGA.BR.7722.01 1 0.2454 0.8856 0.84 0.00 0.00 0.00 0.00 0.16
#> TCGA.BR.7901.01 5 0.3309 0.8380 0.00 0.28 0.00 0.00 0.72 0.00
#> TCGA.BR.6710.01 1 0.0000 0.9446 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.B7.A5TI.01 6 0.6873 0.4062 0.00 0.00 0.26 0.20 0.08 0.46
#> TCGA.D7.6815.01 5 0.5289 0.7722 0.00 0.28 0.00 0.00 0.58 0.14
#> TCGA.BR.8295.01 2 0.0000 0.9600 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.BR.7197.01 2 0.0937 0.9506 0.00 0.96 0.00 0.00 0.00 0.04
#> TCGA.IN.A7NR.01 4 0.0547 0.7500 0.00 0.00 0.00 0.98 0.02 0.00
#> TCGA.BR.6564.01 1 0.0000 0.9446 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.KB.A93J.01 5 0.4172 0.8257 0.00 0.28 0.00 0.00 0.68 0.04
#> TCGA.CD.5798.01 1 0.0000 0.9446 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CD.8530.01 3 0.0000 0.6695 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.CG.5719.01 1 0.2454 0.8856 0.84 0.00 0.00 0.00 0.00 0.16
#> TCGA.BR.6709.01 4 0.0547 0.7500 0.00 0.00 0.00 0.98 0.02 0.00
#> TCGA.R5.A7ZR.01 2 0.0000 0.9600 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.BR.6801.01 4 0.4834 0.7258 0.00 0.00 0.00 0.64 0.26 0.10
#> TCGA.D7.5579.01 4 0.0937 0.7337 0.00 0.00 0.00 0.96 0.00 0.04
#> TCGA.R5.A7ZI.01 4 0.0937 0.7337 0.00 0.00 0.00 0.96 0.00 0.04
#> TCGA.CG.5732.01 3 0.4247 0.2774 0.00 0.00 0.70 0.00 0.24 0.06
#> TCGA.ZQ.A9CR.01 3 0.4873 0.0767 0.00 0.00 0.52 0.00 0.42 0.06
#> TCGA.BR.6803.01 1 0.0000 0.9446 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.SW.A7EB.01 4 0.0547 0.7500 0.00 0.00 0.00 0.98 0.02 0.00
#> TCGA.D7.8574.01 1 0.0000 0.9446 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HJ.7597.01 1 0.2454 0.8856 0.84 0.00 0.00 0.00 0.00 0.16
#> TCGA.R5.A7ZE.01 5 0.3309 0.8380 0.00 0.28 0.00 0.00 0.72 0.00
#> TCGA.CD.5803.01 1 0.2454 0.8856 0.84 0.00 0.00 0.00 0.00 0.16
#> TCGA.CG.5725.01 2 0.0000 0.9600 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.D7.6820.01 5 0.3309 0.8380 0.00 0.28 0.00 0.00 0.72 0.00
#> TCGA.CD.5802.01 4 0.4482 0.1637 0.00 0.00 0.36 0.60 0.00 0.04
#> TCGA.R5.A7ZF.01 4 0.2728 0.6573 0.00 0.00 0.10 0.86 0.00 0.04
#> TCGA.D7.A6F0.01 2 0.0000 0.9600 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.CD.A486.01 5 0.3309 0.8380 0.00 0.28 0.00 0.00 0.72 0.00
#> TCGA.RD.A8N2.01 1 0.0000 0.9446 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.IN.A6RI.01 2 0.0000 0.9600 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.RD.A8N5.01 1 0.0000 0.9446 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.RD.A8N1.01 4 0.2474 0.6774 0.00 0.00 0.08 0.88 0.00 0.04
#> TCGA.HU.A4GF.01 2 0.0937 0.9506 0.00 0.96 0.00 0.00 0.00 0.04
#> TCGA.CD.8532.01 1 0.0000 0.9446 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.VQ.A8E2.01 3 0.3706 -0.3451 0.00 0.00 0.62 0.00 0.00 0.38
#> TCGA.BR.8373.01 2 0.2728 0.8389 0.00 0.86 0.00 0.00 0.10 0.04
#> TCGA.BR.8058.01 1 0.0000 0.9446 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D7.A748.01 1 0.0000 0.9446 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CD.8527.01 6 0.3864 0.6451 0.00 0.00 0.48 0.00 0.00 0.52
#> TCGA.VQ.A8DV.01 2 0.0000 0.9600 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.RD.A8N6.01 3 0.1267 0.6140 0.00 0.00 0.94 0.00 0.00 0.06
#> TCGA.HU.8245.01 5 0.4377 0.7587 0.00 0.12 0.16 0.00 0.72 0.00
#> TCGA.ZA.A8F6.01 3 0.0000 0.6695 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.RD.A8N0.01 1 0.0000 0.9446 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BR.8365.01 1 0.2631 0.8746 0.82 0.00 0.00 0.00 0.00 0.18
#> TCGA.FP.8211.01 4 0.7359 0.4701 0.16 0.00 0.00 0.40 0.18 0.26
#> TCGA.RD.A8N4.01 1 0.0000 0.9446 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.VQ.A8DU.01 2 0.2728 0.8389 0.00 0.86 0.00 0.00 0.10 0.04
#> TCGA.VQ.A8DL.01 3 0.0000 0.6695 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.VQ.A8DZ.01 2 0.0937 0.9506 0.00 0.96 0.00 0.00 0.00 0.04
#> TCGA.D7.8572.01 3 0.0000 0.6695 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.RD.A7BW.01 1 0.2631 0.8746 0.82 0.00 0.00 0.00 0.00 0.18
#> TCGA.CD.A487.01 3 0.0000 0.6695 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.BR.8371.01 1 0.0000 0.9446 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BR.8059.01 3 0.0547 0.6443 0.00 0.00 0.98 0.02 0.00 0.00
#> TCGA.D7.8576.01 4 0.4929 0.7180 0.00 0.00 0.00 0.62 0.28 0.10
#> TCGA.FP.A8CX.01 3 0.0000 0.6695 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.HU.A4GH.01 2 0.0000 0.9600 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.CD.8526.01 3 0.0000 0.6695 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.D7.8578.01 4 0.2728 0.6573 0.00 0.00 0.10 0.86 0.00 0.04
#> TCGA.RD.A8MW.01 3 0.0000 0.6695 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.BR.8364.01 1 0.0000 0.9446 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.KB.A6F7.01 5 0.3309 0.8380 0.00 0.28 0.00 0.00 0.72 0.00
#> TCGA.BR.A4CR.01 6 0.3851 0.6286 0.00 0.00 0.46 0.00 0.00 0.54
#> TCGA.CD.A489.01 4 0.5490 0.6849 0.00 0.00 0.00 0.56 0.26 0.18
#> TCGA.HU.A4GY.01 1 0.0000 0.9446 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FP.8209.01 1 0.0000 0.9446 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BR.8060.01 2 0.0937 0.9506 0.00 0.96 0.00 0.00 0.00 0.04
#> TCGA.BR.8077.01 2 0.0000 0.9600 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.EQ.8122.01 5 0.4172 0.8128 0.00 0.28 0.00 0.00 0.68 0.04
#> TCGA.BR.A44T.01 1 0.0000 0.9446 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BR.8291.01 4 0.0547 0.7408 0.00 0.00 0.00 0.98 0.00 0.02
#> TCGA.FP.8210.01 1 0.0000 0.9446 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.RD.A7BS.01 4 0.0547 0.7500 0.00 0.00 0.00 0.98 0.02 0.00
#> TCGA.CD.8529.01 3 0.4651 -0.0910 0.00 0.00 0.48 0.48 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.VQ.A94P.01 1 0.0000 0.906 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D7.6521.01 1 0.4635 0.792 0.72 0.00 0.00 0.02 0.12 0.12 0.02
#> TCGA.VQ.A8PE.01 5 0.2259 0.867 0.00 0.16 0.00 0.00 0.84 0.00 0.00
#> TCGA.D7.6519.01 6 0.3388 0.843 0.00 0.00 0.20 0.04 0.00 0.76 0.00
#> TCGA.BR.8485.01 5 0.2259 0.867 0.00 0.16 0.00 0.00 0.84 0.00 0.00
#> TCGA.BR.8486.01 5 0.2259 0.867 0.00 0.16 0.00 0.00 0.84 0.00 0.00
#> TCGA.D7.6522.01 1 0.0000 0.906 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.VQ.A8PJ.01 2 0.0000 0.921 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.VQ.A8PH.01 2 0.1433 0.905 0.00 0.92 0.00 0.00 0.00 0.08 0.00
#> TCGA.D7.6520.01 2 0.1433 0.905 0.00 0.92 0.00 0.00 0.00 0.08 0.00
#> TCGA.VQ.AA64.01 7 0.3289 0.689 0.00 0.00 0.00 0.02 0.06 0.10 0.82
#> TCGA.D7.6527.01 2 0.0000 0.921 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.VQ.A8PM.01 4 0.3358 0.835 0.00 0.00 0.00 0.64 0.00 0.00 0.36
#> TCGA.VQ.A928.01 7 0.0504 0.869 0.00 0.00 0.00 0.02 0.00 0.00 0.98
#> TCGA.VQ.A8E0.01 7 0.5232 0.528 0.06 0.00 0.00 0.02 0.12 0.12 0.68
#> TCGA.BR.8678.01 2 0.0000 0.921 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.VQ.A91Q.01 1 0.4635 0.792 0.72 0.00 0.00 0.02 0.12 0.12 0.02
#> TCGA.VQ.A91Z.01 5 0.5281 0.538 0.00 0.00 0.06 0.26 0.60 0.08 0.00
#> TCGA.VQ.A94T.01 7 0.0504 0.869 0.00 0.00 0.00 0.02 0.00 0.00 0.98
#> TCGA.BR.8484.01 4 0.5128 0.493 0.00 0.00 0.00 0.52 0.00 0.32 0.16
#> TCGA.VQ.A91N.01 2 0.1433 0.905 0.00 0.92 0.00 0.00 0.00 0.08 0.00
#> TCGA.VQ.A8PS.01 1 0.0000 0.906 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BR.6454.01 1 0.4635 0.792 0.72 0.00 0.00 0.02 0.12 0.12 0.02
#> TCGA.BR.8590.01 4 0.3358 0.835 0.00 0.00 0.00 0.64 0.00 0.00 0.36
#> TCGA.VQ.A8PQ.01 1 0.0000 0.906 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.VQ.A91U.01 2 0.5040 0.215 0.00 0.54 0.00 0.02 0.36 0.08 0.00
#> TCGA.BR.6565.01 5 0.3617 0.816 0.00 0.16 0.00 0.00 0.76 0.08 0.00
#> TCGA.VQ.A91Y.01 3 0.0863 0.841 0.00 0.00 0.96 0.00 0.04 0.00 0.00
#> TCGA.BR.6456.01 3 0.0000 0.889 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.VQ.A925.01 6 0.3985 0.821 0.00 0.00 0.18 0.10 0.00 0.72 0.00
#> TCGA.VQ.A927.01 1 0.4635 0.792 0.72 0.00 0.00 0.02 0.12 0.12 0.02
#> TCGA.BR.6566.11 1 0.0000 0.906 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.IN.AB1V.01 3 0.0000 0.889 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.VQ.AA6F.01 7 0.0504 0.869 0.00 0.00 0.00 0.02 0.00 0.00 0.98
#> TCGA.VQ.AA6J.01 7 0.0504 0.869 0.00 0.00 0.00 0.02 0.00 0.00 0.98
#> TCGA.VQ.A94O.01 2 0.0000 0.921 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D7.6526.01 2 0.0000 0.921 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.3M.AB46.01 5 0.5559 0.558 0.00 0.00 0.06 0.24 0.58 0.12 0.00
#> TCGA.BR.8677.01 1 0.4635 0.792 0.72 0.00 0.00 0.02 0.12 0.12 0.02
#> TCGA.BR.8687.01 6 0.6337 0.417 0.00 0.00 0.32 0.06 0.22 0.40 0.00
#> TCGA.BR.8690.01 3 0.0000 0.889 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.FP.8631.01 2 0.1433 0.905 0.00 0.92 0.00 0.00 0.00 0.08 0.00
#> TCGA.VQ.A922.01 5 0.2259 0.867 0.00 0.16 0.00 0.00 0.84 0.00 0.00
#> TCGA.BR.A452.01 7 0.0504 0.869 0.00 0.00 0.00 0.02 0.00 0.00 0.98
#> TCGA.VQ.A8PU.01 7 0.0504 0.847 0.00 0.00 0.00 0.02 0.00 0.00 0.98
#> TCGA.HU.A4HD.01 5 0.2829 0.837 0.00 0.08 0.08 0.00 0.84 0.00 0.00
#> TCGA.KB.A6F5.01 5 0.4278 0.138 0.00 0.00 0.46 0.04 0.50 0.00 0.00
#> TCGA.VQ.AA6K.01 1 0.0000 0.906 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HF.7133.01 6 0.3052 0.843 0.00 0.00 0.20 0.02 0.00 0.78 0.00
#> TCGA.F1.6875.01 5 0.5293 0.725 0.00 0.16 0.00 0.24 0.58 0.02 0.00
#> TCGA.MX.A666.01 5 0.2829 0.837 0.00 0.08 0.08 0.00 0.84 0.00 0.00
#> TCGA.VQ.A8PX.01 7 0.0504 0.869 0.00 0.00 0.00 0.02 0.00 0.00 0.98
#> TCGA.BR.A4IV.01 1 0.0000 0.906 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D7.A6EX.01 7 0.4426 0.298 0.00 0.00 0.00 0.06 0.00 0.38 0.56
#> TCGA.BR.A4IZ.01 1 0.0000 0.906 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BR.A4J9.01 1 0.0000 0.906 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.B7.A5TN.01 5 0.5399 0.611 0.00 0.00 0.10 0.20 0.62 0.08 0.00
#> TCGA.BR.7704.01 2 0.1433 0.905 0.00 0.92 0.00 0.00 0.00 0.08 0.00
#> TCGA.BR.A4J1.01 2 0.0000 0.921 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BR.7716.01 3 0.0000 0.889 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.FP.7735.01 7 0.0504 0.869 0.00 0.00 0.00 0.02 0.00 0.00 0.98
#> TCGA.BR.7723.01 3 0.0504 0.872 0.00 0.00 0.98 0.02 0.00 0.00 0.00
#> TCGA.EQ.A4SO.01 7 0.0000 0.860 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.CD.A4MH.01 5 0.3617 0.816 0.00 0.16 0.00 0.00 0.76 0.08 0.00
#> TCGA.BR.A4J7.01 1 0.0000 0.906 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HF.7131.01 5 0.2259 0.756 0.00 0.00 0.16 0.00 0.84 0.00 0.00
#> TCGA.D7.A74B.01 1 0.4635 0.792 0.72 0.00 0.00 0.02 0.12 0.12 0.02
#> TCGA.D7.A6F2.01 5 0.4457 0.821 0.00 0.16 0.00 0.06 0.72 0.06 0.00
#> TCGA.RD.A7BT.01 5 0.3370 0.853 0.00 0.16 0.00 0.06 0.78 0.00 0.00
#> TCGA.BR.A4J6.01 1 0.0000 0.906 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HF.7136.01 6 0.5853 0.621 0.00 0.00 0.32 0.16 0.04 0.48 0.00
#> TCGA.BR.A4PD.01 5 0.2829 0.837 0.00 0.08 0.08 0.00 0.84 0.00 0.00
#> TCGA.VQ.A8PK.01 5 0.2829 0.837 0.00 0.08 0.08 0.00 0.84 0.00 0.00
#> TCGA.IN.A6RN.01 2 0.3617 0.733 0.00 0.76 0.00 0.00 0.16 0.08 0.00
#> TCGA.D7.A747.01 1 0.4635 0.792 0.72 0.00 0.00 0.02 0.12 0.12 0.02
#> TCGA.F1.A72C.01 1 0.0000 0.906 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.MX.A663.01 3 0.0000 0.889 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.VQ.AA6D.01 2 0.0000 0.921 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.VQ.AA6A.01 2 0.0000 0.921 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.IN.7806.01 5 0.2259 0.867 0.00 0.16 0.00 0.00 0.84 0.00 0.00
#> TCGA.HU.A4H5.01 2 0.0000 0.921 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CD.5804.01 4 0.4248 0.797 0.00 0.00 0.08 0.66 0.00 0.00 0.26
#> TCGA.D7.A4YT.01 6 0.4193 0.836 0.00 0.00 0.20 0.04 0.04 0.72 0.00
#> TCGA.EQ.5647.01 6 0.3052 0.843 0.00 0.00 0.20 0.02 0.00 0.78 0.00
#> TCGA.RD.A8N9.01 7 0.0504 0.869 0.00 0.00 0.00 0.02 0.00 0.00 0.98
#> TCGA.CG.5717.01 1 0.4162 0.802 0.74 0.00 0.00 0.02 0.12 0.12 0.00
#> TCGA.D7.6818.01 3 0.0000 0.889 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.CD.8525.01 3 0.0000 0.889 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.BR.4288.01 4 0.4243 0.770 0.00 0.00 0.10 0.68 0.00 0.00 0.22
#> TCGA.CD.5813.01 1 0.4635 0.792 0.72 0.00 0.00 0.02 0.12 0.12 0.02
#> TCGA.CG.5723.01 4 0.3358 0.835 0.00 0.00 0.00 0.64 0.00 0.00 0.36
#> TCGA.CD.5800.01 3 0.5561 -0.516 0.00 0.00 0.42 0.14 0.02 0.42 0.00
#> TCGA.CG.5718.01 5 0.2259 0.867 0.00 0.16 0.00 0.00 0.84 0.00 0.00
#> TCGA.BR.8080.01 4 0.3358 0.835 0.00 0.00 0.00 0.64 0.00 0.00 0.36
#> TCGA.D7.6817.01 5 0.2259 0.756 0.00 0.00 0.16 0.00 0.84 0.00 0.00
#> TCGA.KB.A93G.01 4 0.6372 0.423 0.00 0.00 0.00 0.42 0.12 0.12 0.34
#> TCGA.CD.5799.01 3 0.3841 0.321 0.00 0.00 0.68 0.04 0.00 0.28 0.00
#> TCGA.BR.7722.01 1 0.4635 0.792 0.72 0.00 0.00 0.02 0.12 0.12 0.02
#> TCGA.BR.7901.01 5 0.2259 0.867 0.00 0.16 0.00 0.00 0.84 0.00 0.00
#> TCGA.BR.6710.01 1 0.0000 0.906 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.B7.A5TI.01 6 0.3927 0.787 0.00 0.00 0.14 0.02 0.00 0.76 0.08
#> TCGA.D7.6815.01 5 0.5086 0.757 0.00 0.16 0.00 0.20 0.62 0.02 0.00
#> TCGA.BR.8295.01 2 0.0504 0.918 0.00 0.98 0.00 0.00 0.00 0.02 0.00
#> TCGA.BR.7197.01 2 0.1433 0.905 0.00 0.92 0.00 0.00 0.00 0.08 0.00
#> TCGA.IN.A7NR.01 4 0.3358 0.835 0.00 0.00 0.00 0.64 0.00 0.00 0.36
#> TCGA.BR.6564.01 1 0.0000 0.906 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.KB.A93J.01 5 0.3086 0.859 0.00 0.16 0.00 0.04 0.80 0.00 0.00
#> TCGA.CD.5798.01 1 0.0000 0.906 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CD.8530.01 3 0.0000 0.889 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.CG.5719.01 1 0.4162 0.802 0.74 0.00 0.00 0.02 0.12 0.12 0.00
#> TCGA.BR.6709.01 4 0.3358 0.835 0.00 0.00 0.00 0.64 0.00 0.00 0.36
#> TCGA.R5.A7ZR.01 2 0.0000 0.921 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BR.6801.01 7 0.0504 0.869 0.00 0.00 0.00 0.02 0.00 0.00 0.98
#> TCGA.D7.5579.01 4 0.3358 0.835 0.00 0.00 0.00 0.64 0.00 0.00 0.36
#> TCGA.R5.A7ZI.01 4 0.3294 0.830 0.00 0.00 0.00 0.66 0.00 0.00 0.34
#> TCGA.CG.5732.01 3 0.3637 0.495 0.00 0.00 0.72 0.04 0.24 0.00 0.00
#> TCGA.ZQ.A9CR.01 3 0.3685 0.392 0.00 0.00 0.66 0.02 0.32 0.00 0.00
#> TCGA.BR.6803.01 1 0.0000 0.906 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.SW.A7EB.01 4 0.3358 0.835 0.00 0.00 0.00 0.64 0.00 0.00 0.36
#> TCGA.D7.8574.01 1 0.0000 0.906 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HJ.7597.01 1 0.4635 0.792 0.72 0.00 0.00 0.02 0.12 0.12 0.02
#> TCGA.R5.A7ZE.01 5 0.2259 0.867 0.00 0.16 0.00 0.00 0.84 0.00 0.00
#> TCGA.CD.5803.01 1 0.4162 0.802 0.74 0.00 0.00 0.02 0.12 0.12 0.00
#> TCGA.CG.5725.01 2 0.0000 0.921 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D7.6820.01 5 0.2259 0.867 0.00 0.16 0.00 0.00 0.84 0.00 0.00
#> TCGA.CD.5802.01 4 0.4535 0.625 0.00 0.00 0.24 0.64 0.00 0.00 0.12
#> TCGA.R5.A7ZF.01 4 0.4353 0.783 0.00 0.00 0.10 0.66 0.00 0.00 0.24
#> TCGA.D7.A6F0.01 2 0.0000 0.921 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CD.A486.01 5 0.2259 0.867 0.00 0.16 0.00 0.00 0.84 0.00 0.00
#> TCGA.RD.A8N2.01 1 0.0000 0.906 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.IN.A6RI.01 2 0.0000 0.921 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.RD.A8N5.01 1 0.0000 0.906 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.RD.A8N1.01 4 0.3685 0.826 0.00 0.00 0.02 0.66 0.00 0.00 0.32
#> TCGA.HU.A4GF.01 2 0.1433 0.905 0.00 0.92 0.00 0.00 0.00 0.08 0.00
#> TCGA.CD.8532.01 1 0.0000 0.906 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.VQ.A8E2.01 6 0.4995 0.449 0.00 0.00 0.46 0.04 0.04 0.46 0.00
#> TCGA.BR.8373.01 2 0.4418 0.452 0.00 0.62 0.00 0.00 0.30 0.08 0.00
#> TCGA.BR.8058.01 1 0.0000 0.906 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D7.A748.01 1 0.0000 0.906 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CD.8527.01 6 0.3863 0.840 0.00 0.00 0.20 0.04 0.02 0.74 0.00
#> TCGA.VQ.A8DV.01 2 0.0000 0.921 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.RD.A8N6.01 3 0.1718 0.813 0.00 0.00 0.92 0.04 0.04 0.00 0.00
#> TCGA.HU.8245.01 5 0.2259 0.756 0.00 0.00 0.16 0.00 0.84 0.00 0.00
#> TCGA.ZA.A8F6.01 3 0.0000 0.889 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.RD.A8N0.01 1 0.0000 0.906 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BR.8365.01 1 0.4635 0.792 0.72 0.00 0.00 0.02 0.12 0.12 0.02
#> TCGA.FP.8211.01 7 0.4831 0.581 0.08 0.00 0.00 0.02 0.06 0.12 0.72
#> TCGA.RD.A8N4.01 1 0.0000 0.906 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.VQ.A8DU.01 2 0.4597 0.294 0.00 0.56 0.00 0.00 0.36 0.08 0.00
#> TCGA.VQ.A8DL.01 3 0.0000 0.889 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.VQ.A8DZ.01 2 0.1433 0.905 0.00 0.92 0.00 0.00 0.00 0.08 0.00
#> TCGA.D7.8572.01 3 0.0000 0.889 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.RD.A7BW.01 1 0.4635 0.792 0.72 0.00 0.00 0.02 0.12 0.12 0.02
#> TCGA.CD.A487.01 3 0.0000 0.889 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.BR.8371.01 1 0.0000 0.906 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BR.8059.01 3 0.0000 0.889 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.D7.8576.01 7 0.0504 0.869 0.00 0.00 0.00 0.02 0.00 0.00 0.98
#> TCGA.FP.A8CX.01 3 0.0000 0.889 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.HU.A4GH.01 2 0.0000 0.921 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CD.8526.01 3 0.0000 0.889 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.D7.8578.01 4 0.4353 0.783 0.00 0.00 0.10 0.66 0.00 0.00 0.24
#> TCGA.RD.A8MW.01 3 0.0000 0.889 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.BR.8364.01 1 0.0000 0.906 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.KB.A6F7.01 5 0.2259 0.867 0.00 0.16 0.00 0.00 0.84 0.00 0.00
#> TCGA.BR.A4CR.01 6 0.3908 0.835 0.00 0.00 0.20 0.08 0.00 0.72 0.00
#> TCGA.CD.A489.01 7 0.1006 0.834 0.00 0.00 0.00 0.02 0.00 0.02 0.96
#> TCGA.HU.A4GY.01 1 0.0000 0.906 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FP.8209.01 1 0.0000 0.906 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BR.8060.01 2 0.1433 0.905 0.00 0.92 0.00 0.00 0.00 0.08 0.00
#> TCGA.BR.8077.01 2 0.0000 0.921 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EQ.8122.01 5 0.3086 0.846 0.00 0.16 0.00 0.00 0.80 0.04 0.00
#> TCGA.BR.A44T.01 1 0.0000 0.906 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BR.8291.01 4 0.3358 0.835 0.00 0.00 0.00 0.64 0.00 0.00 0.36
#> TCGA.FP.8210.01 1 0.0000 0.906 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.RD.A7BS.01 4 0.3358 0.835 0.00 0.00 0.00 0.64 0.00 0.00 0.36
#> TCGA.CD.8529.01 4 0.3358 0.426 0.00 0.00 0.36 0.64 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.VQ.A94P.01 1 0.0000 0.914 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D7.6521.01 1 0.3170 0.815 0.76 0.00 0.00 0.00 0.00 0.00 0.20 0.04
#> TCGA.VQ.A8PE.01 5 0.1091 0.835 0.00 0.06 0.00 0.00 0.94 0.00 0.00 0.00
#> TCGA.D7.6519.01 6 0.1607 0.760 0.00 0.00 0.04 0.04 0.00 0.92 0.00 0.00
#> TCGA.BR.8485.01 5 0.1091 0.835 0.00 0.06 0.00 0.00 0.94 0.00 0.00 0.00
#> TCGA.BR.8486.01 5 0.1091 0.835 0.00 0.06 0.00 0.00 0.94 0.00 0.00 0.00
#> TCGA.D7.6522.01 1 0.0000 0.914 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.VQ.A8PJ.01 2 0.0000 0.961 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.VQ.A8PH.01 2 0.1091 0.948 0.00 0.94 0.00 0.00 0.00 0.00 0.00 0.06
#> TCGA.D7.6520.01 2 0.1091 0.948 0.00 0.94 0.00 0.00 0.00 0.00 0.00 0.06
#> TCGA.VQ.AA64.01 8 0.4593 0.827 0.00 0.00 0.00 0.26 0.00 0.02 0.10 0.62
#> TCGA.D7.6527.01 2 0.0000 0.961 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.VQ.A8PM.01 4 0.0000 0.822 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.VQ.A928.01 8 0.3675 0.888 0.00 0.00 0.00 0.30 0.00 0.00 0.04 0.66
#> TCGA.VQ.A8E0.01 8 0.5402 0.610 0.02 0.00 0.00 0.24 0.00 0.00 0.26 0.48
#> TCGA.BR.8678.01 2 0.0000 0.961 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.VQ.A91Q.01 1 0.3504 0.761 0.70 0.00 0.00 0.00 0.00 0.00 0.26 0.04
#> TCGA.VQ.A91Z.01 5 0.5189 0.405 0.00 0.00 0.04 0.00 0.48 0.00 0.38 0.10
#> TCGA.VQ.A94T.01 8 0.2938 0.895 0.00 0.00 0.00 0.30 0.00 0.00 0.00 0.70
#> TCGA.BR.8484.01 4 0.4325 0.278 0.00 0.00 0.00 0.56 0.02 0.38 0.00 0.04
#> TCGA.VQ.A91N.01 2 0.1091 0.948 0.00 0.94 0.00 0.00 0.00 0.00 0.00 0.06
#> TCGA.VQ.A8PS.01 1 0.0000 0.914 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BR.6454.01 1 0.3170 0.815 0.76 0.00 0.00 0.00 0.00 0.00 0.20 0.04
#> TCGA.BR.8590.01 4 0.1275 0.805 0.00 0.00 0.00 0.94 0.00 0.00 0.02 0.04
#> TCGA.VQ.A8PQ.01 1 0.0000 0.914 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.VQ.A91U.01 5 0.5180 0.507 0.00 0.30 0.00 0.00 0.54 0.00 0.04 0.12
#> TCGA.BR.6565.01 5 0.2165 0.821 0.00 0.06 0.00 0.00 0.88 0.00 0.00 0.06
#> TCGA.VQ.A91Y.01 3 0.1091 0.869 0.00 0.00 0.94 0.00 0.00 0.00 0.06 0.00
#> TCGA.BR.6456.01 3 0.0000 0.911 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.VQ.A925.01 6 0.3494 0.736 0.00 0.00 0.04 0.00 0.04 0.78 0.14 0.00
#> TCGA.VQ.A927.01 1 0.3170 0.815 0.76 0.00 0.00 0.00 0.00 0.00 0.20 0.04
#> TCGA.BR.6566.11 1 0.0000 0.914 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.IN.AB1V.01 3 0.0000 0.911 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.VQ.AA6F.01 8 0.3449 0.881 0.00 0.00 0.00 0.32 0.00 0.00 0.02 0.66
#> TCGA.VQ.AA6J.01 8 0.3449 0.881 0.00 0.00 0.00 0.32 0.00 0.00 0.02 0.66
#> TCGA.VQ.A94O.01 2 0.0000 0.961 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D7.6526.01 2 0.0000 0.961 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.3M.AB46.01 5 0.5266 0.582 0.00 0.00 0.04 0.00 0.56 0.02 0.30 0.08
#> TCGA.BR.8677.01 1 0.3170 0.815 0.76 0.00 0.00 0.00 0.00 0.00 0.20 0.04
#> TCGA.BR.8687.01 6 0.6129 0.490 0.00 0.00 0.12 0.00 0.18 0.44 0.26 0.00
#> TCGA.BR.8690.01 3 0.0000 0.911 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FP.8631.01 2 0.1804 0.918 0.00 0.90 0.00 0.00 0.02 0.00 0.00 0.08
#> TCGA.VQ.A922.01 5 0.1557 0.834 0.00 0.06 0.00 0.00 0.92 0.00 0.00 0.02
#> TCGA.BR.A452.01 8 0.2938 0.895 0.00 0.00 0.00 0.30 0.00 0.00 0.00 0.70
#> TCGA.VQ.A8PU.01 8 0.3198 0.879 0.00 0.00 0.00 0.26 0.00 0.02 0.00 0.72
#> TCGA.HU.A4HD.01 5 0.1887 0.806 0.00 0.00 0.06 0.00 0.90 0.00 0.04 0.00
#> TCGA.KB.A6F5.01 3 0.4622 0.363 0.00 0.00 0.56 0.00 0.30 0.00 0.14 0.00
#> TCGA.VQ.AA6K.01 1 0.0000 0.914 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HF.7133.01 6 0.2071 0.759 0.00 0.00 0.04 0.04 0.00 0.90 0.00 0.02
#> TCGA.F1.6875.01 5 0.4759 0.689 0.00 0.06 0.00 0.00 0.64 0.00 0.22 0.08
#> TCGA.MX.A666.01 5 0.1887 0.806 0.00 0.00 0.06 0.00 0.90 0.00 0.04 0.00
#> TCGA.VQ.A8PX.01 8 0.2938 0.895 0.00 0.00 0.00 0.30 0.00 0.00 0.00 0.70
#> TCGA.BR.A4IV.01 1 0.0000 0.914 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D7.A6EX.01 6 0.6726 0.359 0.00 0.00 0.00 0.12 0.04 0.42 0.18 0.24
#> TCGA.BR.A4IZ.01 1 0.0000 0.914 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BR.A4J9.01 1 0.0000 0.914 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.B7.A5TN.01 5 0.5082 0.587 0.00 0.00 0.06 0.00 0.56 0.00 0.30 0.08
#> TCGA.BR.7704.01 2 0.1091 0.948 0.00 0.94 0.00 0.00 0.00 0.00 0.00 0.06
#> TCGA.BR.A4J1.01 2 0.0000 0.961 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BR.7716.01 3 0.0000 0.911 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FP.7735.01 8 0.2938 0.895 0.00 0.00 0.00 0.30 0.00 0.00 0.00 0.70
#> TCGA.BR.7723.01 3 0.2623 0.794 0.00 0.00 0.84 0.00 0.00 0.00 0.10 0.06
#> TCGA.EQ.A4SO.01 8 0.3941 0.866 0.00 0.00 0.00 0.26 0.00 0.02 0.04 0.68
#> TCGA.CD.A4MH.01 5 0.2165 0.821 0.00 0.06 0.00 0.00 0.88 0.00 0.00 0.06
#> TCGA.BR.A4J7.01 1 0.0000 0.914 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HF.7131.01 5 0.2165 0.801 0.00 0.00 0.06 0.00 0.88 0.00 0.06 0.00
#> TCGA.D7.A74B.01 1 0.3170 0.815 0.76 0.00 0.00 0.00 0.00 0.00 0.20 0.04
#> TCGA.D7.A6F2.01 5 0.3454 0.802 0.00 0.06 0.00 0.00 0.80 0.00 0.06 0.08
#> TCGA.RD.A7BT.01 5 0.3850 0.785 0.00 0.06 0.00 0.00 0.76 0.00 0.12 0.06
#> TCGA.BR.A4J6.01 1 0.0000 0.914 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HF.7136.01 6 0.5825 0.579 0.00 0.00 0.14 0.00 0.02 0.44 0.36 0.04
#> TCGA.BR.A4PD.01 5 0.2165 0.801 0.00 0.00 0.06 0.00 0.88 0.00 0.06 0.00
#> TCGA.VQ.A8PK.01 5 0.1887 0.806 0.00 0.00 0.06 0.00 0.90 0.00 0.04 0.00
#> TCGA.IN.A6RN.01 2 0.4059 0.502 0.00 0.64 0.00 0.00 0.28 0.00 0.00 0.08
#> TCGA.D7.A747.01 1 0.3735 0.780 0.72 0.00 0.00 0.02 0.00 0.00 0.22 0.04
#> TCGA.F1.A72C.01 1 0.0000 0.914 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.MX.A663.01 3 0.0000 0.911 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.VQ.AA6D.01 2 0.0000 0.961 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.VQ.AA6A.01 2 0.0000 0.961 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.IN.7806.01 5 0.3218 0.811 0.00 0.06 0.00 0.00 0.82 0.00 0.06 0.06
#> TCGA.HU.A4H5.01 2 0.0000 0.961 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CD.5804.01 4 0.2132 0.801 0.00 0.00 0.08 0.88 0.00 0.04 0.00 0.00
#> TCGA.D7.A4YT.01 6 0.4492 0.743 0.00 0.00 0.02 0.00 0.04 0.70 0.18 0.06
#> TCGA.EQ.5647.01 6 0.1607 0.760 0.00 0.00 0.04 0.04 0.00 0.92 0.00 0.00
#> TCGA.RD.A8N9.01 8 0.2938 0.895 0.00 0.00 0.00 0.30 0.00 0.00 0.00 0.70
#> TCGA.CG.5717.01 1 0.3170 0.815 0.76 0.00 0.00 0.00 0.00 0.00 0.20 0.04
#> TCGA.D7.6818.01 3 0.0000 0.911 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CD.8525.01 3 0.0000 0.911 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BR.4288.01 4 0.3454 0.757 0.00 0.00 0.08 0.80 0.00 0.06 0.06 0.00
#> TCGA.CD.5813.01 1 0.3170 0.815 0.76 0.00 0.00 0.00 0.00 0.00 0.20 0.04
#> TCGA.CG.5723.01 4 0.0808 0.810 0.00 0.00 0.00 0.96 0.00 0.00 0.00 0.04
#> TCGA.CD.5800.01 6 0.5187 0.606 0.00 0.00 0.22 0.06 0.02 0.62 0.08 0.00
#> TCGA.CG.5718.01 5 0.1557 0.834 0.00 0.06 0.00 0.00 0.92 0.00 0.00 0.02
#> TCGA.BR.8080.01 4 0.1275 0.805 0.00 0.00 0.00 0.94 0.00 0.00 0.02 0.04
#> TCGA.D7.6817.01 5 0.2165 0.801 0.00 0.00 0.06 0.00 0.88 0.00 0.06 0.00
#> TCGA.KB.A93G.01 4 0.3774 0.489 0.00 0.00 0.00 0.70 0.00 0.00 0.22 0.08
#> TCGA.CD.5799.01 3 0.3449 0.481 0.00 0.00 0.66 0.00 0.00 0.32 0.02 0.00
#> TCGA.BR.7722.01 1 0.3170 0.815 0.76 0.00 0.00 0.00 0.00 0.00 0.20 0.04
#> TCGA.BR.7901.01 5 0.1091 0.835 0.00 0.06 0.00 0.00 0.94 0.00 0.00 0.00
#> TCGA.BR.6710.01 1 0.0000 0.914 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.B7.A5TI.01 6 0.4422 0.699 0.00 0.00 0.00 0.06 0.04 0.74 0.06 0.10
#> TCGA.D7.6815.01 5 0.4759 0.689 0.00 0.06 0.00 0.00 0.64 0.00 0.22 0.08
#> TCGA.BR.8295.01 2 0.0808 0.954 0.00 0.96 0.00 0.00 0.00 0.00 0.00 0.04
#> TCGA.BR.7197.01 2 0.1091 0.948 0.00 0.94 0.00 0.00 0.00 0.00 0.00 0.06
#> TCGA.IN.A7NR.01 4 0.1275 0.805 0.00 0.00 0.00 0.94 0.00 0.00 0.02 0.04
#> TCGA.BR.6564.01 1 0.0000 0.914 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.KB.A93J.01 5 0.3454 0.802 0.00 0.06 0.00 0.00 0.80 0.00 0.06 0.08
#> TCGA.CD.5798.01 1 0.0000 0.914 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CD.8530.01 3 0.0000 0.911 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CG.5719.01 1 0.3170 0.815 0.76 0.00 0.00 0.00 0.00 0.00 0.20 0.04
#> TCGA.BR.6709.01 4 0.1275 0.805 0.00 0.00 0.00 0.94 0.00 0.00 0.02 0.04
#> TCGA.R5.A7ZR.01 2 0.0000 0.961 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BR.6801.01 8 0.3942 0.790 0.00 0.00 0.00 0.34 0.02 0.02 0.00 0.62
#> TCGA.D7.5579.01 4 0.0000 0.822 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.R5.A7ZI.01 4 0.0808 0.816 0.00 0.00 0.00 0.96 0.00 0.04 0.00 0.00
#> TCGA.CG.5732.01 3 0.2725 0.774 0.00 0.00 0.82 0.00 0.04 0.00 0.14 0.00
#> TCGA.ZQ.A9CR.01 3 0.3054 0.746 0.00 0.00 0.80 0.00 0.08 0.00 0.12 0.00
#> TCGA.BR.6803.01 1 0.0000 0.914 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.SW.A7EB.01 4 0.1275 0.805 0.00 0.00 0.00 0.94 0.00 0.00 0.02 0.04
#> TCGA.D7.8574.01 1 0.0000 0.914 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HJ.7597.01 1 0.3170 0.815 0.76 0.00 0.00 0.00 0.00 0.00 0.20 0.04
#> TCGA.R5.A7ZE.01 5 0.1557 0.834 0.00 0.06 0.00 0.00 0.92 0.00 0.00 0.02
#> TCGA.CD.5803.01 1 0.3170 0.815 0.76 0.00 0.00 0.00 0.00 0.00 0.20 0.04
#> TCGA.CG.5725.01 2 0.0000 0.961 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D7.6820.01 5 0.2165 0.829 0.00 0.06 0.00 0.00 0.88 0.00 0.06 0.00
#> TCGA.CD.5802.01 4 0.3036 0.694 0.00 0.00 0.18 0.78 0.00 0.04 0.00 0.00
#> TCGA.R5.A7ZF.01 4 0.2132 0.801 0.00 0.00 0.08 0.88 0.00 0.04 0.00 0.00
#> TCGA.D7.A6F0.01 2 0.0000 0.961 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CD.A486.01 5 0.1887 0.832 0.00 0.06 0.00 0.00 0.90 0.00 0.04 0.00
#> TCGA.RD.A8N2.01 1 0.0000 0.914 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.IN.A6RI.01 2 0.0808 0.954 0.00 0.96 0.00 0.00 0.00 0.00 0.00 0.04
#> TCGA.RD.A8N5.01 1 0.0000 0.914 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.RD.A8N1.01 4 0.2132 0.801 0.00 0.00 0.08 0.88 0.00 0.04 0.00 0.00
#> TCGA.HU.A4GF.01 2 0.1091 0.948 0.00 0.94 0.00 0.00 0.00 0.00 0.00 0.06
#> TCGA.CD.8532.01 1 0.0000 0.914 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.VQ.A8E2.01 6 0.5725 0.605 0.00 0.00 0.16 0.00 0.02 0.52 0.26 0.04
#> TCGA.BR.8373.01 5 0.4340 0.319 0.00 0.38 0.00 0.00 0.54 0.00 0.00 0.08
#> TCGA.BR.8058.01 1 0.0000 0.914 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D7.A748.01 1 0.0000 0.914 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CD.8527.01 6 0.2940 0.754 0.00 0.00 0.02 0.00 0.02 0.84 0.10 0.02
#> TCGA.VQ.A8DV.01 2 0.0000 0.961 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.RD.A8N6.01 3 0.5072 0.495 0.00 0.00 0.62 0.00 0.02 0.06 0.24 0.06
#> TCGA.HU.8245.01 5 0.2165 0.801 0.00 0.00 0.06 0.00 0.88 0.00 0.06 0.00
#> TCGA.ZA.A8F6.01 3 0.0000 0.911 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.RD.A8N0.01 1 0.0000 0.914 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BR.8365.01 1 0.3170 0.815 0.76 0.00 0.00 0.00 0.00 0.00 0.20 0.04
#> TCGA.FP.8211.01 8 0.5456 0.665 0.10 0.00 0.00 0.14 0.00 0.02 0.12 0.62
#> TCGA.RD.A8N4.01 1 0.0000 0.914 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.VQ.A8DU.01 5 0.4370 0.258 0.00 0.40 0.00 0.00 0.52 0.00 0.00 0.08
#> TCGA.VQ.A8DL.01 3 0.0000 0.911 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.VQ.A8DZ.01 2 0.1091 0.948 0.00 0.94 0.00 0.00 0.00 0.00 0.00 0.06
#> TCGA.D7.8572.01 3 0.0000 0.911 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.RD.A7BW.01 1 0.3170 0.815 0.76 0.00 0.00 0.00 0.00 0.00 0.20 0.04
#> TCGA.CD.A487.01 3 0.0000 0.911 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BR.8371.01 1 0.0000 0.914 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BR.8059.01 3 0.0000 0.911 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D7.8576.01 8 0.2938 0.895 0.00 0.00 0.00 0.30 0.00 0.00 0.00 0.70
#> TCGA.FP.A8CX.01 3 0.0000 0.911 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HU.A4GH.01 2 0.0000 0.961 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CD.8526.01 3 0.0000 0.911 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D7.8578.01 4 0.2132 0.801 0.00 0.00 0.08 0.88 0.00 0.04 0.00 0.00
#> TCGA.RD.A8MW.01 3 0.0000 0.911 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BR.8364.01 1 0.0000 0.914 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.KB.A6F7.01 5 0.1887 0.832 0.00 0.06 0.00 0.00 0.90 0.00 0.04 0.00
#> TCGA.BR.A4CR.01 6 0.3941 0.719 0.00 0.00 0.04 0.00 0.02 0.68 0.26 0.00
#> TCGA.CD.A489.01 8 0.3504 0.872 0.00 0.00 0.00 0.26 0.00 0.00 0.04 0.70
#> TCGA.HU.A4GY.01 1 0.0000 0.914 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FP.8209.01 1 0.0000 0.914 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BR.8060.01 2 0.1341 0.935 0.00 0.92 0.00 0.00 0.00 0.00 0.00 0.08
#> TCGA.BR.8077.01 2 0.0000 0.961 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EQ.8122.01 5 0.1557 0.834 0.00 0.06 0.00 0.00 0.92 0.00 0.00 0.02
#> TCGA.BR.A44T.01 1 0.0000 0.914 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BR.8291.01 4 0.0000 0.822 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.FP.8210.01 1 0.0000 0.914 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.RD.A7BS.01 4 0.1275 0.805 0.00 0.00 0.00 0.94 0.00 0.00 0.02 0.04
#> TCGA.CD.8529.01 4 0.3170 0.661 0.00 0.00 0.20 0.76 0.00 0.04 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 , Node0113 , Node0114-leaf , Node0121 , Node0122 , Node0123 , Node0131 , Node0132-leaf , Node0211-leaf , Node0212-leaf , Node0221-leaf , Node0222 , Node0231-leaf , Node0232-leaf , Node0233-leaf , Node0311 , Node0312-leaf , Node0313-leaf , Node0314-leaf , Node0331-leaf , Node0332-leaf , Node0333-leaf , Node0341 , Node0342-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 67 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 0.4827 0.518 0.518
#> 3 3 1.000 0.999 1.000 0.3876 0.813 0.638
#> 4 4 0.988 0.959 0.979 0.0994 0.931 0.791
#> 5 5 0.784 0.709 0.821 0.0577 0.940 0.772
#> 6 6 0.749 0.676 0.827 0.0346 0.948 0.762
#> 7 7 0.770 0.651 0.792 0.0244 0.953 0.777
#> 8 8 0.734 0.481 0.761 0.0168 0.978 0.882
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.VQ.A94P.01 2 0 1 0 1
#> TCGA.D7.6521.01 2 0 1 0 1
#> TCGA.D7.6522.01 2 0 1 0 1
#> TCGA.VQ.AA64.01 2 0 1 0 1
#> TCGA.VQ.A928.01 2 0 1 0 1
#> TCGA.VQ.A8E0.01 2 0 1 0 1
#> TCGA.VQ.A91Q.01 2 0 1 0 1
#> TCGA.VQ.A94T.01 2 0 1 0 1
#> TCGA.VQ.A8PS.01 2 0 1 0 1
#> TCGA.BR.6454.01 2 0 1 0 1
#> TCGA.BR.8590.01 2 0 1 0 1
#> TCGA.VQ.A8PQ.01 1 0 1 1 0
#> TCGA.VQ.A927.01 2 0 1 0 1
#> TCGA.BR.6566.11 1 0 1 1 0
#> TCGA.VQ.AA6F.01 2 0 1 0 1
#> TCGA.VQ.AA6J.01 2 0 1 0 1
#> TCGA.BR.8677.01 1 0 1 1 0
#> TCGA.BR.A452.01 2 0 1 0 1
#> TCGA.VQ.A8PU.01 2 0 1 0 1
#> TCGA.VQ.AA6K.01 2 0 1 0 1
#> TCGA.VQ.A8PX.01 2 0 1 0 1
#> TCGA.BR.A4IV.01 2 0 1 0 1
#> TCGA.BR.A4IZ.01 1 0 1 1 0
#> TCGA.BR.A4J9.01 2 0 1 0 1
#> TCGA.EQ.A4SO.01 2 0 1 0 1
#> TCGA.BR.A4J7.01 2 0 1 0 1
#> TCGA.D7.A74B.01 1 0 1 1 0
#> TCGA.BR.A4J6.01 1 0 1 1 0
#> TCGA.D7.A747.01 2 0 1 0 1
#> TCGA.F1.A72C.01 2 0 1 0 1
#> TCGA.RD.A8N9.01 1 0 1 1 0
#> TCGA.CG.5717.01 2 0 1 0 1
#> TCGA.CD.5813.01 2 0 1 0 1
#> TCGA.CG.5723.01 2 0 1 0 1
#> TCGA.BR.8080.01 1 0 1 1 0
#> TCGA.KB.A93G.01 2 0 1 0 1
#> TCGA.BR.7722.01 2 0 1 0 1
#> TCGA.BR.6710.01 2 0 1 0 1
#> TCGA.IN.A7NR.01 1 0 1 1 0
#> TCGA.BR.6564.01 1 0 1 1 0
#> TCGA.CD.5798.01 2 0 1 0 1
#> TCGA.CG.5719.01 1 0 1 1 0
#> TCGA.BR.6709.01 1 0 1 1 0
#> TCGA.BR.6803.01 1 0 1 1 0
#> TCGA.SW.A7EB.01 2 0 1 0 1
#> TCGA.D7.8574.01 2 0 1 0 1
#> TCGA.HJ.7597.01 1 0 1 1 0
#> TCGA.CD.5803.01 1 0 1 1 0
#> TCGA.RD.A8N2.01 1 0 1 1 0
#> TCGA.RD.A8N5.01 2 0 1 0 1
#> TCGA.CD.8532.01 2 0 1 0 1
#> TCGA.BR.8058.01 1 0 1 1 0
#> TCGA.D7.A748.01 1 0 1 1 0
#> TCGA.RD.A8N0.01 1 0 1 1 0
#> TCGA.BR.8365.01 1 0 1 1 0
#> TCGA.FP.8211.01 2 0 1 0 1
#> TCGA.RD.A8N4.01 1 0 1 1 0
#> TCGA.RD.A7BW.01 1 0 1 1 0
#> TCGA.BR.8371.01 2 0 1 0 1
#> TCGA.D7.8576.01 1 0 1 1 0
#> TCGA.BR.8364.01 1 0 1 1 0
#> TCGA.CD.A489.01 2 0 1 0 1
#> TCGA.HU.A4GY.01 1 0 1 1 0
#> TCGA.FP.8209.01 2 0 1 0 1
#> TCGA.BR.A44T.01 1 0 1 1 0
#> TCGA.FP.8210.01 2 0 1 0 1
#> TCGA.RD.A7BS.01 2 0 1 0 1
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.VQ.A94P.01 3 0.0000 1.000 0 0.00 1.00
#> TCGA.D7.6521.01 2 0.0000 0.999 0 1.00 0.00
#> TCGA.D7.6522.01 3 0.0000 1.000 0 0.00 1.00
#> TCGA.VQ.AA64.01 2 0.0000 0.999 0 1.00 0.00
#> TCGA.VQ.A928.01 2 0.0000 0.999 0 1.00 0.00
#> TCGA.VQ.A8E0.01 2 0.0000 0.999 0 1.00 0.00
#> TCGA.VQ.A91Q.01 2 0.0000 0.999 0 1.00 0.00
#> TCGA.VQ.A94T.01 2 0.0000 0.999 0 1.00 0.00
#> TCGA.VQ.A8PS.01 2 0.0000 0.999 0 1.00 0.00
#> TCGA.BR.6454.01 2 0.0000 0.999 0 1.00 0.00
#> TCGA.BR.8590.01 3 0.0000 1.000 0 0.00 1.00
#> TCGA.VQ.A8PQ.01 1 0.0000 1.000 1 0.00 0.00
#> TCGA.VQ.A927.01 3 0.0000 1.000 0 0.00 1.00
#> TCGA.BR.6566.11 1 0.0000 1.000 1 0.00 0.00
#> TCGA.VQ.AA6F.01 2 0.0892 0.980 0 0.98 0.02
#> TCGA.VQ.AA6J.01 2 0.0000 0.999 0 1.00 0.00
#> TCGA.BR.8677.01 1 0.0000 1.000 1 0.00 0.00
#> TCGA.BR.A452.01 2 0.0000 0.999 0 1.00 0.00
#> TCGA.VQ.A8PU.01 2 0.0000 0.999 0 1.00 0.00
#> TCGA.VQ.AA6K.01 2 0.0000 0.999 0 1.00 0.00
#> TCGA.VQ.A8PX.01 2 0.0000 0.999 0 1.00 0.00
#> TCGA.BR.A4IV.01 3 0.0000 1.000 0 0.00 1.00
#> TCGA.BR.A4IZ.01 1 0.0000 1.000 1 0.00 0.00
#> TCGA.BR.A4J9.01 3 0.0000 1.000 0 0.00 1.00
#> TCGA.EQ.A4SO.01 2 0.0000 0.999 0 1.00 0.00
#> TCGA.BR.A4J7.01 2 0.0000 0.999 0 1.00 0.00
#> TCGA.D7.A74B.01 1 0.0000 1.000 1 0.00 0.00
#> TCGA.BR.A4J6.01 1 0.0000 1.000 1 0.00 0.00
#> TCGA.D7.A747.01 3 0.0000 1.000 0 0.00 1.00
#> TCGA.F1.A72C.01 2 0.0000 0.999 0 1.00 0.00
#> TCGA.RD.A8N9.01 1 0.0000 1.000 1 0.00 0.00
#> TCGA.CG.5717.01 3 0.0000 1.000 0 0.00 1.00
#> TCGA.CD.5813.01 2 0.0000 0.999 0 1.00 0.00
#> TCGA.CG.5723.01 2 0.0000 0.999 0 1.00 0.00
#> TCGA.BR.8080.01 1 0.0000 1.000 1 0.00 0.00
#> TCGA.KB.A93G.01 3 0.0000 1.000 0 0.00 1.00
#> TCGA.BR.7722.01 2 0.0000 0.999 0 1.00 0.00
#> TCGA.BR.6710.01 3 0.0000 1.000 0 0.00 1.00
#> TCGA.IN.A7NR.01 1 0.0000 1.000 1 0.00 0.00
#> TCGA.BR.6564.01 1 0.0000 1.000 1 0.00 0.00
#> TCGA.CD.5798.01 3 0.0000 1.000 0 0.00 1.00
#> TCGA.CG.5719.01 1 0.0000 1.000 1 0.00 0.00
#> TCGA.BR.6709.01 1 0.0000 1.000 1 0.00 0.00
#> TCGA.BR.6803.01 1 0.0000 1.000 1 0.00 0.00
#> TCGA.SW.A7EB.01 3 0.0000 1.000 0 0.00 1.00
#> TCGA.D7.8574.01 3 0.0000 1.000 0 0.00 1.00
#> TCGA.HJ.7597.01 1 0.0000 1.000 1 0.00 0.00
#> TCGA.CD.5803.01 1 0.0000 1.000 1 0.00 0.00
#> TCGA.RD.A8N2.01 1 0.0000 1.000 1 0.00 0.00
#> TCGA.RD.A8N5.01 3 0.0000 1.000 0 0.00 1.00
#> TCGA.CD.8532.01 2 0.0000 0.999 0 1.00 0.00
#> TCGA.BR.8058.01 1 0.0000 1.000 1 0.00 0.00
#> TCGA.D7.A748.01 1 0.0000 1.000 1 0.00 0.00
#> TCGA.RD.A8N0.01 1 0.0000 1.000 1 0.00 0.00
#> TCGA.BR.8365.01 1 0.0000 1.000 1 0.00 0.00
#> TCGA.FP.8211.01 2 0.0000 0.999 0 1.00 0.00
#> TCGA.RD.A8N4.01 1 0.0000 1.000 1 0.00 0.00
#> TCGA.RD.A7BW.01 1 0.0000 1.000 1 0.00 0.00
#> TCGA.BR.8371.01 3 0.0000 1.000 0 0.00 1.00
#> TCGA.D7.8576.01 1 0.0000 1.000 1 0.00 0.00
#> TCGA.BR.8364.01 1 0.0000 1.000 1 0.00 0.00
#> TCGA.CD.A489.01 2 0.0000 0.999 0 1.00 0.00
#> TCGA.HU.A4GY.01 1 0.0000 1.000 1 0.00 0.00
#> TCGA.FP.8209.01 3 0.0000 1.000 0 0.00 1.00
#> TCGA.BR.A44T.01 1 0.0000 1.000 1 0.00 0.00
#> TCGA.FP.8210.01 3 0.0000 1.000 0 0.00 1.00
#> TCGA.RD.A7BS.01 3 0.0000 1.000 0 0.00 1.00
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> TCGA.VQ.A94P.01 3 0.0000 0.999 0.00 0.00 1.00 0.00
#> TCGA.D7.6521.01 2 0.0000 0.981 0.00 1.00 0.00 0.00
#> TCGA.D7.6522.01 3 0.0000 0.999 0.00 0.00 1.00 0.00
#> TCGA.VQ.AA64.01 2 0.0000 0.981 0.00 1.00 0.00 0.00
#> TCGA.VQ.A928.01 2 0.0000 0.981 0.00 1.00 0.00 0.00
#> TCGA.VQ.A8E0.01 2 0.0000 0.981 0.00 1.00 0.00 0.00
#> TCGA.VQ.A91Q.01 2 0.0000 0.981 0.00 1.00 0.00 0.00
#> TCGA.VQ.A94T.01 2 0.0000 0.981 0.00 1.00 0.00 0.00
#> TCGA.VQ.A8PS.01 2 0.0000 0.981 0.00 1.00 0.00 0.00
#> TCGA.BR.6454.01 2 0.0000 0.981 0.00 1.00 0.00 0.00
#> TCGA.BR.8590.01 3 0.0000 0.999 0.00 0.00 1.00 0.00
#> TCGA.VQ.A8PQ.01 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.VQ.A927.01 3 0.0000 0.999 0.00 0.00 1.00 0.00
#> TCGA.BR.6566.11 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.VQ.AA6F.01 2 0.2011 0.892 0.00 0.92 0.08 0.00
#> TCGA.VQ.AA6J.01 2 0.0000 0.981 0.00 1.00 0.00 0.00
#> TCGA.BR.8677.01 4 0.4522 0.639 0.32 0.00 0.00 0.68
#> TCGA.BR.A452.01 2 0.0000 0.981 0.00 1.00 0.00 0.00
#> TCGA.VQ.A8PU.01 2 0.4522 0.563 0.00 0.68 0.00 0.32
#> TCGA.VQ.AA6K.01 2 0.0000 0.981 0.00 1.00 0.00 0.00
#> TCGA.VQ.A8PX.01 2 0.0000 0.981 0.00 1.00 0.00 0.00
#> TCGA.BR.A4IV.01 3 0.0000 0.999 0.00 0.00 1.00 0.00
#> TCGA.BR.A4IZ.01 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.BR.A4J9.01 3 0.0000 0.999 0.00 0.00 1.00 0.00
#> TCGA.EQ.A4SO.01 2 0.0000 0.981 0.00 1.00 0.00 0.00
#> TCGA.BR.A4J7.01 2 0.0000 0.981 0.00 1.00 0.00 0.00
#> TCGA.D7.A74B.01 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.BR.A4J6.01 4 0.0000 0.872 0.00 0.00 0.00 1.00
#> TCGA.D7.A747.01 3 0.0000 0.999 0.00 0.00 1.00 0.00
#> TCGA.F1.A72C.01 2 0.0000 0.981 0.00 1.00 0.00 0.00
#> TCGA.RD.A8N9.01 4 0.0000 0.872 0.00 0.00 0.00 1.00
#> TCGA.CG.5717.01 3 0.0000 0.999 0.00 0.00 1.00 0.00
#> TCGA.CD.5813.01 2 0.0000 0.981 0.00 1.00 0.00 0.00
#> TCGA.CG.5723.01 2 0.0000 0.981 0.00 1.00 0.00 0.00
#> TCGA.BR.8080.01 4 0.2921 0.830 0.14 0.00 0.00 0.86
#> TCGA.KB.A93G.01 3 0.0000 0.999 0.00 0.00 1.00 0.00
#> TCGA.BR.7722.01 2 0.0000 0.981 0.00 1.00 0.00 0.00
#> TCGA.BR.6710.01 3 0.0000 0.999 0.00 0.00 1.00 0.00
#> TCGA.IN.A7NR.01 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.BR.6564.01 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.CD.5798.01 3 0.0000 0.999 0.00 0.00 1.00 0.00
#> TCGA.CG.5719.01 4 0.0000 0.872 0.00 0.00 0.00 1.00
#> TCGA.BR.6709.01 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.BR.6803.01 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.SW.A7EB.01 3 0.0707 0.975 0.00 0.02 0.98 0.00
#> TCGA.D7.8574.01 3 0.0000 0.999 0.00 0.00 1.00 0.00
#> TCGA.HJ.7597.01 4 0.0000 0.872 0.00 0.00 0.00 1.00
#> TCGA.CD.5803.01 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.RD.A8N2.01 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.RD.A8N5.01 3 0.0000 0.999 0.00 0.00 1.00 0.00
#> TCGA.CD.8532.01 2 0.0000 0.981 0.00 1.00 0.00 0.00
#> TCGA.BR.8058.01 4 0.4713 0.569 0.36 0.00 0.00 0.64
#> TCGA.D7.A748.01 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.RD.A8N0.01 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.BR.8365.01 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.FP.8211.01 2 0.0000 0.981 0.00 1.00 0.00 0.00
#> TCGA.RD.A8N4.01 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.RD.A7BW.01 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.BR.8371.01 3 0.0000 0.999 0.00 0.00 1.00 0.00
#> TCGA.D7.8576.01 4 0.0000 0.872 0.00 0.00 0.00 1.00
#> TCGA.BR.8364.01 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.CD.A489.01 2 0.0000 0.981 0.00 1.00 0.00 0.00
#> TCGA.HU.A4GY.01 4 0.3172 0.818 0.16 0.00 0.00 0.84
#> TCGA.FP.8209.01 3 0.0000 0.999 0.00 0.00 1.00 0.00
#> TCGA.BR.A44T.01 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.FP.8210.01 3 0.0000 0.999 0.00 0.00 1.00 0.00
#> TCGA.RD.A7BS.01 3 0.0000 0.999 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.VQ.A94P.01 3 0.0000 0.861 0.00 0.00 1.00 0.00 0.00
#> TCGA.D7.6521.01 2 0.1410 0.566 0.00 0.94 0.00 0.00 0.06
#> TCGA.D7.6522.01 3 0.0000 0.861 0.00 0.00 1.00 0.00 0.00
#> TCGA.VQ.AA64.01 5 0.4262 0.646 0.00 0.44 0.00 0.00 0.56
#> TCGA.VQ.A928.01 5 0.4302 0.539 0.00 0.48 0.00 0.00 0.52
#> TCGA.VQ.A8E0.01 5 0.4262 0.706 0.00 0.44 0.00 0.00 0.56
#> TCGA.VQ.A91Q.01 5 0.4182 0.717 0.00 0.40 0.00 0.00 0.60
#> TCGA.VQ.A94T.01 5 0.4182 0.673 0.00 0.40 0.00 0.00 0.60
#> TCGA.VQ.A8PS.01 5 0.4060 0.699 0.00 0.36 0.00 0.00 0.64
#> TCGA.BR.6454.01 2 0.3895 0.205 0.00 0.68 0.00 0.00 0.32
#> TCGA.BR.8590.01 3 0.3424 0.793 0.00 0.24 0.76 0.00 0.00
#> TCGA.VQ.A8PQ.01 1 0.0000 0.995 1.00 0.00 0.00 0.00 0.00
#> TCGA.VQ.A927.01 3 0.2929 0.829 0.00 0.18 0.82 0.00 0.00
#> TCGA.BR.6566.11 1 0.0000 0.995 1.00 0.00 0.00 0.00 0.00
#> TCGA.VQ.AA6F.01 2 0.1410 0.542 0.00 0.94 0.06 0.00 0.00
#> TCGA.VQ.AA6J.01 2 0.0000 0.591 0.00 1.00 0.00 0.00 0.00
#> TCGA.BR.8677.01 4 0.4182 0.513 0.40 0.00 0.00 0.60 0.00
#> TCGA.BR.A452.01 2 0.4287 -0.503 0.00 0.54 0.00 0.00 0.46
#> TCGA.VQ.A8PU.01 5 0.6244 0.298 0.00 0.20 0.00 0.26 0.54
#> TCGA.VQ.AA6K.01 2 0.4302 -0.560 0.00 0.52 0.00 0.00 0.48
#> TCGA.VQ.A8PX.01 5 0.4302 0.467 0.00 0.48 0.00 0.00 0.52
#> TCGA.BR.A4IV.01 3 0.0609 0.865 0.00 0.02 0.98 0.00 0.00
#> TCGA.BR.A4IZ.01 1 0.0000 0.995 1.00 0.00 0.00 0.00 0.00
#> TCGA.BR.A4J9.01 3 0.3796 0.745 0.00 0.30 0.70 0.00 0.00
#> TCGA.EQ.A4SO.01 5 0.4182 0.717 0.00 0.40 0.00 0.00 0.60
#> TCGA.BR.A4J7.01 2 0.1410 0.571 0.00 0.94 0.00 0.00 0.06
#> TCGA.D7.A74B.01 1 0.0000 0.995 1.00 0.00 0.00 0.00 0.00
#> TCGA.BR.A4J6.01 4 0.0609 0.799 0.00 0.00 0.00 0.98 0.02
#> TCGA.D7.A747.01 3 0.0609 0.865 0.00 0.02 0.98 0.00 0.00
#> TCGA.F1.A72C.01 2 0.3561 0.304 0.00 0.74 0.00 0.00 0.26
#> TCGA.RD.A8N9.01 4 0.1043 0.825 0.04 0.00 0.00 0.96 0.00
#> TCGA.CG.5717.01 3 0.2012 0.857 0.00 0.06 0.92 0.00 0.02
#> TCGA.CD.5813.01 2 0.1732 0.585 0.00 0.92 0.00 0.00 0.08
#> TCGA.CG.5723.01 2 0.2020 0.582 0.00 0.90 0.00 0.00 0.10
#> TCGA.BR.8080.01 4 0.2929 0.791 0.18 0.00 0.00 0.82 0.00
#> TCGA.KB.A93G.01 3 0.0000 0.861 0.00 0.00 1.00 0.00 0.00
#> TCGA.BR.7722.01 5 0.4307 0.439 0.00 0.50 0.00 0.00 0.50
#> TCGA.BR.6710.01 3 0.4132 0.687 0.00 0.02 0.72 0.00 0.26
#> TCGA.IN.A7NR.01 1 0.0609 0.974 0.98 0.00 0.00 0.02 0.00
#> TCGA.BR.6564.01 1 0.0000 0.995 1.00 0.00 0.00 0.00 0.00
#> TCGA.CD.5798.01 3 0.2732 0.835 0.00 0.16 0.84 0.00 0.00
#> TCGA.CG.5719.01 4 0.1043 0.825 0.04 0.00 0.00 0.96 0.00
#> TCGA.BR.6709.01 1 0.0000 0.995 1.00 0.00 0.00 0.00 0.00
#> TCGA.BR.6803.01 1 0.0000 0.995 1.00 0.00 0.00 0.00 0.00
#> TCGA.SW.A7EB.01 3 0.6619 0.410 0.00 0.36 0.42 0.00 0.22
#> TCGA.D7.8574.01 3 0.3684 0.765 0.00 0.28 0.72 0.00 0.00
#> TCGA.HJ.7597.01 4 0.0609 0.817 0.02 0.00 0.00 0.98 0.00
#> TCGA.CD.5803.01 1 0.1043 0.951 0.96 0.00 0.00 0.04 0.00
#> TCGA.RD.A8N2.01 1 0.0000 0.995 1.00 0.00 0.00 0.00 0.00
#> TCGA.RD.A8N5.01 3 0.1043 0.864 0.00 0.04 0.96 0.00 0.00
#> TCGA.CD.8532.01 2 0.4182 -0.291 0.00 0.60 0.00 0.00 0.40
#> TCGA.BR.8058.01 4 0.4262 0.423 0.44 0.00 0.00 0.56 0.00
#> TCGA.D7.A748.01 1 0.0000 0.995 1.00 0.00 0.00 0.00 0.00
#> TCGA.RD.A8N0.01 1 0.0000 0.995 1.00 0.00 0.00 0.00 0.00
#> TCGA.BR.8365.01 1 0.0000 0.995 1.00 0.00 0.00 0.00 0.00
#> TCGA.FP.8211.01 5 0.4227 0.715 0.00 0.42 0.00 0.00 0.58
#> TCGA.RD.A8N4.01 1 0.0000 0.995 1.00 0.00 0.00 0.00 0.00
#> TCGA.RD.A7BW.01 1 0.0000 0.995 1.00 0.00 0.00 0.00 0.00
#> TCGA.BR.8371.01 3 0.0000 0.861 0.00 0.00 1.00 0.00 0.00
#> TCGA.D7.8576.01 4 0.0609 0.799 0.00 0.00 0.00 0.98 0.02
#> TCGA.BR.8364.01 1 0.0000 0.995 1.00 0.00 0.00 0.00 0.00
#> TCGA.CD.A489.01 2 0.2280 0.559 0.00 0.88 0.00 0.00 0.12
#> TCGA.HU.A4GY.01 4 0.3109 0.778 0.20 0.00 0.00 0.80 0.00
#> TCGA.FP.8209.01 3 0.0000 0.861 0.00 0.00 1.00 0.00 0.00
#> TCGA.BR.A44T.01 1 0.0000 0.995 1.00 0.00 0.00 0.00 0.00
#> TCGA.FP.8210.01 3 0.0609 0.865 0.00 0.02 0.98 0.00 0.00
#> TCGA.RD.A7BS.01 3 0.4227 0.598 0.00 0.42 0.58 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.VQ.A94P.01 3 0.1556 0.6642 0.00 0.00 0.92 0.00 0.00 0.08
#> TCGA.D7.6521.01 2 0.4903 0.6071 0.00 0.70 0.02 0.00 0.14 0.14
#> TCGA.D7.6522.01 3 0.1556 0.6642 0.00 0.00 0.92 0.00 0.00 0.08
#> TCGA.VQ.AA64.01 5 0.2631 0.6884 0.00 0.18 0.00 0.00 0.82 0.00
#> TCGA.VQ.A928.01 5 0.3711 0.6164 0.00 0.26 0.00 0.00 0.72 0.02
#> TCGA.VQ.A8E0.01 5 0.3460 0.6324 0.00 0.22 0.00 0.00 0.76 0.02
#> TCGA.VQ.A91Q.01 5 0.2094 0.7026 0.00 0.08 0.00 0.00 0.90 0.02
#> TCGA.VQ.A94T.01 5 0.2048 0.6939 0.00 0.12 0.00 0.00 0.88 0.00
#> TCGA.VQ.A8PS.01 5 0.1480 0.7011 0.00 0.04 0.00 0.00 0.94 0.02
#> TCGA.BR.6454.01 2 0.4632 -0.0486 0.00 0.52 0.00 0.00 0.44 0.04
#> TCGA.BR.8590.01 3 0.4613 0.4496 0.00 0.26 0.66 0.00 0.00 0.08
#> TCGA.VQ.A8PQ.01 1 0.0000 0.9720 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.VQ.A927.01 3 0.4094 0.4276 0.00 0.08 0.74 0.00 0.00 0.18
#> TCGA.BR.6566.11 1 0.0000 0.9720 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.VQ.AA6F.01 2 0.3697 0.6281 0.00 0.82 0.06 0.00 0.08 0.04
#> TCGA.VQ.AA6J.01 2 0.3600 0.6362 0.00 0.82 0.08 0.00 0.08 0.02
#> TCGA.BR.8677.01 4 0.3578 0.6156 0.34 0.00 0.00 0.66 0.00 0.00
#> TCGA.BR.A452.01 5 0.3916 0.5660 0.00 0.30 0.00 0.00 0.68 0.02
#> TCGA.VQ.A8PU.01 5 0.6012 0.4191 0.00 0.06 0.00 0.16 0.60 0.18
#> TCGA.VQ.AA6K.01 5 0.3819 0.5881 0.00 0.28 0.00 0.00 0.70 0.02
#> TCGA.VQ.A8PX.01 5 0.4566 0.5857 0.00 0.16 0.00 0.00 0.70 0.14
#> TCGA.BR.A4IV.01 3 0.2474 0.6713 0.00 0.08 0.88 0.00 0.00 0.04
#> TCGA.BR.A4IZ.01 1 0.1267 0.9346 0.94 0.00 0.00 0.06 0.00 0.00
#> TCGA.BR.A4J9.01 3 0.4552 0.4035 0.00 0.30 0.64 0.00 0.00 0.06
#> TCGA.EQ.A4SO.01 5 0.2512 0.6776 0.00 0.06 0.00 0.00 0.88 0.06
#> TCGA.BR.A4J7.01 2 0.4468 0.6109 0.00 0.76 0.06 0.00 0.12 0.06
#> TCGA.D7.A74B.01 1 0.0000 0.9720 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BR.A4J6.01 4 0.2581 0.6367 0.00 0.02 0.00 0.86 0.00 0.12
#> TCGA.D7.A747.01 3 0.2094 0.6828 0.00 0.08 0.90 0.00 0.00 0.02
#> TCGA.F1.A72C.01 2 0.4534 0.2917 0.00 0.58 0.00 0.00 0.38 0.04
#> TCGA.RD.A8N9.01 4 0.1556 0.7856 0.08 0.00 0.00 0.92 0.00 0.00
#> TCGA.CG.5717.01 3 0.3592 0.4378 0.00 0.02 0.74 0.00 0.00 0.24
#> TCGA.CD.5813.01 2 0.3523 0.5986 0.00 0.78 0.00 0.00 0.18 0.04
#> TCGA.CG.5723.01 2 0.4711 0.4876 0.00 0.64 0.00 0.00 0.28 0.08
#> TCGA.BR.8080.01 4 0.2454 0.7934 0.16 0.00 0.00 0.84 0.00 0.00
#> TCGA.KB.A93G.01 3 0.1556 0.6642 0.00 0.00 0.92 0.00 0.00 0.08
#> TCGA.BR.7722.01 5 0.3523 0.6228 0.00 0.18 0.00 0.00 0.78 0.04
#> TCGA.BR.6710.01 6 0.3578 0.5958 0.00 0.00 0.34 0.00 0.00 0.66
#> TCGA.IN.A7NR.01 1 0.1556 0.9143 0.92 0.00 0.00 0.08 0.00 0.00
#> TCGA.BR.6564.01 1 0.0000 0.9720 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CD.5798.01 3 0.3073 0.6603 0.00 0.08 0.84 0.00 0.00 0.08
#> TCGA.CG.5719.01 4 0.1814 0.7988 0.10 0.00 0.00 0.90 0.00 0.00
#> TCGA.BR.6709.01 1 0.1267 0.9337 0.94 0.00 0.00 0.06 0.00 0.00
#> TCGA.BR.6803.01 1 0.0000 0.9720 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.SW.A7EB.01 6 0.5802 0.5825 0.00 0.12 0.34 0.00 0.02 0.52
#> TCGA.D7.8574.01 3 0.4576 0.2563 0.00 0.40 0.56 0.00 0.00 0.04
#> TCGA.HJ.7597.01 4 0.1814 0.7988 0.10 0.00 0.00 0.90 0.00 0.00
#> TCGA.CD.5803.01 1 0.2048 0.8654 0.88 0.00 0.00 0.12 0.00 0.00
#> TCGA.RD.A8N2.01 1 0.0000 0.9720 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.RD.A8N5.01 3 0.1092 0.6897 0.00 0.02 0.96 0.00 0.00 0.02
#> TCGA.CD.8532.01 5 0.4609 0.1776 0.00 0.42 0.00 0.00 0.54 0.04
#> TCGA.BR.8058.01 4 0.3828 0.3970 0.44 0.00 0.00 0.56 0.00 0.00
#> TCGA.D7.A748.01 1 0.1267 0.9346 0.94 0.00 0.00 0.06 0.00 0.00
#> TCGA.RD.A8N0.01 1 0.0000 0.9720 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BR.8365.01 1 0.0000 0.9720 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FP.8211.01 5 0.0937 0.7133 0.00 0.04 0.00 0.00 0.96 0.00
#> TCGA.RD.A8N4.01 1 0.0000 0.9720 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.RD.A7BW.01 1 0.0000 0.9720 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BR.8371.01 3 0.1556 0.6642 0.00 0.00 0.92 0.00 0.00 0.08
#> TCGA.D7.8576.01 4 0.2350 0.6495 0.00 0.02 0.00 0.88 0.00 0.10
#> TCGA.BR.8364.01 1 0.0000 0.9720 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CD.A489.01 2 0.3523 0.6038 0.00 0.78 0.00 0.00 0.18 0.04
#> TCGA.HU.A4GY.01 4 0.2454 0.7934 0.16 0.00 0.00 0.84 0.00 0.00
#> TCGA.FP.8209.01 3 0.1556 0.6642 0.00 0.00 0.92 0.00 0.00 0.08
#> TCGA.BR.A44T.01 1 0.0000 0.9720 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FP.8210.01 3 0.1556 0.6891 0.00 0.08 0.92 0.00 0.00 0.00
#> TCGA.RD.A7BS.01 2 0.5189 0.1214 0.00 0.58 0.34 0.00 0.02 0.06
cbind(get_classes(res, k = 7), get_membership(res, k = 7))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7
#> TCGA.VQ.A94P.01 3 0.0504 0.7994 0.00 0.00 0.98 0.00 0.00 0.02 0.00
#> TCGA.D7.6521.01 2 0.4766 0.2886 0.00 0.70 0.00 0.00 0.12 0.12 0.06
#> TCGA.D7.6522.01 3 0.0504 0.7994 0.00 0.00 0.98 0.00 0.00 0.02 0.00
#> TCGA.VQ.AA64.01 7 0.4108 0.6435 0.00 0.06 0.00 0.00 0.28 0.00 0.66
#> TCGA.VQ.A928.01 7 0.4615 0.6302 0.00 0.10 0.00 0.00 0.30 0.00 0.60
#> TCGA.VQ.A8E0.01 7 0.4429 0.6039 0.00 0.12 0.00 0.00 0.22 0.00 0.66
#> TCGA.VQ.A91Q.01 7 0.1363 0.6608 0.00 0.04 0.00 0.00 0.02 0.00 0.94
#> TCGA.VQ.A94T.01 7 0.3927 0.6382 0.00 0.04 0.00 0.00 0.30 0.00 0.66
#> TCGA.VQ.A8PS.01 7 0.1860 0.6380 0.00 0.04 0.00 0.00 0.02 0.02 0.92
#> TCGA.BR.6454.01 7 0.6009 0.3450 0.00 0.28 0.00 0.00 0.34 0.02 0.36
#> TCGA.BR.8590.01 2 0.4977 0.0046 0.00 0.50 0.42 0.00 0.04 0.04 0.00
#> TCGA.VQ.A8PQ.01 1 0.0000 0.9678 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.VQ.A927.01 3 0.5477 0.3659 0.00 0.34 0.52 0.00 0.04 0.10 0.00
#> TCGA.BR.6566.11 1 0.0000 0.9678 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.VQ.AA6F.01 2 0.3656 0.4580 0.00 0.80 0.08 0.00 0.04 0.00 0.08
#> TCGA.VQ.AA6J.01 2 0.2355 0.4461 0.00 0.90 0.04 0.00 0.02 0.02 0.02
#> TCGA.BR.8677.01 4 0.3047 0.5883 0.28 0.00 0.00 0.72 0.00 0.00 0.00
#> TCGA.BR.A452.01 7 0.4945 0.5898 0.00 0.12 0.00 0.00 0.36 0.00 0.52
#> TCGA.VQ.A8PU.01 7 0.5077 0.3398 0.00 0.00 0.00 0.08 0.38 0.02 0.52
#> TCGA.VQ.AA6K.01 7 0.4487 0.6252 0.00 0.08 0.00 0.00 0.32 0.00 0.60
#> TCGA.VQ.A8PX.01 7 0.5404 0.4575 0.00 0.16 0.00 0.00 0.16 0.06 0.62
#> TCGA.BR.A4IV.01 3 0.2912 0.7849 0.00 0.14 0.82 0.00 0.04 0.00 0.00
#> TCGA.BR.A4IZ.01 1 0.1433 0.9198 0.92 0.00 0.00 0.08 0.00 0.00 0.00
#> TCGA.BR.A4J9.01 2 0.4127 0.1760 0.00 0.60 0.36 0.00 0.04 0.00 0.00
#> TCGA.EQ.A4SO.01 7 0.0863 0.6398 0.00 0.00 0.00 0.00 0.04 0.00 0.96
#> TCGA.BR.A4J7.01 2 0.4842 0.2816 0.00 0.60 0.00 0.00 0.16 0.00 0.24
#> TCGA.D7.A74B.01 1 0.0000 0.9678 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BR.A4J6.01 4 0.2569 0.6875 0.00 0.00 0.00 0.84 0.14 0.02 0.00
#> TCGA.D7.A747.01 3 0.2912 0.7855 0.00 0.14 0.82 0.00 0.04 0.00 0.00
#> TCGA.F1.A72C.01 7 0.5134 0.1953 0.00 0.40 0.00 0.00 0.14 0.00 0.46
#> TCGA.RD.A8N9.01 4 0.1006 0.7839 0.02 0.00 0.00 0.96 0.02 0.00 0.00
#> TCGA.CG.5717.01 3 0.3744 0.7369 0.00 0.08 0.78 0.00 0.02 0.12 0.00
#> TCGA.CD.5813.01 2 0.6096 0.1232 0.00 0.48 0.00 0.00 0.28 0.06 0.18
#> TCGA.CG.5723.01 2 0.5551 0.1257 0.00 0.56 0.00 0.00 0.10 0.06 0.28
#> TCGA.BR.8080.01 4 0.1166 0.7898 0.06 0.00 0.00 0.94 0.00 0.00 0.00
#> TCGA.KB.A93G.01 3 0.0504 0.7994 0.00 0.00 0.98 0.00 0.00 0.02 0.00
#> TCGA.BR.7722.01 7 0.4698 0.5172 0.00 0.14 0.00 0.00 0.24 0.00 0.62
#> TCGA.BR.6710.01 6 0.2422 0.5399 0.00 0.00 0.18 0.00 0.00 0.82 0.00
#> TCGA.IN.A7NR.01 1 0.1166 0.9346 0.94 0.00 0.00 0.06 0.00 0.00 0.00
#> TCGA.BR.6564.01 1 0.0000 0.9678 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CD.5798.01 3 0.3908 0.7180 0.00 0.20 0.72 0.00 0.08 0.00 0.00
#> TCGA.CG.5719.01 4 0.1718 0.7915 0.04 0.00 0.00 0.92 0.04 0.00 0.00
#> TCGA.BR.6709.01 1 0.1671 0.9016 0.90 0.00 0.00 0.10 0.00 0.00 0.00
#> TCGA.BR.6803.01 1 0.0000 0.9678 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.SW.A7EB.01 6 0.6292 0.4009 0.00 0.28 0.10 0.00 0.06 0.52 0.04
#> TCGA.D7.8574.01 2 0.4547 0.2501 0.00 0.58 0.34 0.00 0.08 0.00 0.00
#> TCGA.HJ.7597.01 4 0.1363 0.7932 0.04 0.00 0.00 0.94 0.02 0.00 0.00
#> TCGA.CD.5803.01 1 0.2081 0.8560 0.86 0.00 0.00 0.14 0.00 0.00 0.00
#> TCGA.RD.A8N2.01 1 0.0000 0.9678 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.RD.A8N5.01 3 0.3244 0.7501 0.00 0.18 0.78 0.00 0.00 0.04 0.00
#> TCGA.CD.8532.01 7 0.4998 0.3808 0.00 0.32 0.00 0.00 0.14 0.00 0.54
#> TCGA.BR.8058.01 4 0.3496 0.3181 0.42 0.00 0.00 0.58 0.00 0.00 0.00
#> TCGA.D7.A748.01 1 0.1671 0.9032 0.90 0.00 0.00 0.10 0.00 0.00 0.00
#> TCGA.RD.A8N0.01 1 0.0000 0.9678 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BR.8365.01 1 0.0000 0.9678 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FP.8211.01 7 0.0863 0.6470 0.00 0.00 0.00 0.00 0.04 0.00 0.96
#> TCGA.RD.A8N4.01 1 0.0000 0.9678 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.RD.A7BW.01 1 0.0000 0.9678 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BR.8371.01 3 0.0504 0.7994 0.00 0.00 0.98 0.00 0.00 0.02 0.00
#> TCGA.D7.8576.01 4 0.2569 0.6919 0.00 0.00 0.00 0.84 0.14 0.02 0.00
#> TCGA.BR.8364.01 1 0.0000 0.9678 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CD.A489.01 2 0.5504 0.2551 0.00 0.58 0.00 0.00 0.22 0.04 0.16
#> TCGA.HU.A4GY.01 4 0.1433 0.7810 0.08 0.00 0.00 0.92 0.00 0.00 0.00
#> TCGA.FP.8209.01 3 0.0504 0.7994 0.00 0.00 0.98 0.00 0.00 0.02 0.00
#> TCGA.BR.A44T.01 1 0.0000 0.9678 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FP.8210.01 3 0.2722 0.7927 0.00 0.12 0.84 0.00 0.04 0.00 0.00
#> TCGA.RD.A7BS.01 2 0.3667 0.4131 0.00 0.74 0.20 0.00 0.06 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.VQ.A94P.01 3 0.0000 0.8299 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D7.6521.01 2 0.5082 -0.1474 0.00 0.56 0.00 0.00 0.08 0.00 0.06 0.30
#> TCGA.D7.6522.01 3 0.0000 0.8299 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.VQ.AA64.01 7 0.2994 0.2323 0.00 0.06 0.00 0.00 0.00 0.00 0.80 0.14
#> TCGA.VQ.A928.01 7 0.5131 0.1273 0.00 0.16 0.00 0.00 0.08 0.00 0.62 0.14
#> TCGA.VQ.A8E0.01 7 0.6146 -0.0299 0.00 0.10 0.00 0.00 0.22 0.00 0.42 0.26
#> TCGA.VQ.A91Q.01 7 0.4522 0.1236 0.00 0.04 0.00 0.00 0.04 0.00 0.58 0.34
#> TCGA.VQ.A94T.01 7 0.0941 0.2760 0.00 0.00 0.00 0.00 0.02 0.00 0.96 0.02
#> TCGA.VQ.A8PS.01 7 0.3690 0.0810 0.00 0.02 0.00 0.00 0.00 0.00 0.56 0.42
#> TCGA.BR.6454.01 7 0.6485 -0.3937 0.00 0.26 0.00 0.00 0.18 0.00 0.36 0.20
#> TCGA.BR.8590.01 2 0.3658 0.0768 0.00 0.58 0.40 0.00 0.00 0.00 0.00 0.02
#> TCGA.VQ.A8PQ.01 1 0.1275 0.8922 0.94 0.00 0.00 0.00 0.02 0.04 0.00 0.00
#> TCGA.VQ.A927.01 3 0.5281 0.4391 0.00 0.26 0.56 0.00 0.00 0.12 0.00 0.06
#> TCGA.BR.6566.11 1 0.0808 0.8913 0.96 0.00 0.00 0.00 0.04 0.00 0.00 0.00
#> TCGA.VQ.AA6F.01 2 0.4345 0.1196 0.00 0.74 0.04 0.00 0.06 0.00 0.04 0.12
#> TCGA.VQ.AA6J.01 2 0.3135 0.2054 0.00 0.82 0.02 0.00 0.02 0.00 0.02 0.12
#> TCGA.BR.8677.01 4 0.3845 0.5913 0.28 0.00 0.00 0.66 0.06 0.00 0.00 0.00
#> TCGA.BR.A452.01 7 0.4514 0.1615 0.00 0.16 0.00 0.00 0.12 0.00 0.68 0.04
#> TCGA.VQ.A8PU.01 7 0.6014 -0.0016 0.00 0.00 0.00 0.20 0.20 0.00 0.48 0.12
#> TCGA.VQ.AA6K.01 7 0.3710 0.2035 0.00 0.12 0.00 0.00 0.02 0.00 0.76 0.10
#> TCGA.VQ.A8PX.01 8 0.5245 0.2805 0.00 0.10 0.00 0.00 0.00 0.08 0.24 0.58
#> TCGA.BR.A4IV.01 3 0.2114 0.8055 0.00 0.16 0.84 0.00 0.00 0.00 0.00 0.00
#> TCGA.BR.A4IZ.01 1 0.2623 0.8235 0.84 0.00 0.00 0.10 0.06 0.00 0.00 0.00
#> TCGA.BR.A4J9.01 2 0.3374 0.3355 0.00 0.68 0.30 0.00 0.02 0.00 0.00 0.00
#> TCGA.EQ.A4SO.01 7 0.4325 0.0736 0.00 0.00 0.00 0.00 0.04 0.02 0.56 0.38
#> TCGA.BR.A4J7.01 2 0.5315 -0.2505 0.00 0.60 0.00 0.00 0.14 0.00 0.16 0.10
#> TCGA.D7.A74B.01 1 0.1607 0.8859 0.92 0.00 0.00 0.00 0.04 0.04 0.00 0.00
#> TCGA.BR.A4J6.01 4 0.2114 0.6437 0.00 0.00 0.00 0.84 0.16 0.00 0.00 0.00
#> TCGA.D7.A747.01 3 0.1563 0.8282 0.00 0.10 0.90 0.00 0.00 0.00 0.00 0.00
#> TCGA.F1.A72C.01 8 0.5727 0.1303 0.00 0.22 0.00 0.00 0.04 0.00 0.32 0.42
#> TCGA.RD.A8N9.01 4 0.0808 0.7243 0.00 0.00 0.00 0.96 0.04 0.00 0.00 0.00
#> TCGA.CG.5717.01 3 0.4521 0.6724 0.00 0.12 0.72 0.00 0.02 0.08 0.00 0.06
#> TCGA.CD.5813.01 5 0.6255 0.0000 0.00 0.32 0.00 0.00 0.38 0.00 0.14 0.16
#> TCGA.CG.5723.01 2 0.5994 -0.3181 0.00 0.46 0.00 0.00 0.10 0.00 0.18 0.26
#> TCGA.BR.8080.01 4 0.2818 0.7335 0.12 0.00 0.00 0.82 0.06 0.00 0.00 0.00
#> TCGA.KB.A93G.01 3 0.0000 0.8299 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BR.7722.01 8 0.6269 0.2591 0.00 0.12 0.00 0.00 0.08 0.04 0.30 0.46
#> TCGA.BR.6710.01 6 0.1765 0.5033 0.00 0.00 0.12 0.00 0.00 0.88 0.00 0.00
#> TCGA.IN.A7NR.01 1 0.2994 0.7800 0.80 0.00 0.00 0.14 0.06 0.00 0.00 0.00
#> TCGA.BR.6564.01 1 0.0000 0.9030 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CD.5798.01 3 0.3637 0.6749 0.00 0.26 0.70 0.00 0.02 0.00 0.00 0.02
#> TCGA.CG.5719.01 4 0.0808 0.7506 0.04 0.00 0.00 0.96 0.00 0.00 0.00 0.00
#> TCGA.BR.6709.01 1 0.3154 0.7637 0.78 0.00 0.00 0.16 0.06 0.00 0.00 0.00
#> TCGA.BR.6803.01 1 0.0471 0.9003 0.98 0.00 0.00 0.00 0.00 0.02 0.00 0.00
#> TCGA.SW.A7EB.01 6 0.6521 0.4400 0.00 0.18 0.12 0.00 0.02 0.42 0.00 0.26
#> TCGA.D7.8574.01 2 0.3015 0.3119 0.00 0.68 0.32 0.00 0.00 0.00 0.00 0.00
#> TCGA.HJ.7597.01 4 0.0000 0.7345 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.CD.5803.01 1 0.3299 0.7360 0.76 0.00 0.00 0.18 0.06 0.00 0.00 0.00
#> TCGA.RD.A8N2.01 1 0.1607 0.8859 0.92 0.00 0.00 0.00 0.04 0.04 0.00 0.00
#> TCGA.RD.A8N5.01 3 0.2719 0.7854 0.00 0.18 0.80 0.00 0.00 0.00 0.00 0.02
#> TCGA.CD.8532.01 7 0.6114 -0.2825 0.00 0.16 0.00 0.00 0.06 0.02 0.42 0.34
#> TCGA.BR.8058.01 4 0.3991 0.5206 0.32 0.00 0.00 0.62 0.06 0.00 0.00 0.00
#> TCGA.D7.A748.01 1 0.2818 0.8060 0.82 0.00 0.00 0.12 0.06 0.00 0.00 0.00
#> TCGA.RD.A8N0.01 1 0.0000 0.9030 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BR.8365.01 1 0.0000 0.9030 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FP.8211.01 7 0.3942 0.0918 0.00 0.00 0.00 0.00 0.02 0.02 0.62 0.34
#> TCGA.RD.A8N4.01 1 0.1607 0.8859 0.92 0.00 0.00 0.00 0.04 0.04 0.00 0.00
#> TCGA.RD.A7BW.01 1 0.1607 0.8859 0.92 0.00 0.00 0.00 0.04 0.04 0.00 0.00
#> TCGA.BR.8371.01 3 0.0000 0.8299 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D7.8576.01 4 0.2114 0.6414 0.00 0.00 0.00 0.84 0.16 0.00 0.00 0.00
#> TCGA.BR.8364.01 1 0.0000 0.9030 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CD.A489.01 2 0.6294 -0.6488 0.00 0.42 0.00 0.00 0.24 0.00 0.16 0.18
#> TCGA.HU.A4GY.01 4 0.2818 0.7327 0.12 0.00 0.00 0.82 0.06 0.00 0.00 0.00
#> TCGA.FP.8209.01 3 0.0471 0.8159 0.00 0.00 0.98 0.00 0.00 0.02 0.00 0.00
#> TCGA.BR.A44T.01 1 0.0000 0.9030 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FP.8210.01 3 0.1765 0.8238 0.00 0.12 0.88 0.00 0.00 0.00 0.00 0.00
#> TCGA.RD.A7BS.01 2 0.1947 0.3909 0.00 0.86 0.14 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: Node011. Child nodes: Node01111-leaf , Node01112-leaf , Node01113-leaf , Node01114-leaf , Node01115-leaf , Node01116-leaf , Node01121-leaf , Node01122-leaf , Node01123-leaf , Node01131-leaf , Node01132-leaf , Node01133-leaf , Node01134-leaf , Node01211-leaf , Node01212-leaf , Node01221-leaf , Node01222-leaf , Node01231-leaf , Node01232-leaf , Node01233-leaf , Node01311-leaf , Node01312 , Node02221-leaf , Node02222-leaf , Node02223-leaf , Node02224-leaf , Node03111-leaf , Node03112-leaf , Node03113-leaf , Node03411-leaf , Node03412-leaf , Node03413-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 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 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 1.0000 1.000 0.5152 0.485 0.485
#> 3 3 0.882 0.0222 0.591 0.2847 0.559 0.318
#> 4 4 1.000 0.9976 0.999 0.0898 0.662 0.313
#> 5 5 0.868 0.9125 0.894 0.0931 0.926 0.737
#> 6 6 0.963 0.9751 0.980 0.0757 0.941 0.714
#> 7 7 0.941 0.8862 0.927 0.0227 1.000 1.000
#> 8 8 0.912 0.7131 0.914 0.0208 0.971 0.800
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 6
There is also optional best \(k\) = 2 4 6 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.VQ.A8PQ.01 2 0 1 0 1
#> TCGA.BR.6566.11 2 0 1 0 1
#> TCGA.BR.A4IZ.01 2 0 1 0 1
#> TCGA.D7.A74B.01 1 0 1 1 0
#> TCGA.IN.A7NR.01 2 0 1 0 1
#> TCGA.BR.6564.01 1 0 1 1 0
#> TCGA.BR.6709.01 2 0 1 0 1
#> TCGA.BR.6803.01 2 0 1 0 1
#> TCGA.CD.5803.01 2 0 1 0 1
#> TCGA.RD.A8N2.01 1 0 1 1 0
#> TCGA.D7.A748.01 2 0 1 0 1
#> TCGA.RD.A8N0.01 2 0 1 0 1
#> TCGA.BR.8365.01 1 0 1 1 0
#> TCGA.RD.A8N4.01 1 0 1 1 0
#> TCGA.RD.A7BW.01 1 0 1 1 0
#> TCGA.BR.8364.01 1 0 1 1 0
#> TCGA.BR.A44T.01 2 0 1 0 1
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.VQ.A8PQ.01 2 0.631 0.1766 0.50 0.50 0.0
#> TCGA.BR.6566.11 2 0.630 -0.2644 0.48 0.52 0.0
#> TCGA.BR.A4IZ.01 1 0.631 -0.3825 0.50 0.50 0.0
#> TCGA.D7.A74B.01 1 0.631 -0.2509 0.50 0.00 0.5
#> TCGA.IN.A7NR.01 2 0.630 -0.2644 0.48 0.52 0.0
#> TCGA.BR.6564.01 1 0.631 0.0437 0.50 0.50 0.0
#> TCGA.BR.6709.01 1 0.631 -0.3825 0.50 0.50 0.0
#> TCGA.BR.6803.01 1 0.631 0.0437 0.50 0.50 0.0
#> TCGA.CD.5803.01 1 0.631 -0.3825 0.50 0.50 0.0
#> TCGA.RD.A8N2.01 3 0.000 1.0000 0.00 0.00 1.0
#> TCGA.D7.A748.01 2 0.631 0.1766 0.50 0.50 0.0
#> TCGA.RD.A8N0.01 2 0.631 0.1766 0.50 0.50 0.0
#> TCGA.BR.8365.01 1 0.631 0.0437 0.50 0.50 0.0
#> TCGA.RD.A8N4.01 3 0.000 1.0000 0.00 0.00 1.0
#> TCGA.RD.A7BW.01 1 0.631 -0.2509 0.50 0.00 0.5
#> TCGA.BR.8364.01 2 0.631 -0.2828 0.50 0.50 0.0
#> TCGA.BR.A44T.01 2 0.631 0.1766 0.50 0.50 0.0
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> TCGA.VQ.A8PQ.01 2 0.0000 1.000 0.00 1 0 0.00
#> TCGA.BR.6566.11 4 0.0000 1.000 0.00 0 0 1.00
#> TCGA.BR.A4IZ.01 2 0.0000 1.000 0.00 1 0 0.00
#> TCGA.D7.A74B.01 1 0.0000 0.996 1.00 0 0 0.00
#> TCGA.IN.A7NR.01 4 0.0000 1.000 0.00 0 0 1.00
#> TCGA.BR.6564.01 1 0.0000 0.996 1.00 0 0 0.00
#> TCGA.BR.6709.01 2 0.0000 1.000 0.00 1 0 0.00
#> TCGA.BR.6803.01 1 0.0707 0.980 0.98 0 0 0.02
#> TCGA.CD.5803.01 2 0.0000 1.000 0.00 1 0 0.00
#> TCGA.RD.A8N2.01 3 0.0000 1.000 0.00 0 1 0.00
#> TCGA.D7.A748.01 2 0.0000 1.000 0.00 1 0 0.00
#> TCGA.RD.A8N0.01 2 0.0000 1.000 0.00 1 0 0.00
#> TCGA.BR.8365.01 1 0.0000 0.996 1.00 0 0 0.00
#> TCGA.RD.A8N4.01 3 0.0000 1.000 0.00 0 1 0.00
#> TCGA.RD.A7BW.01 1 0.0000 0.996 1.00 0 0 0.00
#> TCGA.BR.8364.01 1 0.0000 0.996 1.00 0 0 0.00
#> TCGA.BR.A44T.01 2 0.0000 1.000 0.00 1 0 0.00
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> TCGA.VQ.A8PQ.01 2 0.426 1.000 0.00 0.56 0 0.00 0.44
#> TCGA.BR.6566.11 4 0.000 1.000 0.00 0.00 0 1.00 0.00
#> TCGA.BR.A4IZ.01 5 0.000 1.000 0.00 0.00 0 0.00 1.00
#> TCGA.D7.A74B.01 1 0.000 0.618 1.00 0.00 0 0.00 0.00
#> TCGA.IN.A7NR.01 4 0.000 1.000 0.00 0.00 0 1.00 0.00
#> TCGA.BR.6564.01 1 0.480 0.817 0.54 0.44 0 0.02 0.00
#> TCGA.BR.6709.01 2 0.426 1.000 0.00 0.56 0 0.00 0.44
#> TCGA.BR.6803.01 1 0.480 0.817 0.54 0.44 0 0.02 0.00
#> TCGA.CD.5803.01 2 0.426 1.000 0.00 0.56 0 0.00 0.44
#> TCGA.RD.A8N2.01 3 0.000 1.000 0.00 0.00 1 0.00 0.00
#> TCGA.D7.A748.01 5 0.000 1.000 0.00 0.00 0 0.00 1.00
#> TCGA.RD.A8N0.01 2 0.426 1.000 0.00 0.56 0 0.00 0.44
#> TCGA.BR.8365.01 1 0.426 0.822 0.56 0.44 0 0.00 0.00
#> TCGA.RD.A8N4.01 3 0.000 1.000 0.00 0.00 1 0.00 0.00
#> TCGA.RD.A7BW.01 1 0.000 0.618 1.00 0.00 0 0.00 0.00
#> TCGA.BR.8364.01 1 0.426 0.822 0.56 0.44 0 0.00 0.00
#> TCGA.BR.A44T.01 2 0.426 1.000 0.00 0.56 0 0.00 0.44
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> TCGA.VQ.A8PQ.01 2 0.0000 1.000 0.00 1.00 0 0.00 0.00 0.00
#> TCGA.BR.6566.11 4 0.0000 0.971 0.00 0.00 0 1.00 0.00 0.00
#> TCGA.BR.A4IZ.01 5 0.0547 0.891 0.00 0.02 0 0.00 0.98 0.00
#> TCGA.D7.A74B.01 6 0.0547 1.000 0.02 0.00 0 0.00 0.00 0.98
#> TCGA.IN.A7NR.01 4 0.1092 0.971 0.00 0.00 0 0.96 0.02 0.02
#> TCGA.BR.6564.01 1 0.0547 0.969 0.98 0.00 0 0.00 0.00 0.02
#> TCGA.BR.6709.01 2 0.0000 1.000 0.00 1.00 0 0.00 0.00 0.00
#> TCGA.BR.6803.01 1 0.0547 0.952 0.98 0.00 0 0.00 0.02 0.00
#> TCGA.CD.5803.01 2 0.0000 1.000 0.00 1.00 0 0.00 0.00 0.00
#> TCGA.RD.A8N2.01 3 0.0000 1.000 0.00 0.00 1 0.00 0.00 0.00
#> TCGA.D7.A748.01 5 0.1814 0.892 0.00 0.10 0 0.00 0.90 0.00
#> TCGA.RD.A8N0.01 2 0.0000 1.000 0.00 1.00 0 0.00 0.00 0.00
#> TCGA.BR.8365.01 1 0.1267 0.962 0.94 0.00 0 0.00 0.00 0.06
#> TCGA.RD.A8N4.01 3 0.0000 1.000 0.00 0.00 1 0.00 0.00 0.00
#> TCGA.RD.A7BW.01 6 0.0547 1.000 0.02 0.00 0 0.00 0.00 0.98
#> TCGA.BR.8364.01 1 0.0937 0.969 0.96 0.00 0 0.00 0.00 0.04
#> TCGA.BR.A44T.01 2 0.0000 1.000 0.00 1.00 0 0.00 0.00 0.00
cbind(get_classes(res, k = 7), get_membership(res, k = 7))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7
#> TCGA.VQ.A8PQ.01 2 0.1006 0.950 0.00 0.96 0.02 0.00 0.02 0.00 0
#> TCGA.BR.6566.11 4 0.3558 0.610 0.00 0.00 0.48 0.52 0.00 0.00 0
#> TCGA.BR.A4IZ.01 5 0.0000 0.859 0.00 0.00 0.00 0.00 1.00 0.00 0
#> TCGA.D7.A74B.01 6 0.0000 1.000 0.00 0.00 0.00 0.00 0.00 1.00 0
#> TCGA.IN.A7NR.01 4 0.0000 0.610 0.00 0.00 0.00 1.00 0.00 0.00 0
#> TCGA.BR.6564.01 1 0.0000 0.867 1.00 0.00 0.00 0.00 0.00 0.00 0
#> TCGA.BR.6709.01 2 0.0863 0.960 0.00 0.96 0.04 0.00 0.00 0.00 0
#> TCGA.BR.6803.01 1 0.0863 0.859 0.96 0.00 0.04 0.00 0.00 0.00 0
#> TCGA.CD.5803.01 2 0.0504 0.969 0.00 0.98 0.02 0.00 0.00 0.00 0
#> TCGA.RD.A8N2.01 7 0.0000 1.000 0.00 0.00 0.00 0.00 0.00 0.00 1
#> TCGA.D7.A748.01 5 0.2572 0.859 0.00 0.06 0.08 0.00 0.86 0.00 0
#> TCGA.RD.A8N0.01 2 0.0504 0.969 0.00 0.98 0.02 0.00 0.00 0.00 0
#> TCGA.BR.8365.01 1 0.3047 0.749 0.72 0.00 0.28 0.00 0.00 0.00 0
#> TCGA.RD.A8N4.01 7 0.0000 1.000 0.00 0.00 0.00 0.00 0.00 0.00 1
#> TCGA.RD.A7BW.01 6 0.0000 1.000 0.00 0.00 0.00 0.00 0.00 1.00 0
#> TCGA.BR.8364.01 1 0.2569 0.838 0.84 0.00 0.14 0.00 0.00 0.02 0
#> TCGA.BR.A44T.01 2 0.0504 0.967 0.00 0.98 0.02 0.00 0.00 0.00 0
cbind(get_classes(res, k = 8), get_membership(res, k = 8))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7 p8
#> TCGA.VQ.A8PQ.01 2 0.0471 0.934 0.00 0.98 0.00 0.00 0.00 0 0 0.02
#> TCGA.BR.6566.11 4 0.0000 0.000 0.00 0.00 0.00 1.00 0.00 0 0 0.00
#> TCGA.BR.A4IZ.01 5 0.0000 0.842 0.00 0.00 0.00 0.00 1.00 0 0 0.00
#> TCGA.D7.A74B.01 6 0.0000 1.000 0.00 0.00 0.00 0.00 0.00 1 0 0.00
#> TCGA.IN.A7NR.01 8 0.2267 0.000 0.00 0.00 0.00 0.18 0.00 0 0 0.82
#> TCGA.BR.6564.01 1 0.1341 0.661 0.92 0.00 0.08 0.00 0.00 0 0 0.00
#> TCGA.BR.6709.01 2 0.2818 0.834 0.00 0.82 0.12 0.00 0.00 0 0 0.06
#> TCGA.BR.6803.01 1 0.1563 0.666 0.90 0.00 0.10 0.00 0.00 0 0 0.00
#> TCGA.CD.5803.01 2 0.0941 0.926 0.00 0.96 0.02 0.00 0.00 0 0 0.02
#> TCGA.RD.A8N2.01 7 0.0000 1.000 0.00 0.00 0.00 0.00 0.00 0 1 0.00
#> TCGA.D7.A748.01 5 0.3078 0.842 0.00 0.02 0.10 0.00 0.82 0 0 0.06
#> TCGA.RD.A8N0.01 2 0.0471 0.933 0.00 0.98 0.02 0.00 0.00 0 0 0.00
#> TCGA.BR.8365.01 3 0.3299 0.000 0.44 0.00 0.56 0.00 0.00 0 0 0.00
#> TCGA.RD.A8N4.01 7 0.0000 1.000 0.00 0.00 0.00 0.00 0.00 0 1 0.00
#> TCGA.RD.A7BW.01 6 0.0000 1.000 0.00 0.00 0.00 0.00 0.00 1 0 0.00
#> TCGA.BR.8364.01 1 0.2725 0.556 0.82 0.00 0.14 0.00 0.00 0 0 0.04
#> TCGA.BR.A44T.01 2 0.0941 0.930 0.00 0.96 0.02 0.00 0.00 0 0 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: Node011. Child nodes: Node01111-leaf , Node01112-leaf , Node01113-leaf , Node01114-leaf , Node01115-leaf , Node01116-leaf , Node01121-leaf , Node01122-leaf , Node01123-leaf , Node01131-leaf , Node01132-leaf , Node01133-leaf , Node01134-leaf , Node01211-leaf , Node01212-leaf , Node01221-leaf , Node01222-leaf , Node01231-leaf , Node01232-leaf , Node01233-leaf , Node01311-leaf , Node01312 , Node02221-leaf , Node02222-leaf , Node02223-leaf , Node02224-leaf , Node03111-leaf , Node03112-leaf , Node03113-leaf , Node03411-leaf , Node03412-leaf , Node03413-leaf .
The object with results only for a single top-value method and a single partitioning method can be extracted as:
res = res_rh["0112"]
A summary of res and all the functions that can be applied to it:
res
#> A 'ConsensusPartition' object with k = 2, 3, 4, 5, 6, 7, 8.
#> On a matrix with 30000 rows and 23 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 0.533 0.945 0.922 0.4266 0.502 0.502
#> 3 3 1.000 1.000 1.000 0.2982 0.945 0.890
#> 4 4 0.624 0.653 0.819 0.2712 0.802 0.573
#> 5 5 0.610 0.303 0.672 0.0970 0.862 0.583
#> 6 6 0.695 0.532 0.739 0.0643 0.767 0.298
#> 7 7 0.805 0.767 0.810 0.0472 0.941 0.681
#> 8 8 0.833 0.762 0.860 0.0194 0.941 0.605
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.D7.6521.01 1 0.000 0.988 1.00 0.00
#> TCGA.VQ.AA64.01 2 0.795 0.924 0.24 0.76
#> TCGA.VQ.A928.01 2 0.795 0.924 0.24 0.76
#> TCGA.VQ.A8E0.01 2 0.795 0.924 0.24 0.76
#> TCGA.VQ.A91Q.01 2 0.795 0.924 0.24 0.76
#> TCGA.VQ.A94T.01 2 0.000 0.767 0.00 1.00
#> TCGA.VQ.A8PS.01 2 0.795 0.924 0.24 0.76
#> TCGA.BR.6454.01 1 0.000 0.988 1.00 0.00
#> TCGA.VQ.AA6F.01 1 0.000 0.988 1.00 0.00
#> TCGA.VQ.AA6J.01 1 0.000 0.988 1.00 0.00
#> TCGA.BR.A452.01 1 0.242 0.957 0.96 0.04
#> TCGA.VQ.A8PU.01 2 0.000 0.767 0.00 1.00
#> TCGA.VQ.AA6K.01 1 0.000 0.988 1.00 0.00
#> TCGA.VQ.A8PX.01 1 0.242 0.957 0.96 0.04
#> TCGA.EQ.A4SO.01 2 0.795 0.924 0.24 0.76
#> TCGA.BR.A4J7.01 1 0.000 0.988 1.00 0.00
#> TCGA.F1.A72C.01 1 0.000 0.988 1.00 0.00
#> TCGA.CD.5813.01 1 0.000 0.988 1.00 0.00
#> TCGA.CG.5723.01 1 0.000 0.988 1.00 0.00
#> TCGA.BR.7722.01 1 0.242 0.957 0.96 0.04
#> TCGA.CD.8532.01 1 0.000 0.988 1.00 0.00
#> TCGA.FP.8211.01 2 0.795 0.924 0.24 0.76
#> TCGA.CD.A489.01 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.D7.6521.01 1 0 1 1 0 0
#> TCGA.VQ.AA64.01 2 0 1 0 1 0
#> TCGA.VQ.A928.01 2 0 1 0 1 0
#> TCGA.VQ.A8E0.01 2 0 1 0 1 0
#> TCGA.VQ.A91Q.01 2 0 1 0 1 0
#> TCGA.VQ.A94T.01 3 0 1 0 0 1
#> TCGA.VQ.A8PS.01 2 0 1 0 1 0
#> TCGA.BR.6454.01 1 0 1 1 0 0
#> TCGA.VQ.AA6F.01 1 0 1 1 0 0
#> TCGA.VQ.AA6J.01 1 0 1 1 0 0
#> TCGA.BR.A452.01 1 0 1 1 0 0
#> TCGA.VQ.A8PU.01 3 0 1 0 0 1
#> TCGA.VQ.AA6K.01 1 0 1 1 0 0
#> TCGA.VQ.A8PX.01 1 0 1 1 0 0
#> TCGA.EQ.A4SO.01 2 0 1 0 1 0
#> TCGA.BR.A4J7.01 1 0 1 1 0 0
#> TCGA.F1.A72C.01 1 0 1 1 0 0
#> TCGA.CD.5813.01 1 0 1 1 0 0
#> TCGA.CG.5723.01 1 0 1 1 0 0
#> TCGA.BR.7722.01 1 0 1 1 0 0
#> TCGA.CD.8532.01 1 0 1 1 0 0
#> TCGA.FP.8211.01 2 0 1 0 1 0
#> TCGA.CD.A489.01 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.D7.6521.01 1 0.000 0.72771 1.00 0.00 0.00 0.00
#> TCGA.VQ.AA64.01 4 0.491 0.16656 0.00 0.42 0.00 0.58
#> TCGA.VQ.A928.01 2 0.265 0.83694 0.00 0.88 0.00 0.12
#> TCGA.VQ.A8E0.01 2 0.265 0.83694 0.00 0.88 0.00 0.12
#> TCGA.VQ.A91Q.01 2 0.000 0.88119 0.00 1.00 0.00 0.00
#> TCGA.VQ.A94T.01 3 0.000 0.97846 0.00 0.00 1.00 0.00
#> TCGA.VQ.A8PS.01 2 0.000 0.88119 0.00 1.00 0.00 0.00
#> TCGA.BR.6454.01 1 0.452 0.00289 0.68 0.00 0.00 0.32
#> TCGA.VQ.AA6F.01 1 0.000 0.72771 1.00 0.00 0.00 0.00
#> TCGA.VQ.AA6J.01 1 0.000 0.72771 1.00 0.00 0.00 0.00
#> TCGA.BR.A452.01 1 0.398 0.66564 0.76 0.00 0.00 0.24
#> TCGA.VQ.A8PU.01 3 0.121 0.97846 0.00 0.00 0.96 0.04
#> TCGA.VQ.AA6K.01 4 0.462 0.62775 0.34 0.00 0.00 0.66
#> TCGA.VQ.A8PX.01 1 0.398 0.66564 0.76 0.00 0.00 0.24
#> TCGA.EQ.A4SO.01 2 0.292 0.83362 0.00 0.86 0.00 0.14
#> TCGA.BR.A4J7.01 4 0.491 0.66936 0.42 0.00 0.00 0.58
#> TCGA.F1.A72C.01 1 0.498 -0.47881 0.54 0.00 0.00 0.46
#> TCGA.CD.5813.01 4 0.491 0.66936 0.42 0.00 0.00 0.58
#> TCGA.CG.5723.01 4 0.684 0.66707 0.28 0.14 0.00 0.58
#> TCGA.BR.7722.01 1 0.398 0.66564 0.76 0.00 0.00 0.24
#> TCGA.CD.8532.01 1 0.000 0.72771 1.00 0.00 0.00 0.00
#> TCGA.FP.8211.01 2 0.292 0.83362 0.00 0.86 0.00 0.14
#> TCGA.CD.A489.01 1 0.201 0.71557 0.92 0.00 0.00 0.08
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> TCGA.D7.6521.01 1 0.000 0.5268 1.00 0.00 0.00 0.00 0.00
#> TCGA.VQ.AA64.01 4 0.634 0.1384 0.00 0.32 0.00 0.50 0.18
#> TCGA.VQ.A928.01 2 0.327 0.6267 0.00 0.78 0.00 0.22 0.00
#> TCGA.VQ.A8E0.01 2 0.327 0.6267 0.00 0.78 0.00 0.22 0.00
#> TCGA.VQ.A91Q.01 2 0.000 0.7039 0.00 1.00 0.00 0.00 0.00
#> TCGA.VQ.A94T.01 3 0.104 0.9735 0.00 0.00 0.96 0.04 0.00
#> TCGA.VQ.A8PS.01 2 0.000 0.7039 0.00 1.00 0.00 0.00 0.00
#> TCGA.BR.6454.01 1 0.398 0.2053 0.66 0.00 0.00 0.00 0.34
#> TCGA.VQ.AA6F.01 1 0.000 0.5268 1.00 0.00 0.00 0.00 0.00
#> TCGA.VQ.AA6J.01 1 0.000 0.5268 1.00 0.00 0.00 0.00 0.00
#> TCGA.BR.A452.01 5 0.418 -0.3676 0.40 0.00 0.00 0.00 0.60
#> TCGA.VQ.A8PU.01 3 0.000 0.9735 0.00 0.00 1.00 0.00 0.00
#> TCGA.VQ.AA6K.01 4 0.607 -0.0398 0.12 0.00 0.00 0.44 0.44
#> TCGA.VQ.A8PX.01 1 0.517 0.1037 0.50 0.00 0.00 0.04 0.46
#> TCGA.EQ.A4SO.01 2 0.389 0.3303 0.00 0.68 0.00 0.32 0.00
#> TCGA.BR.A4J7.01 1 0.655 -0.4673 0.40 0.00 0.00 0.20 0.40
#> TCGA.F1.A72C.01 1 0.468 -0.1202 0.60 0.00 0.00 0.02 0.38
#> TCGA.CD.5813.01 5 0.655 0.1122 0.40 0.00 0.00 0.20 0.40
#> TCGA.CG.5723.01 5 0.676 0.1482 0.28 0.00 0.00 0.32 0.40
#> TCGA.BR.7722.01 1 0.517 0.1037 0.50 0.00 0.00 0.04 0.46
#> TCGA.CD.8532.01 1 0.000 0.5268 1.00 0.00 0.00 0.00 0.00
#> TCGA.FP.8211.01 4 0.430 -0.3122 0.00 0.48 0.00 0.52 0.00
#> TCGA.CD.A489.01 1 0.311 0.4108 0.80 0.00 0.00 0.00 0.20
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> TCGA.D7.6521.01 1 0.7194 0.516 0.32 0.00 0.0 0.08 0.30 0.30
#> TCGA.VQ.AA64.01 2 0.5778 0.255 0.08 0.64 0.0 0.12 0.16 0.00
#> TCGA.VQ.A928.01 2 0.0547 0.592 0.02 0.98 0.0 0.00 0.00 0.00
#> TCGA.VQ.A8E0.01 2 0.0547 0.592 0.02 0.98 0.0 0.00 0.00 0.00
#> TCGA.VQ.A91Q.01 2 0.3309 0.354 0.00 0.72 0.0 0.28 0.00 0.00
#> TCGA.VQ.A94T.01 3 0.1814 0.932 0.00 0.00 0.9 0.10 0.00 0.00
#> TCGA.VQ.A8PS.01 2 0.3309 0.354 0.00 0.72 0.0 0.28 0.00 0.00
#> TCGA.BR.6454.01 5 0.3475 0.500 0.14 0.00 0.0 0.00 0.80 0.06
#> TCGA.VQ.AA6F.01 1 0.7194 0.516 0.32 0.00 0.0 0.08 0.30 0.30
#> TCGA.VQ.AA6J.01 1 0.7194 0.516 0.32 0.00 0.0 0.08 0.30 0.30
#> TCGA.BR.A452.01 5 0.4328 0.142 0.00 0.00 0.0 0.02 0.52 0.46
#> TCGA.VQ.A8PU.01 3 0.0000 0.932 0.00 0.00 1.0 0.00 0.00 0.00
#> TCGA.VQ.AA6K.01 5 0.4967 0.403 0.10 0.06 0.0 0.12 0.72 0.00
#> TCGA.VQ.A8PX.01 6 0.0000 1.000 0.00 0.00 0.0 0.00 0.00 1.00
#> TCGA.EQ.A4SO.01 4 0.3578 0.651 0.00 0.34 0.0 0.66 0.00 0.00
#> TCGA.BR.A4J7.01 1 0.0000 0.316 1.00 0.00 0.0 0.00 0.00 0.00
#> TCGA.F1.A72C.01 1 0.6904 0.490 0.46 0.00 0.0 0.10 0.28 0.16
#> TCGA.CD.5813.01 1 0.1092 0.325 0.96 0.00 0.0 0.02 0.02 0.00
#> TCGA.CG.5723.01 1 0.2793 0.140 0.80 0.20 0.0 0.00 0.00 0.00
#> TCGA.BR.7722.01 6 0.0000 1.000 0.00 0.00 0.0 0.00 0.00 1.00
#> TCGA.CD.8532.01 1 0.7180 0.521 0.34 0.00 0.0 0.08 0.28 0.30
#> TCGA.FP.8211.01 4 0.4121 0.683 0.00 0.22 0.0 0.72 0.06 0.00
#> TCGA.CD.A489.01 5 0.4066 0.516 0.12 0.00 0.0 0.02 0.78 0.08
cbind(get_classes(res, k = 7), get_membership(res, k = 7))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7
#> TCGA.D7.6521.01 1 0.0000 0.952 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.VQ.AA64.01 2 0.6109 0.279 0.00 0.54 0.00 0.04 0.28 0.08 0.06
#> TCGA.VQ.A928.01 2 0.0000 0.649 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.VQ.A8E0.01 2 0.0000 0.649 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.VQ.A91Q.01 2 0.4108 0.517 0.00 0.66 0.00 0.28 0.00 0.06 0.00
#> TCGA.VQ.A94T.01 3 0.0504 0.985 0.00 0.00 0.98 0.00 0.02 0.00 0.00
#> TCGA.VQ.A8PS.01 2 0.4108 0.517 0.00 0.66 0.00 0.28 0.00 0.06 0.00
#> TCGA.BR.6454.01 5 0.3867 0.524 0.38 0.00 0.00 0.00 0.60 0.00 0.02
#> TCGA.VQ.AA6F.01 1 0.0000 0.952 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.VQ.AA6J.01 1 0.0000 0.952 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BR.A452.01 5 0.3841 0.426 0.04 0.00 0.00 0.00 0.68 0.28 0.00
#> TCGA.VQ.A8PU.01 3 0.0000 0.985 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.VQ.AA6K.01 5 0.4136 0.396 0.00 0.02 0.00 0.04 0.78 0.08 0.08
#> TCGA.VQ.A8PX.01 6 0.3047 0.985 0.28 0.00 0.00 0.00 0.00 0.72 0.00
#> TCGA.EQ.A4SO.01 4 0.1166 0.823 0.00 0.06 0.00 0.94 0.00 0.00 0.00
#> TCGA.BR.A4J7.01 7 0.1166 0.970 0.06 0.00 0.00 0.00 0.00 0.00 0.94
#> TCGA.F1.A72C.01 1 0.1886 0.806 0.88 0.00 0.00 0.00 0.00 0.00 0.12
#> TCGA.CD.5813.01 7 0.1166 0.970 0.06 0.00 0.00 0.00 0.00 0.00 0.94
#> TCGA.CG.5723.01 7 0.1363 0.939 0.02 0.04 0.00 0.00 0.00 0.00 0.94
#> TCGA.BR.7722.01 6 0.3517 0.985 0.28 0.00 0.00 0.02 0.00 0.70 0.00
#> TCGA.CD.8532.01 1 0.0000 0.952 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FP.8211.01 4 0.3691 0.830 0.00 0.04 0.00 0.80 0.02 0.12 0.02
#> TCGA.CD.A489.01 5 0.3606 0.610 0.30 0.00 0.00 0.00 0.68 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.D7.6521.01 1 0.0471 0.839 0.98 0.00 0.0 0.00 0.00 0.02 0.00 0.00
#> TCGA.VQ.AA64.01 8 0.2406 0.634 0.00 0.20 0.0 0.00 0.00 0.00 0.00 0.80
#> TCGA.VQ.A928.01 2 0.1557 0.752 0.00 0.92 0.0 0.00 0.00 0.00 0.02 0.06
#> TCGA.VQ.A8E0.01 2 0.1557 0.752 0.00 0.92 0.0 0.00 0.00 0.00 0.02 0.06
#> TCGA.VQ.A91Q.01 2 0.2534 0.718 0.00 0.78 0.0 0.22 0.00 0.00 0.00 0.00
#> TCGA.VQ.A94T.01 3 0.3454 0.844 0.00 0.00 0.8 0.00 0.08 0.06 0.00 0.06
#> TCGA.VQ.A8PS.01 2 0.2534 0.718 0.00 0.78 0.0 0.22 0.00 0.00 0.00 0.00
#> TCGA.BR.6454.01 1 0.4593 0.232 0.62 0.00 0.0 0.00 0.26 0.00 0.02 0.10
#> TCGA.VQ.AA6F.01 1 0.0471 0.839 0.98 0.00 0.0 0.00 0.00 0.02 0.00 0.00
#> TCGA.VQ.AA6J.01 1 0.0471 0.839 0.98 0.00 0.0 0.00 0.00 0.02 0.00 0.00
#> TCGA.BR.A452.01 5 0.3299 0.564 0.06 0.00 0.0 0.00 0.76 0.18 0.00 0.00
#> TCGA.VQ.A8PU.01 3 0.0000 0.844 0.00 0.00 1.0 0.00 0.00 0.00 0.00 0.00
#> TCGA.VQ.AA6K.01 8 0.2114 0.592 0.00 0.00 0.0 0.00 0.16 0.00 0.00 0.84
#> TCGA.VQ.A8PX.01 6 0.2680 0.967 0.12 0.00 0.0 0.02 0.00 0.84 0.02 0.00
#> TCGA.EQ.A4SO.01 4 0.3503 0.717 0.00 0.12 0.0 0.78 0.08 0.00 0.00 0.02
#> TCGA.BR.A4J7.01 7 0.1741 0.950 0.04 0.02 0.0 0.00 0.00 0.02 0.92 0.00
#> TCGA.F1.A72C.01 1 0.3264 0.753 0.84 0.00 0.0 0.04 0.02 0.02 0.06 0.02
#> TCGA.CD.5813.01 7 0.1741 0.936 0.04 0.00 0.0 0.00 0.02 0.02 0.92 0.00
#> TCGA.CG.5723.01 7 0.0941 0.946 0.02 0.02 0.0 0.00 0.00 0.00 0.96 0.00
#> TCGA.BR.7722.01 6 0.1765 0.967 0.12 0.00 0.0 0.00 0.00 0.88 0.00 0.00
#> TCGA.CD.8532.01 1 0.1741 0.807 0.92 0.00 0.0 0.04 0.02 0.00 0.00 0.02
#> TCGA.FP.8211.01 4 0.2348 0.716 0.00 0.00 0.0 0.88 0.04 0.02 0.00 0.06
#> TCGA.CD.A489.01 5 0.3594 0.596 0.28 0.00 0.0 0.00 0.68 0.00 0.00 0.04
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
consensus_heatmap(res, k = 7)
consensus_heatmap(res, k = 8)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
membership_heatmap(res, k = 7)
membership_heatmap(res, k = 8)
As soon as the classes for columns are determined, the signatures that are significantly different between subgroups can be looked for. Following are the heatmaps for signatures.
get_signatures(res, k = 2)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
get_signatures(res, k = 7)
get_signatures(res, k = 8)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. To get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows (which is done by automatically selecting number of clusters).If there are too many signatures, top_signatures = ... can be set to only show the
signatures with the highest FDRs:
# code only for demonstration
# e.g. to show the top 500 most significant rows
tb = get_signature(res, k = ..., top_signatures = 500)
If the signatures are defined as these which are uniquely high in current group, diff_method argument
can be set to "uniquely_high_in_one_group":
# code only for demonstration
tb = get_signature(res, k = ..., diff_method = "uniquely_high_in_one_group")
UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
dimension_reduction(res, k = 7, method = "UMAP")
dimension_reduction(res, k = 8, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
If matrix rows can be associated to genes, consider to use functional_enrichment(res,
...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.
Parent node: Node011. Child nodes: Node01111-leaf , Node01112-leaf , Node01113-leaf , Node01114-leaf , Node01115-leaf , Node01116-leaf , Node01121-leaf , Node01122-leaf , Node01123-leaf , Node01131-leaf , Node01132-leaf , Node01133-leaf , Node01134-leaf , Node01211-leaf , Node01212-leaf , Node01221-leaf , Node01222-leaf , Node01231-leaf , Node01232-leaf , Node01233-leaf , Node01311-leaf , Node01312 , Node02221-leaf , Node02222-leaf , Node02223-leaf , Node02224-leaf , Node03111-leaf , Node03112-leaf , Node03113-leaf , Node03411-leaf , Node03412-leaf , Node03413-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 18 columns.
#> Top rows (1000) are extracted by 'ATC' method.
#> Subgroups are detected by 'kmeans' method.
#> Performed in total 350 partitions by row resampling.
#> Best k for subgroups seems to be 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 0.4711 0.529 0.529
#> 3 3 0.686 0.695 0.811 0.3102 0.654 0.418
#> 4 4 0.732 0.961 0.942 0.1984 0.830 0.527
#> 5 5 0.791 0.751 0.870 0.1137 0.948 0.778
#> 6 6 0.824 0.629 0.829 0.0438 0.922 0.613
#> 7 7 0.850 0.774 0.881 0.0311 0.948 0.652
#> 8 8 0.869 0.705 0.847 0.0195 1.000 1.000
suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:
suggest_best_k(res)
#> [1] 2
Following is the table of the partitions (You need to click the show/hide
code output link to see it). The membership matrix (columns with name p*)
is inferred by
clue::cl_consensus()
function with the SE method. Basically the value in the membership matrix
represents the probability to belong to a certain group. The finall subgroup
label for an item is determined with the group with highest probability it
belongs to.
In get_classes() function, the entropy is calculated from the membership
matrix and the silhouette score is calculated from the consensus matrix.
cbind(get_classes(res, k = 2), get_membership(res, k = 2))
#> class entropy silhouette p1 p2
#> TCGA.VQ.A94P.01 1 0 1 1 0
#> TCGA.D7.6522.01 1 0 1 1 0
#> TCGA.BR.8590.01 1 0 1 1 0
#> TCGA.VQ.A927.01 2 0 1 0 1
#> TCGA.BR.A4IV.01 1 0 1 1 0
#> TCGA.BR.A4J9.01 1 0 1 1 0
#> TCGA.D7.A747.01 1 0 1 1 0
#> TCGA.CG.5717.01 2 0 1 0 1
#> TCGA.KB.A93G.01 1 0 1 1 0
#> TCGA.BR.6710.01 2 0 1 0 1
#> TCGA.CD.5798.01 2 0 1 0 1
#> TCGA.SW.A7EB.01 2 0 1 0 1
#> TCGA.D7.8574.01 1 0 1 1 0
#> TCGA.RD.A8N5.01 1 0 1 1 0
#> TCGA.BR.8371.01 1 0 1 1 0
#> TCGA.FP.8209.01 1 0 1 1 0
#> TCGA.FP.8210.01 1 0 1 1 0
#> TCGA.RD.A7BS.01 2 0 1 0 1
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.VQ.A94P.01 3 0.6302 0.577 0.48 0.00 0.52
#> TCGA.D7.6522.01 1 0.0000 1.000 1.00 0.00 0.00
#> TCGA.BR.8590.01 3 0.6302 0.577 0.48 0.00 0.52
#> TCGA.VQ.A927.01 2 0.0892 0.854 0.00 0.98 0.02
#> TCGA.BR.A4IV.01 1 0.0000 1.000 1.00 0.00 0.00
#> TCGA.BR.A4J9.01 3 0.6302 0.577 0.48 0.00 0.52
#> TCGA.D7.A747.01 3 0.6302 0.577 0.48 0.00 0.52
#> TCGA.CG.5717.01 2 0.6302 0.529 0.00 0.52 0.48
#> TCGA.KB.A93G.01 3 0.6302 0.577 0.48 0.00 0.52
#> TCGA.BR.6710.01 2 0.0000 0.856 0.00 1.00 0.00
#> TCGA.CD.5798.01 3 0.0000 0.158 0.00 0.00 1.00
#> TCGA.SW.A7EB.01 2 0.0000 0.856 0.00 1.00 0.00
#> TCGA.D7.8574.01 1 0.0000 1.000 1.00 0.00 0.00
#> TCGA.RD.A8N5.01 1 0.0000 1.000 1.00 0.00 0.00
#> TCGA.BR.8371.01 1 0.0000 1.000 1.00 0.00 0.00
#> TCGA.FP.8209.01 1 0.0000 1.000 1.00 0.00 0.00
#> TCGA.FP.8210.01 1 0.0000 1.000 1.00 0.00 0.00
#> TCGA.RD.A7BS.01 3 0.6280 -0.629 0.00 0.46 0.54
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> TCGA.VQ.A94P.01 3 0.0707 0.981 0.02 0.00 0.98 0.00
#> TCGA.D7.6522.01 1 0.2345 1.000 0.90 0.00 0.10 0.00
#> TCGA.BR.8590.01 3 0.0707 0.981 0.02 0.00 0.98 0.00
#> TCGA.VQ.A927.01 2 0.3935 0.845 0.10 0.84 0.00 0.06
#> TCGA.BR.A4IV.01 3 0.2011 0.925 0.08 0.00 0.92 0.00
#> TCGA.BR.A4J9.01 3 0.0707 0.981 0.02 0.00 0.98 0.00
#> TCGA.D7.A747.01 3 0.0000 0.963 0.00 0.00 1.00 0.00
#> TCGA.CG.5717.01 4 0.2345 0.903 0.10 0.00 0.00 0.90
#> TCGA.KB.A93G.01 3 0.0707 0.981 0.02 0.00 0.98 0.00
#> TCGA.BR.6710.01 2 0.0000 0.929 0.00 1.00 0.00 0.00
#> TCGA.CD.5798.01 4 0.0707 0.941 0.00 0.00 0.02 0.98
#> TCGA.SW.A7EB.01 2 0.0000 0.929 0.00 1.00 0.00 0.00
#> TCGA.D7.8574.01 1 0.2345 1.000 0.90 0.00 0.10 0.00
#> TCGA.RD.A8N5.01 1 0.2345 1.000 0.90 0.00 0.10 0.00
#> TCGA.BR.8371.01 1 0.2345 1.000 0.90 0.00 0.10 0.00
#> TCGA.FP.8209.01 1 0.2345 1.000 0.90 0.00 0.10 0.00
#> TCGA.FP.8210.01 1 0.2345 1.000 0.90 0.00 0.10 0.00
#> TCGA.RD.A7BS.01 4 0.0000 0.946 0.00 0.00 0.00 1.00
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> TCGA.VQ.A94P.01 3 0.0000 0.684 0.00 0.00 1.00 0.00 0.00
#> TCGA.D7.6522.01 1 0.0000 0.838 1.00 0.00 0.00 0.00 0.00
#> TCGA.BR.8590.01 5 0.3424 1.000 0.00 0.00 0.24 0.00 0.76
#> TCGA.VQ.A927.01 2 0.0609 0.736 0.00 0.98 0.00 0.02 0.00
#> TCGA.BR.A4IV.01 3 0.1043 0.658 0.04 0.00 0.96 0.00 0.00
#> TCGA.BR.A4J9.01 3 0.3274 0.604 0.00 0.00 0.78 0.00 0.22
#> TCGA.D7.A747.01 3 0.3983 0.378 0.00 0.00 0.66 0.00 0.34
#> TCGA.CG.5717.01 4 0.3424 0.760 0.00 0.24 0.00 0.76 0.00
#> TCGA.KB.A93G.01 5 0.3424 1.000 0.00 0.00 0.24 0.00 0.76
#> TCGA.BR.6710.01 2 0.3424 0.882 0.00 0.76 0.00 0.00 0.24
#> TCGA.CD.5798.01 4 0.0000 0.890 0.00 0.00 0.00 1.00 0.00
#> TCGA.SW.A7EB.01 2 0.3424 0.882 0.00 0.76 0.00 0.00 0.24
#> TCGA.D7.8574.01 1 0.0000 0.838 1.00 0.00 0.00 0.00 0.00
#> TCGA.RD.A8N5.01 1 0.4227 0.302 0.58 0.00 0.00 0.00 0.42
#> TCGA.BR.8371.01 1 0.3983 0.503 0.66 0.00 0.34 0.00 0.00
#> TCGA.FP.8209.01 1 0.0000 0.838 1.00 0.00 0.00 0.00 0.00
#> TCGA.FP.8210.01 1 0.0000 0.838 1.00 0.00 0.00 0.00 0.00
#> TCGA.RD.A7BS.01 4 0.0000 0.890 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.VQ.A94P.01 3 0.0547 0.6564 0.00 0.00 0.98 0.00 0.02 0.00
#> TCGA.D7.6522.01 1 0.0000 0.7959 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BR.8590.01 5 0.2350 0.5941 0.00 0.10 0.02 0.00 0.88 0.00
#> TCGA.VQ.A927.01 6 0.0000 0.0142 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.BR.A4IV.01 3 0.2981 0.5636 0.02 0.16 0.82 0.00 0.00 0.00
#> TCGA.BR.A4J9.01 3 0.4608 0.6209 0.00 0.10 0.68 0.00 0.22 0.00
#> TCGA.D7.A747.01 3 0.5012 0.5377 0.00 0.10 0.60 0.00 0.30 0.00
#> TCGA.CG.5717.01 6 0.4310 0.0053 0.00 0.00 0.02 0.44 0.00 0.54
#> TCGA.KB.A93G.01 5 0.0547 0.6440 0.00 0.00 0.02 0.00 0.98 0.00
#> TCGA.BR.6710.01 2 0.3828 1.0000 0.00 0.56 0.00 0.00 0.00 0.44
#> TCGA.CD.5798.01 4 0.0547 0.9807 0.00 0.00 0.00 0.98 0.02 0.00
#> TCGA.SW.A7EB.01 2 0.3828 1.0000 0.00 0.56 0.00 0.00 0.00 0.44
#> TCGA.D7.8574.01 1 0.0000 0.7959 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.RD.A8N5.01 5 0.5144 0.3382 0.34 0.10 0.00 0.00 0.56 0.00
#> TCGA.BR.8371.01 1 0.6010 0.1848 0.40 0.24 0.36 0.00 0.00 0.00
#> TCGA.FP.8209.01 1 0.1556 0.8046 0.92 0.08 0.00 0.00 0.00 0.00
#> TCGA.FP.8210.01 1 0.1556 0.8046 0.92 0.08 0.00 0.00 0.00 0.00
#> TCGA.RD.A7BS.01 4 0.0000 0.9807 0.00 0.00 0.00 1.00 0.00 0.00
cbind(get_classes(res, k = 7), get_membership(res, k = 7))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7
#> TCGA.VQ.A94P.01 3 0.3496 0.366 0.00 0.00 0.58 0.00 0.00 0.00 0.42
#> TCGA.D7.6522.01 1 0.0504 0.959 0.98 0.00 0.00 0.00 0.00 0.02 0.00
#> TCGA.BR.8590.01 5 0.2832 0.656 0.00 0.00 0.24 0.00 0.76 0.00 0.00
#> TCGA.VQ.A927.01 6 0.2422 0.728 0.00 0.18 0.00 0.00 0.00 0.82 0.00
#> TCGA.BR.A4IV.01 7 0.2422 0.500 0.00 0.00 0.18 0.00 0.00 0.00 0.82
#> TCGA.BR.A4J9.01 3 0.2422 0.663 0.00 0.00 0.82 0.00 0.00 0.00 0.18
#> TCGA.D7.A747.01 3 0.0504 0.614 0.00 0.00 0.98 0.00 0.00 0.00 0.02
#> TCGA.CG.5717.01 6 0.2422 0.726 0.00 0.00 0.00 0.18 0.00 0.82 0.00
#> TCGA.KB.A93G.01 5 0.0863 0.753 0.00 0.00 0.04 0.00 0.96 0.00 0.00
#> TCGA.BR.6710.01 2 0.0000 0.967 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CD.5798.01 4 0.1166 0.951 0.00 0.00 0.00 0.94 0.00 0.00 0.06
#> TCGA.SW.A7EB.01 2 0.0863 0.967 0.00 0.96 0.00 0.00 0.04 0.00 0.00
#> TCGA.D7.8574.01 1 0.0504 0.959 0.98 0.00 0.00 0.00 0.00 0.02 0.00
#> TCGA.RD.A8N5.01 5 0.4696 0.646 0.06 0.00 0.00 0.00 0.70 0.16 0.08
#> TCGA.BR.8371.01 7 0.2422 0.605 0.18 0.00 0.00 0.00 0.00 0.00 0.82
#> TCGA.FP.8209.01 1 0.0863 0.958 0.96 0.00 0.00 0.00 0.00 0.00 0.04
#> TCGA.FP.8210.01 1 0.0863 0.958 0.96 0.00 0.00 0.00 0.00 0.00 0.04
#> TCGA.RD.A7BS.01 4 0.0000 0.951 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.VQ.A94P.01 3 0.4971 0.266 0.00 0.00 0.46 0.00 0.18 0.00 0.36 0.00
#> TCGA.D7.6522.01 1 0.0000 0.824 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BR.8590.01 8 0.3785 0.563 0.00 0.00 0.14 0.00 0.14 0.00 0.00 0.72
#> TCGA.VQ.A927.01 6 0.1741 0.923 0.00 0.04 0.00 0.00 0.02 0.92 0.02 0.00
#> TCGA.BR.A4IV.01 7 0.4180 0.420 0.00 0.00 0.06 0.00 0.20 0.04 0.70 0.00
#> TCGA.BR.A4J9.01 3 0.4672 0.567 0.00 0.00 0.60 0.00 0.28 0.00 0.10 0.02
#> TCGA.D7.A747.01 3 0.0471 0.501 0.00 0.00 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.CG.5717.01 6 0.0808 0.923 0.00 0.00 0.00 0.04 0.00 0.96 0.00 0.00
#> TCGA.KB.A93G.01 8 0.0000 0.721 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.BR.6710.01 2 0.0000 0.844 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CD.5798.01 4 0.0000 0.844 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.SW.A7EB.01 2 0.3021 0.844 0.00 0.80 0.02 0.00 0.16 0.00 0.02 0.00
#> TCGA.D7.8574.01 1 0.0000 0.824 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.RD.A8N5.01 8 0.3404 0.631 0.04 0.00 0.00 0.00 0.24 0.00 0.00 0.72
#> TCGA.BR.8371.01 7 0.1341 0.527 0.08 0.00 0.00 0.00 0.00 0.00 0.92 0.00
#> TCGA.FP.8209.01 1 0.2650 0.814 0.76 0.00 0.00 0.00 0.00 0.00 0.24 0.00
#> TCGA.FP.8210.01 1 0.2650 0.814 0.76 0.00 0.00 0.00 0.00 0.00 0.24 0.00
#> TCGA.RD.A7BS.01 4 0.2406 0.844 0.00 0.00 0.00 0.80 0.20 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 , Node0113 , Node0114-leaf , Node0121 , Node0122 , Node0123 , Node0131 , Node0132-leaf , Node0211-leaf , Node0212-leaf , Node0221-leaf , Node0222 , Node0231-leaf , Node0232-leaf , Node0233-leaf , Node0311 , Node0312-leaf , Node0313-leaf , Node0314-leaf , Node0331-leaf , Node0332-leaf , Node0333-leaf , Node0341 , Node0342-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 59 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 0.5090 0.492 0.492
#> 3 3 1.000 0.987 0.994 0.3308 0.728 0.499
#> 4 4 0.820 0.782 0.864 0.1055 0.843 0.564
#> 5 5 0.828 0.812 0.846 0.0542 0.901 0.635
#> 6 6 0.814 0.779 0.831 0.0225 0.987 0.938
#> 7 7 0.800 0.665 0.812 0.0284 0.970 0.850
#> 8 8 0.807 0.666 0.818 0.0166 0.982 0.897
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.VQ.A8PE.01 2 0 1 0 1
#> TCGA.BR.8485.01 1 0 1 1 0
#> TCGA.BR.8486.01 2 0 1 0 1
#> TCGA.VQ.A8PJ.01 2 0 1 0 1
#> TCGA.VQ.A8PH.01 2 0 1 0 1
#> TCGA.D7.6520.01 1 0 1 1 0
#> TCGA.D7.6527.01 1 0 1 1 0
#> TCGA.BR.8678.01 2 0 1 0 1
#> TCGA.VQ.A91Z.01 2 0 1 0 1
#> TCGA.VQ.A91N.01 2 0 1 0 1
#> TCGA.VQ.A91U.01 2 0 1 0 1
#> TCGA.BR.6565.01 1 0 1 1 0
#> TCGA.VQ.A94O.01 1 0 1 1 0
#> TCGA.D7.6526.01 1 0 1 1 0
#> TCGA.3M.AB46.01 2 0 1 0 1
#> TCGA.FP.8631.01 1 0 1 1 0
#> TCGA.VQ.A922.01 1 0 1 1 0
#> TCGA.HU.A4HD.01 1 0 1 1 0
#> TCGA.F1.6875.01 2 0 1 0 1
#> TCGA.MX.A666.01 1 0 1 1 0
#> TCGA.B7.A5TN.01 2 0 1 0 1
#> TCGA.BR.7704.01 2 0 1 0 1
#> TCGA.BR.A4J1.01 1 0 1 1 0
#> TCGA.CD.A4MH.01 1 0 1 1 0
#> TCGA.HF.7131.01 2 0 1 0 1
#> TCGA.D7.A6F2.01 2 0 1 0 1
#> TCGA.RD.A7BT.01 2 0 1 0 1
#> TCGA.BR.A4PD.01 2 0 1 0 1
#> TCGA.VQ.A8PK.01 1 0 1 1 0
#> TCGA.IN.A6RN.01 1 0 1 1 0
#> TCGA.VQ.AA6D.01 1 0 1 1 0
#> TCGA.VQ.AA6A.01 2 0 1 0 1
#> TCGA.IN.7806.01 2 0 1 0 1
#> TCGA.HU.A4H5.01 2 0 1 0 1
#> TCGA.CG.5718.01 1 0 1 1 0
#> TCGA.D7.6817.01 1 0 1 1 0
#> TCGA.BR.7901.01 1 0 1 1 0
#> TCGA.D7.6815.01 2 0 1 0 1
#> TCGA.BR.8295.01 1 0 1 1 0
#> TCGA.BR.7197.01 2 0 1 0 1
#> TCGA.KB.A93J.01 2 0 1 0 1
#> TCGA.R5.A7ZR.01 2 0 1 0 1
#> TCGA.R5.A7ZE.01 2 0 1 0 1
#> TCGA.CG.5725.01 1 0 1 1 0
#> TCGA.D7.6820.01 2 0 1 0 1
#> TCGA.D7.A6F0.01 1 0 1 1 0
#> TCGA.CD.A486.01 1 0 1 1 0
#> TCGA.IN.A6RI.01 1 0 1 1 0
#> TCGA.HU.A4GF.01 2 0 1 0 1
#> TCGA.BR.8373.01 2 0 1 0 1
#> TCGA.VQ.A8DV.01 1 0 1 1 0
#> TCGA.HU.8245.01 1 0 1 1 0
#> TCGA.VQ.A8DU.01 1 0 1 1 0
#> TCGA.VQ.A8DZ.01 1 0 1 1 0
#> TCGA.HU.A4GH.01 1 0 1 1 0
#> TCGA.KB.A6F7.01 1 0 1 1 0
#> TCGA.BR.8060.01 1 0 1 1 0
#> TCGA.BR.8077.01 2 0 1 0 1
#> TCGA.EQ.8122.01 2 0 1 0 1
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.VQ.A8PE.01 3 0.000 1.000 0.00 0 1.00
#> TCGA.BR.8485.01 3 0.000 1.000 0.00 0 1.00
#> TCGA.BR.8486.01 3 0.000 1.000 0.00 0 1.00
#> TCGA.VQ.A8PJ.01 2 0.000 1.000 0.00 1 0.00
#> TCGA.VQ.A8PH.01 3 0.000 1.000 0.00 0 1.00
#> TCGA.D7.6520.01 1 0.000 0.980 1.00 0 0.00
#> TCGA.D7.6527.01 3 0.000 1.000 0.00 0 1.00
#> TCGA.BR.8678.01 2 0.000 1.000 0.00 1 0.00
#> TCGA.VQ.A91Z.01 2 0.000 1.000 0.00 1 0.00
#> TCGA.VQ.A91N.01 2 0.000 1.000 0.00 1 0.00
#> TCGA.VQ.A91U.01 2 0.000 1.000 0.00 1 0.00
#> TCGA.BR.6565.01 1 0.369 0.840 0.86 0 0.14
#> TCGA.VQ.A94O.01 1 0.000 0.980 1.00 0 0.00
#> TCGA.D7.6526.01 3 0.000 1.000 0.00 0 1.00
#> TCGA.3M.AB46.01 2 0.000 1.000 0.00 1 0.00
#> TCGA.FP.8631.01 1 0.000 0.980 1.00 0 0.00
#> TCGA.VQ.A922.01 1 0.000 0.980 1.00 0 0.00
#> TCGA.HU.A4HD.01 1 0.000 0.980 1.00 0 0.00
#> TCGA.F1.6875.01 2 0.000 1.000 0.00 1 0.00
#> TCGA.MX.A666.01 1 0.000 0.980 1.00 0 0.00
#> TCGA.B7.A5TN.01 2 0.000 1.000 0.00 1 0.00
#> TCGA.BR.7704.01 3 0.000 1.000 0.00 0 1.00
#> TCGA.BR.A4J1.01 1 0.000 0.980 1.00 0 0.00
#> TCGA.CD.A4MH.01 3 0.000 1.000 0.00 0 1.00
#> TCGA.HF.7131.01 3 0.000 1.000 0.00 0 1.00
#> TCGA.D7.A6F2.01 2 0.000 1.000 0.00 1 0.00
#> TCGA.RD.A7BT.01 2 0.000 1.000 0.00 1 0.00
#> TCGA.BR.A4PD.01 2 0.000 1.000 0.00 1 0.00
#> TCGA.VQ.A8PK.01 1 0.000 0.980 1.00 0 0.00
#> TCGA.IN.A6RN.01 1 0.000 0.980 1.00 0 0.00
#> TCGA.VQ.AA6D.01 3 0.000 1.000 0.00 0 1.00
#> TCGA.VQ.AA6A.01 3 0.000 1.000 0.00 0 1.00
#> TCGA.IN.7806.01 2 0.000 1.000 0.00 1 0.00
#> TCGA.HU.A4H5.01 3 0.000 1.000 0.00 0 1.00
#> TCGA.CG.5718.01 3 0.000 1.000 0.00 0 1.00
#> TCGA.D7.6817.01 3 0.000 1.000 0.00 0 1.00
#> TCGA.BR.7901.01 1 0.000 0.980 1.00 0 0.00
#> TCGA.D7.6815.01 2 0.000 1.000 0.00 1 0.00
#> TCGA.BR.8295.01 1 0.000 0.980 1.00 0 0.00
#> TCGA.BR.7197.01 2 0.000 1.000 0.00 1 0.00
#> TCGA.KB.A93J.01 2 0.000 1.000 0.00 1 0.00
#> TCGA.R5.A7ZR.01 2 0.000 1.000 0.00 1 0.00
#> TCGA.R5.A7ZE.01 2 0.000 1.000 0.00 1 0.00
#> TCGA.CG.5725.01 1 0.000 0.980 1.00 0 0.00
#> TCGA.D7.6820.01 3 0.000 1.000 0.00 0 1.00
#> TCGA.D7.A6F0.01 1 0.000 0.980 1.00 0 0.00
#> TCGA.CD.A486.01 1 0.000 0.980 1.00 0 0.00
#> TCGA.IN.A6RI.01 1 0.000 0.980 1.00 0 0.00
#> TCGA.HU.A4GF.01 2 0.000 1.000 0.00 1 0.00
#> TCGA.BR.8373.01 2 0.000 1.000 0.00 1 0.00
#> TCGA.VQ.A8DV.01 3 0.000 1.000 0.00 0 1.00
#> TCGA.HU.8245.01 3 0.000 1.000 0.00 0 1.00
#> TCGA.VQ.A8DU.01 3 0.000 1.000 0.00 0 1.00
#> TCGA.VQ.A8DZ.01 3 0.000 1.000 0.00 0 1.00
#> TCGA.HU.A4GH.01 1 0.480 0.731 0.78 0 0.22
#> TCGA.KB.A6F7.01 1 0.000 0.980 1.00 0 0.00
#> TCGA.BR.8060.01 1 0.000 0.980 1.00 0 0.00
#> TCGA.BR.8077.01 2 0.000 1.000 0.00 1 0.00
#> TCGA.EQ.8122.01 2 0.000 1.000 0.00 1 0.00
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> TCGA.VQ.A8PE.01 4 0.471 0.702 0.00 0.00 0.36 0.64
#> TCGA.BR.8485.01 3 0.000 0.875 0.00 0.00 1.00 0.00
#> TCGA.BR.8486.01 4 0.485 0.676 0.00 0.00 0.40 0.60
#> TCGA.VQ.A8PJ.01 2 0.441 0.804 0.00 0.70 0.00 0.30
#> TCGA.VQ.A8PH.01 4 0.485 0.676 0.00 0.00 0.40 0.60
#> TCGA.D7.6520.01 1 0.000 0.976 1.00 0.00 0.00 0.00
#> TCGA.D7.6527.01 3 0.000 0.875 0.00 0.00 1.00 0.00
#> TCGA.BR.8678.01 2 0.452 0.795 0.00 0.68 0.00 0.32
#> TCGA.VQ.A91Z.01 2 0.164 0.772 0.00 0.94 0.00 0.06
#> TCGA.VQ.A91N.01 2 0.471 0.762 0.00 0.64 0.00 0.36
#> TCGA.VQ.A91U.01 2 0.164 0.772 0.00 0.94 0.00 0.06
#> TCGA.BR.6565.01 3 0.428 0.594 0.28 0.00 0.72 0.00
#> TCGA.VQ.A94O.01 1 0.000 0.976 1.00 0.00 0.00 0.00
#> TCGA.D7.6526.01 3 0.000 0.875 0.00 0.00 1.00 0.00
#> TCGA.3M.AB46.01 2 0.000 0.797 0.00 1.00 0.00 0.00
#> TCGA.FP.8631.01 3 0.485 0.317 0.40 0.00 0.60 0.00
#> TCGA.VQ.A922.01 1 0.000 0.976 1.00 0.00 0.00 0.00
#> TCGA.HU.A4HD.01 1 0.000 0.976 1.00 0.00 0.00 0.00
#> TCGA.F1.6875.01 2 0.164 0.772 0.00 0.94 0.00 0.06
#> TCGA.MX.A666.01 1 0.000 0.976 1.00 0.00 0.00 0.00
#> TCGA.B7.A5TN.01 2 0.000 0.797 0.00 1.00 0.00 0.00
#> TCGA.BR.7704.01 4 0.485 0.676 0.00 0.00 0.40 0.60
#> TCGA.BR.A4J1.01 1 0.000 0.976 1.00 0.00 0.00 0.00
#> TCGA.CD.A4MH.01 3 0.000 0.875 0.00 0.00 1.00 0.00
#> TCGA.HF.7131.01 4 0.485 0.676 0.00 0.00 0.40 0.60
#> TCGA.D7.A6F2.01 2 0.452 0.795 0.00 0.68 0.00 0.32
#> TCGA.RD.A7BT.01 2 0.000 0.797 0.00 1.00 0.00 0.00
#> TCGA.BR.A4PD.01 2 0.471 0.762 0.00 0.64 0.00 0.36
#> TCGA.VQ.A8PK.01 1 0.452 0.475 0.68 0.00 0.32 0.00
#> TCGA.IN.A6RN.01 1 0.000 0.976 1.00 0.00 0.00 0.00
#> TCGA.VQ.AA6D.01 3 0.000 0.875 0.00 0.00 1.00 0.00
#> TCGA.VQ.AA6A.01 4 0.471 0.702 0.00 0.00 0.36 0.64
#> TCGA.IN.7806.01 2 0.413 0.808 0.00 0.74 0.00 0.26
#> TCGA.HU.A4H5.01 4 0.471 0.702 0.00 0.00 0.36 0.64
#> TCGA.CG.5718.01 3 0.000 0.875 0.00 0.00 1.00 0.00
#> TCGA.D7.6817.01 3 0.000 0.875 0.00 0.00 1.00 0.00
#> TCGA.BR.7901.01 1 0.000 0.976 1.00 0.00 0.00 0.00
#> TCGA.D7.6815.01 2 0.164 0.772 0.00 0.94 0.00 0.06
#> TCGA.BR.8295.01 1 0.000 0.976 1.00 0.00 0.00 0.00
#> TCGA.BR.7197.01 4 0.164 0.497 0.00 0.06 0.00 0.94
#> TCGA.KB.A93J.01 4 0.164 0.497 0.00 0.06 0.00 0.94
#> TCGA.R5.A7ZR.01 2 0.441 0.804 0.00 0.70 0.00 0.30
#> TCGA.R5.A7ZE.01 4 0.499 -0.560 0.00 0.48 0.00 0.52
#> TCGA.CG.5725.01 1 0.000 0.976 1.00 0.00 0.00 0.00
#> TCGA.D7.6820.01 4 0.471 0.702 0.00 0.00 0.36 0.64
#> TCGA.D7.A6F0.01 1 0.000 0.976 1.00 0.00 0.00 0.00
#> TCGA.CD.A486.01 1 0.000 0.976 1.00 0.00 0.00 0.00
#> TCGA.IN.A6RI.01 1 0.000 0.976 1.00 0.00 0.00 0.00
#> TCGA.HU.A4GF.01 4 0.164 0.497 0.00 0.06 0.00 0.94
#> TCGA.BR.8373.01 2 0.000 0.797 0.00 1.00 0.00 0.00
#> TCGA.VQ.A8DV.01 3 0.000 0.875 0.00 0.00 1.00 0.00
#> TCGA.HU.8245.01 3 0.000 0.875 0.00 0.00 1.00 0.00
#> TCGA.VQ.A8DU.01 3 0.000 0.875 0.00 0.00 1.00 0.00
#> TCGA.VQ.A8DZ.01 3 0.000 0.875 0.00 0.00 1.00 0.00
#> TCGA.HU.A4GH.01 3 0.413 0.615 0.26 0.00 0.74 0.00
#> TCGA.KB.A6F7.01 1 0.000 0.976 1.00 0.00 0.00 0.00
#> TCGA.BR.8060.01 1 0.000 0.976 1.00 0.00 0.00 0.00
#> TCGA.BR.8077.01 2 0.452 0.795 0.00 0.68 0.00 0.32
#> TCGA.EQ.8122.01 2 0.441 0.804 0.00 0.70 0.00 0.30
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> TCGA.VQ.A8PE.01 4 0.2873 0.9601 0.00 0.00 0.12 0.86 0.02
#> TCGA.BR.8485.01 3 0.0000 0.8195 0.00 0.00 1.00 0.00 0.00
#> TCGA.BR.8486.01 4 0.2020 0.9562 0.00 0.00 0.10 0.90 0.00
#> TCGA.VQ.A8PJ.01 2 0.1648 0.6651 0.00 0.94 0.00 0.04 0.02
#> TCGA.VQ.A8PH.01 4 0.2873 0.9601 0.00 0.00 0.12 0.86 0.02
#> TCGA.D7.6520.01 1 0.3274 0.7556 0.78 0.00 0.00 0.00 0.22
#> TCGA.D7.6527.01 3 0.2020 0.8229 0.00 0.00 0.90 0.00 0.10
#> TCGA.BR.8678.01 2 0.0000 0.7001 0.00 1.00 0.00 0.00 0.00
#> TCGA.VQ.A91Z.01 5 0.4726 0.9270 0.00 0.40 0.00 0.02 0.58
#> TCGA.VQ.A91N.01 2 0.1043 0.7054 0.00 0.96 0.00 0.04 0.00
#> TCGA.VQ.A91U.01 5 0.4182 0.9299 0.00 0.40 0.00 0.00 0.60
#> TCGA.BR.6565.01 3 0.4263 0.7838 0.06 0.00 0.76 0.00 0.18
#> TCGA.VQ.A94O.01 1 0.0000 0.9853 1.00 0.00 0.00 0.00 0.00
#> TCGA.D7.6526.01 3 0.1043 0.8250 0.00 0.00 0.96 0.00 0.04
#> TCGA.3M.AB46.01 5 0.4287 0.9284 0.00 0.46 0.00 0.00 0.54
#> TCGA.FP.8631.01 3 0.4876 0.7475 0.08 0.00 0.70 0.00 0.22
#> TCGA.VQ.A922.01 1 0.0000 0.9853 1.00 0.00 0.00 0.00 0.00
#> TCGA.HU.A4HD.01 1 0.0000 0.9853 1.00 0.00 0.00 0.00 0.00
#> TCGA.F1.6875.01 5 0.4726 0.9270 0.00 0.40 0.00 0.02 0.58
#> TCGA.MX.A666.01 1 0.0000 0.9853 1.00 0.00 0.00 0.00 0.00
#> TCGA.B7.A5TN.01 5 0.4287 0.9284 0.00 0.46 0.00 0.00 0.54
#> TCGA.BR.7704.01 4 0.2873 0.9601 0.00 0.00 0.12 0.86 0.02
#> TCGA.BR.A4J1.01 1 0.0000 0.9853 1.00 0.00 0.00 0.00 0.00
#> TCGA.CD.A4MH.01 3 0.0000 0.8195 0.00 0.00 1.00 0.00 0.00
#> TCGA.HF.7131.01 4 0.2873 0.9601 0.00 0.00 0.12 0.86 0.02
#> TCGA.D7.A6F2.01 2 0.0000 0.7001 0.00 1.00 0.00 0.00 0.00
#> TCGA.RD.A7BT.01 5 0.4287 0.9284 0.00 0.46 0.00 0.00 0.54
#> TCGA.BR.A4PD.01 2 0.1410 0.7013 0.00 0.94 0.00 0.06 0.00
#> TCGA.VQ.A8PK.01 3 0.6638 0.3891 0.32 0.00 0.44 0.00 0.24
#> TCGA.IN.A6RN.01 1 0.0000 0.9853 1.00 0.00 0.00 0.00 0.00
#> TCGA.VQ.AA6D.01 3 0.1410 0.8059 0.00 0.00 0.94 0.00 0.06
#> TCGA.VQ.AA6A.01 4 0.1732 0.9485 0.00 0.00 0.08 0.92 0.00
#> TCGA.IN.7806.01 2 0.2280 0.4892 0.00 0.88 0.00 0.00 0.12
#> TCGA.HU.A4H5.01 4 0.3110 0.8956 0.00 0.00 0.06 0.86 0.08
#> TCGA.CG.5718.01 3 0.0609 0.8136 0.00 0.00 0.98 0.00 0.02
#> TCGA.D7.6817.01 3 0.4767 -0.0508 0.00 0.00 0.56 0.42 0.02
#> TCGA.BR.7901.01 1 0.0000 0.9853 1.00 0.00 0.00 0.00 0.00
#> TCGA.D7.6815.01 5 0.4726 0.9270 0.00 0.40 0.00 0.02 0.58
#> TCGA.BR.8295.01 1 0.0000 0.9853 1.00 0.00 0.00 0.00 0.00
#> TCGA.BR.7197.01 2 0.4262 0.3082 0.00 0.56 0.00 0.44 0.00
#> TCGA.KB.A93J.01 2 0.4302 0.2053 0.00 0.52 0.00 0.48 0.00
#> TCGA.R5.A7ZR.01 2 0.1648 0.6651 0.00 0.94 0.00 0.04 0.02
#> TCGA.R5.A7ZE.01 2 0.2516 0.6577 0.00 0.86 0.00 0.14 0.00
#> TCGA.CG.5725.01 1 0.0000 0.9853 1.00 0.00 0.00 0.00 0.00
#> TCGA.D7.6820.01 4 0.1732 0.9485 0.00 0.00 0.08 0.92 0.00
#> TCGA.D7.A6F0.01 1 0.0000 0.9853 1.00 0.00 0.00 0.00 0.00
#> TCGA.CD.A486.01 1 0.0000 0.9853 1.00 0.00 0.00 0.00 0.00
#> TCGA.IN.A6RI.01 1 0.0000 0.9853 1.00 0.00 0.00 0.00 0.00
#> TCGA.HU.A4GF.01 2 0.4182 0.3915 0.00 0.60 0.00 0.40 0.00
#> TCGA.BR.8373.01 5 0.4302 0.9016 0.00 0.48 0.00 0.00 0.52
#> TCGA.VQ.A8DV.01 3 0.1410 0.8059 0.00 0.00 0.94 0.00 0.06
#> TCGA.HU.8245.01 3 0.2929 0.8052 0.00 0.00 0.82 0.00 0.18
#> TCGA.VQ.A8DU.01 3 0.2020 0.7877 0.00 0.00 0.90 0.00 0.10
#> TCGA.VQ.A8DZ.01 3 0.2732 0.8115 0.00 0.00 0.84 0.00 0.16
#> TCGA.HU.A4GH.01 3 0.4263 0.7838 0.06 0.00 0.76 0.00 0.18
#> TCGA.KB.A6F7.01 1 0.0000 0.9853 1.00 0.00 0.00 0.00 0.00
#> TCGA.BR.8060.01 1 0.0000 0.9853 1.00 0.00 0.00 0.00 0.00
#> TCGA.BR.8077.01 2 0.0000 0.7001 0.00 1.00 0.00 0.00 0.00
#> TCGA.EQ.8122.01 2 0.0609 0.6867 0.00 0.98 0.00 0.00 0.02
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> TCGA.VQ.A8PE.01 4 0.1480 0.874 0.02 0.00 0.04 0.94 0.00 0.00
#> TCGA.BR.8485.01 3 0.2454 0.818 0.16 0.00 0.84 0.00 0.00 0.00
#> TCGA.BR.8486.01 4 0.2190 0.873 0.06 0.00 0.04 0.90 0.00 0.00
#> TCGA.VQ.A8PJ.01 2 0.4094 0.504 0.18 0.74 0.00 0.00 0.08 0.00
#> TCGA.VQ.A8PH.01 4 0.1480 0.874 0.02 0.00 0.04 0.94 0.00 0.00
#> TCGA.D7.6520.01 6 0.5256 0.644 0.08 0.00 0.06 0.00 0.18 0.68
#> TCGA.D7.6527.01 3 0.0547 0.823 0.00 0.00 0.98 0.00 0.02 0.00
#> TCGA.BR.8678.01 2 0.2474 0.655 0.08 0.88 0.00 0.04 0.00 0.00
#> TCGA.VQ.A91Z.01 5 0.4711 0.814 0.08 0.28 0.00 0.00 0.64 0.00
#> TCGA.VQ.A91N.01 2 0.0547 0.700 0.02 0.98 0.00 0.00 0.00 0.00
#> TCGA.VQ.A91U.01 5 0.3409 0.836 0.00 0.30 0.00 0.00 0.70 0.00
#> TCGA.BR.6565.01 3 0.1480 0.811 0.00 0.00 0.94 0.00 0.02 0.04
#> TCGA.VQ.A94O.01 6 0.0000 0.979 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.D7.6526.01 3 0.2260 0.819 0.14 0.00 0.86 0.00 0.00 0.00
#> TCGA.3M.AB46.01 5 0.3797 0.831 0.00 0.42 0.00 0.00 0.58 0.00
#> TCGA.FP.8631.01 3 0.5106 0.661 0.08 0.00 0.68 0.00 0.20 0.04
#> TCGA.VQ.A922.01 6 0.0000 0.979 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.HU.A4HD.01 6 0.0000 0.979 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.F1.6875.01 5 0.4711 0.814 0.08 0.28 0.00 0.00 0.64 0.00
#> TCGA.MX.A666.01 6 0.0000 0.979 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.B7.A5TN.01 5 0.3797 0.831 0.00 0.42 0.00 0.00 0.58 0.00
#> TCGA.BR.7704.01 4 0.0937 0.878 0.00 0.00 0.04 0.96 0.00 0.00
#> TCGA.BR.A4J1.01 6 0.0000 0.979 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.CD.A4MH.01 3 0.2454 0.818 0.16 0.00 0.84 0.00 0.00 0.00
#> TCGA.HF.7131.01 4 0.0937 0.878 0.00 0.00 0.04 0.96 0.00 0.00
#> TCGA.D7.A6F2.01 2 0.0000 0.697 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.RD.A7BT.01 5 0.3797 0.831 0.00 0.42 0.00 0.00 0.58 0.00
#> TCGA.BR.A4PD.01 2 0.0547 0.700 0.02 0.98 0.00 0.00 0.00 0.00
#> TCGA.VQ.A8PK.01 3 0.6873 0.386 0.08 0.00 0.46 0.00 0.20 0.26
#> TCGA.IN.A6RN.01 6 0.0000 0.979 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.VQ.AA6D.01 3 0.3198 0.785 0.26 0.00 0.74 0.00 0.00 0.00
#> TCGA.VQ.AA6A.01 4 0.2728 0.862 0.10 0.00 0.04 0.86 0.00 0.00
#> TCGA.IN.7806.01 2 0.3076 0.294 0.00 0.76 0.00 0.00 0.24 0.00
#> TCGA.HU.A4H5.01 4 0.5107 0.725 0.30 0.00 0.04 0.62 0.04 0.00
#> TCGA.CG.5718.01 3 0.2790 0.754 0.02 0.00 0.84 0.14 0.00 0.00
#> TCGA.D7.6817.01 4 0.4609 0.203 0.04 0.00 0.42 0.54 0.00 0.00
#> TCGA.BR.7901.01 6 0.0000 0.979 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.D7.6815.01 5 0.4711 0.814 0.08 0.28 0.00 0.00 0.64 0.00
#> TCGA.BR.8295.01 6 0.0000 0.979 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.BR.7197.01 2 0.5291 0.397 0.08 0.60 0.00 0.30 0.02 0.00
#> TCGA.KB.A93J.01 2 0.5626 0.279 0.10 0.54 0.00 0.34 0.02 0.00
#> TCGA.R5.A7ZR.01 2 0.3928 0.524 0.16 0.76 0.00 0.00 0.08 0.00
#> TCGA.R5.A7ZE.01 2 0.1480 0.693 0.02 0.94 0.00 0.04 0.00 0.00
#> TCGA.CG.5725.01 6 0.0000 0.979 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.D7.6820.01 4 0.2728 0.862 0.10 0.00 0.04 0.86 0.00 0.00
#> TCGA.D7.A6F0.01 6 0.0000 0.979 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.CD.A486.01 6 0.0000 0.979 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.IN.A6RI.01 6 0.0000 0.979 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.HU.A4GF.01 2 0.4887 0.525 0.08 0.68 0.00 0.22 0.02 0.00
#> TCGA.BR.8373.01 5 0.3797 0.831 0.00 0.42 0.00 0.00 0.58 0.00
#> TCGA.VQ.A8DV.01 3 0.3309 0.776 0.28 0.00 0.72 0.00 0.00 0.00
#> TCGA.HU.8245.01 3 0.0547 0.820 0.00 0.00 0.98 0.00 0.02 0.00
#> TCGA.VQ.A8DU.01 3 0.4983 0.740 0.22 0.00 0.68 0.06 0.04 0.00
#> TCGA.VQ.A8DZ.01 3 0.0547 0.823 0.00 0.00 0.98 0.00 0.02 0.00
#> TCGA.HU.A4GH.01 3 0.1480 0.811 0.00 0.00 0.94 0.00 0.02 0.04
#> TCGA.KB.A6F7.01 6 0.0000 0.979 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.BR.8060.01 6 0.0000 0.979 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.BR.8077.01 2 0.0000 0.697 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.EQ.8122.01 2 0.1556 0.639 0.00 0.92 0.00 0.00 0.08 0.00
cbind(get_classes(res, k = 7), get_membership(res, k = 7))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7
#> TCGA.VQ.A8PE.01 4 0.1166 0.6922 0.06 0.00 0.00 0.94 0.00 0.00 0.00
#> TCGA.BR.8485.01 3 0.1006 0.5458 0.02 0.00 0.96 0.02 0.00 0.00 0.00
#> TCGA.BR.8486.01 4 0.3417 0.7197 0.26 0.00 0.00 0.72 0.02 0.00 0.00
#> TCGA.VQ.A8PJ.01 2 0.5652 0.4624 0.12 0.60 0.00 0.00 0.10 0.00 0.18
#> TCGA.VQ.A8PH.01 4 0.0504 0.7189 0.02 0.00 0.00 0.98 0.00 0.00 0.00
#> TCGA.D7.6520.01 7 0.3867 0.4193 0.00 0.00 0.02 0.00 0.00 0.38 0.60
#> TCGA.D7.6527.01 3 0.3661 0.6156 0.00 0.00 0.74 0.02 0.02 0.00 0.22
#> TCGA.BR.8678.01 2 0.2722 0.6861 0.04 0.84 0.00 0.00 0.00 0.00 0.12
#> TCGA.VQ.A91Z.01 5 0.3927 0.7552 0.02 0.14 0.00 0.00 0.76 0.00 0.08
#> TCGA.VQ.A91N.01 2 0.0000 0.7498 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.VQ.A91U.01 5 0.2081 0.7667 0.00 0.14 0.00 0.00 0.86 0.00 0.00
#> TCGA.BR.6565.01 3 0.3047 0.5690 0.00 0.00 0.72 0.00 0.00 0.00 0.28
#> TCGA.VQ.A94O.01 6 0.0000 0.9946 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.D7.6526.01 3 0.0000 0.5726 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.3M.AB46.01 5 0.3358 0.7354 0.00 0.36 0.00 0.00 0.64 0.00 0.00
#> TCGA.FP.8631.01 7 0.3358 0.1103 0.00 0.00 0.36 0.00 0.00 0.00 0.64
#> TCGA.VQ.A922.01 6 0.0000 0.9946 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.HU.A4HD.01 6 0.0504 0.9766 0.00 0.00 0.00 0.00 0.02 0.98 0.00
#> TCGA.F1.6875.01 5 0.3927 0.7552 0.02 0.14 0.00 0.00 0.76 0.00 0.08
#> TCGA.MX.A666.01 6 0.0000 0.9946 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.B7.A5TN.01 5 0.3358 0.7354 0.00 0.36 0.00 0.00 0.64 0.00 0.00
#> TCGA.BR.7704.01 4 0.1006 0.7197 0.02 0.00 0.00 0.96 0.02 0.00 0.00
#> TCGA.BR.A4J1.01 6 0.0000 0.9946 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.CD.A4MH.01 3 0.1006 0.5458 0.02 0.00 0.96 0.02 0.00 0.00 0.00
#> TCGA.HF.7131.01 4 0.0000 0.7265 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.D7.A6F2.01 2 0.0504 0.7476 0.00 0.98 0.00 0.00 0.02 0.00 0.00
#> TCGA.RD.A7BT.01 5 0.3358 0.7354 0.00 0.36 0.00 0.00 0.64 0.00 0.00
#> TCGA.BR.A4PD.01 2 0.0000 0.7498 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.VQ.A8PK.01 7 0.5278 0.5288 0.00 0.00 0.18 0.00 0.04 0.16 0.62
#> TCGA.IN.A6RN.01 6 0.0000 0.9946 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.VQ.AA6D.01 3 0.3887 -0.0149 0.26 0.00 0.70 0.02 0.02 0.00 0.00
#> TCGA.VQ.AA6A.01 4 0.3517 0.7103 0.28 0.00 0.00 0.70 0.02 0.00 0.00
#> TCGA.IN.7806.01 2 0.3221 0.2618 0.00 0.68 0.00 0.00 0.32 0.00 0.00
#> TCGA.HU.A4H5.01 4 0.4386 0.5744 0.42 0.00 0.00 0.54 0.02 0.00 0.02
#> TCGA.CG.5718.01 3 0.4447 0.1404 0.02 0.00 0.66 0.28 0.02 0.00 0.02
#> TCGA.D7.6817.01 4 0.4249 0.2334 0.02 0.00 0.24 0.70 0.02 0.00 0.02
#> TCGA.BR.7901.01 6 0.0000 0.9946 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.D7.6815.01 5 0.3927 0.7552 0.02 0.14 0.00 0.00 0.76 0.00 0.08
#> TCGA.BR.8295.01 6 0.0000 0.9946 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.BR.7197.01 2 0.4242 0.5744 0.08 0.72 0.00 0.18 0.02 0.00 0.00
#> TCGA.KB.A93J.01 2 0.4248 0.4736 0.08 0.66 0.00 0.26 0.00 0.00 0.00
#> TCGA.R5.A7ZR.01 2 0.5022 0.5459 0.10 0.68 0.00 0.00 0.10 0.00 0.12
#> TCGA.R5.A7ZE.01 2 0.0863 0.7445 0.00 0.96 0.00 0.04 0.00 0.00 0.00
#> TCGA.CG.5725.01 6 0.0000 0.9946 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.D7.6820.01 4 0.2945 0.7214 0.26 0.00 0.00 0.74 0.00 0.00 0.00
#> TCGA.D7.A6F0.01 6 0.0000 0.9946 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.CD.A486.01 6 0.0000 0.9946 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.IN.A6RI.01 6 0.0000 0.9946 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.HU.A4GF.01 2 0.3494 0.6591 0.06 0.80 0.00 0.12 0.02 0.00 0.00
#> TCGA.BR.8373.01 5 0.3358 0.7354 0.00 0.36 0.00 0.00 0.64 0.00 0.00
#> TCGA.VQ.A8DV.01 3 0.3815 -0.2955 0.36 0.00 0.62 0.02 0.00 0.00 0.00
#> TCGA.HU.8245.01 3 0.3417 0.5792 0.00 0.00 0.72 0.00 0.02 0.00 0.26
#> TCGA.VQ.A8DU.01 1 0.5976 0.0000 0.38 0.00 0.34 0.26 0.00 0.00 0.02
#> TCGA.VQ.A8DZ.01 3 0.3307 0.5955 0.00 0.00 0.74 0.00 0.02 0.00 0.24
#> TCGA.HU.A4GH.01 3 0.3047 0.5690 0.00 0.00 0.72 0.00 0.00 0.00 0.28
#> TCGA.KB.A6F7.01 6 0.0000 0.9946 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.BR.8060.01 6 0.0863 0.9507 0.00 0.00 0.00 0.00 0.00 0.96 0.04
#> TCGA.BR.8077.01 2 0.0504 0.7476 0.00 0.98 0.00 0.00 0.02 0.00 0.00
#> TCGA.EQ.8122.01 2 0.1671 0.6975 0.00 0.90 0.00 0.00 0.10 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.VQ.A8PE.01 4 0.1557 0.7790 0.06 0.00 0.00 0.92 0.00 0.00 0.00 0.02
#> TCGA.BR.8485.01 3 0.3318 -0.0966 0.46 0.00 0.54 0.00 0.00 0.00 0.00 0.00
#> TCGA.BR.8486.01 4 0.2132 0.7868 0.00 0.00 0.00 0.88 0.00 0.00 0.08 0.04
#> TCGA.VQ.A8PJ.01 2 0.3570 0.5631 0.00 0.62 0.00 0.00 0.00 0.00 0.02 0.36
#> TCGA.VQ.A8PH.01 4 0.1091 0.7858 0.06 0.00 0.00 0.94 0.00 0.00 0.00 0.00
#> TCGA.D7.6520.01 7 0.5073 0.4519 0.00 0.00 0.22 0.00 0.00 0.32 0.46 0.00
#> TCGA.D7.6527.01 3 0.0000 0.6051 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BR.8678.01 2 0.4979 0.6190 0.12 0.64 0.00 0.00 0.00 0.00 0.08 0.16
#> TCGA.VQ.A91Z.01 5 0.0808 0.6789 0.00 0.04 0.00 0.00 0.96 0.00 0.00 0.00
#> TCGA.VQ.A91N.01 2 0.0000 0.7596 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.VQ.A91U.01 5 0.3299 0.7405 0.00 0.06 0.00 0.00 0.76 0.00 0.00 0.18
#> TCGA.BR.6565.01 3 0.1765 0.5292 0.00 0.00 0.88 0.00 0.00 0.00 0.12 0.00
#> TCGA.VQ.A94O.01 6 0.0000 0.9902 0.00 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.D7.6526.01 3 0.2938 0.2787 0.30 0.00 0.70 0.00 0.00 0.00 0.00 0.00
#> TCGA.3M.AB46.01 5 0.4757 0.7219 0.00 0.24 0.00 0.00 0.56 0.00 0.00 0.20
#> TCGA.FP.8631.01 3 0.3318 -0.3874 0.00 0.00 0.54 0.00 0.00 0.00 0.46 0.00
#> TCGA.VQ.A922.01 6 0.0000 0.9902 0.00 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.HU.A4HD.01 6 0.0000 0.9902 0.00 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.F1.6875.01 5 0.1275 0.6695 0.00 0.04 0.00 0.00 0.94 0.00 0.02 0.00
#> TCGA.MX.A666.01 6 0.0000 0.9902 0.00 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.B7.A5TN.01 5 0.4757 0.7219 0.00 0.24 0.00 0.00 0.56 0.00 0.00 0.20
#> TCGA.BR.7704.01 4 0.0941 0.7920 0.02 0.00 0.00 0.96 0.00 0.00 0.00 0.02
#> TCGA.BR.A4J1.01 6 0.0000 0.9902 0.00 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.CD.A4MH.01 3 0.3318 -0.0966 0.46 0.00 0.54 0.00 0.00 0.00 0.00 0.00
#> TCGA.HF.7131.01 4 0.0000 0.7970 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.D7.A6F2.01 2 0.1341 0.7505 0.00 0.92 0.00 0.00 0.00 0.00 0.00 0.08
#> TCGA.RD.A7BT.01 5 0.4757 0.7219 0.00 0.24 0.00 0.00 0.56 0.00 0.00 0.20
#> TCGA.BR.A4PD.01 2 0.0471 0.7597 0.00 0.98 0.00 0.00 0.00 0.00 0.02 0.00
#> TCGA.VQ.A8PK.01 7 0.4407 0.1586 0.02 0.00 0.46 0.00 0.00 0.04 0.48 0.00
#> TCGA.IN.A6RN.01 6 0.0000 0.9902 0.00 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.VQ.AA6D.01 1 0.4530 0.5527 0.66 0.00 0.24 0.00 0.02 0.00 0.02 0.06
#> TCGA.VQ.AA6A.01 4 0.4211 0.7227 0.02 0.00 0.00 0.70 0.00 0.00 0.12 0.16
#> TCGA.IN.7806.01 2 0.4033 0.5103 0.00 0.68 0.00 0.00 0.12 0.00 0.00 0.20
#> TCGA.HU.A4H5.01 4 0.5718 0.4754 0.04 0.00 0.00 0.44 0.00 0.00 0.24 0.28
#> TCGA.CG.5718.01 3 0.4028 0.1986 0.04 0.00 0.66 0.28 0.00 0.00 0.00 0.02
#> TCGA.D7.6817.01 4 0.3551 0.5526 0.06 0.00 0.22 0.72 0.00 0.00 0.00 0.00
#> TCGA.BR.7901.01 6 0.0000 0.9902 0.00 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.D7.6815.01 5 0.1275 0.6695 0.00 0.04 0.00 0.00 0.94 0.00 0.02 0.00
#> TCGA.BR.8295.01 6 0.0000 0.9902 0.00 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.BR.7197.01 2 0.4211 0.6071 0.00 0.70 0.00 0.16 0.00 0.00 0.02 0.12
#> TCGA.KB.A93J.01 2 0.3991 0.5429 0.00 0.70 0.00 0.22 0.00 0.00 0.02 0.06
#> TCGA.R5.A7ZR.01 2 0.3514 0.5792 0.00 0.64 0.00 0.00 0.00 0.00 0.02 0.34
#> TCGA.R5.A7ZE.01 2 0.0471 0.7600 0.00 0.98 0.00 0.02 0.00 0.00 0.00 0.00
#> TCGA.CG.5725.01 6 0.0000 0.9902 0.00 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.D7.6820.01 4 0.3879 0.7313 0.02 0.00 0.00 0.74 0.00 0.00 0.10 0.14
#> TCGA.D7.A6F0.01 6 0.0000 0.9902 0.00 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.CD.A486.01 6 0.0000 0.9902 0.00 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.IN.A6RI.01 6 0.0000 0.9902 0.00 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.HU.A4GF.01 2 0.3270 0.7065 0.00 0.80 0.00 0.06 0.00 0.00 0.02 0.12
#> TCGA.BR.8373.01 5 0.4757 0.7219 0.00 0.24 0.00 0.00 0.56 0.00 0.00 0.20
#> TCGA.VQ.A8DV.01 1 0.2852 0.5690 0.72 0.00 0.28 0.00 0.00 0.00 0.00 0.00
#> TCGA.HU.8245.01 3 0.0000 0.6051 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.VQ.A8DU.01 1 0.7216 0.4351 0.44 0.00 0.20 0.10 0.02 0.00 0.12 0.12
#> TCGA.VQ.A8DZ.01 3 0.0000 0.6051 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HU.A4GH.01 3 0.1765 0.5292 0.00 0.00 0.88 0.00 0.00 0.00 0.12 0.00
#> TCGA.KB.A6F7.01 6 0.0000 0.9902 0.00 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.BR.8060.01 6 0.1563 0.8564 0.00 0.00 0.00 0.00 0.00 0.90 0.10 0.00
#> TCGA.BR.8077.01 2 0.1563 0.7534 0.00 0.90 0.00 0.00 0.00 0.00 0.00 0.10
#> TCGA.EQ.8122.01 2 0.2856 0.6497 0.00 0.78 0.00 0.00 0.02 0.00 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: Node012. Child nodes: Node01111-leaf , Node01112-leaf , Node01113-leaf , Node01114-leaf , Node01115-leaf , Node01116-leaf , Node01121-leaf , Node01122-leaf , Node01123-leaf , Node01131-leaf , Node01132-leaf , Node01133-leaf , Node01134-leaf , Node01211-leaf , Node01212-leaf , Node01221-leaf , Node01222-leaf , Node01231-leaf , Node01232-leaf , Node01233-leaf , Node01311-leaf , Node01312 , Node02221-leaf , Node02222-leaf , Node02223-leaf , Node02224-leaf , Node03111-leaf , Node03112-leaf , Node03113-leaf , Node03411-leaf , Node03412-leaf , Node03413-leaf .
The object with results only for a single top-value method and a single partitioning method can be extracted as:
res = res_rh["0121"]
A summary of res and all the functions that can be applied to it:
res
#> A 'ConsensusPartition' object with k = 2, 3, 4, 5, 6, 7, 8.
#> On a matrix with 30000 rows and 19 columns.
#> Top rows (1000) are extracted by 'ATC' method.
#> Subgroups are detected by 'kmeans' method.
#> Performed in total 350 partitions by row resampling.
#> Best k for subgroups seems to be 2.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_partitions"
#> [7] "compare_signatures" "consensus_heatmap" "dimension_reduction"
#> [10] "functional_enrichment" "get_anno_col" "get_anno"
#> [13] "get_classes" "get_consensus" "get_matrix"
#> [16] "get_membership" "get_param" "get_signatures"
#> [19] "get_stats" "is_best_k" "is_stable_k"
#> [22] "membership_heatmap" "ncol" "nrow"
#> [25] "plot_ecdf" "predict_classes" "rownames"
#> [28] "select_partition_number" "show" "suggest_best_k"
#> [31] "test_to_known_factors" "top_rows_heatmap"
collect_plots() function collects all the plots made from res for all k (number of subgroups)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
The plots are:
k and the heatmap of
predicted classes for each k.k.k.k.All the plots in panels can be made by individual functions and they are plotted later in this section.
select_partition_number() produces several plots showing different
statistics for choosing “optimized” k. There are following statistics:
k;k, the area increased is defined as \(A_k - A_{k-1}\).The detailed explanations of these statistics can be found in the cola vignette.
Generally speaking, higher 1-PAC score, higher mean silhouette score or higher
concordance corresponds to better partition. Rand index and Jaccard index
measure how similar the current partition is compared to partition with k-1.
If they are too similar, we won't accept k is better than k-1.
select_partition_number(res)
The numeric values for all these statistics can be obtained by get_stats().
get_stats(res)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> 2 2 1.000 1.000 1.000 0.5268 0.474 0.474
#> 3 3 0.772 0.914 0.941 0.2543 0.854 0.699
#> 4 4 0.784 0.898 0.868 0.1289 0.883 0.667
#> 5 5 0.778 0.918 0.876 0.0673 0.942 0.750
#> 6 6 0.749 0.654 0.755 0.0388 0.942 0.688
#> 7 7 0.842 0.735 0.864 0.0420 0.965 0.786
#> 8 8 0.819 0.735 0.819 0.0231 0.953 0.692
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.D7.6520.01 1 0 1 1 0
#> TCGA.BR.6565.01 2 0 1 0 1
#> TCGA.VQ.A94O.01 1 0 1 1 0
#> TCGA.FP.8631.01 2 0 1 0 1
#> TCGA.VQ.A922.01 2 0 1 0 1
#> TCGA.HU.A4HD.01 1 0 1 1 0
#> TCGA.MX.A666.01 1 0 1 1 0
#> TCGA.BR.A4J1.01 1 0 1 1 0
#> TCGA.VQ.A8PK.01 2 0 1 0 1
#> TCGA.IN.A6RN.01 2 0 1 0 1
#> TCGA.BR.7901.01 2 0 1 0 1
#> TCGA.BR.8295.01 1 0 1 1 0
#> TCGA.CG.5725.01 2 0 1 0 1
#> TCGA.D7.A6F0.01 1 0 1 1 0
#> TCGA.CD.A486.01 1 0 1 1 0
#> TCGA.IN.A6RI.01 2 0 1 0 1
#> TCGA.HU.A4GH.01 2 0 1 0 1
#> TCGA.KB.A6F7.01 1 0 1 1 0
#> TCGA.BR.8060.01 2 0 1 0 1
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.D7.6520.01 3 0.153 0.973 0.04 0.00 0.96
#> TCGA.BR.6565.01 3 0.000 0.945 0.00 0.00 1.00
#> TCGA.VQ.A94O.01 3 0.153 0.973 0.04 0.00 0.96
#> TCGA.FP.8631.01 2 0.400 0.870 0.00 0.84 0.16
#> TCGA.VQ.A922.01 2 0.400 0.870 0.00 0.84 0.16
#> TCGA.HU.A4HD.01 1 0.000 1.000 1.00 0.00 0.00
#> TCGA.MX.A666.01 1 0.000 1.000 1.00 0.00 0.00
#> TCGA.BR.A4J1.01 1 0.000 1.000 1.00 0.00 0.00
#> TCGA.VQ.A8PK.01 2 0.400 0.870 0.00 0.84 0.16
#> TCGA.IN.A6RN.01 2 0.000 0.864 0.00 1.00 0.00
#> TCGA.BR.7901.01 2 0.400 0.870 0.00 0.84 0.16
#> TCGA.BR.8295.01 1 0.000 1.000 1.00 0.00 0.00
#> TCGA.CG.5725.01 2 0.613 0.542 0.00 0.60 0.40
#> TCGA.D7.A6F0.01 1 0.000 1.000 1.00 0.00 0.00
#> TCGA.CD.A486.01 1 0.000 1.000 1.00 0.00 0.00
#> TCGA.IN.A6RI.01 2 0.000 0.864 0.00 1.00 0.00
#> TCGA.HU.A4GH.01 2 0.000 0.864 0.00 1.00 0.00
#> TCGA.KB.A6F7.01 1 0.000 1.000 1.00 0.00 0.00
#> TCGA.BR.8060.01 2 0.000 0.864 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.D7.6520.01 3 0.000 1.000 0.00 0.00 1.00 0.00
#> TCGA.BR.6565.01 3 0.000 1.000 0.00 0.00 1.00 0.00
#> TCGA.VQ.A94O.01 3 0.000 1.000 0.00 0.00 1.00 0.00
#> TCGA.FP.8631.01 2 0.491 0.871 0.00 0.58 0.00 0.42
#> TCGA.VQ.A922.01 2 0.491 0.871 0.00 0.58 0.00 0.42
#> TCGA.HU.A4HD.01 1 0.000 0.906 1.00 0.00 0.00 0.00
#> TCGA.MX.A666.01 1 0.000 0.906 1.00 0.00 0.00 0.00
#> TCGA.BR.A4J1.01 1 0.452 0.740 0.68 0.32 0.00 0.00
#> TCGA.VQ.A8PK.01 2 0.491 0.871 0.00 0.58 0.00 0.42
#> TCGA.IN.A6RN.01 4 0.000 1.000 0.00 0.00 0.00 1.00
#> TCGA.BR.7901.01 2 0.491 0.871 0.00 0.58 0.00 0.42
#> TCGA.BR.8295.01 1 0.000 0.906 1.00 0.00 0.00 0.00
#> TCGA.CG.5725.01 2 0.610 0.560 0.00 0.68 0.18 0.14
#> TCGA.D7.A6F0.01 1 0.452 0.740 0.68 0.32 0.00 0.00
#> TCGA.CD.A486.01 1 0.000 0.906 1.00 0.00 0.00 0.00
#> TCGA.IN.A6RI.01 4 0.000 1.000 0.00 0.00 0.00 1.00
#> TCGA.HU.A4GH.01 4 0.000 1.000 0.00 0.00 0.00 1.00
#> TCGA.KB.A6F7.01 1 0.000 0.906 1.00 0.00 0.00 0.00
#> TCGA.BR.8060.01 4 0.000 1.000 0.00 0.00 0.00 1.00
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> TCGA.D7.6520.01 3 0.000 1.000 0.00 0.00 1.00 0.00 0.00
#> TCGA.BR.6565.01 3 0.000 1.000 0.00 0.00 1.00 0.00 0.00
#> TCGA.VQ.A94O.01 3 0.000 1.000 0.00 0.00 1.00 0.00 0.00
#> TCGA.FP.8631.01 2 0.252 0.811 0.00 0.86 0.00 0.00 0.14
#> TCGA.VQ.A922.01 2 0.000 0.826 0.00 1.00 0.00 0.00 0.00
#> TCGA.HU.A4HD.01 1 0.000 0.955 1.00 0.00 0.00 0.00 0.00
#> TCGA.MX.A666.01 1 0.000 0.955 1.00 0.00 0.00 0.00 0.00
#> TCGA.BR.A4J1.01 5 0.423 1.000 0.42 0.00 0.00 0.00 0.58
#> TCGA.VQ.A8PK.01 2 0.252 0.811 0.00 0.86 0.00 0.00 0.14
#> TCGA.IN.A6RN.01 4 0.311 1.000 0.00 0.20 0.00 0.80 0.00
#> TCGA.BR.7901.01 2 0.000 0.826 0.00 1.00 0.00 0.00 0.00
#> TCGA.BR.8295.01 1 0.228 0.803 0.88 0.00 0.00 0.12 0.00
#> TCGA.CG.5725.01 2 0.617 0.547 0.00 0.60 0.04 0.08 0.28
#> TCGA.D7.A6F0.01 5 0.423 1.000 0.42 0.00 0.00 0.00 0.58
#> TCGA.CD.A486.01 1 0.000 0.955 1.00 0.00 0.00 0.00 0.00
#> TCGA.IN.A6RI.01 4 0.311 1.000 0.00 0.20 0.00 0.80 0.00
#> TCGA.HU.A4GH.01 4 0.311 1.000 0.00 0.20 0.00 0.80 0.00
#> TCGA.KB.A6F7.01 1 0.000 0.955 1.00 0.00 0.00 0.00 0.00
#> TCGA.BR.8060.01 4 0.311 1.000 0.00 0.20 0.00 0.80 0.00
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> TCGA.D7.6520.01 3 0.0547 0.917 0.02 0.00 0.98 0.00 0.00 0.00
#> TCGA.BR.6565.01 3 0.0000 0.912 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.VQ.A94O.01 3 0.3321 0.855 0.10 0.00 0.82 0.00 0.00 0.08
#> TCGA.FP.8631.01 2 0.2454 0.558 0.16 0.84 0.00 0.00 0.00 0.00
#> TCGA.VQ.A922.01 2 0.4195 0.479 0.00 0.74 0.02 0.04 0.00 0.20
#> TCGA.HU.A4HD.01 1 0.3756 0.939 0.60 0.00 0.00 0.00 0.40 0.00
#> TCGA.MX.A666.01 1 0.3706 0.960 0.62 0.00 0.00 0.00 0.38 0.00
#> TCGA.BR.A4J1.01 5 0.0000 0.568 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.VQ.A8PK.01 2 0.2454 0.558 0.16 0.84 0.00 0.00 0.00 0.00
#> TCGA.IN.A6RN.01 4 0.1814 0.899 0.00 0.10 0.00 0.90 0.00 0.00
#> TCGA.BR.7901.01 2 0.4195 0.479 0.00 0.74 0.02 0.04 0.00 0.20
#> TCGA.BR.8295.01 5 0.6868 -0.619 0.38 0.00 0.00 0.08 0.38 0.16
#> TCGA.CG.5725.01 6 0.3076 0.000 0.00 0.24 0.00 0.00 0.00 0.76
#> TCGA.D7.A6F0.01 5 0.0000 0.568 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.CD.A486.01 1 0.4199 0.951 0.60 0.00 0.00 0.02 0.38 0.00
#> TCGA.IN.A6RI.01 4 0.1814 0.899 0.00 0.10 0.00 0.90 0.00 0.00
#> TCGA.HU.A4GH.01 4 0.1814 0.899 0.00 0.10 0.00 0.90 0.00 0.00
#> TCGA.KB.A6F7.01 1 0.4199 0.948 0.60 0.00 0.00 0.00 0.38 0.02
#> TCGA.BR.8060.01 4 0.5202 0.651 0.14 0.26 0.00 0.60 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.D7.6520.01 3 0.0504 0.839 0.00 0.00 0.98 0.00 0.00 0.00 0.02
#> TCGA.BR.6565.01 3 0.0000 0.839 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.VQ.A94O.01 3 0.4479 0.668 0.00 0.02 0.66 0.00 0.26 0.06 0.00
#> TCGA.FP.8631.01 2 0.4777 0.575 0.00 0.70 0.02 0.02 0.16 0.00 0.10
#> TCGA.VQ.A922.01 2 0.3519 0.525 0.00 0.74 0.00 0.04 0.00 0.22 0.00
#> TCGA.HU.A4HD.01 1 0.0000 0.914 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.MX.A666.01 1 0.0000 0.914 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BR.A4J1.01 7 0.2081 1.000 0.14 0.00 0.00 0.00 0.00 0.00 0.86
#> TCGA.VQ.A8PK.01 2 0.4635 0.586 0.00 0.70 0.00 0.04 0.16 0.00 0.10
#> TCGA.IN.A6RN.01 4 0.0504 0.861 0.00 0.00 0.00 0.98 0.00 0.00 0.02
#> TCGA.BR.7901.01 2 0.3519 0.525 0.00 0.74 0.00 0.04 0.00 0.22 0.00
#> TCGA.BR.8295.01 1 0.3221 0.618 0.68 0.00 0.00 0.00 0.32 0.00 0.00
#> TCGA.CG.5725.01 6 0.1166 0.000 0.00 0.06 0.00 0.00 0.00 0.94 0.00
#> TCGA.D7.A6F0.01 7 0.2081 1.000 0.14 0.00 0.00 0.00 0.00 0.00 0.86
#> TCGA.CD.A486.01 1 0.0504 0.906 0.98 0.02 0.00 0.00 0.00 0.00 0.00
#> TCGA.IN.A6RI.01 4 0.0000 0.866 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.HU.A4GH.01 4 0.0000 0.866 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.KB.A6F7.01 1 0.0000 0.914 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BR.8060.01 4 0.4789 0.539 0.00 0.14 0.00 0.60 0.26 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.D7.6520.01 3 0.0941 0.761 0.00 0.00 0.96 0.00 0.02 0.00 0.02 0.00
#> TCGA.BR.6565.01 3 0.0000 0.761 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.VQ.A94O.01 3 0.5954 0.501 0.00 0.00 0.52 0.00 0.14 0.08 0.02 0.24
#> TCGA.FP.8631.01 2 0.1887 0.888 0.00 0.90 0.00 0.00 0.00 0.04 0.06 0.00
#> TCGA.VQ.A922.01 8 0.3862 1.000 0.00 0.36 0.00 0.04 0.00 0.00 0.00 0.60
#> TCGA.HU.A4HD.01 1 0.2547 0.700 0.84 0.00 0.00 0.00 0.00 0.04 0.00 0.12
#> TCGA.MX.A666.01 1 0.0000 0.888 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BR.A4J1.01 7 0.2224 0.983 0.12 0.00 0.00 0.00 0.00 0.02 0.86 0.00
#> TCGA.VQ.A8PK.01 2 0.0000 0.888 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.IN.A6RN.01 4 0.0471 0.823 0.00 0.00 0.00 0.98 0.00 0.00 0.02 0.00
#> TCGA.BR.7901.01 8 0.3862 1.000 0.00 0.36 0.00 0.04 0.00 0.00 0.00 0.60
#> TCGA.BR.8295.01 5 0.3272 0.000 0.42 0.00 0.00 0.00 0.58 0.00 0.00 0.00
#> TCGA.CG.5725.01 6 0.2888 0.000 0.00 0.04 0.00 0.00 0.00 0.80 0.00 0.16
#> TCGA.D7.A6F0.01 7 0.1765 0.983 0.12 0.00 0.00 0.00 0.00 0.00 0.88 0.00
#> TCGA.CD.A486.01 1 0.0471 0.882 0.98 0.00 0.00 0.00 0.00 0.00 0.00 0.02
#> TCGA.IN.A6RI.01 4 0.0000 0.828 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.HU.A4GH.01 4 0.0000 0.828 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.KB.A6F7.01 1 0.0471 0.879 0.98 0.00 0.00 0.00 0.02 0.00 0.00 0.00
#> TCGA.BR.8060.01 4 0.5329 0.371 0.00 0.00 0.00 0.50 0.26 0.02 0.00 0.22
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
consensus_heatmap(res, k = 7)
consensus_heatmap(res, k = 8)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
membership_heatmap(res, k = 7)
membership_heatmap(res, k = 8)
As soon as the classes for columns are determined, the signatures that are significantly different between subgroups can be looked for. Following are the heatmaps for signatures.
get_signatures(res, k = 2)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
get_signatures(res, k = 7)
get_signatures(res, k = 8)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. To get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows (which is done by automatically selecting number of clusters).If there are too many signatures, top_signatures = ... can be set to only show the
signatures with the highest FDRs:
# code only for demonstration
# e.g. to show the top 500 most significant rows
tb = get_signature(res, k = ..., top_signatures = 500)
If the signatures are defined as these which are uniquely high in current group, diff_method argument
can be set to "uniquely_high_in_one_group":
# code only for demonstration
tb = get_signature(res, k = ..., diff_method = "uniquely_high_in_one_group")
UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
dimension_reduction(res, k = 7, method = "UMAP")
dimension_reduction(res, k = 8, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
If matrix rows can be associated to genes, consider to use functional_enrichment(res,
...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.
Parent node: Node012. Child nodes: Node01111-leaf , Node01112-leaf , Node01113-leaf , Node01114-leaf , Node01115-leaf , Node01116-leaf , Node01121-leaf , Node01122-leaf , Node01123-leaf , Node01131-leaf , Node01132-leaf , Node01133-leaf , Node01134-leaf , Node01211-leaf , Node01212-leaf , Node01221-leaf , Node01222-leaf , Node01231-leaf , Node01232-leaf , Node01233-leaf , Node01311-leaf , Node01312 , Node02221-leaf , Node02222-leaf , Node02223-leaf , Node02224-leaf , Node03111-leaf , Node03112-leaf , Node03113-leaf , Node03411-leaf , Node03412-leaf , Node03413-leaf .
The object with results only for a single top-value method and a single partitioning method can be extracted as:
res = res_rh["0122"]
A summary of res and all the functions that can be applied to it:
res
#> A 'ConsensusPartition' object with k = 2, 3, 4, 5, 6, 7, 8.
#> On a matrix with 30000 rows and 21 columns.
#> Top rows (1000) are extracted by 'ATC' method.
#> Subgroups are detected by 'kmeans' method.
#> Performed in total 350 partitions by row resampling.
#> Best k for subgroups seems to be 2.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_partitions"
#> [7] "compare_signatures" "consensus_heatmap" "dimension_reduction"
#> [10] "functional_enrichment" "get_anno_col" "get_anno"
#> [13] "get_classes" "get_consensus" "get_matrix"
#> [16] "get_membership" "get_param" "get_signatures"
#> [19] "get_stats" "is_best_k" "is_stable_k"
#> [22] "membership_heatmap" "ncol" "nrow"
#> [25] "plot_ecdf" "predict_classes" "rownames"
#> [28] "select_partition_number" "show" "suggest_best_k"
#> [31] "test_to_known_factors" "top_rows_heatmap"
collect_plots() function collects all the plots made from res for all k (number of subgroups)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
The plots are:
k and the heatmap of
predicted classes for each k.k.k.k.All the plots in panels can be made by individual functions and they are plotted later in this section.
select_partition_number() produces several plots showing different
statistics for choosing “optimized” k. There are following statistics:
k;k, the area increased is defined as \(A_k - A_{k-1}\).The detailed explanations of these statistics can be found in the cola vignette.
Generally speaking, higher 1-PAC score, higher mean silhouette score or higher
concordance corresponds to better partition. Rand index and Jaccard index
measure how similar the current partition is compared to partition with k-1.
If they are too similar, we won't accept k is better than k-1.
select_partition_number(res)
The numeric values for all these statistics can be obtained by get_stats().
get_stats(res)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> 2 2 1.000 1.000 1.000 0.2579 0.743 0.743
#> 3 3 0.526 0.795 0.870 1.2144 0.657 0.538
#> 4 4 0.605 0.737 0.835 0.2342 0.833 0.611
#> 5 5 0.616 0.654 0.789 0.0894 0.952 0.836
#> 6 6 0.653 0.669 0.742 0.0551 0.914 0.647
#> 7 7 0.689 0.579 0.710 0.0385 1.000 1.000
#> 8 8 0.726 0.613 0.768 0.0341 0.943 0.636
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.VQ.A8PJ.01 2 0 1 0 1
#> TCGA.BR.8678.01 1 0 1 1 0
#> TCGA.VQ.A91Z.01 1 0 1 1 0
#> TCGA.VQ.A91N.01 2 0 1 0 1
#> TCGA.VQ.A91U.01 2 0 1 0 1
#> TCGA.3M.AB46.01 2 0 1 0 1
#> TCGA.F1.6875.01 1 0 1 1 0
#> TCGA.B7.A5TN.01 2 0 1 0 1
#> TCGA.D7.A6F2.01 2 0 1 0 1
#> TCGA.RD.A7BT.01 2 0 1 0 1
#> TCGA.BR.A4PD.01 2 0 1 0 1
#> TCGA.IN.7806.01 2 0 1 0 1
#> TCGA.D7.6815.01 2 0 1 0 1
#> TCGA.BR.7197.01 2 0 1 0 1
#> TCGA.KB.A93J.01 2 0 1 0 1
#> TCGA.R5.A7ZR.01 2 0 1 0 1
#> TCGA.R5.A7ZE.01 2 0 1 0 1
#> TCGA.HU.A4GF.01 2 0 1 0 1
#> TCGA.BR.8373.01 2 0 1 0 1
#> TCGA.BR.8077.01 2 0 1 0 1
#> TCGA.EQ.8122.01 2 0 1 0 1
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.VQ.A8PJ.01 2 0.5560 0.733 0.00 0.70 0.30
#> TCGA.BR.8678.01 1 0.0892 0.989 0.98 0.00 0.02
#> TCGA.VQ.A91Z.01 1 0.0000 0.994 1.00 0.00 0.00
#> TCGA.VQ.A91N.01 2 0.5016 0.747 0.00 0.76 0.24
#> TCGA.VQ.A91U.01 2 0.0000 0.775 0.00 1.00 0.00
#> TCGA.3M.AB46.01 3 0.5216 0.837 0.00 0.26 0.74
#> TCGA.F1.6875.01 1 0.0000 0.994 1.00 0.00 0.00
#> TCGA.B7.A5TN.01 2 0.4796 0.390 0.00 0.78 0.22
#> TCGA.D7.A6F2.01 2 0.0000 0.775 0.00 1.00 0.00
#> TCGA.RD.A7BT.01 2 0.0000 0.775 0.00 1.00 0.00
#> TCGA.BR.A4PD.01 2 0.5216 0.744 0.00 0.74 0.26
#> TCGA.IN.7806.01 2 0.0892 0.773 0.00 0.98 0.02
#> TCGA.D7.6815.01 3 0.6280 0.799 0.00 0.46 0.54
#> TCGA.BR.7197.01 3 0.5397 0.847 0.00 0.28 0.72
#> TCGA.KB.A93J.01 2 0.5216 0.744 0.00 0.74 0.26
#> TCGA.R5.A7ZR.01 2 0.5560 0.733 0.00 0.70 0.30
#> TCGA.R5.A7ZE.01 3 0.6244 0.821 0.00 0.44 0.56
#> TCGA.HU.A4GF.01 2 0.0000 0.775 0.00 1.00 0.00
#> TCGA.BR.8373.01 3 0.5397 0.847 0.00 0.28 0.72
#> TCGA.BR.8077.01 2 0.0000 0.775 0.00 1.00 0.00
#> TCGA.EQ.8122.01 3 0.6244 0.821 0.00 0.44 0.56
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> TCGA.VQ.A8PJ.01 4 0.2011 1.000 0.00 0.08 0.00 0.92
#> TCGA.BR.8678.01 1 0.2011 0.942 0.92 0.00 0.00 0.08
#> TCGA.VQ.A91Z.01 1 0.0000 0.971 1.00 0.00 0.00 0.00
#> TCGA.VQ.A91N.01 2 0.4855 0.525 0.00 0.60 0.00 0.40
#> TCGA.VQ.A91U.01 2 0.2706 0.765 0.00 0.90 0.02 0.08
#> TCGA.3M.AB46.01 3 0.3198 0.694 0.00 0.04 0.88 0.08
#> TCGA.F1.6875.01 1 0.0000 0.971 1.00 0.00 0.00 0.00
#> TCGA.B7.A5TN.01 3 0.7249 0.476 0.00 0.20 0.54 0.26
#> TCGA.D7.A6F2.01 2 0.2706 0.765 0.00 0.90 0.02 0.08
#> TCGA.RD.A7BT.01 2 0.2706 0.765 0.00 0.90 0.02 0.08
#> TCGA.BR.A4PD.01 2 0.4855 0.525 0.00 0.60 0.00 0.40
#> TCGA.IN.7806.01 2 0.5077 0.693 0.00 0.76 0.08 0.16
#> TCGA.D7.6815.01 3 0.5594 0.614 0.00 0.46 0.52 0.02
#> TCGA.BR.7197.01 3 0.0000 0.685 0.00 0.00 1.00 0.00
#> TCGA.KB.A93J.01 2 0.4855 0.525 0.00 0.60 0.00 0.40
#> TCGA.R5.A7ZR.01 4 0.2011 1.000 0.00 0.08 0.00 0.92
#> TCGA.R5.A7ZE.01 3 0.5062 0.732 0.00 0.30 0.68 0.02
#> TCGA.HU.A4GF.01 2 0.0707 0.711 0.00 0.98 0.02 0.00
#> TCGA.BR.8373.01 3 0.1211 0.685 0.00 0.04 0.96 0.00
#> TCGA.BR.8077.01 2 0.0707 0.711 0.00 0.98 0.02 0.00
#> TCGA.EQ.8122.01 3 0.5062 0.732 0.00 0.30 0.68 0.02
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> TCGA.VQ.A8PJ.01 4 0.400 1.000 0.0 0.24 0.02 0.74 0.00
#> TCGA.BR.8678.01 1 0.351 0.836 0.8 0.00 0.00 0.18 0.02
#> TCGA.VQ.A91Z.01 1 0.000 0.921 1.0 0.00 0.00 0.00 0.00
#> TCGA.VQ.A91N.01 2 0.273 0.430 0.0 0.84 0.00 0.16 0.00
#> TCGA.VQ.A91U.01 2 0.342 0.651 0.0 0.76 0.24 0.00 0.00
#> TCGA.3M.AB46.01 3 0.516 0.484 0.0 0.00 0.62 0.06 0.32
#> TCGA.F1.6875.01 1 0.000 0.921 1.0 0.00 0.00 0.00 0.00
#> TCGA.B7.A5TN.01 3 0.461 0.454 0.0 0.36 0.62 0.02 0.00
#> TCGA.D7.A6F2.01 2 0.342 0.651 0.0 0.76 0.24 0.00 0.00
#> TCGA.RD.A7BT.01 2 0.342 0.651 0.0 0.76 0.24 0.00 0.00
#> TCGA.BR.A4PD.01 2 0.273 0.430 0.0 0.84 0.00 0.16 0.00
#> TCGA.IN.7806.01 2 0.413 0.122 0.0 0.62 0.38 0.00 0.00
#> TCGA.D7.6815.01 3 0.104 0.545 0.0 0.00 0.96 0.00 0.04
#> TCGA.BR.7197.01 5 0.141 0.916 0.0 0.00 0.06 0.00 0.94
#> TCGA.KB.A93J.01 2 0.273 0.430 0.0 0.84 0.00 0.16 0.00
#> TCGA.R5.A7ZR.01 4 0.400 1.000 0.0 0.24 0.02 0.74 0.00
#> TCGA.R5.A7ZE.01 3 0.440 0.675 0.0 0.04 0.72 0.00 0.24
#> TCGA.HU.A4GF.01 2 0.595 0.515 0.0 0.54 0.38 0.04 0.04
#> TCGA.BR.8373.01 5 0.104 0.918 0.0 0.00 0.04 0.00 0.96
#> TCGA.BR.8077.01 2 0.595 0.515 0.0 0.54 0.38 0.04 0.04
#> TCGA.EQ.8122.01 3 0.440 0.675 0.0 0.04 0.72 0.00 0.24
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> TCGA.VQ.A8PJ.01 4 0.3711 1.000 0.00 0.02 0.00 0.72 0.00 0.26
#> TCGA.BR.8678.01 1 0.3631 0.850 0.82 0.00 0.04 0.10 0.00 0.04
#> TCGA.VQ.A91Z.01 1 0.0547 0.921 0.98 0.00 0.02 0.00 0.00 0.00
#> TCGA.VQ.A91N.01 6 0.3647 0.946 0.00 0.36 0.00 0.00 0.00 0.64
#> TCGA.VQ.A91U.01 2 0.0000 0.569 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.3M.AB46.01 3 0.3324 0.413 0.00 0.06 0.84 0.02 0.08 0.00
#> TCGA.F1.6875.01 1 0.0000 0.921 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.B7.A5TN.01 3 0.5020 0.327 0.00 0.38 0.56 0.02 0.00 0.04
#> TCGA.D7.A6F2.01 2 0.0000 0.569 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.RD.A7BT.01 2 0.0000 0.569 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.BR.A4PD.01 6 0.3706 0.963 0.00 0.38 0.00 0.00 0.00 0.62
#> TCGA.IN.7806.01 2 0.5087 -0.238 0.00 0.52 0.42 0.02 0.00 0.04
#> TCGA.D7.6815.01 3 0.6998 0.611 0.00 0.22 0.48 0.00 0.14 0.16
#> TCGA.BR.7197.01 5 0.4733 0.778 0.00 0.00 0.06 0.08 0.74 0.12
#> TCGA.KB.A93J.01 6 0.3756 0.948 0.00 0.40 0.00 0.00 0.00 0.60
#> TCGA.R5.A7ZR.01 4 0.3711 1.000 0.00 0.02 0.00 0.72 0.00 0.26
#> TCGA.R5.A7ZE.01 3 0.7644 0.648 0.00 0.16 0.40 0.02 0.28 0.14
#> TCGA.HU.A4GF.01 2 0.5822 0.424 0.00 0.58 0.06 0.08 0.00 0.28
#> TCGA.BR.8373.01 5 0.0000 0.767 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.BR.8077.01 2 0.5822 0.424 0.00 0.58 0.06 0.08 0.00 0.28
#> TCGA.EQ.8122.01 3 0.7644 0.648 0.00 0.16 0.40 0.02 0.28 0.14
cbind(get_classes(res, k = 7), get_membership(res, k = 7))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7
#> TCGA.VQ.A8PJ.01 4 0.2509 0.9549 0.00 0.00 0.04 0.88 0.00 0.06 0.02
#> TCGA.BR.8678.01 1 0.0504 0.7069 0.98 0.00 0.00 0.02 0.00 0.00 0.00
#> TCGA.VQ.A91Z.01 1 0.3139 0.8634 0.70 0.00 0.30 0.00 0.00 0.00 0.00
#> TCGA.VQ.A91N.01 6 0.3221 0.9244 0.00 0.32 0.00 0.00 0.00 0.68 0.00
#> TCGA.VQ.A91U.01 2 0.0000 0.4966 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.3M.AB46.01 7 0.5840 0.2927 0.00 0.02 0.12 0.04 0.00 0.26 0.56
#> TCGA.F1.6875.01 1 0.3139 0.8634 0.70 0.00 0.30 0.00 0.00 0.00 0.00
#> TCGA.B7.A5TN.01 7 0.5408 0.1277 0.00 0.42 0.04 0.00 0.00 0.08 0.46
#> TCGA.D7.A6F2.01 2 0.0000 0.4966 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.RD.A7BT.01 2 0.0000 0.4966 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BR.A4PD.01 6 0.3294 0.9413 0.00 0.34 0.00 0.00 0.00 0.66 0.00
#> TCGA.IN.7806.01 2 0.5023 0.0693 0.00 0.62 0.04 0.00 0.00 0.08 0.26
#> TCGA.D7.6815.01 7 0.4242 0.4305 0.00 0.18 0.08 0.00 0.00 0.02 0.72
#> TCGA.BR.7197.01 5 0.0000 0.6725 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.KB.A93J.01 6 0.3413 0.9050 0.00 0.38 0.00 0.00 0.00 0.62 0.00
#> TCGA.R5.A7ZR.01 4 0.1166 0.9549 0.00 0.00 0.00 0.94 0.00 0.06 0.00
#> TCGA.R5.A7ZE.01 7 0.4587 0.4632 0.00 0.10 0.00 0.00 0.20 0.02 0.68
#> TCGA.HU.A4GF.01 2 0.6470 0.1996 0.00 0.38 0.36 0.00 0.00 0.16 0.10
#> TCGA.BR.8373.01 5 0.4908 0.6341 0.00 0.00 0.10 0.00 0.66 0.04 0.20
#> TCGA.BR.8077.01 2 0.6470 0.1996 0.00 0.38 0.36 0.00 0.00 0.16 0.10
#> TCGA.EQ.8122.01 7 0.4587 0.4632 0.00 0.10 0.00 0.00 0.20 0.02 0.68
cbind(get_classes(res, k = 8), get_membership(res, k = 8))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7 p8
#> TCGA.VQ.A8PJ.01 4 0.0471 0.8697 0.00 0.00 0.00 0.98 0.00 0.02 0.00 0.00
#> TCGA.BR.8678.01 1 0.3660 0.7257 0.70 0.00 0.24 0.00 0.00 0.00 0.00 0.06
#> TCGA.VQ.A91Z.01 1 0.0471 0.8564 0.98 0.00 0.00 0.00 0.00 0.00 0.00 0.02
#> TCGA.VQ.A91N.01 6 0.0000 0.9852 0.00 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.VQ.A91U.01 2 0.5171 0.7800 0.00 0.54 0.00 0.00 0.00 0.20 0.02 0.24
#> TCGA.3M.AB46.01 3 0.4004 0.0000 0.00 0.04 0.50 0.00 0.00 0.00 0.46 0.00
#> TCGA.F1.6875.01 1 0.0471 0.8564 0.98 0.00 0.00 0.00 0.00 0.00 0.00 0.02
#> TCGA.B7.A5TN.01 7 0.4698 -0.2263 0.00 0.44 0.00 0.00 0.00 0.12 0.44 0.00
#> TCGA.D7.A6F2.01 2 0.5171 0.7800 0.00 0.54 0.00 0.00 0.00 0.20 0.02 0.24
#> TCGA.RD.A7BT.01 2 0.5171 0.7800 0.00 0.54 0.00 0.00 0.00 0.20 0.02 0.24
#> TCGA.BR.A4PD.01 6 0.0000 0.9852 0.00 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.IN.7806.01 2 0.4677 0.1479 0.00 0.54 0.00 0.00 0.00 0.14 0.32 0.00
#> TCGA.D7.6815.01 7 0.4119 0.0367 0.00 0.14 0.08 0.02 0.00 0.00 0.74 0.02
#> TCGA.BR.7197.01 5 0.0000 0.3693 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.KB.A93J.01 6 0.0471 0.9700 0.00 0.02 0.00 0.00 0.00 0.98 0.00 0.00
#> TCGA.R5.A7ZR.01 4 0.3369 0.8697 0.00 0.04 0.08 0.82 0.00 0.02 0.00 0.04
#> TCGA.R5.A7ZE.01 7 0.2267 0.3854 0.00 0.00 0.00 0.00 0.18 0.00 0.82 0.00
#> TCGA.HU.A4GF.01 8 0.3073 1.0000 0.00 0.00 0.00 0.00 0.00 0.10 0.10 0.80
#> TCGA.BR.8373.01 5 0.6859 0.3190 0.00 0.26 0.10 0.00 0.34 0.00 0.26 0.04
#> TCGA.BR.8077.01 8 0.3073 1.0000 0.00 0.00 0.00 0.00 0.00 0.10 0.10 0.80
#> TCGA.EQ.8122.01 7 0.2267 0.3854 0.00 0.00 0.00 0.00 0.18 0.00 0.82 0.00
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
consensus_heatmap(res, k = 7)
consensus_heatmap(res, k = 8)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
membership_heatmap(res, k = 7)
membership_heatmap(res, k = 8)
As soon as the classes for columns are determined, the signatures that are significantly different between subgroups can be looked for. Following are the heatmaps for signatures.
get_signatures(res, k = 2)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
get_signatures(res, k = 7)
get_signatures(res, k = 8)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. To get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows (which is done by automatically selecting number of clusters).If there are too many signatures, top_signatures = ... can be set to only show the
signatures with the highest FDRs:
# code only for demonstration
# e.g. to show the top 500 most significant rows
tb = get_signature(res, k = ..., top_signatures = 500)
If the signatures are defined as these which are uniquely high in current group, diff_method argument
can be set to "uniquely_high_in_one_group":
# code only for demonstration
tb = get_signature(res, k = ..., diff_method = "uniquely_high_in_one_group")
UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
dimension_reduction(res, k = 7, method = "UMAP")
dimension_reduction(res, k = 8, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
If matrix rows can be associated to genes, consider to use functional_enrichment(res,
...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.
Parent node: Node012. Child nodes: Node01111-leaf , Node01112-leaf , Node01113-leaf , Node01114-leaf , Node01115-leaf , Node01116-leaf , Node01121-leaf , Node01122-leaf , Node01123-leaf , Node01131-leaf , Node01132-leaf , Node01133-leaf , Node01134-leaf , Node01211-leaf , Node01212-leaf , Node01221-leaf , Node01222-leaf , Node01231-leaf , Node01232-leaf , Node01233-leaf , Node01311-leaf , Node01312 , Node02221-leaf , Node02222-leaf , Node02223-leaf , Node02224-leaf , Node03111-leaf , Node03112-leaf , Node03113-leaf , Node03411-leaf , Node03412-leaf , Node03413-leaf .
The object with results only for a single top-value method and a single partitioning method can be extracted as:
res = res_rh["0123"]
A summary of res and all the functions that can be applied to it:
res
#> A 'ConsensusPartition' object with k = 2, 3, 4, 5, 6, 7, 8.
#> On a matrix with 30000 rows and 19 columns.
#> Top rows (1000) are extracted by 'ATC' method.
#> Subgroups are detected by 'kmeans' method.
#> Performed in total 350 partitions by row resampling.
#> Best k for subgroups seems to be 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 0.996 0.998 0.4578 0.544 0.544
#> 3 3 0.977 0.987 0.974 0.4296 0.789 0.613
#> 4 4 0.825 0.676 0.872 0.1327 0.971 0.912
#> 5 5 0.749 0.776 0.854 0.0828 0.865 0.566
#> 6 6 0.766 0.781 0.873 0.0498 0.971 0.844
#> 7 7 0.871 0.762 0.863 0.0322 1.000 1.000
#> 8 8 0.842 0.540 0.762 0.0329 0.912 0.483
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.VQ.A8PE.01 1 0.141 0.981 0.98 0.02
#> TCGA.BR.8485.01 2 0.000 1.000 0.00 1.00
#> TCGA.BR.8486.01 2 0.000 1.000 0.00 1.00
#> TCGA.VQ.A8PH.01 1 0.141 0.981 0.98 0.02
#> TCGA.D7.6527.01 1 0.000 0.997 1.00 0.00
#> TCGA.D7.6526.01 1 0.000 0.997 1.00 0.00
#> TCGA.BR.7704.01 2 0.000 1.000 0.00 1.00
#> TCGA.CD.A4MH.01 2 0.000 1.000 0.00 1.00
#> TCGA.HF.7131.01 1 0.000 0.997 1.00 0.00
#> TCGA.VQ.AA6D.01 2 0.000 1.000 0.00 1.00
#> TCGA.VQ.AA6A.01 1 0.000 0.997 1.00 0.00
#> TCGA.HU.A4H5.01 1 0.000 0.997 1.00 0.00
#> TCGA.CG.5718.01 2 0.000 1.000 0.00 1.00
#> TCGA.D7.6817.01 1 0.000 0.997 1.00 0.00
#> TCGA.D7.6820.01 1 0.000 0.997 1.00 0.00
#> TCGA.VQ.A8DV.01 1 0.000 0.997 1.00 0.00
#> TCGA.HU.8245.01 1 0.000 0.997 1.00 0.00
#> TCGA.VQ.A8DU.01 1 0.000 0.997 1.00 0.00
#> TCGA.VQ.A8DZ.01 1 0.000 0.997 1.00 0.00
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.VQ.A8PE.01 3 0.2537 1.000 0.08 0.00 0.92
#> TCGA.BR.8485.01 2 0.0000 0.975 0.00 1.00 0.00
#> TCGA.BR.8486.01 2 0.0000 0.975 0.00 1.00 0.00
#> TCGA.VQ.A8PH.01 3 0.2537 1.000 0.08 0.00 0.92
#> TCGA.D7.6527.01 1 0.0000 0.997 1.00 0.00 0.00
#> TCGA.D7.6526.01 1 0.0000 0.997 1.00 0.00 0.00
#> TCGA.BR.7704.01 2 0.2537 0.949 0.00 0.92 0.08
#> TCGA.CD.A4MH.01 2 0.0000 0.975 0.00 1.00 0.00
#> TCGA.HF.7131.01 1 0.0000 0.997 1.00 0.00 0.00
#> TCGA.VQ.AA6D.01 2 0.0000 0.975 0.00 1.00 0.00
#> TCGA.VQ.AA6A.01 1 0.0000 0.997 1.00 0.00 0.00
#> TCGA.HU.A4H5.01 1 0.0000 0.997 1.00 0.00 0.00
#> TCGA.CG.5718.01 2 0.2537 0.949 0.00 0.92 0.08
#> TCGA.D7.6817.01 1 0.0000 0.997 1.00 0.00 0.00
#> TCGA.D7.6820.01 1 0.0000 0.997 1.00 0.00 0.00
#> TCGA.VQ.A8DV.01 3 0.2537 1.000 0.08 0.00 0.92
#> TCGA.HU.8245.01 1 0.0000 0.997 1.00 0.00 0.00
#> TCGA.VQ.A8DU.01 3 0.2537 1.000 0.08 0.00 0.92
#> TCGA.VQ.A8DZ.01 1 0.0892 0.978 0.98 0.00 0.02
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> TCGA.VQ.A8PE.01 3 0.000 1.000 0.00 0.00 1.00 0.00
#> TCGA.BR.8485.01 2 0.000 0.699 0.00 1.00 0.00 0.00
#> TCGA.BR.8486.01 2 0.000 0.699 0.00 1.00 0.00 0.00
#> TCGA.VQ.A8PH.01 3 0.000 1.000 0.00 0.00 1.00 0.00
#> TCGA.D7.6527.01 1 0.000 0.624 1.00 0.00 0.00 0.00
#> TCGA.D7.6526.01 1 0.498 0.824 0.54 0.00 0.00 0.46
#> TCGA.BR.7704.01 2 0.380 0.261 0.00 0.78 0.00 0.22
#> TCGA.CD.A4MH.01 2 0.000 0.699 0.00 1.00 0.00 0.00
#> TCGA.HF.7131.01 1 0.495 0.824 0.56 0.00 0.00 0.44
#> TCGA.VQ.AA6D.01 2 0.517 -0.323 0.00 0.66 0.02 0.32
#> TCGA.VQ.AA6A.01 1 0.000 0.624 1.00 0.00 0.00 0.00
#> TCGA.HU.A4H5.01 1 0.498 0.824 0.54 0.00 0.00 0.46
#> TCGA.CG.5718.01 4 0.557 0.000 0.02 0.44 0.00 0.54
#> TCGA.D7.6817.01 1 0.495 0.824 0.56 0.00 0.00 0.44
#> TCGA.D7.6820.01 1 0.000 0.624 1.00 0.00 0.00 0.00
#> TCGA.VQ.A8DV.01 3 0.000 1.000 0.00 0.00 1.00 0.00
#> TCGA.HU.8245.01 1 0.498 0.824 0.54 0.00 0.00 0.46
#> TCGA.VQ.A8DU.01 3 0.000 1.000 0.00 0.00 1.00 0.00
#> TCGA.VQ.A8DZ.01 1 0.559 0.813 0.52 0.00 0.02 0.46
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> TCGA.VQ.A8PE.01 3 0.387 0.850 0.00 0.00 0.80 0.06 0.14
#> TCGA.BR.8485.01 2 0.000 0.794 0.00 1.00 0.00 0.00 0.00
#> TCGA.BR.8486.01 2 0.000 0.794 0.00 1.00 0.00 0.00 0.00
#> TCGA.VQ.A8PH.01 3 0.387 0.850 0.00 0.00 0.80 0.06 0.14
#> TCGA.D7.6527.01 5 0.356 1.000 0.26 0.00 0.00 0.00 0.74
#> TCGA.D7.6526.01 1 0.000 0.872 1.00 0.00 0.00 0.00 0.00
#> TCGA.BR.7704.01 2 0.429 0.181 0.00 0.54 0.00 0.46 0.00
#> TCGA.CD.A4MH.01 2 0.000 0.794 0.00 1.00 0.00 0.00 0.00
#> TCGA.HF.7131.01 1 0.000 0.872 1.00 0.00 0.00 0.00 0.00
#> TCGA.VQ.AA6D.01 4 0.640 0.333 0.00 0.30 0.00 0.50 0.20
#> TCGA.VQ.AA6A.01 5 0.356 1.000 0.26 0.00 0.00 0.00 0.74
#> TCGA.HU.A4H5.01 1 0.141 0.874 0.94 0.00 0.00 0.00 0.06
#> TCGA.CG.5718.01 4 0.280 0.404 0.06 0.06 0.00 0.88 0.00
#> TCGA.D7.6817.01 1 0.244 0.874 0.90 0.00 0.00 0.04 0.06
#> TCGA.D7.6820.01 5 0.356 1.000 0.26 0.00 0.00 0.00 0.74
#> TCGA.VQ.A8DV.01 3 0.000 0.855 0.00 0.00 1.00 0.00 0.00
#> TCGA.HU.8245.01 1 0.244 0.874 0.90 0.00 0.00 0.04 0.06
#> TCGA.VQ.A8DU.01 3 0.000 0.855 0.00 0.00 1.00 0.00 0.00
#> TCGA.VQ.A8DZ.01 1 0.425 0.672 0.74 0.00 0.22 0.04 0.00
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> TCGA.VQ.A8PE.01 3 0.4733 0.793 0.00 0.00 0.74 0.12 0.08 0.06
#> TCGA.BR.8485.01 2 0.0000 1.000 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.BR.8486.01 2 0.0000 1.000 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.VQ.A8PH.01 3 0.4733 0.793 0.00 0.00 0.74 0.12 0.08 0.06
#> TCGA.D7.6527.01 5 0.1814 0.991 0.10 0.00 0.00 0.00 0.90 0.00
#> TCGA.D7.6526.01 1 0.2728 0.833 0.86 0.00 0.00 0.10 0.00 0.04
#> TCGA.BR.7704.01 4 0.3309 0.535 0.00 0.28 0.00 0.72 0.00 0.00
#> TCGA.CD.A4MH.01 2 0.0000 1.000 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.HF.7131.01 1 0.0547 0.838 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.VQ.AA6D.01 6 0.1814 0.000 0.00 0.10 0.00 0.00 0.00 0.90
#> TCGA.VQ.AA6A.01 5 0.1814 0.991 0.10 0.00 0.00 0.00 0.90 0.00
#> TCGA.HU.A4H5.01 1 0.2350 0.837 0.88 0.00 0.00 0.10 0.00 0.02
#> TCGA.CG.5718.01 4 0.3819 0.438 0.00 0.00 0.00 0.70 0.02 0.28
#> TCGA.D7.6817.01 1 0.1480 0.844 0.94 0.00 0.00 0.02 0.00 0.04
#> TCGA.D7.6820.01 5 0.2350 0.983 0.10 0.00 0.00 0.00 0.88 0.02
#> TCGA.VQ.A8DV.01 3 0.0937 0.772 0.00 0.00 0.96 0.04 0.00 0.00
#> TCGA.HU.8245.01 1 0.1480 0.844 0.94 0.00 0.00 0.02 0.00 0.04
#> TCGA.VQ.A8DU.01 3 0.0000 0.793 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.VQ.A8DZ.01 1 0.6347 0.555 0.54 0.00 0.24 0.16 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.VQ.A8PE.01 3 0.0504 0.748 0.00 0.00 0.98 0.00 0.00 0.02 0.00
#> TCGA.BR.8485.01 2 0.0504 0.982 0.02 0.98 0.00 0.00 0.00 0.00 0.00
#> TCGA.BR.8486.01 2 0.0000 0.991 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.VQ.A8PH.01 3 0.0504 0.748 0.00 0.00 0.98 0.00 0.00 0.02 0.00
#> TCGA.D7.6527.01 5 0.0863 0.945 0.00 0.00 0.00 0.00 0.96 0.00 0.04
#> TCGA.D7.6526.01 7 0.3525 0.678 0.44 0.00 0.00 0.00 0.00 0.00 0.56
#> TCGA.BR.7704.01 4 0.0000 0.844 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.CD.A4MH.01 2 0.0000 0.991 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HF.7131.01 7 0.3047 0.690 0.28 0.00 0.00 0.00 0.00 0.00 0.72
#> TCGA.VQ.AA6D.01 6 0.1006 0.000 0.00 0.02 0.02 0.00 0.00 0.96 0.00
#> TCGA.VQ.AA6A.01 5 0.1860 0.935 0.02 0.00 0.00 0.00 0.92 0.02 0.04
#> TCGA.HU.A4H5.01 7 0.3221 0.722 0.32 0.00 0.00 0.00 0.00 0.00 0.68
#> TCGA.CG.5718.01 4 0.2912 0.844 0.14 0.00 0.00 0.82 0.04 0.00 0.00
#> TCGA.D7.6817.01 7 0.1006 0.703 0.02 0.00 0.00 0.00 0.02 0.00 0.96
#> TCGA.D7.6820.01 5 0.2509 0.916 0.06 0.00 0.00 0.00 0.88 0.02 0.04
#> TCGA.VQ.A8DV.01 3 0.3221 0.754 0.32 0.00 0.68 0.00 0.00 0.00 0.00
#> TCGA.HU.8245.01 7 0.0000 0.719 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.VQ.A8DU.01 3 0.3221 0.754 0.32 0.00 0.68 0.00 0.00 0.00 0.00
#> TCGA.VQ.A8DZ.01 7 0.3815 0.513 0.36 0.00 0.02 0.00 0.00 0.00 0.62
cbind(get_classes(res, k = 8), get_membership(res, k = 8))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7 p8
#> TCGA.VQ.A8PE.01 3 0.0000 0.6698 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BR.8485.01 2 0.0000 0.9911 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BR.8486.01 2 0.0471 0.9821 0.02 0.98 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.VQ.A8PH.01 3 0.2265 0.6447 0.08 0.00 0.88 0.00 0.00 0.00 0.02 0.02
#> TCGA.D7.6527.01 5 0.0471 0.8467 0.02 0.00 0.00 0.00 0.98 0.00 0.00 0.00
#> TCGA.D7.6526.01 7 0.0471 0.5504 0.00 0.00 0.00 0.00 0.02 0.00 0.98 0.00
#> TCGA.BR.7704.01 4 0.0000 0.7697 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.CD.A4MH.01 2 0.0000 0.9911 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HF.7131.01 7 0.3142 -0.0526 0.36 0.00 0.00 0.00 0.00 0.00 0.64 0.00
#> TCGA.VQ.AA6D.01 6 0.0471 0.0000 0.00 0.02 0.00 0.00 0.00 0.98 0.00 0.00
#> TCGA.VQ.AA6A.01 5 0.0471 0.8370 0.00 0.00 0.00 0.00 0.98 0.00 0.00 0.02
#> TCGA.HU.A4H5.01 7 0.3270 0.4595 0.12 0.00 0.00 0.00 0.02 0.00 0.80 0.06
#> TCGA.CG.5718.01 4 0.3095 0.7697 0.02 0.00 0.00 0.74 0.00 0.00 0.00 0.24
#> TCGA.D7.6817.01 1 0.2267 0.7958 0.82 0.00 0.00 0.00 0.00 0.00 0.18 0.00
#> TCGA.D7.6820.01 5 0.4169 0.7041 0.18 0.00 0.00 0.00 0.70 0.02 0.00 0.10
#> TCGA.VQ.A8DV.01 8 0.3299 -0.4876 0.00 0.00 0.44 0.00 0.00 0.00 0.00 0.56
#> TCGA.HU.8245.01 1 0.2852 0.7752 0.72 0.00 0.00 0.00 0.00 0.00 0.28 0.00
#> TCGA.VQ.A8DU.01 3 0.3193 0.2432 0.00 0.00 0.62 0.00 0.00 0.00 0.00 0.38
#> TCGA.VQ.A8DZ.01 8 0.5259 -0.2367 0.30 0.00 0.00 0.00 0.00 0.00 0.32 0.38
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 , Node0113 , Node0114-leaf , Node0121 , Node0122 , Node0123 , Node0131 , Node0132-leaf , Node0211-leaf , Node0212-leaf , Node0221-leaf , Node0222 , Node0231-leaf , Node0232-leaf , Node0233-leaf , Node0311 , Node0312-leaf , Node0313-leaf , Node0314-leaf , Node0331-leaf , Node0332-leaf , Node0333-leaf , Node0341 , Node0342-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 50 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 0.998 0.999 0.4452 0.556 0.556
#> 3 3 0.543 0.763 0.824 0.3445 0.650 0.458
#> 4 4 0.743 0.748 0.886 0.1404 0.970 0.922
#> 5 5 0.805 0.870 0.909 0.0671 0.878 0.674
#> 6 6 0.820 0.875 0.889 0.0629 0.978 0.918
#> 7 7 0.806 0.761 0.864 0.0511 0.927 0.701
#> 8 8 0.804 0.736 0.831 0.0320 0.956 0.764
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.D7.6519.01 2 0.000 1.000 0.00 1.00
#> TCGA.VQ.A8PM.01 1 0.000 0.999 1.00 0.00
#> TCGA.BR.8484.01 2 0.000 1.000 0.00 1.00
#> TCGA.VQ.A91Y.01 1 0.000 0.999 1.00 0.00
#> TCGA.BR.6456.01 1 0.000 0.999 1.00 0.00
#> TCGA.VQ.A925.01 2 0.000 1.000 0.00 1.00
#> TCGA.IN.AB1V.01 1 0.000 0.999 1.00 0.00
#> TCGA.BR.8687.01 2 0.000 1.000 0.00 1.00
#> TCGA.BR.8690.01 1 0.242 0.958 0.96 0.04
#> TCGA.KB.A6F5.01 1 0.000 0.999 1.00 0.00
#> TCGA.HF.7133.01 2 0.000 1.000 0.00 1.00
#> TCGA.D7.A6EX.01 2 0.000 1.000 0.00 1.00
#> TCGA.BR.7716.01 1 0.000 0.999 1.00 0.00
#> TCGA.FP.7735.01 2 0.000 1.000 0.00 1.00
#> TCGA.BR.7723.01 1 0.000 0.999 1.00 0.00
#> TCGA.HF.7136.01 2 0.000 1.000 0.00 1.00
#> TCGA.MX.A663.01 1 0.000 0.999 1.00 0.00
#> TCGA.CD.5804.01 1 0.000 0.999 1.00 0.00
#> TCGA.D7.A4YT.01 2 0.000 1.000 0.00 1.00
#> TCGA.EQ.5647.01 2 0.000 1.000 0.00 1.00
#> TCGA.D7.6818.01 1 0.000 0.999 1.00 0.00
#> TCGA.CD.8525.01 1 0.000 0.999 1.00 0.00
#> TCGA.BR.4288.01 1 0.000 0.999 1.00 0.00
#> TCGA.CD.5800.01 1 0.000 0.999 1.00 0.00
#> TCGA.CD.5799.01 1 0.000 0.999 1.00 0.00
#> TCGA.B7.A5TI.01 2 0.000 1.000 0.00 1.00
#> TCGA.CD.8530.01 1 0.000 0.999 1.00 0.00
#> TCGA.BR.6801.01 2 0.000 1.000 0.00 1.00
#> TCGA.D7.5579.01 1 0.000 0.999 1.00 0.00
#> TCGA.R5.A7ZI.01 1 0.000 0.999 1.00 0.00
#> TCGA.CG.5732.01 1 0.000 0.999 1.00 0.00
#> TCGA.ZQ.A9CR.01 1 0.000 0.999 1.00 0.00
#> TCGA.CD.5802.01 1 0.000 0.999 1.00 0.00
#> TCGA.R5.A7ZF.01 1 0.000 0.999 1.00 0.00
#> TCGA.RD.A8N1.01 1 0.000 0.999 1.00 0.00
#> TCGA.VQ.A8E2.01 1 0.000 0.999 1.00 0.00
#> TCGA.CD.8527.01 2 0.000 1.000 0.00 1.00
#> TCGA.RD.A8N6.01 2 0.000 1.000 0.00 1.00
#> TCGA.ZA.A8F6.01 1 0.000 0.999 1.00 0.00
#> TCGA.VQ.A8DL.01 1 0.000 0.999 1.00 0.00
#> TCGA.D7.8572.01 1 0.000 0.999 1.00 0.00
#> TCGA.CD.A487.01 2 0.000 1.000 0.00 1.00
#> TCGA.BR.8059.01 1 0.000 0.999 1.00 0.00
#> TCGA.FP.A8CX.01 1 0.000 0.999 1.00 0.00
#> TCGA.CD.8526.01 1 0.000 0.999 1.00 0.00
#> TCGA.D7.8578.01 1 0.000 0.999 1.00 0.00
#> TCGA.RD.A8MW.01 1 0.000 0.999 1.00 0.00
#> TCGA.BR.A4CR.01 2 0.000 1.000 0.00 1.00
#> TCGA.BR.8291.01 1 0.000 0.999 1.00 0.00
#> TCGA.CD.8529.01 1 0.000 0.999 1.00 0.00
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.D7.6519.01 2 0.0000 0.8896 0.00 1.00 0.00
#> TCGA.VQ.A8PM.01 1 0.5948 0.1403 0.64 0.00 0.36
#> TCGA.BR.8484.01 1 0.6677 0.6135 0.74 0.08 0.18
#> TCGA.VQ.A91Y.01 3 0.5216 0.9918 0.26 0.00 0.74
#> TCGA.BR.6456.01 3 0.5216 0.9918 0.26 0.00 0.74
#> TCGA.VQ.A925.01 2 0.0000 0.8896 0.00 1.00 0.00
#> TCGA.IN.AB1V.01 1 0.3686 0.6501 0.86 0.00 0.14
#> TCGA.BR.8687.01 2 0.3686 0.8677 0.00 0.86 0.14
#> TCGA.BR.8690.01 1 0.4291 0.7045 0.82 0.00 0.18
#> TCGA.KB.A6F5.01 3 0.5216 0.9918 0.26 0.00 0.74
#> TCGA.HF.7133.01 2 0.4002 0.8598 0.00 0.84 0.16
#> TCGA.D7.A6EX.01 2 0.0000 0.8896 0.00 1.00 0.00
#> TCGA.BR.7716.01 3 0.5216 0.9918 0.26 0.00 0.74
#> TCGA.FP.7735.01 1 0.6677 0.6135 0.74 0.08 0.18
#> TCGA.BR.7723.01 3 0.5016 0.9755 0.24 0.00 0.76
#> TCGA.HF.7136.01 2 0.9823 0.3654 0.32 0.42 0.26
#> TCGA.MX.A663.01 3 0.5216 0.9918 0.26 0.00 0.74
#> TCGA.CD.5804.01 1 0.0000 0.8052 1.00 0.00 0.00
#> TCGA.D7.A4YT.01 2 0.0000 0.8896 0.00 1.00 0.00
#> TCGA.EQ.5647.01 2 0.3686 0.8677 0.00 0.86 0.14
#> TCGA.D7.6818.01 1 0.0000 0.8052 1.00 0.00 0.00
#> TCGA.CD.8525.01 1 0.5948 0.1403 0.64 0.00 0.36
#> TCGA.BR.4288.01 3 0.5016 0.9755 0.24 0.00 0.76
#> TCGA.CD.5800.01 1 0.0892 0.7978 0.98 0.00 0.02
#> TCGA.CD.5799.01 1 0.0000 0.8052 1.00 0.00 0.00
#> TCGA.B7.A5TI.01 1 0.6677 0.6135 0.74 0.08 0.18
#> TCGA.CD.8530.01 1 0.6045 0.0545 0.62 0.00 0.38
#> TCGA.BR.6801.01 2 0.7398 0.7511 0.12 0.70 0.18
#> TCGA.D7.5579.01 1 0.0892 0.8004 0.98 0.00 0.02
#> TCGA.R5.A7ZI.01 1 0.0892 0.8004 0.98 0.00 0.02
#> TCGA.CG.5732.01 1 0.0000 0.8052 1.00 0.00 0.00
#> TCGA.ZQ.A9CR.01 1 0.0000 0.8052 1.00 0.00 0.00
#> TCGA.CD.5802.01 1 0.0000 0.8052 1.00 0.00 0.00
#> TCGA.R5.A7ZF.01 1 0.5948 0.1403 0.64 0.00 0.36
#> TCGA.RD.A8N1.01 1 0.5706 0.2695 0.68 0.00 0.32
#> TCGA.VQ.A8E2.01 3 0.5016 0.9755 0.24 0.00 0.76
#> TCGA.CD.8527.01 2 0.0000 0.8896 0.00 1.00 0.00
#> TCGA.RD.A8N6.01 1 0.5216 0.6300 0.74 0.00 0.26
#> TCGA.ZA.A8F6.01 1 0.0000 0.8052 1.00 0.00 0.00
#> TCGA.VQ.A8DL.01 1 0.0000 0.8052 1.00 0.00 0.00
#> TCGA.D7.8572.01 3 0.5216 0.9918 0.26 0.00 0.74
#> TCGA.CD.A487.01 1 0.6677 0.6135 0.74 0.08 0.18
#> TCGA.BR.8059.01 1 0.0892 0.8004 0.98 0.00 0.02
#> TCGA.FP.A8CX.01 1 0.0000 0.8052 1.00 0.00 0.00
#> TCGA.CD.8526.01 3 0.5216 0.9918 0.26 0.00 0.74
#> TCGA.D7.8578.01 1 0.0000 0.8052 1.00 0.00 0.00
#> TCGA.RD.A8MW.01 3 0.5216 0.9918 0.26 0.00 0.74
#> TCGA.BR.A4CR.01 2 0.0000 0.8896 0.00 1.00 0.00
#> TCGA.BR.8291.01 3 0.5216 0.9918 0.26 0.00 0.74
#> TCGA.CD.8529.01 1 0.0000 0.8052 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.D7.6519.01 2 0.121 0.826 0.00 0.96 0.04 0.00
#> TCGA.VQ.A8PM.01 1 0.485 0.320 0.60 0.00 0.40 0.00
#> TCGA.BR.8484.01 1 0.491 0.269 0.58 0.00 0.00 0.42
#> TCGA.VQ.A91Y.01 3 0.121 1.000 0.04 0.00 0.96 0.00
#> TCGA.BR.6456.01 3 0.121 1.000 0.04 0.00 0.96 0.00
#> TCGA.VQ.A925.01 2 0.000 0.825 0.00 1.00 0.00 0.00
#> TCGA.IN.AB1V.01 1 0.000 0.798 1.00 0.00 0.00 0.00
#> TCGA.BR.8687.01 2 0.361 0.728 0.00 0.80 0.00 0.20
#> TCGA.BR.8690.01 1 0.491 0.269 0.58 0.00 0.00 0.42
#> TCGA.KB.A6F5.01 3 0.121 1.000 0.04 0.00 0.96 0.00
#> TCGA.HF.7133.01 2 0.452 0.567 0.00 0.68 0.00 0.32
#> TCGA.D7.A6EX.01 2 0.121 0.826 0.00 0.96 0.04 0.00
#> TCGA.BR.7716.01 3 0.121 1.000 0.04 0.00 0.96 0.00
#> TCGA.FP.7735.01 1 0.491 0.269 0.58 0.00 0.00 0.42
#> TCGA.BR.7723.01 3 0.121 1.000 0.04 0.00 0.96 0.00
#> TCGA.HF.7136.01 4 0.000 1.000 0.00 0.00 0.00 1.00
#> TCGA.MX.A663.01 3 0.121 1.000 0.04 0.00 0.96 0.00
#> TCGA.CD.5804.01 1 0.000 0.798 1.00 0.00 0.00 0.00
#> TCGA.D7.A4YT.01 2 0.121 0.826 0.00 0.96 0.04 0.00
#> TCGA.EQ.5647.01 2 0.361 0.728 0.00 0.80 0.00 0.20
#> TCGA.D7.6818.01 1 0.000 0.798 1.00 0.00 0.00 0.00
#> TCGA.CD.8525.01 1 0.485 0.320 0.60 0.00 0.40 0.00
#> TCGA.BR.4288.01 3 0.121 1.000 0.04 0.00 0.96 0.00
#> TCGA.CD.5800.01 1 0.000 0.798 1.00 0.00 0.00 0.00
#> TCGA.CD.5799.01 1 0.000 0.798 1.00 0.00 0.00 0.00
#> TCGA.B7.A5TI.01 1 0.491 0.269 0.58 0.00 0.00 0.42
#> TCGA.CD.8530.01 1 0.485 0.320 0.60 0.00 0.40 0.00
#> TCGA.BR.6801.01 2 0.479 0.443 0.00 0.62 0.00 0.38
#> TCGA.D7.5579.01 1 0.000 0.798 1.00 0.00 0.00 0.00
#> TCGA.R5.A7ZI.01 1 0.000 0.798 1.00 0.00 0.00 0.00
#> TCGA.CG.5732.01 1 0.000 0.798 1.00 0.00 0.00 0.00
#> TCGA.ZQ.A9CR.01 1 0.000 0.798 1.00 0.00 0.00 0.00
#> TCGA.CD.5802.01 1 0.000 0.798 1.00 0.00 0.00 0.00
#> TCGA.R5.A7ZF.01 1 0.485 0.320 0.60 0.00 0.40 0.00
#> TCGA.RD.A8N1.01 1 0.413 0.571 0.74 0.00 0.26 0.00
#> TCGA.VQ.A8E2.01 3 0.121 1.000 0.04 0.00 0.96 0.00
#> TCGA.CD.8527.01 2 0.121 0.826 0.00 0.96 0.04 0.00
#> TCGA.RD.A8N6.01 4 0.000 1.000 0.00 0.00 0.00 1.00
#> TCGA.ZA.A8F6.01 1 0.000 0.798 1.00 0.00 0.00 0.00
#> TCGA.VQ.A8DL.01 1 0.000 0.798 1.00 0.00 0.00 0.00
#> TCGA.D7.8572.01 3 0.121 1.000 0.04 0.00 0.96 0.00
#> TCGA.CD.A487.01 1 0.491 0.269 0.58 0.00 0.00 0.42
#> TCGA.BR.8059.01 1 0.000 0.798 1.00 0.00 0.00 0.00
#> TCGA.FP.A8CX.01 1 0.000 0.798 1.00 0.00 0.00 0.00
#> TCGA.CD.8526.01 3 0.121 1.000 0.04 0.00 0.96 0.00
#> TCGA.D7.8578.01 1 0.000 0.798 1.00 0.00 0.00 0.00
#> TCGA.RD.A8MW.01 3 0.121 1.000 0.04 0.00 0.96 0.00
#> TCGA.BR.A4CR.01 2 0.000 0.825 0.00 1.00 0.00 0.00
#> TCGA.BR.8291.01 3 0.121 1.000 0.04 0.00 0.96 0.00
#> TCGA.CD.8529.01 1 0.000 0.798 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.D7.6519.01 2 0.3274 0.991 0.00 0.78 0.00 0.00 0.22
#> TCGA.VQ.A8PM.01 1 0.3110 0.879 0.86 0.06 0.08 0.00 0.00
#> TCGA.BR.8484.01 5 0.3274 0.724 0.22 0.00 0.00 0.00 0.78
#> TCGA.VQ.A91Y.01 3 0.0000 0.907 0.00 0.00 1.00 0.00 0.00
#> TCGA.BR.6456.01 3 0.0000 0.907 0.00 0.00 1.00 0.00 0.00
#> TCGA.VQ.A925.01 2 0.3274 0.991 0.00 0.78 0.00 0.00 0.22
#> TCGA.IN.AB1V.01 1 0.1410 0.934 0.94 0.06 0.00 0.00 0.00
#> TCGA.BR.8687.01 5 0.2929 0.483 0.00 0.18 0.00 0.00 0.82
#> TCGA.BR.8690.01 5 0.3274 0.724 0.22 0.00 0.00 0.00 0.78
#> TCGA.KB.A6F5.01 3 0.0609 0.895 0.00 0.02 0.98 0.00 0.00
#> TCGA.HF.7133.01 5 0.1043 0.614 0.00 0.04 0.00 0.00 0.96
#> TCGA.D7.A6EX.01 2 0.3274 0.991 0.00 0.78 0.00 0.00 0.22
#> TCGA.BR.7716.01 3 0.0000 0.907 0.00 0.00 1.00 0.00 0.00
#> TCGA.FP.7735.01 5 0.3274 0.724 0.22 0.00 0.00 0.00 0.78
#> TCGA.BR.7723.01 3 0.5444 0.685 0.00 0.18 0.66 0.16 0.00
#> TCGA.HF.7136.01 4 0.2732 1.000 0.00 0.00 0.00 0.84 0.16
#> TCGA.MX.A663.01 3 0.0000 0.907 0.00 0.00 1.00 0.00 0.00
#> TCGA.CD.5804.01 1 0.0000 0.949 1.00 0.00 0.00 0.00 0.00
#> TCGA.D7.A4YT.01 2 0.3274 0.991 0.00 0.78 0.00 0.00 0.22
#> TCGA.EQ.5647.01 5 0.2929 0.483 0.00 0.18 0.00 0.00 0.82
#> TCGA.D7.6818.01 1 0.0000 0.949 1.00 0.00 0.00 0.00 0.00
#> TCGA.CD.8525.01 1 0.3110 0.879 0.86 0.06 0.08 0.00 0.00
#> TCGA.BR.4288.01 3 0.5444 0.685 0.00 0.18 0.66 0.16 0.00
#> TCGA.CD.5800.01 1 0.1410 0.934 0.94 0.06 0.00 0.00 0.00
#> TCGA.CD.5799.01 1 0.0000 0.949 1.00 0.00 0.00 0.00 0.00
#> TCGA.B7.A5TI.01 5 0.3274 0.724 0.22 0.00 0.00 0.00 0.78
#> TCGA.CD.8530.01 1 0.3110 0.879 0.86 0.06 0.08 0.00 0.00
#> TCGA.BR.6801.01 5 0.0000 0.621 0.00 0.00 0.00 0.00 1.00
#> TCGA.D7.5579.01 1 0.0000 0.949 1.00 0.00 0.00 0.00 0.00
#> TCGA.R5.A7ZI.01 1 0.0000 0.949 1.00 0.00 0.00 0.00 0.00
#> TCGA.CG.5732.01 1 0.0000 0.949 1.00 0.00 0.00 0.00 0.00
#> TCGA.ZQ.A9CR.01 1 0.0000 0.949 1.00 0.00 0.00 0.00 0.00
#> TCGA.CD.5802.01 1 0.1410 0.934 0.94 0.06 0.00 0.00 0.00
#> TCGA.R5.A7ZF.01 1 0.3110 0.879 0.86 0.06 0.08 0.00 0.00
#> TCGA.RD.A8N1.01 1 0.2438 0.912 0.90 0.06 0.04 0.00 0.00
#> TCGA.VQ.A8E2.01 3 0.5444 0.685 0.00 0.18 0.66 0.16 0.00
#> TCGA.CD.8527.01 2 0.3274 0.991 0.00 0.78 0.00 0.00 0.22
#> TCGA.RD.A8N6.01 4 0.2732 1.000 0.00 0.00 0.00 0.84 0.16
#> TCGA.ZA.A8F6.01 1 0.0000 0.949 1.00 0.00 0.00 0.00 0.00
#> TCGA.VQ.A8DL.01 1 0.0000 0.949 1.00 0.00 0.00 0.00 0.00
#> TCGA.D7.8572.01 3 0.0000 0.907 0.00 0.00 1.00 0.00 0.00
#> TCGA.CD.A487.01 5 0.3274 0.724 0.22 0.00 0.00 0.00 0.78
#> TCGA.BR.8059.01 1 0.0000 0.949 1.00 0.00 0.00 0.00 0.00
#> TCGA.FP.A8CX.01 1 0.0000 0.949 1.00 0.00 0.00 0.00 0.00
#> TCGA.CD.8526.01 3 0.0000 0.907 0.00 0.00 1.00 0.00 0.00
#> TCGA.D7.8578.01 1 0.1410 0.934 0.94 0.06 0.00 0.00 0.00
#> TCGA.RD.A8MW.01 3 0.0000 0.907 0.00 0.00 1.00 0.00 0.00
#> TCGA.BR.A4CR.01 2 0.2929 0.955 0.00 0.82 0.00 0.00 0.18
#> TCGA.BR.8291.01 3 0.0000 0.907 0.00 0.00 1.00 0.00 0.00
#> TCGA.CD.8529.01 1 0.0000 0.949 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.D7.6519.01 2 0.0000 0.923 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.VQ.A8PM.01 1 0.3985 0.827 0.76 0.00 0.00 0.10 0.00 0.14
#> TCGA.BR.8484.01 5 0.0547 0.829 0.00 0.00 0.00 0.00 0.98 0.02
#> TCGA.VQ.A91Y.01 3 0.0000 0.990 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.BR.6456.01 3 0.0000 0.990 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.VQ.A925.01 2 0.3787 0.768 0.00 0.78 0.00 0.00 0.10 0.12
#> TCGA.IN.AB1V.01 1 0.3073 0.848 0.84 0.00 0.00 0.08 0.00 0.08
#> TCGA.BR.8687.01 5 0.4200 0.692 0.00 0.14 0.00 0.00 0.74 0.12
#> TCGA.BR.8690.01 5 0.4503 0.441 0.24 0.00 0.00 0.00 0.68 0.08
#> TCGA.KB.A6F5.01 3 0.1092 0.916 0.02 0.00 0.96 0.02 0.00 0.00
#> TCGA.HF.7133.01 5 0.2581 0.776 0.00 0.02 0.00 0.00 0.86 0.12
#> TCGA.D7.A6EX.01 2 0.0000 0.923 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.BR.7716.01 3 0.0000 0.990 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.FP.7735.01 5 0.0547 0.829 0.00 0.00 0.00 0.00 0.98 0.02
#> TCGA.BR.7723.01 6 0.3706 1.000 0.00 0.00 0.38 0.00 0.00 0.62
#> TCGA.HF.7136.01 4 0.1814 1.000 0.00 0.00 0.00 0.90 0.10 0.00
#> TCGA.MX.A663.01 3 0.0000 0.990 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.CD.5804.01 1 0.2094 0.858 0.90 0.00 0.00 0.02 0.00 0.08
#> TCGA.D7.A4YT.01 2 0.0000 0.923 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.EQ.5647.01 5 0.4200 0.692 0.00 0.14 0.00 0.00 0.74 0.12
#> TCGA.D7.6818.01 1 0.0547 0.870 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.CD.8525.01 1 0.3787 0.832 0.78 0.00 0.00 0.10 0.00 0.12
#> TCGA.BR.4288.01 6 0.3706 1.000 0.00 0.00 0.38 0.00 0.00 0.62
#> TCGA.CD.5800.01 1 0.3985 0.827 0.76 0.00 0.00 0.10 0.00 0.14
#> TCGA.CD.5799.01 1 0.1814 0.849 0.90 0.00 0.00 0.00 0.00 0.10
#> TCGA.B7.A5TI.01 5 0.0000 0.828 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.CD.8530.01 1 0.3073 0.848 0.84 0.00 0.00 0.08 0.00 0.08
#> TCGA.BR.6801.01 5 0.0000 0.828 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.D7.5579.01 1 0.1556 0.859 0.92 0.00 0.00 0.00 0.00 0.08
#> TCGA.R5.A7ZI.01 1 0.1556 0.859 0.92 0.00 0.00 0.00 0.00 0.08
#> TCGA.CG.5732.01 1 0.2094 0.858 0.90 0.00 0.00 0.02 0.00 0.08
#> TCGA.ZQ.A9CR.01 1 0.1267 0.862 0.94 0.00 0.00 0.00 0.00 0.06
#> TCGA.CD.5802.01 1 0.3985 0.827 0.76 0.00 0.00 0.10 0.00 0.14
#> TCGA.R5.A7ZF.01 1 0.3544 0.837 0.80 0.00 0.00 0.08 0.00 0.12
#> TCGA.RD.A8N1.01 1 0.3270 0.850 0.82 0.00 0.00 0.06 0.00 0.12
#> TCGA.VQ.A8E2.01 6 0.3706 1.000 0.00 0.00 0.38 0.00 0.00 0.62
#> TCGA.CD.8527.01 2 0.0000 0.923 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.RD.A8N6.01 4 0.1814 1.000 0.00 0.00 0.00 0.90 0.10 0.00
#> TCGA.ZA.A8F6.01 1 0.1267 0.862 0.94 0.00 0.00 0.00 0.00 0.06
#> TCGA.VQ.A8DL.01 1 0.2350 0.856 0.88 0.00 0.00 0.02 0.00 0.10
#> TCGA.D7.8572.01 3 0.0000 0.990 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.CD.A487.01 5 0.0547 0.829 0.00 0.00 0.00 0.00 0.98 0.02
#> TCGA.BR.8059.01 1 0.1267 0.862 0.94 0.00 0.00 0.00 0.00 0.06
#> TCGA.FP.A8CX.01 1 0.1267 0.862 0.94 0.00 0.00 0.00 0.00 0.06
#> TCGA.CD.8526.01 3 0.0000 0.990 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.D7.8578.01 1 0.3985 0.827 0.76 0.00 0.00 0.10 0.00 0.14
#> TCGA.RD.A8MW.01 3 0.0000 0.990 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.BR.A4CR.01 2 0.2260 0.854 0.00 0.86 0.00 0.00 0.00 0.14
#> TCGA.BR.8291.01 3 0.0000 0.990 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.CD.8529.01 1 0.1267 0.862 0.94 0.00 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.D7.6519.01 2 0.0000 0.915 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.VQ.A8PM.01 7 0.3358 0.936 0.36 0.00 0.00 0.00 0.00 0.00 0.64
#> TCGA.BR.8484.01 5 0.0504 0.811 0.00 0.00 0.00 0.02 0.98 0.00 0.00
#> TCGA.VQ.A91Y.01 3 0.1433 0.924 0.00 0.00 0.92 0.00 0.00 0.00 0.08
#> TCGA.BR.6456.01 3 0.0504 0.945 0.00 0.00 0.98 0.00 0.00 0.00 0.02
#> TCGA.VQ.A925.01 2 0.4161 0.748 0.00 0.76 0.00 0.00 0.08 0.10 0.06
#> TCGA.IN.AB1V.01 1 0.3562 -0.771 0.50 0.00 0.00 0.00 0.00 0.00 0.50
#> TCGA.BR.8687.01 5 0.4574 0.684 0.00 0.12 0.00 0.00 0.72 0.10 0.06
#> TCGA.BR.8690.01 5 0.3496 0.272 0.42 0.00 0.00 0.00 0.58 0.00 0.00
#> TCGA.KB.A6F5.01 3 0.1671 0.866 0.00 0.00 0.90 0.00 0.00 0.00 0.10
#> TCGA.HF.7133.01 5 0.2803 0.762 0.00 0.00 0.00 0.00 0.84 0.10 0.06
#> TCGA.D7.A6EX.01 2 0.0000 0.915 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BR.7716.01 3 0.0504 0.945 0.00 0.00 0.98 0.00 0.00 0.00 0.02
#> TCGA.FP.7735.01 5 0.0504 0.811 0.00 0.00 0.00 0.02 0.98 0.00 0.00
#> TCGA.BR.7723.01 6 0.2722 0.969 0.00 0.00 0.12 0.00 0.00 0.84 0.04
#> TCGA.HF.7136.01 4 0.0000 0.987 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.MX.A663.01 3 0.1433 0.924 0.00 0.00 0.92 0.00 0.00 0.00 0.08
#> TCGA.CD.5804.01 1 0.2572 0.659 0.80 0.00 0.00 0.00 0.00 0.00 0.20
#> TCGA.D7.A4YT.01 2 0.0000 0.915 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.EQ.5647.01 5 0.4574 0.684 0.00 0.12 0.00 0.00 0.72 0.10 0.06
#> TCGA.D7.6818.01 1 0.1433 0.738 0.92 0.00 0.00 0.00 0.00 0.00 0.08
#> TCGA.CD.8525.01 7 0.3358 0.936 0.36 0.00 0.00 0.00 0.00 0.00 0.64
#> TCGA.BR.4288.01 6 0.1886 0.985 0.00 0.00 0.12 0.00 0.00 0.88 0.00
#> TCGA.CD.5800.01 7 0.3413 0.950 0.38 0.00 0.00 0.00 0.00 0.00 0.62
#> TCGA.CD.5799.01 1 0.1671 0.716 0.90 0.00 0.00 0.00 0.00 0.00 0.10
#> TCGA.B7.A5TI.01 5 0.0504 0.811 0.00 0.00 0.00 0.02 0.98 0.00 0.00
#> TCGA.CD.8530.01 1 0.3562 -0.771 0.50 0.00 0.00 0.00 0.00 0.00 0.50
#> TCGA.BR.6801.01 5 0.0863 0.804 0.00 0.00 0.00 0.00 0.96 0.04 0.00
#> TCGA.D7.5579.01 1 0.0000 0.769 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.R5.A7ZI.01 1 0.0000 0.769 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CG.5732.01 1 0.2572 0.659 0.80 0.00 0.00 0.00 0.00 0.00 0.20
#> TCGA.ZQ.A9CR.01 1 0.0000 0.769 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CD.5802.01 7 0.3413 0.950 0.38 0.00 0.00 0.00 0.00 0.00 0.62
#> TCGA.R5.A7ZF.01 7 0.3546 0.809 0.46 0.00 0.00 0.00 0.00 0.00 0.54
#> TCGA.RD.A8N1.01 1 0.3221 0.247 0.68 0.00 0.00 0.00 0.00 0.00 0.32
#> TCGA.VQ.A8E2.01 6 0.1886 0.985 0.00 0.00 0.12 0.00 0.00 0.88 0.00
#> TCGA.CD.8527.01 2 0.0000 0.915 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.RD.A8N6.01 4 0.0504 0.987 0.00 0.00 0.00 0.98 0.00 0.00 0.02
#> TCGA.ZA.A8F6.01 1 0.0000 0.769 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.VQ.A8DL.01 1 0.2081 0.701 0.86 0.00 0.00 0.00 0.00 0.00 0.14
#> TCGA.D7.8572.01 3 0.0504 0.945 0.00 0.00 0.98 0.00 0.00 0.00 0.02
#> TCGA.CD.A487.01 5 0.0504 0.811 0.00 0.00 0.00 0.02 0.98 0.00 0.00
#> TCGA.BR.8059.01 1 0.0000 0.769 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FP.A8CX.01 1 0.0000 0.769 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CD.8526.01 3 0.1433 0.924 0.00 0.00 0.92 0.00 0.00 0.00 0.08
#> TCGA.D7.8578.01 7 0.3413 0.950 0.38 0.00 0.00 0.00 0.00 0.00 0.62
#> TCGA.RD.A8MW.01 3 0.0000 0.947 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.BR.A4CR.01 2 0.3011 0.829 0.00 0.82 0.00 0.00 0.00 0.06 0.12
#> TCGA.BR.8291.01 3 0.0000 0.947 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.CD.8529.01 1 0.0000 0.769 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.D7.6519.01 2 0.0000 0.764 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.VQ.A8PM.01 8 0.0000 0.742 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.BR.8484.01 5 0.0471 0.708 0.02 0.00 0.00 0.00 0.98 0.00 0.00 0.00
#> TCGA.VQ.A91Y.01 3 0.2025 0.898 0.02 0.00 0.88 0.00 0.00 0.00 0.10 0.00
#> TCGA.BR.6456.01 3 0.0000 0.925 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.VQ.A925.01 2 0.4914 0.270 0.00 0.42 0.00 0.00 0.16 0.00 0.42 0.00
#> TCGA.IN.AB1V.01 8 0.3660 0.587 0.24 0.00 0.00 0.00 0.00 0.00 0.06 0.70
#> TCGA.BR.8687.01 5 0.4199 0.490 0.00 0.06 0.00 0.00 0.52 0.00 0.42 0.00
#> TCGA.BR.8690.01 5 0.3237 0.244 0.40 0.00 0.00 0.00 0.60 0.00 0.00 0.00
#> TCGA.KB.A6F5.01 3 0.2267 0.750 0.00 0.00 0.82 0.00 0.00 0.00 0.00 0.18
#> TCGA.HF.7133.01 5 0.3272 0.552 0.00 0.00 0.00 0.00 0.58 0.00 0.42 0.00
#> TCGA.D7.A6EX.01 2 0.0000 0.764 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BR.7716.01 3 0.0000 0.925 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FP.7735.01 5 0.0000 0.713 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.BR.7723.01 6 0.2020 0.936 0.02 0.00 0.02 0.00 0.00 0.90 0.06 0.00
#> TCGA.HF.7136.01 4 0.0941 0.974 0.02 0.00 0.00 0.96 0.00 0.00 0.02 0.00
#> TCGA.MX.A663.01 3 0.2025 0.898 0.02 0.00 0.88 0.00 0.00 0.00 0.10 0.00
#> TCGA.CD.5804.01 1 0.4628 0.641 0.52 0.00 0.00 0.00 0.00 0.00 0.12 0.36
#> TCGA.D7.A4YT.01 2 0.0471 0.758 0.00 0.98 0.00 0.00 0.00 0.02 0.00 0.00
#> TCGA.EQ.5647.01 5 0.4199 0.490 0.00 0.06 0.00 0.00 0.52 0.00 0.42 0.00
#> TCGA.D7.6818.01 1 0.3198 0.791 0.72 0.00 0.00 0.00 0.00 0.00 0.02 0.26
#> TCGA.CD.8525.01 8 0.0471 0.744 0.00 0.00 0.00 0.00 0.00 0.00 0.02 0.98
#> TCGA.BR.4288.01 6 0.0471 0.968 0.00 0.00 0.02 0.00 0.00 0.98 0.00 0.00
#> TCGA.CD.5800.01 8 0.2025 0.731 0.02 0.00 0.00 0.00 0.00 0.00 0.10 0.88
#> TCGA.CD.5799.01 1 0.4458 0.755 0.62 0.00 0.00 0.00 0.00 0.00 0.18 0.20
#> TCGA.B7.A5TI.01 5 0.0000 0.713 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.CD.8530.01 8 0.4180 0.621 0.20 0.00 0.04 0.00 0.00 0.00 0.06 0.70
#> TCGA.BR.6801.01 5 0.1804 0.698 0.02 0.00 0.00 0.00 0.90 0.00 0.08 0.00
#> TCGA.D7.5579.01 1 0.2267 0.858 0.82 0.00 0.00 0.00 0.00 0.00 0.00 0.18
#> TCGA.R5.A7ZI.01 1 0.2267 0.858 0.82 0.00 0.00 0.00 0.00 0.00 0.00 0.18
#> TCGA.CG.5732.01 1 0.4658 0.610 0.50 0.00 0.00 0.00 0.00 0.00 0.12 0.38
#> TCGA.ZQ.A9CR.01 1 0.2267 0.858 0.82 0.00 0.00 0.00 0.00 0.00 0.00 0.18
#> TCGA.CD.5802.01 8 0.2569 0.729 0.02 0.00 0.00 0.00 0.00 0.00 0.16 0.82
#> TCGA.R5.A7ZF.01 8 0.3601 0.668 0.16 0.00 0.02 0.00 0.00 0.00 0.06 0.76
#> TCGA.RD.A8N1.01 8 0.4340 -0.208 0.38 0.00 0.00 0.00 0.00 0.00 0.08 0.54
#> TCGA.VQ.A8E2.01 6 0.0471 0.968 0.00 0.00 0.02 0.00 0.00 0.98 0.00 0.00
#> TCGA.CD.8527.01 2 0.0000 0.764 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.RD.A8N6.01 4 0.0000 0.974 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.ZA.A8F6.01 1 0.2406 0.851 0.80 0.00 0.00 0.00 0.00 0.00 0.00 0.20
#> TCGA.VQ.A8DL.01 1 0.4480 0.687 0.58 0.00 0.00 0.00 0.00 0.00 0.12 0.30
#> TCGA.D7.8572.01 3 0.0000 0.925 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CD.A487.01 5 0.0471 0.708 0.02 0.00 0.00 0.00 0.98 0.00 0.00 0.00
#> TCGA.BR.8059.01 1 0.2267 0.858 0.82 0.00 0.00 0.00 0.00 0.00 0.00 0.18
#> TCGA.FP.A8CX.01 1 0.2406 0.851 0.80 0.00 0.00 0.00 0.00 0.00 0.00 0.20
#> TCGA.CD.8526.01 3 0.2025 0.898 0.02 0.00 0.88 0.00 0.00 0.00 0.10 0.00
#> TCGA.D7.8578.01 8 0.2025 0.731 0.02 0.00 0.00 0.00 0.00 0.00 0.10 0.88
#> TCGA.RD.A8MW.01 3 0.0471 0.923 0.00 0.00 0.98 0.00 0.00 0.00 0.02 0.00
#> TCGA.BR.A4CR.01 2 0.4511 0.489 0.10 0.52 0.00 0.00 0.00 0.00 0.38 0.00
#> TCGA.BR.8291.01 3 0.0471 0.917 0.00 0.00 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.CD.8529.01 1 0.2267 0.858 0.82 0.00 0.00 0.00 0.00 0.00 0.00 0.18
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
consensus_heatmap(res, k = 7)
consensus_heatmap(res, k = 8)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
membership_heatmap(res, k = 7)
membership_heatmap(res, k = 8)
As soon as the classes for columns are determined, the signatures that are significantly different between subgroups can be looked for. Following are the heatmaps for signatures.
get_signatures(res, k = 2)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
get_signatures(res, k = 7)
get_signatures(res, k = 8)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. To get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows (which is done by automatically selecting number of clusters).If there are too many signatures, top_signatures = ... can be set to only show the
signatures with the highest FDRs:
# code only for demonstration
# e.g. to show the top 500 most significant rows
tb = get_signature(res, k = ..., top_signatures = 500)
If the signatures are defined as these which are uniquely high in current group, diff_method argument
can be set to "uniquely_high_in_one_group":
# code only for demonstration
tb = get_signature(res, k = ..., diff_method = "uniquely_high_in_one_group")
UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
dimension_reduction(res, k = 7, method = "UMAP")
dimension_reduction(res, k = 8, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
If matrix rows can be associated to genes, consider to use functional_enrichment(res,
...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.
Parent node: Node013. Child nodes: Node01111-leaf , Node01112-leaf , Node01113-leaf , Node01114-leaf , Node01115-leaf , Node01116-leaf , Node01121-leaf , Node01122-leaf , Node01123-leaf , Node01131-leaf , Node01132-leaf , Node01133-leaf , Node01134-leaf , Node01211-leaf , Node01212-leaf , Node01221-leaf , Node01222-leaf , Node01231-leaf , Node01232-leaf , Node01233-leaf , Node01311-leaf , Node01312 , Node02221-leaf , Node02222-leaf , Node02223-leaf , Node02224-leaf , Node03111-leaf , Node03112-leaf , Node03113-leaf , Node03411-leaf , Node03412-leaf , Node03413-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 34 columns.
#> Top rows (1000) are extracted by 'SD' method.
#> Subgroups are detected by 'kmeans' method.
#> Performed in total 350 partitions by row resampling.
#> Best k for subgroups seems to be 2.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_partitions"
#> [7] "compare_signatures" "consensus_heatmap" "dimension_reduction"
#> [10] "functional_enrichment" "get_anno_col" "get_anno"
#> [13] "get_classes" "get_consensus" "get_matrix"
#> [16] "get_membership" "get_param" "get_signatures"
#> [19] "get_stats" "is_best_k" "is_stable_k"
#> [22] "membership_heatmap" "ncol" "nrow"
#> [25] "plot_ecdf" "predict_classes" "rownames"
#> [28] "select_partition_number" "show" "suggest_best_k"
#> [31] "test_to_known_factors" "top_rows_heatmap"
collect_plots() function collects all the plots made from res for all k (number of subgroups)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
The plots are:
k and the heatmap of
predicted classes for each k.k.k.k.All the plots in panels can be made by individual functions and they are plotted later in this section.
select_partition_number() produces several plots showing different
statistics for choosing “optimized” k. There are following statistics:
k;k, the area increased is defined as \(A_k - A_{k-1}\).The detailed explanations of these statistics can be found in the cola vignette.
Generally speaking, higher 1-PAC score, higher mean silhouette score or higher
concordance corresponds to better partition. Rand index and Jaccard index
measure how similar the current partition is compared to partition with k-1.
If they are too similar, we won't accept k is better than k-1.
select_partition_number(res)
The numeric values for all these statistics can be obtained by get_stats().
get_stats(res)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> 2 2 1.000 1.000 1.000 0.4284 0.572 0.572
#> 3 3 0.667 0.924 0.926 0.5359 0.750 0.564
#> 4 4 0.796 0.869 0.882 0.1217 0.929 0.779
#> 5 5 0.706 0.674 0.798 0.0626 0.936 0.776
#> 6 6 0.669 0.434 0.562 0.0429 0.911 0.669
#> 7 7 0.677 0.547 0.616 0.0294 0.900 0.533
#> 8 8 0.734 0.454 0.609 0.0277 0.877 0.361
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.VQ.A8PM.01 2 0 1 0 1
#> TCGA.VQ.A91Y.01 2 0 1 0 1
#> TCGA.BR.6456.01 1 0 1 1 0
#> TCGA.IN.AB1V.01 2 0 1 0 1
#> TCGA.BR.8690.01 1 0 1 1 0
#> TCGA.KB.A6F5.01 2 0 1 0 1
#> TCGA.BR.7716.01 1 0 1 1 0
#> TCGA.BR.7723.01 2 0 1 0 1
#> TCGA.MX.A663.01 2 0 1 0 1
#> TCGA.CD.5804.01 2 0 1 0 1
#> TCGA.D7.6818.01 2 0 1 0 1
#> TCGA.CD.8525.01 1 0 1 1 0
#> TCGA.BR.4288.01 2 0 1 0 1
#> TCGA.CD.5800.01 1 0 1 1 0
#> TCGA.CD.5799.01 2 0 1 0 1
#> TCGA.CD.8530.01 2 0 1 0 1
#> TCGA.D7.5579.01 2 0 1 0 1
#> TCGA.R5.A7ZI.01 1 0 1 1 0
#> TCGA.CG.5732.01 2 0 1 0 1
#> TCGA.ZQ.A9CR.01 1 0 1 1 0
#> TCGA.CD.5802.01 2 0 1 0 1
#> TCGA.R5.A7ZF.01 1 0 1 1 0
#> TCGA.RD.A8N1.01 2 0 1 0 1
#> TCGA.VQ.A8E2.01 2 0 1 0 1
#> TCGA.ZA.A8F6.01 2 0 1 0 1
#> TCGA.VQ.A8DL.01 1 0 1 1 0
#> TCGA.D7.8572.01 2 0 1 0 1
#> TCGA.BR.8059.01 2 0 1 0 1
#> TCGA.FP.A8CX.01 2 0 1 0 1
#> TCGA.CD.8526.01 1 0 1 1 0
#> TCGA.D7.8578.01 2 0 1 0 1
#> TCGA.RD.A8MW.01 2 0 1 0 1
#> TCGA.BR.8291.01 2 0 1 0 1
#> TCGA.CD.8529.01 2 0 1 0 1
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.VQ.A8PM.01 2 0.0892 0.906 0.00 0.98 0.02
#> TCGA.VQ.A91Y.01 2 0.0000 0.912 0.00 1.00 0.00
#> TCGA.BR.6456.01 1 0.0892 0.963 0.98 0.00 0.02
#> TCGA.IN.AB1V.01 3 0.3686 0.953 0.00 0.14 0.86
#> TCGA.BR.8690.01 1 0.0000 0.965 1.00 0.00 0.00
#> TCGA.KB.A6F5.01 2 0.0000 0.912 0.00 1.00 0.00
#> TCGA.BR.7716.01 1 0.2959 0.963 0.90 0.00 0.10
#> TCGA.BR.7723.01 2 0.1529 0.892 0.00 0.96 0.04
#> TCGA.MX.A663.01 2 0.0000 0.912 0.00 1.00 0.00
#> TCGA.CD.5804.01 2 0.5216 0.669 0.00 0.74 0.26
#> TCGA.D7.6818.01 3 0.2959 0.989 0.00 0.10 0.90
#> TCGA.CD.8525.01 1 0.2537 0.965 0.92 0.00 0.08
#> TCGA.BR.4288.01 2 0.0000 0.912 0.00 1.00 0.00
#> TCGA.CD.5800.01 1 0.2537 0.965 0.92 0.00 0.08
#> TCGA.CD.5799.01 3 0.3686 0.953 0.00 0.14 0.86
#> TCGA.CD.8530.01 3 0.2959 0.989 0.00 0.10 0.90
#> TCGA.D7.5579.01 3 0.2959 0.989 0.00 0.10 0.90
#> TCGA.R5.A7ZI.01 1 0.0000 0.965 1.00 0.00 0.00
#> TCGA.CG.5732.01 2 0.2537 0.869 0.00 0.92 0.08
#> TCGA.ZQ.A9CR.01 1 0.2537 0.965 0.92 0.00 0.08
#> TCGA.CD.5802.01 2 0.0000 0.912 0.00 1.00 0.00
#> TCGA.R5.A7ZF.01 1 0.0000 0.965 1.00 0.00 0.00
#> TCGA.RD.A8N1.01 2 0.5216 0.669 0.00 0.74 0.26
#> TCGA.VQ.A8E2.01 2 0.0000 0.912 0.00 1.00 0.00
#> TCGA.ZA.A8F6.01 3 0.2959 0.989 0.00 0.10 0.90
#> TCGA.VQ.A8DL.01 1 0.0892 0.963 0.98 0.00 0.02
#> TCGA.D7.8572.01 2 0.1529 0.892 0.00 0.96 0.04
#> TCGA.BR.8059.01 3 0.2959 0.989 0.00 0.10 0.90
#> TCGA.FP.A8CX.01 3 0.2959 0.989 0.00 0.10 0.90
#> TCGA.CD.8526.01 1 0.2959 0.963 0.90 0.00 0.10
#> TCGA.D7.8578.01 3 0.2959 0.989 0.00 0.10 0.90
#> TCGA.RD.A8MW.01 2 0.0000 0.912 0.00 1.00 0.00
#> TCGA.BR.8291.01 2 0.5216 0.669 0.00 0.74 0.26
#> TCGA.CD.8529.01 3 0.2959 0.989 0.00 0.10 0.90
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> TCGA.VQ.A8PM.01 2 0.0000 0.912 0.00 1.00 0.00 0.00
#> TCGA.VQ.A91Y.01 2 0.1211 0.913 0.00 0.96 0.00 0.04
#> TCGA.BR.6456.01 1 0.4522 0.850 0.68 0.00 0.00 0.32
#> TCGA.IN.AB1V.01 3 0.3975 0.710 0.00 0.24 0.76 0.00
#> TCGA.BR.8690.01 1 0.3400 0.872 0.82 0.00 0.00 0.18
#> TCGA.KB.A6F5.01 2 0.1211 0.913 0.00 0.96 0.00 0.04
#> TCGA.BR.7716.01 1 0.2921 0.850 0.86 0.00 0.00 0.14
#> TCGA.BR.7723.01 4 0.5062 0.916 0.00 0.30 0.02 0.68
#> TCGA.MX.A663.01 2 0.1637 0.889 0.00 0.94 0.00 0.06
#> TCGA.CD.5804.01 2 0.1637 0.876 0.00 0.94 0.06 0.00
#> TCGA.D7.6818.01 3 0.1211 0.902 0.00 0.04 0.96 0.00
#> TCGA.CD.8525.01 1 0.0000 0.872 1.00 0.00 0.00 0.00
#> TCGA.BR.4288.01 4 0.4948 0.753 0.00 0.44 0.00 0.56
#> TCGA.CD.5800.01 1 0.0000 0.872 1.00 0.00 0.00 0.00
#> TCGA.CD.5799.01 3 0.4790 0.471 0.00 0.38 0.62 0.00
#> TCGA.CD.8530.01 3 0.0000 0.911 0.00 0.00 1.00 0.00
#> TCGA.D7.5579.01 3 0.1211 0.902 0.00 0.04 0.96 0.00
#> TCGA.R5.A7ZI.01 1 0.3400 0.872 0.82 0.00 0.00 0.18
#> TCGA.CG.5732.01 2 0.0707 0.906 0.00 0.98 0.02 0.00
#> TCGA.ZQ.A9CR.01 1 0.0000 0.872 1.00 0.00 0.00 0.00
#> TCGA.CD.5802.01 2 0.1211 0.913 0.00 0.96 0.00 0.04
#> TCGA.R5.A7ZF.01 1 0.3400 0.872 0.82 0.00 0.00 0.18
#> TCGA.RD.A8N1.01 2 0.1637 0.876 0.00 0.94 0.06 0.00
#> TCGA.VQ.A8E2.01 4 0.4522 0.910 0.00 0.32 0.00 0.68
#> TCGA.ZA.A8F6.01 3 0.0000 0.911 0.00 0.00 1.00 0.00
#> TCGA.VQ.A8DL.01 1 0.4522 0.850 0.68 0.00 0.00 0.32
#> TCGA.D7.8572.01 4 0.5062 0.916 0.00 0.30 0.02 0.68
#> TCGA.BR.8059.01 3 0.0000 0.911 0.00 0.00 1.00 0.00
#> TCGA.FP.A8CX.01 3 0.0000 0.911 0.00 0.00 1.00 0.00
#> TCGA.CD.8526.01 1 0.2921 0.850 0.86 0.00 0.00 0.14
#> TCGA.D7.8578.01 3 0.0707 0.908 0.00 0.02 0.98 0.00
#> TCGA.RD.A8MW.01 2 0.1211 0.913 0.00 0.96 0.00 0.04
#> TCGA.BR.8291.01 2 0.1637 0.876 0.00 0.94 0.06 0.00
#> TCGA.CD.8529.01 3 0.0000 0.911 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.VQ.A8PM.01 5 0.0609 0.6781 0.00 0.00 0.02 0.00 0.98
#> TCGA.VQ.A91Y.01 5 0.3110 0.5976 0.00 0.06 0.00 0.08 0.86
#> TCGA.BR.6456.01 1 0.2732 0.7413 0.84 0.16 0.00 0.00 0.00
#> TCGA.IN.AB1V.01 5 0.6593 -0.0227 0.00 0.22 0.34 0.00 0.44
#> TCGA.BR.8690.01 1 0.4287 0.7863 0.54 0.46 0.00 0.00 0.00
#> TCGA.KB.A6F5.01 5 0.4854 0.3696 0.00 0.06 0.00 0.26 0.68
#> TCGA.BR.7716.01 1 0.0609 0.7376 0.98 0.00 0.00 0.02 0.00
#> TCGA.BR.7723.01 4 0.4263 0.7671 0.00 0.18 0.00 0.76 0.06
#> TCGA.MX.A663.01 5 0.5068 0.2768 0.00 0.06 0.00 0.30 0.64
#> TCGA.CD.5804.01 5 0.3999 0.6274 0.00 0.24 0.02 0.00 0.74
#> TCGA.D7.6818.01 3 0.5759 0.6380 0.00 0.20 0.62 0.00 0.18
#> TCGA.CD.8525.01 1 0.4644 0.7834 0.68 0.28 0.00 0.04 0.00
#> TCGA.BR.4288.01 4 0.4840 0.4902 0.00 0.04 0.00 0.64 0.32
#> TCGA.CD.5800.01 1 0.4644 0.7834 0.68 0.28 0.00 0.04 0.00
#> TCGA.CD.5799.01 5 0.6054 0.4233 0.00 0.28 0.16 0.00 0.56
#> TCGA.CD.8530.01 3 0.0000 0.8307 0.00 0.00 1.00 0.00 0.00
#> TCGA.D7.5579.01 3 0.5759 0.6380 0.00 0.20 0.62 0.00 0.18
#> TCGA.R5.A7ZI.01 1 0.4262 0.7899 0.56 0.44 0.00 0.00 0.00
#> TCGA.CG.5732.01 5 0.3513 0.6580 0.00 0.18 0.02 0.00 0.80
#> TCGA.ZQ.A9CR.01 1 0.4644 0.7834 0.68 0.28 0.00 0.04 0.00
#> TCGA.CD.5802.01 5 0.2438 0.6473 0.00 0.04 0.00 0.06 0.90
#> TCGA.R5.A7ZF.01 1 0.4262 0.7899 0.56 0.44 0.00 0.00 0.00
#> TCGA.RD.A8N1.01 5 0.3513 0.6580 0.00 0.18 0.02 0.00 0.80
#> TCGA.VQ.A8E2.01 4 0.1410 0.8110 0.00 0.00 0.00 0.94 0.06
#> TCGA.ZA.A8F6.01 3 0.0000 0.8307 0.00 0.00 1.00 0.00 0.00
#> TCGA.VQ.A8DL.01 1 0.2732 0.7413 0.84 0.16 0.00 0.00 0.00
#> TCGA.D7.8572.01 4 0.2797 0.8159 0.00 0.06 0.00 0.88 0.06
#> TCGA.BR.8059.01 3 0.0000 0.8307 0.00 0.00 1.00 0.00 0.00
#> TCGA.FP.A8CX.01 3 0.0000 0.8307 0.00 0.00 1.00 0.00 0.00
#> TCGA.CD.8526.01 1 0.0609 0.7376 0.98 0.00 0.00 0.02 0.00
#> TCGA.D7.8578.01 3 0.4373 0.7475 0.00 0.08 0.76 0.00 0.16
#> TCGA.RD.A8MW.01 5 0.3390 0.5819 0.00 0.06 0.00 0.10 0.84
#> TCGA.BR.8291.01 5 0.1648 0.6759 0.00 0.04 0.02 0.00 0.94
#> TCGA.CD.8529.01 3 0.2012 0.8238 0.00 0.06 0.92 0.00 0.02
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> TCGA.VQ.A8PM.01 5 0.148 0.57288 0.00 0.02 0.00 0.04 0.94 0.00
#> TCGA.VQ.A91Y.01 5 0.341 0.24471 0.00 0.00 0.00 0.30 0.70 0.00
#> TCGA.BR.6456.01 1 0.320 0.13602 0.74 0.00 0.00 0.00 0.00 0.26
#> TCGA.IN.AB1V.01 5 0.680 0.16227 0.00 0.12 0.24 0.00 0.50 0.14
#> TCGA.BR.8690.01 6 0.427 0.86201 0.30 0.04 0.00 0.00 0.00 0.66
#> TCGA.KB.A6F5.01 4 0.385 0.23323 0.00 0.00 0.00 0.54 0.46 0.00
#> TCGA.BR.7716.01 1 0.000 0.37640 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BR.7723.01 2 0.365 0.00000 0.00 0.64 0.00 0.36 0.00 0.00
#> TCGA.MX.A663.01 4 0.376 0.35420 0.00 0.00 0.00 0.60 0.40 0.00
#> TCGA.CD.5804.01 5 0.409 0.57974 0.00 0.08 0.00 0.00 0.74 0.18
#> TCGA.D7.6818.01 3 0.648 0.53859 0.00 0.08 0.54 0.00 0.22 0.16
#> TCGA.CD.8525.01 1 0.580 0.00958 0.48 0.20 0.00 0.00 0.00 0.32
#> TCGA.BR.4288.01 4 0.127 0.40287 0.00 0.00 0.00 0.94 0.06 0.00
#> TCGA.CD.5800.01 1 0.580 0.00958 0.48 0.20 0.00 0.00 0.00 0.32
#> TCGA.CD.5799.01 5 0.695 0.36349 0.00 0.14 0.14 0.00 0.48 0.24
#> TCGA.CD.8530.01 3 0.000 0.76932 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.D7.5579.01 3 0.648 0.53859 0.00 0.08 0.54 0.00 0.22 0.16
#> TCGA.R5.A7ZI.01 6 0.350 0.93211 0.32 0.00 0.00 0.00 0.00 0.68
#> TCGA.CG.5732.01 5 0.316 0.59802 0.00 0.02 0.00 0.00 0.80 0.18
#> TCGA.ZQ.A9CR.01 1 0.580 0.00958 0.48 0.20 0.00 0.00 0.00 0.32
#> TCGA.CD.5802.01 5 0.536 0.42502 0.00 0.08 0.00 0.16 0.68 0.08
#> TCGA.R5.A7ZF.01 6 0.350 0.93211 0.32 0.00 0.00 0.00 0.00 0.68
#> TCGA.RD.A8N1.01 5 0.279 0.60352 0.00 0.02 0.00 0.00 0.84 0.14
#> TCGA.VQ.A8E2.01 4 0.127 0.24808 0.00 0.06 0.00 0.94 0.00 0.00
#> TCGA.ZA.A8F6.01 3 0.000 0.76932 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.VQ.A8DL.01 1 0.331 0.11040 0.72 0.00 0.00 0.00 0.00 0.28
#> TCGA.D7.8572.01 4 0.352 -0.08190 0.00 0.18 0.00 0.78 0.00 0.04
#> TCGA.BR.8059.01 3 0.000 0.76932 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.FP.A8CX.01 3 0.000 0.76932 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.CD.8526.01 1 0.000 0.37640 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D7.8578.01 3 0.585 0.57963 0.00 0.10 0.60 0.00 0.24 0.06
#> TCGA.RD.A8MW.01 5 0.392 0.21904 0.00 0.00 0.00 0.30 0.68 0.02
#> TCGA.BR.8291.01 5 0.338 0.57439 0.00 0.08 0.00 0.04 0.84 0.04
#> TCGA.CD.8529.01 3 0.209 0.75342 0.00 0.08 0.90 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.VQ.A8PM.01 5 0.4765 0.554 0.00 0.28 0.00 0.02 0.64 0.04 0.02
#> TCGA.VQ.A91Y.01 5 0.3795 0.616 0.00 0.22 0.00 0.06 0.72 0.00 0.00
#> TCGA.BR.6456.01 1 0.4242 0.573 0.72 0.02 0.00 0.00 0.08 0.18 0.00
#> TCGA.IN.AB1V.01 2 0.6714 0.450 0.00 0.54 0.12 0.00 0.14 0.06 0.14
#> TCGA.BR.8690.01 6 0.5638 0.141 0.32 0.00 0.00 0.00 0.00 0.36 0.32
#> TCGA.KB.A6F5.01 5 0.5293 0.404 0.00 0.12 0.00 0.32 0.54 0.00 0.02
#> TCGA.BR.7716.01 1 0.1671 0.643 0.90 0.00 0.00 0.00 0.00 0.00 0.10
#> TCGA.BR.7723.01 6 0.5438 -0.473 0.00 0.02 0.00 0.42 0.12 0.44 0.00
#> TCGA.MX.A663.01 5 0.5707 0.173 0.00 0.10 0.00 0.40 0.46 0.02 0.02
#> TCGA.CD.5804.01 2 0.2864 0.651 0.00 0.84 0.02 0.00 0.12 0.00 0.02
#> TCGA.D7.6818.01 3 0.5665 0.307 0.00 0.40 0.42 0.00 0.00 0.02 0.16
#> TCGA.CD.8525.01 7 0.2708 0.987 0.22 0.00 0.00 0.00 0.00 0.00 0.78
#> TCGA.BR.4288.01 4 0.3780 0.596 0.00 0.00 0.00 0.72 0.24 0.02 0.02
#> TCGA.CD.5800.01 7 0.3186 0.974 0.22 0.02 0.00 0.00 0.00 0.00 0.76
#> TCGA.CD.5799.01 2 0.3546 0.627 0.00 0.82 0.06 0.00 0.02 0.02 0.08
#> TCGA.CD.8530.01 3 0.0000 0.732 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.D7.5579.01 3 0.5298 0.350 0.00 0.44 0.44 0.00 0.00 0.02 0.10
#> TCGA.R5.A7ZI.01 6 0.5798 0.351 0.34 0.00 0.00 0.00 0.02 0.44 0.20
#> TCGA.CG.5732.01 2 0.2906 0.603 0.00 0.80 0.00 0.00 0.18 0.00 0.02
#> TCGA.ZQ.A9CR.01 7 0.2708 0.987 0.22 0.00 0.00 0.00 0.00 0.00 0.78
#> TCGA.CD.5802.01 5 0.5411 0.519 0.00 0.30 0.00 0.02 0.58 0.04 0.06
#> TCGA.R5.A7ZF.01 6 0.5375 0.355 0.34 0.00 0.00 0.00 0.00 0.46 0.20
#> TCGA.RD.A8N1.01 2 0.4447 0.466 0.00 0.66 0.02 0.00 0.28 0.02 0.02
#> TCGA.VQ.A8E2.01 4 0.0863 0.789 0.00 0.00 0.00 0.96 0.04 0.00 0.00
#> TCGA.ZA.A8F6.01 3 0.0000 0.732 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.VQ.A8DL.01 1 0.4644 0.543 0.68 0.00 0.00 0.02 0.12 0.18 0.00
#> TCGA.D7.8572.01 4 0.2421 0.737 0.00 0.00 0.00 0.88 0.08 0.02 0.02
#> TCGA.BR.8059.01 3 0.0000 0.732 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.FP.A8CX.01 3 0.0000 0.732 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.CD.8526.01 1 0.1671 0.643 0.90 0.00 0.00 0.00 0.00 0.00 0.10
#> TCGA.D7.8578.01 3 0.6812 0.430 0.00 0.16 0.52 0.00 0.16 0.06 0.10
#> TCGA.RD.A8MW.01 5 0.4139 0.622 0.00 0.20 0.00 0.06 0.72 0.00 0.02
#> TCGA.BR.8291.01 5 0.5225 0.395 0.00 0.34 0.02 0.00 0.56 0.06 0.02
#> TCGA.CD.8529.01 3 0.4092 0.655 0.00 0.16 0.74 0.00 0.00 0.02 0.08
cbind(get_classes(res, k = 8), get_membership(res, k = 8))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7 p8
#> TCGA.VQ.A8PM.01 8 0.2114 0.4644 0.00 0.00 0.00 0.00 0.16 0.00 0.00 0.84
#> TCGA.VQ.A91Y.01 5 0.4137 0.2866 0.00 0.02 0.00 0.02 0.50 0.00 0.00 0.46
#> TCGA.BR.6456.01 1 0.1091 0.4777 0.94 0.00 0.00 0.06 0.00 0.00 0.00 0.00
#> TCGA.IN.AB1V.01 8 0.6116 -0.1479 0.00 0.24 0.04 0.10 0.00 0.00 0.10 0.52
#> TCGA.BR.8690.01 1 0.5766 -0.0911 0.50 0.10 0.00 0.04 0.00 0.00 0.32 0.04
#> TCGA.KB.A6F5.01 5 0.2484 0.4967 0.00 0.02 0.00 0.02 0.86 0.00 0.00 0.10
#> TCGA.BR.7716.01 1 0.5257 0.2605 0.54 0.04 0.00 0.28 0.00 0.00 0.14 0.00
#> TCGA.BR.7723.01 6 0.0471 0.0000 0.00 0.00 0.00 0.00 0.02 0.98 0.00 0.00
#> TCGA.MX.A663.01 5 0.1275 0.4305 0.00 0.00 0.00 0.02 0.94 0.00 0.00 0.04
#> TCGA.CD.5804.01 2 0.3928 0.4693 0.00 0.74 0.00 0.02 0.02 0.00 0.04 0.18
#> TCGA.D7.6818.01 2 0.6822 0.2698 0.00 0.44 0.24 0.10 0.00 0.00 0.12 0.10
#> TCGA.CD.8525.01 7 0.2756 0.9714 0.26 0.00 0.00 0.00 0.00 0.00 0.74 0.00
#> TCGA.BR.4288.01 5 0.2864 0.0913 0.00 0.00 0.00 0.08 0.84 0.02 0.06 0.00
#> TCGA.CD.5800.01 7 0.2756 0.9714 0.26 0.00 0.00 0.00 0.00 0.00 0.74 0.00
#> TCGA.CD.5799.01 2 0.4466 0.3861 0.00 0.60 0.00 0.04 0.00 0.00 0.04 0.32
#> TCGA.CD.8530.01 3 0.0000 0.8760 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D7.5579.01 2 0.6667 0.2691 0.00 0.46 0.24 0.08 0.00 0.00 0.12 0.10
#> TCGA.R5.A7ZI.01 1 0.3924 0.3234 0.72 0.04 0.00 0.04 0.00 0.00 0.20 0.00
#> TCGA.CG.5732.01 2 0.4276 0.4226 0.00 0.70 0.00 0.04 0.08 0.00 0.00 0.18
#> TCGA.ZQ.A9CR.01 7 0.3504 0.9422 0.26 0.04 0.00 0.00 0.00 0.00 0.70 0.00
#> TCGA.CD.5802.01 8 0.3227 0.4521 0.00 0.00 0.00 0.08 0.14 0.00 0.00 0.78
#> TCGA.R5.A7ZF.01 1 0.4363 0.3153 0.70 0.04 0.00 0.04 0.00 0.00 0.20 0.02
#> TCGA.RD.A8N1.01 2 0.3737 0.2246 0.00 0.50 0.00 0.00 0.02 0.00 0.00 0.48
#> TCGA.VQ.A8E2.01 4 0.4954 0.7746 0.00 0.00 0.00 0.46 0.42 0.10 0.02 0.00
#> TCGA.ZA.A8F6.01 3 0.0000 0.8760 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.VQ.A8DL.01 1 0.1874 0.4712 0.92 0.02 0.00 0.02 0.00 0.02 0.00 0.02
#> TCGA.D7.8572.01 4 0.5575 0.7539 0.00 0.00 0.00 0.46 0.32 0.18 0.00 0.04
#> TCGA.BR.8059.01 3 0.0000 0.8760 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FP.A8CX.01 3 0.0000 0.8760 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CD.8526.01 1 0.5257 0.2605 0.54 0.04 0.00 0.28 0.00 0.00 0.14 0.00
#> TCGA.D7.8578.01 8 0.5891 0.1898 0.00 0.12 0.26 0.08 0.00 0.00 0.02 0.52
#> TCGA.RD.A8MW.01 5 0.4586 0.3363 0.00 0.02 0.00 0.06 0.52 0.00 0.00 0.40
#> TCGA.BR.8291.01 8 0.2025 0.5201 0.00 0.00 0.00 0.00 0.10 0.00 0.02 0.88
#> TCGA.CD.8529.01 3 0.5781 0.3548 0.00 0.20 0.56 0.08 0.00 0.00 0.14 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: Node0131. Child nodes: Node013121-leaf , Node013122-leaf , Node013123-leaf .
The object with results only for a single top-value method and a single partitioning method can be extracted as:
res = res_rh["01312"]
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 24 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 0.930 0.968 0.3987 0.569 0.569
#> 3 3 1.000 0.970 0.986 0.6739 0.659 0.450
#> 4 4 0.762 0.828 0.887 0.0759 0.833 0.586
#> 5 5 0.751 0.351 0.725 0.0907 0.851 0.586
#> 6 6 0.762 0.774 0.845 0.0404 0.899 0.646
#> 7 7 0.835 0.747 0.838 0.0337 0.877 0.500
#> 8 8 0.797 0.648 0.696 0.0196 0.953 0.717
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.VQ.A8PM.01 1 0.000 1.000 1.00 0.00
#> TCGA.VQ.A91Y.01 1 0.000 1.000 1.00 0.00
#> TCGA.IN.AB1V.01 1 0.000 1.000 1.00 0.00
#> TCGA.KB.A6F5.01 2 0.958 0.489 0.38 0.62
#> TCGA.BR.7723.01 2 0.000 0.868 0.00 1.00
#> TCGA.MX.A663.01 2 0.000 0.868 0.00 1.00
#> TCGA.CD.5804.01 1 0.000 1.000 1.00 0.00
#> TCGA.D7.6818.01 1 0.000 1.000 1.00 0.00
#> TCGA.BR.4288.01 2 0.000 0.868 0.00 1.00
#> TCGA.CD.5799.01 1 0.000 1.000 1.00 0.00
#> TCGA.CD.8530.01 1 0.000 1.000 1.00 0.00
#> TCGA.D7.5579.01 1 0.000 1.000 1.00 0.00
#> TCGA.CG.5732.01 1 0.000 1.000 1.00 0.00
#> TCGA.CD.5802.01 2 0.958 0.489 0.38 0.62
#> TCGA.RD.A8N1.01 1 0.000 1.000 1.00 0.00
#> TCGA.VQ.A8E2.01 2 0.000 0.868 0.00 1.00
#> TCGA.ZA.A8F6.01 1 0.000 1.000 1.00 0.00
#> TCGA.D7.8572.01 2 0.000 0.868 0.00 1.00
#> TCGA.BR.8059.01 1 0.000 1.000 1.00 0.00
#> TCGA.FP.A8CX.01 1 0.000 1.000 1.00 0.00
#> TCGA.D7.8578.01 1 0.000 1.000 1.00 0.00
#> TCGA.RD.A8MW.01 1 0.000 1.000 1.00 0.00
#> TCGA.BR.8291.01 1 0.000 1.000 1.00 0.00
#> TCGA.CD.8529.01 1 0.000 1.000 1.00 0.00
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.VQ.A8PM.01 3 0.000 0.951 0.00 0 1.00
#> TCGA.VQ.A91Y.01 3 0.000 0.951 0.00 0 1.00
#> TCGA.IN.AB1V.01 1 0.000 1.000 1.00 0 0.00
#> TCGA.KB.A6F5.01 3 0.000 0.951 0.00 0 1.00
#> TCGA.BR.7723.01 2 0.000 1.000 0.00 1 0.00
#> TCGA.MX.A663.01 2 0.000 1.000 0.00 1 0.00
#> TCGA.CD.5804.01 3 0.000 0.951 0.00 0 1.00
#> TCGA.D7.6818.01 1 0.000 1.000 1.00 0 0.00
#> TCGA.BR.4288.01 2 0.000 1.000 0.00 1 0.00
#> TCGA.CD.5799.01 1 0.000 1.000 1.00 0 0.00
#> TCGA.CD.8530.01 1 0.000 1.000 1.00 0 0.00
#> TCGA.D7.5579.01 1 0.000 1.000 1.00 0 0.00
#> TCGA.CG.5732.01 3 0.429 0.797 0.18 0 0.82
#> TCGA.CD.5802.01 3 0.000 0.951 0.00 0 1.00
#> TCGA.RD.A8N1.01 1 0.000 1.000 1.00 0 0.00
#> TCGA.VQ.A8E2.01 2 0.000 1.000 0.00 1 0.00
#> TCGA.ZA.A8F6.01 1 0.000 1.000 1.00 0 0.00
#> TCGA.D7.8572.01 2 0.000 1.000 0.00 1 0.00
#> TCGA.BR.8059.01 1 0.000 1.000 1.00 0 0.00
#> TCGA.FP.A8CX.01 1 0.000 1.000 1.00 0 0.00
#> TCGA.D7.8578.01 3 0.000 0.951 0.00 0 1.00
#> TCGA.RD.A8MW.01 3 0.000 0.951 0.00 0 1.00
#> TCGA.BR.8291.01 3 0.400 0.820 0.16 0 0.84
#> TCGA.CD.8529.01 1 0.000 1.000 1.00 0 0.00
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> TCGA.VQ.A8PM.01 3 0.317 0.811 0.00 0 0.84 0.16
#> TCGA.VQ.A91Y.01 4 0.201 0.894 0.00 0 0.08 0.92
#> TCGA.IN.AB1V.01 1 0.317 0.851 0.84 0 0.16 0.00
#> TCGA.KB.A6F5.01 4 0.292 0.778 0.00 0 0.14 0.86
#> TCGA.BR.7723.01 2 0.000 1.000 0.00 1 0.00 0.00
#> TCGA.MX.A663.01 2 0.000 1.000 0.00 1 0.00 0.00
#> TCGA.CD.5804.01 3 0.380 0.365 0.00 0 0.78 0.22
#> TCGA.D7.6818.01 1 0.317 0.851 0.84 0 0.16 0.00
#> TCGA.BR.4288.01 2 0.000 1.000 0.00 1 0.00 0.00
#> TCGA.CD.5799.01 1 0.121 0.819 0.96 0 0.00 0.04
#> TCGA.CD.8530.01 1 0.000 0.838 1.00 0 0.00 0.00
#> TCGA.D7.5579.01 1 0.317 0.851 0.84 0 0.16 0.00
#> TCGA.CG.5732.01 1 0.738 0.535 0.52 0 0.22 0.26
#> TCGA.CD.5802.01 3 0.317 0.811 0.00 0 0.84 0.16
#> TCGA.RD.A8N1.01 1 0.559 0.780 0.72 0 0.18 0.10
#> TCGA.VQ.A8E2.01 2 0.000 1.000 0.00 1 0.00 0.00
#> TCGA.ZA.A8F6.01 1 0.000 0.838 1.00 0 0.00 0.00
#> TCGA.D7.8572.01 2 0.000 1.000 0.00 1 0.00 0.00
#> TCGA.BR.8059.01 1 0.000 0.838 1.00 0 0.00 0.00
#> TCGA.FP.A8CX.01 1 0.000 0.838 1.00 0 0.00 0.00
#> TCGA.D7.8578.01 3 0.317 0.811 0.00 0 0.84 0.16
#> TCGA.RD.A8MW.01 4 0.201 0.894 0.00 0 0.08 0.92
#> TCGA.BR.8291.01 1 0.700 0.628 0.58 0 0.22 0.20
#> TCGA.CD.8529.01 1 0.317 0.851 0.84 0 0.16 0.00
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> TCGA.VQ.A8PM.01 3 0.0609 0.9768 0.00 0.02 0.98 0.00 0.00
#> TCGA.VQ.A91Y.01 4 0.0609 0.8862 0.00 0.00 0.02 0.98 0.00
#> TCGA.IN.AB1V.01 1 0.0000 0.7230 1.00 0.00 0.00 0.00 0.00
#> TCGA.KB.A6F5.01 4 0.3922 0.7589 0.00 0.00 0.04 0.78 0.18
#> TCGA.BR.7723.01 2 0.4227 -0.8645 0.00 0.58 0.00 0.00 0.42
#> TCGA.MX.A663.01 5 0.4829 0.0000 0.00 0.48 0.00 0.02 0.50
#> TCGA.CD.5804.01 2 0.7909 0.0389 0.28 0.42 0.10 0.20 0.00
#> TCGA.D7.6818.01 1 0.0000 0.7230 1.00 0.00 0.00 0.00 0.00
#> TCGA.BR.4288.01 2 0.4227 -0.8645 0.00 0.58 0.00 0.00 0.42
#> TCGA.CD.5799.01 1 0.4060 0.6927 0.64 0.00 0.00 0.00 0.36
#> TCGA.CD.8530.01 1 0.3684 0.7469 0.72 0.00 0.00 0.00 0.28
#> TCGA.D7.5579.01 1 0.0000 0.7230 1.00 0.00 0.00 0.00 0.00
#> TCGA.CG.5732.01 2 0.6619 0.0718 0.36 0.42 0.00 0.22 0.00
#> TCGA.CD.5802.01 3 0.0000 0.9885 0.00 0.00 1.00 0.00 0.00
#> TCGA.RD.A8N1.01 1 0.6555 -0.2684 0.40 0.40 0.00 0.20 0.00
#> TCGA.VQ.A8E2.01 2 0.4227 -0.8645 0.00 0.58 0.00 0.00 0.42
#> TCGA.ZA.A8F6.01 1 0.3684 0.7469 0.72 0.00 0.00 0.00 0.28
#> TCGA.D7.8572.01 2 0.4818 -0.9367 0.00 0.52 0.00 0.02 0.46
#> TCGA.BR.8059.01 1 0.3684 0.7469 0.72 0.00 0.00 0.00 0.28
#> TCGA.FP.A8CX.01 1 0.3684 0.7469 0.72 0.00 0.00 0.00 0.28
#> TCGA.D7.8578.01 3 0.0000 0.9885 0.00 0.00 1.00 0.00 0.00
#> TCGA.RD.A8MW.01 4 0.0609 0.8862 0.00 0.00 0.02 0.98 0.00
#> TCGA.BR.8291.01 2 0.6555 0.0517 0.40 0.40 0.00 0.20 0.00
#> TCGA.CD.8529.01 1 0.0000 0.7230 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.VQ.A8PM.01 3 0.0937 0.953 0.00 0.00 0.96 0.00 0.04 0.00
#> TCGA.VQ.A91Y.01 4 0.2631 0.828 0.00 0.00 0.00 0.82 0.18 0.00
#> TCGA.IN.AB1V.01 1 0.0000 0.727 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.KB.A6F5.01 4 0.2454 0.684 0.00 0.00 0.00 0.84 0.00 0.16
#> TCGA.BR.7723.01 2 0.0000 0.808 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.MX.A663.01 2 0.3797 0.695 0.00 0.58 0.00 0.00 0.00 0.42
#> TCGA.CD.5804.01 5 0.4810 0.748 0.12 0.00 0.00 0.00 0.66 0.22
#> TCGA.D7.6818.01 1 0.0000 0.727 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BR.4288.01 2 0.0000 0.808 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.CD.5799.01 1 0.5618 0.646 0.50 0.00 0.00 0.00 0.34 0.16
#> TCGA.CD.8530.01 1 0.2048 0.748 0.88 0.00 0.00 0.00 0.12 0.00
#> TCGA.D7.5579.01 1 0.0000 0.727 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CG.5732.01 5 0.5029 0.735 0.12 0.00 0.00 0.00 0.62 0.26
#> TCGA.CD.5802.01 3 0.0000 0.977 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.RD.A8N1.01 5 0.3647 0.771 0.36 0.00 0.00 0.00 0.64 0.00
#> TCGA.VQ.A8E2.01 2 0.0000 0.808 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.ZA.A8F6.01 1 0.4420 0.731 0.62 0.00 0.00 0.00 0.34 0.04
#> TCGA.D7.8572.01 2 0.3797 0.695 0.00 0.58 0.00 0.00 0.00 0.42
#> TCGA.BR.8059.01 1 0.4420 0.731 0.62 0.00 0.00 0.00 0.34 0.04
#> TCGA.FP.A8CX.01 1 0.4420 0.731 0.62 0.00 0.00 0.00 0.34 0.04
#> TCGA.D7.8578.01 3 0.0000 0.977 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.RD.A8MW.01 4 0.2631 0.828 0.00 0.00 0.00 0.82 0.18 0.00
#> TCGA.BR.8291.01 5 0.3647 0.771 0.36 0.00 0.00 0.00 0.64 0.00
#> TCGA.CD.8529.01 1 0.0000 0.727 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.VQ.A8PM.01 3 0.0863 0.917 0.00 0.00 0.96 0.00 0.04 0.00 0.00
#> TCGA.VQ.A91Y.01 6 0.0504 0.879 0.00 0.00 0.00 0.00 0.02 0.98 0.00
#> TCGA.IN.AB1V.01 1 0.0000 0.741 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.KB.A6F5.01 6 0.4092 0.745 0.00 0.00 0.00 0.16 0.02 0.74 0.08
#> TCGA.BR.7723.01 2 0.0000 0.817 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.MX.A663.01 2 0.3459 0.699 0.00 0.60 0.00 0.40 0.00 0.00 0.00
#> TCGA.CD.5804.01 5 0.3780 0.766 0.02 0.00 0.02 0.24 0.72 0.00 0.00
#> TCGA.D7.6818.01 1 0.0000 0.741 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BR.4288.01 2 0.0000 0.817 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CD.5799.01 7 0.4204 0.541 0.16 0.00 0.00 0.14 0.00 0.00 0.70
#> TCGA.CD.8530.01 1 0.2259 0.482 0.84 0.00 0.00 0.00 0.00 0.00 0.16
#> TCGA.D7.5579.01 1 0.0000 0.741 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CG.5732.01 5 0.1363 0.761 0.02 0.00 0.00 0.00 0.94 0.00 0.04
#> TCGA.CD.5802.01 3 0.1671 0.902 0.00 0.00 0.90 0.10 0.00 0.00 0.00
#> TCGA.RD.A8N1.01 1 0.4789 0.384 0.60 0.00 0.00 0.14 0.26 0.00 0.00
#> TCGA.VQ.A8E2.01 2 0.0863 0.812 0.00 0.96 0.00 0.00 0.00 0.00 0.04
#> TCGA.ZA.A8F6.01 7 0.3413 0.842 0.38 0.00 0.00 0.00 0.00 0.00 0.62
#> TCGA.D7.8572.01 2 0.3358 0.722 0.00 0.64 0.00 0.36 0.00 0.00 0.00
#> TCGA.BR.8059.01 7 0.3413 0.842 0.38 0.00 0.00 0.00 0.00 0.00 0.62
#> TCGA.FP.A8CX.01 7 0.3413 0.842 0.38 0.00 0.00 0.00 0.00 0.00 0.62
#> TCGA.D7.8578.01 3 0.0000 0.932 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.RD.A8MW.01 6 0.0504 0.879 0.00 0.00 0.00 0.00 0.02 0.98 0.00
#> TCGA.BR.8291.01 1 0.4789 0.384 0.60 0.00 0.00 0.14 0.26 0.00 0.00
#> TCGA.CD.8529.01 1 0.0000 0.741 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.VQ.A8PM.01 3 0.0941 0.911 0.00 0.00 0.96 0.00 0.02 0.00 0.00 0.02
#> TCGA.VQ.A91Y.01 6 0.4077 0.785 0.00 0.00 0.00 0.40 0.02 0.56 0.02 0.00
#> TCGA.IN.AB1V.01 1 0.0471 0.878 0.98 0.00 0.00 0.00 0.00 0.00 0.02 0.00
#> TCGA.KB.A6F5.01 6 0.0000 0.547 0.00 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.BR.7723.01 2 0.0000 0.733 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.MX.A663.01 2 0.5837 0.570 0.00 0.48 0.00 0.16 0.00 0.04 0.02 0.30
#> TCGA.CD.5804.01 8 0.4511 -0.215 0.00 0.00 0.00 0.10 0.38 0.00 0.00 0.52
#> TCGA.D7.6818.01 1 0.0808 0.853 0.96 0.00 0.00 0.04 0.00 0.00 0.00 0.00
#> TCGA.BR.4288.01 2 0.0000 0.733 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CD.5799.01 7 0.4590 0.193 0.10 0.00 0.00 0.16 0.00 0.00 0.68 0.06
#> TCGA.CD.8530.01 1 0.2534 0.520 0.78 0.00 0.00 0.00 0.00 0.00 0.22 0.00
#> TCGA.D7.5579.01 1 0.0000 0.887 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CG.5732.01 5 0.0471 0.000 0.02 0.00 0.00 0.00 0.98 0.00 0.00 0.00
#> TCGA.CD.5802.01 3 0.2348 0.880 0.00 0.00 0.88 0.06 0.00 0.00 0.04 0.02
#> TCGA.RD.A8N1.01 8 0.4804 0.617 0.40 0.00 0.00 0.00 0.14 0.00 0.00 0.46
#> TCGA.VQ.A8E2.01 2 0.1557 0.720 0.00 0.92 0.00 0.06 0.00 0.00 0.02 0.00
#> TCGA.ZA.A8F6.01 7 0.3272 0.709 0.42 0.00 0.00 0.00 0.00 0.00 0.58 0.00
#> TCGA.D7.8572.01 2 0.5159 0.598 0.00 0.52 0.00 0.16 0.00 0.00 0.02 0.30
#> TCGA.BR.8059.01 7 0.3272 0.709 0.42 0.00 0.00 0.00 0.00 0.00 0.58 0.00
#> TCGA.FP.A8CX.01 7 0.3272 0.709 0.42 0.00 0.00 0.00 0.00 0.00 0.58 0.00
#> TCGA.D7.8578.01 3 0.0000 0.923 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.RD.A8MW.01 6 0.3690 0.785 0.00 0.00 0.00 0.42 0.02 0.56 0.00 0.00
#> TCGA.BR.8291.01 8 0.4804 0.617 0.40 0.00 0.00 0.00 0.14 0.00 0.00 0.46
#> TCGA.CD.8529.01 1 0.0000 0.887 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
consensus_heatmap(res, k = 7)
consensus_heatmap(res, k = 8)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
membership_heatmap(res, k = 7)
membership_heatmap(res, k = 8)
As soon as the classes for columns are determined, the signatures that are significantly different between subgroups can be looked for. Following are the heatmaps for signatures.
get_signatures(res, k = 2)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
get_signatures(res, k = 7)
get_signatures(res, k = 8)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. To get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows (which is done by automatically selecting number of clusters).If there are too many signatures, top_signatures = ... can be set to only show the
signatures with the highest FDRs:
# code only for demonstration
# e.g. to show the top 500 most significant rows
tb = get_signature(res, k = ..., top_signatures = 500)
If the signatures are defined as these which are uniquely high in current group, diff_method argument
can be set to "uniquely_high_in_one_group":
# code only for demonstration
tb = get_signature(res, k = ..., diff_method = "uniquely_high_in_one_group")
UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
dimension_reduction(res, k = 7, method = "UMAP")
dimension_reduction(res, k = 8, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
If matrix rows can be associated to genes, consider to use functional_enrichment(res,
...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.
Parent node: Node0. Child nodes: Node011 , Node012 , Node013 , Node021 , Node022 , Node023 , Node031 , Node032-leaf , Node033 , Node034 .
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 105 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 0.3955 0.605 0.605
#> 3 3 0.981 0.986 0.970 0.5967 0.745 0.579
#> 4 4 0.799 0.517 0.696 0.1047 0.778 0.581
#> 5 5 0.751 0.785 0.873 0.0709 0.751 0.491
#> 6 6 0.731 0.800 0.865 0.0321 0.969 0.877
#> 7 7 0.844 0.681 0.853 0.0357 0.964 0.841
#> 8 8 0.831 0.688 0.808 0.0216 0.971 0.855
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.BR.6452.01 2 0 1 0 1
#> TCGA.VQ.A8PO.01 2 0 1 0 1
#> TCGA.VQ.AA69.01 1 0 1 1 0
#> TCGA.BR.8589.01 1 0 1 1 0
#> TCGA.BR.8382.01 2 0 1 0 1
#> TCGA.HU.8604.01 2 0 1 0 1
#> TCGA.BR.8676.01 1 0 1 1 0
#> TCGA.VQ.A923.01 1 0 1 1 0
#> TCGA.BR.8679.01 2 0 1 0 1
#> TCGA.VQ.A92D.01 2 0 1 0 1
#> TCGA.BR.6455.01 1 0 1 1 0
#> TCGA.BR.8591.01 2 0 1 0 1
#> TCGA.HU.8608.01 1 0 1 1 0
#> TCGA.VQ.A91D.01 2 0 1 0 1
#> TCGA.HU.8602.01 2 0 1 0 1
#> TCGA.BR.8381.01 1 0 1 1 0
#> TCGA.IN.8663.01 2 0 1 0 1
#> TCGA.VQ.A91W.01 1 0 1 1 0
#> TCGA.F1.6177.01 2 0 1 0 1
#> TCGA.VQ.AA6I.01 2 0 1 0 1
#> TCGA.CG.4437.01 2 0 1 0 1
#> TCGA.VQ.A8PP.01 2 0 1 0 1
#> TCGA.VQ.A8PF.01 1 0 1 1 0
#> TCGA.BR.8487.01 2 0 1 0 1
#> TCGA.VQ.A91K.01 2 0 1 0 1
#> TCGA.BR.8686.01 1 0 1 1 0
#> TCGA.IN.A6RO.01 2 0 1 0 1
#> TCGA.BR.A4QI.01 2 0 1 0 1
#> TCGA.HU.A4G2.01 1 0 1 1 0
#> TCGA.BR.A4IY.01 1 0 1 1 0
#> TCGA.BR.A4J4.01 1 0 1 1 0
#> TCGA.VQ.A94R.01 2 0 1 0 1
#> TCGA.BR.7707.01 2 0 1 0 1
#> TCGA.FP.7829.01 2 0 1 0 1
#> TCGA.HU.A4H0.01 1 0 1 1 0
#> TCGA.BR.A4PF.01 2 0 1 0 1
#> TCGA.CD.A4MJ.01 2 0 1 0 1
#> TCGA.HU.A4GP.01 2 0 1 0 1
#> TCGA.D7.A4YY.01 2 0 1 0 1
#> TCGA.VQ.AA6G.01 2 0 1 0 1
#> TCGA.CD.A4MI.01 2 0 1 0 1
#> TCGA.VQ.A924.01 2 0 1 0 1
#> TCGA.HU.A4H8.01 2 0 1 0 1
#> TCGA.HU.A4H3.01 2 0 1 0 1
#> TCGA.BR.A4PE.01 2 0 1 0 1
#> TCGA.BR.A4J8.01 2 0 1 0 1
#> TCGA.HU.A4GT.01 2 0 1 0 1
#> TCGA.BR.A4CQ.01 2 0 1 0 1
#> TCGA.HU.A4GQ.01 2 0 1 0 1
#> TCGA.BR.A4QM.01 2 0 1 0 1
#> TCGA.D7.A4YX.01 1 0 1 1 0
#> TCGA.VQ.A8PT.01 2 0 1 0 1
#> TCGA.CD.A4MG.01 2 0 1 0 1
#> TCGA.D7.A4YV.01 2 0 1 0 1
#> TCGA.BR.A4QL.01 2 0 1 0 1
#> TCGA.BR.7703.01 2 0 1 0 1
#> TCGA.D7.A6EZ.01 1 0 1 1 0
#> TCGA.D7.A4YU.01 2 0 1 0 1
#> TCGA.IN.A6RP.01 2 0 1 0 1
#> TCGA.HU.A4GU.01 2 0 1 0 1
#> TCGA.MX.A5UJ.01 2 0 1 0 1
#> TCGA.HU.A4GN.01 2 0 1 0 1
#> TCGA.HU.A4H6.01 2 0 1 0 1
#> TCGA.HF.7132.01 2 0 1 0 1
#> TCGA.HF.7134.01 2 0 1 0 1
#> TCGA.BR.8370.01 2 0 1 0 1
#> TCGA.D7.5577.01 1 0 1 1 0
#> TCGA.BR.6707.01 1 0 1 1 0
#> TCGA.B7.5818.01 1 0 1 1 0
#> TCGA.CG.5733.01 2 0 1 0 1
#> TCGA.BR.7851.01 2 0 1 0 1
#> TCGA.CG.5726.01 2 0 1 0 1
#> TCGA.BR.8363.01 2 0 1 0 1
#> TCGA.CG.5720.01 2 0 1 0 1
#> TCGA.D7.8570.01 1 0 1 1 0
#> TCGA.BR.8284.01 2 0 1 0 1
#> TCGA.B7.A5TJ.01 2 0 1 0 1
#> TCGA.BR.8366.01 1 0 1 1 0
#> TCGA.VQ.A8E3.01 2 0 1 0 1
#> TCGA.CD.5801.01 1 0 1 1 0
#> TCGA.BR.7958.01 1 0 1 1 0
#> TCGA.FP.7916.01 1 0 1 1 0
#> TCGA.SW.A7EA.01 2 0 1 0 1
#> TCGA.BR.8368.01 2 0 1 0 1
#> TCGA.BR.8081.01 2 0 1 0 1
#> TCGA.CD.8535.01 2 0 1 0 1
#> TCGA.HF.A5NB.01 2 0 1 0 1
#> TCGA.CD.A48C.01 2 0 1 0 1
#> TCGA.BR.8285.01 1 0 1 1 0
#> TCGA.BR.8361.01 2 0 1 0 1
#> TCGA.HU.A4G9.01 2 0 1 0 1
#> TCGA.CD.8528.01 2 0 1 0 1
#> TCGA.FP.A4BE.01 2 0 1 0 1
#> TCGA.BR.8078.01 2 0 1 0 1
#> TCGA.CD.8531.01 1 0 1 1 0
#> TCGA.VQ.A8DT.01 2 0 1 0 1
#> TCGA.HU.A4G6.01 1 0 1 1 0
#> TCGA.HU.A4G3.01 2 0 1 0 1
#> TCGA.D7.A74A.01 2 0 1 0 1
#> TCGA.BR.8372.01 2 0 1 0 1
#> TCGA.HU.8244.01 2 0 1 0 1
#> TCGA.IN.A6RR.01 2 0 1 0 1
#> TCGA.VQ.A8P2.01 2 0 1 0 1
#> TCGA.D7.8573.01 1 0 1 1 0
#> TCGA.BR.8360.01 2 0 1 0 1
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.BR.6452.01 3 0.254 0.994 0.00 0.08 0.92
#> TCGA.VQ.A8PO.01 2 0.000 0.993 0.00 1.00 0.00
#> TCGA.VQ.AA69.01 1 0.000 0.991 1.00 0.00 0.00
#> TCGA.BR.8589.01 1 0.000 0.991 1.00 0.00 0.00
#> TCGA.BR.8382.01 3 0.254 0.994 0.00 0.08 0.92
#> TCGA.HU.8604.01 3 0.254 0.994 0.00 0.08 0.92
#> TCGA.BR.8676.01 1 0.000 0.991 1.00 0.00 0.00
#> TCGA.VQ.A923.01 1 0.000 0.991 1.00 0.00 0.00
#> TCGA.BR.8679.01 2 0.000 0.993 0.00 1.00 0.00
#> TCGA.VQ.A92D.01 2 0.000 0.993 0.00 1.00 0.00
#> TCGA.BR.6455.01 1 0.000 0.991 1.00 0.00 0.00
#> TCGA.BR.8591.01 3 0.254 0.994 0.00 0.08 0.92
#> TCGA.HU.8608.01 1 0.000 0.991 1.00 0.00 0.00
#> TCGA.VQ.A91D.01 3 0.254 0.994 0.00 0.08 0.92
#> TCGA.HU.8602.01 3 0.254 0.994 0.00 0.08 0.92
#> TCGA.BR.8381.01 1 0.000 0.991 1.00 0.00 0.00
#> TCGA.IN.8663.01 2 0.000 0.993 0.00 1.00 0.00
#> TCGA.VQ.A91W.01 1 0.000 0.991 1.00 0.00 0.00
#> TCGA.F1.6177.01 2 0.000 0.993 0.00 1.00 0.00
#> TCGA.VQ.AA6I.01 2 0.000 0.993 0.00 1.00 0.00
#> TCGA.CG.4437.01 3 0.254 0.994 0.00 0.08 0.92
#> TCGA.VQ.A8PP.01 3 0.334 0.954 0.00 0.12 0.88
#> TCGA.VQ.A8PF.01 1 0.000 0.991 1.00 0.00 0.00
#> TCGA.BR.8487.01 2 0.000 0.993 0.00 1.00 0.00
#> TCGA.VQ.A91K.01 2 0.000 0.993 0.00 1.00 0.00
#> TCGA.BR.8686.01 1 0.000 0.991 1.00 0.00 0.00
#> TCGA.IN.A6RO.01 2 0.000 0.993 0.00 1.00 0.00
#> TCGA.BR.A4QI.01 3 0.254 0.994 0.00 0.08 0.92
#> TCGA.HU.A4G2.01 1 0.000 0.991 1.00 0.00 0.00
#> TCGA.BR.A4IY.01 1 0.334 0.912 0.88 0.00 0.12
#> TCGA.BR.A4J4.01 1 0.000 0.991 1.00 0.00 0.00
#> TCGA.VQ.A94R.01 2 0.000 0.993 0.00 1.00 0.00
#> TCGA.BR.7707.01 2 0.000 0.993 0.00 1.00 0.00
#> TCGA.FP.7829.01 2 0.000 0.993 0.00 1.00 0.00
#> TCGA.HU.A4H0.01 1 0.000 0.991 1.00 0.00 0.00
#> TCGA.BR.A4PF.01 3 0.254 0.994 0.00 0.08 0.92
#> TCGA.CD.A4MJ.01 3 0.254 0.994 0.00 0.08 0.92
#> TCGA.HU.A4GP.01 2 0.000 0.993 0.00 1.00 0.00
#> TCGA.D7.A4YY.01 2 0.000 0.993 0.00 1.00 0.00
#> TCGA.VQ.AA6G.01 2 0.000 0.993 0.00 1.00 0.00
#> TCGA.CD.A4MI.01 3 0.254 0.994 0.00 0.08 0.92
#> TCGA.VQ.A924.01 3 0.254 0.994 0.00 0.08 0.92
#> TCGA.HU.A4H8.01 2 0.000 0.993 0.00 1.00 0.00
#> TCGA.HU.A4H3.01 2 0.000 0.993 0.00 1.00 0.00
#> TCGA.BR.A4PE.01 2 0.000 0.993 0.00 1.00 0.00
#> TCGA.BR.A4J8.01 3 0.254 0.994 0.00 0.08 0.92
#> TCGA.HU.A4GT.01 2 0.000 0.993 0.00 1.00 0.00
#> TCGA.BR.A4CQ.01 2 0.000 0.993 0.00 1.00 0.00
#> TCGA.HU.A4GQ.01 3 0.254 0.994 0.00 0.08 0.92
#> TCGA.BR.A4QM.01 3 0.254 0.994 0.00 0.08 0.92
#> TCGA.D7.A4YX.01 1 0.000 0.991 1.00 0.00 0.00
#> TCGA.VQ.A8PT.01 2 0.000 0.993 0.00 1.00 0.00
#> TCGA.CD.A4MG.01 2 0.254 0.906 0.00 0.92 0.08
#> TCGA.D7.A4YV.01 3 0.254 0.994 0.00 0.08 0.92
#> TCGA.BR.A4QL.01 2 0.000 0.993 0.00 1.00 0.00
#> TCGA.BR.7703.01 2 0.000 0.993 0.00 1.00 0.00
#> TCGA.D7.A6EZ.01 1 0.000 0.991 1.00 0.00 0.00
#> TCGA.D7.A4YU.01 3 0.254 0.994 0.00 0.08 0.92
#> TCGA.IN.A6RP.01 2 0.000 0.993 0.00 1.00 0.00
#> TCGA.HU.A4GU.01 2 0.000 0.993 0.00 1.00 0.00
#> TCGA.MX.A5UJ.01 2 0.000 0.993 0.00 1.00 0.00
#> TCGA.HU.A4GN.01 3 0.254 0.994 0.00 0.08 0.92
#> TCGA.HU.A4H6.01 3 0.254 0.994 0.00 0.08 0.92
#> TCGA.HF.7132.01 3 0.334 0.954 0.00 0.12 0.88
#> TCGA.HF.7134.01 2 0.000 0.993 0.00 1.00 0.00
#> TCGA.BR.8370.01 3 0.254 0.994 0.00 0.08 0.92
#> TCGA.D7.5577.01 1 0.000 0.991 1.00 0.00 0.00
#> TCGA.BR.6707.01 1 0.000 0.991 1.00 0.00 0.00
#> TCGA.B7.5818.01 1 0.000 0.991 1.00 0.00 0.00
#> TCGA.CG.5733.01 2 0.000 0.993 0.00 1.00 0.00
#> TCGA.BR.7851.01 3 0.254 0.994 0.00 0.08 0.92
#> TCGA.CG.5726.01 2 0.000 0.993 0.00 1.00 0.00
#> TCGA.BR.8363.01 3 0.254 0.994 0.00 0.08 0.92
#> TCGA.CG.5720.01 2 0.000 0.993 0.00 1.00 0.00
#> TCGA.D7.8570.01 1 0.000 0.991 1.00 0.00 0.00
#> TCGA.BR.8284.01 3 0.254 0.994 0.00 0.08 0.92
#> TCGA.B7.A5TJ.01 2 0.000 0.993 0.00 1.00 0.00
#> TCGA.BR.8366.01 1 0.000 0.991 1.00 0.00 0.00
#> TCGA.VQ.A8E3.01 2 0.296 0.881 0.00 0.90 0.10
#> TCGA.CD.5801.01 1 0.000 0.991 1.00 0.00 0.00
#> TCGA.BR.7958.01 1 0.254 0.943 0.92 0.00 0.08
#> TCGA.FP.7916.01 1 0.000 0.991 1.00 0.00 0.00
#> TCGA.SW.A7EA.01 2 0.000 0.993 0.00 1.00 0.00
#> TCGA.BR.8368.01 2 0.000 0.993 0.00 1.00 0.00
#> TCGA.BR.8081.01 3 0.254 0.994 0.00 0.08 0.92
#> TCGA.CD.8535.01 2 0.000 0.993 0.00 1.00 0.00
#> TCGA.HF.A5NB.01 2 0.000 0.993 0.00 1.00 0.00
#> TCGA.CD.A48C.01 2 0.000 0.993 0.00 1.00 0.00
#> TCGA.BR.8285.01 1 0.000 0.991 1.00 0.00 0.00
#> TCGA.BR.8361.01 2 0.000 0.993 0.00 1.00 0.00
#> TCGA.HU.A4G9.01 2 0.000 0.993 0.00 1.00 0.00
#> TCGA.CD.8528.01 2 0.000 0.993 0.00 1.00 0.00
#> TCGA.FP.A4BE.01 3 0.254 0.994 0.00 0.08 0.92
#> TCGA.BR.8078.01 3 0.254 0.994 0.00 0.08 0.92
#> TCGA.CD.8531.01 1 0.334 0.912 0.88 0.00 0.12
#> TCGA.VQ.A8DT.01 2 0.000 0.993 0.00 1.00 0.00
#> TCGA.HU.A4G6.01 1 0.000 0.991 1.00 0.00 0.00
#> TCGA.HU.A4G3.01 2 0.369 0.826 0.00 0.86 0.14
#> TCGA.D7.A74A.01 2 0.000 0.993 0.00 1.00 0.00
#> TCGA.BR.8372.01 2 0.000 0.993 0.00 1.00 0.00
#> TCGA.HU.8244.01 2 0.000 0.993 0.00 1.00 0.00
#> TCGA.IN.A6RR.01 2 0.000 0.993 0.00 1.00 0.00
#> TCGA.VQ.A8P2.01 2 0.000 0.993 0.00 1.00 0.00
#> TCGA.D7.8573.01 1 0.000 0.991 1.00 0.00 0.00
#> TCGA.BR.8360.01 3 0.369 0.932 0.00 0.14 0.86
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> TCGA.BR.6452.01 4 0.7021 -0.224 0.40 0.12 0.00 0.48
#> TCGA.VQ.A8PO.01 4 0.0000 0.414 0.00 0.00 0.00 1.00
#> TCGA.VQ.AA69.01 1 0.4855 0.987 0.60 0.40 0.00 0.00
#> TCGA.BR.8589.01 1 0.4855 0.987 0.60 0.40 0.00 0.00
#> TCGA.BR.8382.01 4 0.7021 -0.217 0.40 0.00 0.12 0.48
#> TCGA.HU.8604.01 3 0.4713 0.882 0.36 0.00 0.64 0.00
#> TCGA.BR.8676.01 1 0.4855 0.987 0.60 0.40 0.00 0.00
#> TCGA.VQ.A923.01 1 0.4855 0.987 0.60 0.40 0.00 0.00
#> TCGA.BR.8679.01 4 0.4994 0.562 0.00 0.48 0.00 0.52
#> TCGA.VQ.A92D.01 4 0.4855 0.540 0.00 0.40 0.00 0.60
#> TCGA.BR.6455.01 1 0.4855 0.987 0.60 0.40 0.00 0.00
#> TCGA.BR.8591.01 4 0.7021 -0.217 0.40 0.00 0.12 0.48
#> TCGA.HU.8608.01 1 0.4855 0.987 0.60 0.40 0.00 0.00
#> TCGA.VQ.A91D.01 4 0.7021 -0.224 0.40 0.12 0.00 0.48
#> TCGA.HU.8602.01 3 0.7021 0.830 0.40 0.12 0.48 0.00
#> TCGA.BR.8381.01 1 0.4855 0.987 0.60 0.40 0.00 0.00
#> TCGA.IN.8663.01 4 0.4994 0.562 0.00 0.48 0.00 0.52
#> TCGA.VQ.A91W.01 1 0.4855 0.987 0.60 0.40 0.00 0.00
#> TCGA.F1.6177.01 4 0.4994 0.562 0.00 0.48 0.00 0.52
#> TCGA.VQ.AA6I.01 4 0.4994 0.562 0.00 0.48 0.00 0.52
#> TCGA.CG.4437.01 4 0.7021 -0.217 0.40 0.00 0.12 0.48
#> TCGA.VQ.A8PP.01 4 0.7021 -0.217 0.40 0.00 0.12 0.48
#> TCGA.VQ.A8PF.01 1 0.4855 0.987 0.60 0.40 0.00 0.00
#> TCGA.BR.8487.01 4 0.4994 0.562 0.00 0.48 0.00 0.52
#> TCGA.VQ.A91K.01 4 0.4994 0.562 0.00 0.48 0.00 0.52
#> TCGA.BR.8686.01 1 0.4855 0.987 0.60 0.40 0.00 0.00
#> TCGA.IN.A6RO.01 4 0.4994 0.562 0.00 0.48 0.00 0.52
#> TCGA.BR.A4QI.01 3 0.4713 0.882 0.36 0.00 0.64 0.00
#> TCGA.HU.A4G2.01 1 0.4855 0.987 0.60 0.40 0.00 0.00
#> TCGA.BR.A4IY.01 3 0.3247 0.555 0.06 0.06 0.88 0.00
#> TCGA.BR.A4J4.01 1 0.4855 0.987 0.60 0.40 0.00 0.00
#> TCGA.VQ.A94R.01 4 0.4994 0.562 0.00 0.48 0.00 0.52
#> TCGA.BR.7707.01 4 0.0000 0.414 0.00 0.00 0.00 1.00
#> TCGA.FP.7829.01 4 0.4994 0.562 0.00 0.48 0.00 0.52
#> TCGA.HU.A4H0.01 1 0.4855 0.987 0.60 0.40 0.00 0.00
#> TCGA.BR.A4PF.01 4 0.7021 -0.217 0.40 0.00 0.12 0.48
#> TCGA.CD.A4MJ.01 4 0.7021 -0.224 0.40 0.12 0.00 0.48
#> TCGA.HU.A4GP.01 4 0.4994 0.562 0.00 0.48 0.00 0.52
#> TCGA.D7.A4YY.01 4 0.4994 0.562 0.00 0.48 0.00 0.52
#> TCGA.VQ.AA6G.01 4 0.4994 0.562 0.00 0.48 0.00 0.52
#> TCGA.CD.A4MI.01 3 0.4713 0.882 0.36 0.00 0.64 0.00
#> TCGA.VQ.A924.01 4 0.7621 -0.218 0.40 0.06 0.06 0.48
#> TCGA.HU.A4H8.01 4 0.4994 0.562 0.00 0.48 0.00 0.52
#> TCGA.HU.A4H3.01 4 0.0000 0.414 0.00 0.00 0.00 1.00
#> TCGA.BR.A4PE.01 4 0.0000 0.414 0.00 0.00 0.00 1.00
#> TCGA.BR.A4J8.01 4 0.7620 -0.250 0.40 0.12 0.02 0.46
#> TCGA.HU.A4GT.01 4 0.4994 0.562 0.00 0.48 0.00 0.52
#> TCGA.BR.A4CQ.01 4 0.4994 0.562 0.00 0.48 0.00 0.52
#> TCGA.HU.A4GQ.01 3 0.4855 0.857 0.40 0.00 0.60 0.00
#> TCGA.BR.A4QM.01 4 0.7021 -0.217 0.40 0.00 0.12 0.48
#> TCGA.D7.A4YX.01 1 0.4855 0.987 0.60 0.40 0.00 0.00
#> TCGA.VQ.A8PT.01 4 0.0707 0.422 0.00 0.02 0.00 0.98
#> TCGA.CD.A4MG.01 4 0.2706 0.325 0.08 0.00 0.02 0.90
#> TCGA.D7.A4YV.01 4 0.7021 -0.217 0.40 0.00 0.12 0.48
#> TCGA.BR.A4QL.01 4 0.4994 0.562 0.00 0.48 0.00 0.52
#> TCGA.BR.7703.01 4 0.4994 0.562 0.00 0.48 0.00 0.52
#> TCGA.D7.A6EZ.01 1 0.4855 0.987 0.60 0.40 0.00 0.00
#> TCGA.D7.A4YU.01 4 0.7021 -0.217 0.40 0.00 0.12 0.48
#> TCGA.IN.A6RP.01 4 0.4994 0.562 0.00 0.48 0.00 0.52
#> TCGA.HU.A4GU.01 4 0.2345 0.447 0.00 0.10 0.00 0.90
#> TCGA.MX.A5UJ.01 4 0.0000 0.414 0.00 0.00 0.00 1.00
#> TCGA.HU.A4GN.01 4 0.7021 -0.217 0.40 0.00 0.12 0.48
#> TCGA.HU.A4H6.01 3 0.4713 0.882 0.36 0.00 0.64 0.00
#> TCGA.HF.7132.01 4 0.7021 -0.217 0.40 0.00 0.12 0.48
#> TCGA.HF.7134.01 4 0.4994 0.562 0.00 0.48 0.00 0.52
#> TCGA.BR.8370.01 3 0.7021 0.830 0.40 0.12 0.48 0.00
#> TCGA.D7.5577.01 1 0.4855 0.987 0.60 0.40 0.00 0.00
#> TCGA.BR.6707.01 1 0.4855 0.987 0.60 0.40 0.00 0.00
#> TCGA.B7.5818.01 1 0.4855 0.987 0.60 0.40 0.00 0.00
#> TCGA.CG.5733.01 4 0.3610 0.478 0.00 0.20 0.00 0.80
#> TCGA.BR.7851.01 4 0.7021 -0.217 0.40 0.00 0.12 0.48
#> TCGA.CG.5726.01 4 0.4994 0.562 0.00 0.48 0.00 0.52
#> TCGA.BR.8363.01 3 0.4713 0.882 0.36 0.00 0.64 0.00
#> TCGA.CG.5720.01 4 0.0707 0.422 0.00 0.02 0.00 0.98
#> TCGA.D7.8570.01 1 0.4855 0.987 0.60 0.40 0.00 0.00
#> TCGA.BR.8284.01 4 0.7021 -0.217 0.40 0.00 0.12 0.48
#> TCGA.B7.A5TJ.01 4 0.4994 0.562 0.00 0.48 0.00 0.52
#> TCGA.BR.8366.01 1 0.4855 0.987 0.60 0.40 0.00 0.00
#> TCGA.VQ.A8E3.01 4 0.2706 0.325 0.08 0.00 0.02 0.90
#> TCGA.CD.5801.01 1 0.4855 0.987 0.60 0.40 0.00 0.00
#> TCGA.BR.7958.01 1 0.5793 0.582 0.60 0.04 0.36 0.00
#> TCGA.FP.7916.01 1 0.4855 0.987 0.60 0.40 0.00 0.00
#> TCGA.SW.A7EA.01 4 0.0000 0.414 0.00 0.00 0.00 1.00
#> TCGA.BR.8368.01 4 0.4994 0.562 0.00 0.48 0.00 0.52
#> TCGA.BR.8081.01 3 0.4713 0.882 0.36 0.00 0.64 0.00
#> TCGA.CD.8535.01 4 0.4994 0.562 0.00 0.48 0.00 0.52
#> TCGA.HF.A5NB.01 4 0.4994 0.562 0.00 0.48 0.00 0.52
#> TCGA.CD.A48C.01 4 0.4994 0.562 0.00 0.48 0.00 0.52
#> TCGA.BR.8285.01 1 0.4855 0.987 0.60 0.40 0.00 0.00
#> TCGA.BR.8361.01 4 0.0000 0.414 0.00 0.00 0.00 1.00
#> TCGA.HU.A4G9.01 4 0.4994 0.562 0.00 0.48 0.00 0.52
#> TCGA.CD.8528.01 4 0.4994 0.562 0.00 0.48 0.00 0.52
#> TCGA.FP.A4BE.01 4 0.7620 -0.250 0.40 0.12 0.02 0.46
#> TCGA.BR.8078.01 4 0.7411 -0.222 0.40 0.10 0.02 0.48
#> TCGA.CD.8531.01 3 0.3037 0.521 0.10 0.02 0.88 0.00
#> TCGA.VQ.A8DT.01 4 0.4994 0.562 0.00 0.48 0.00 0.52
#> TCGA.HU.A4G6.01 1 0.4855 0.987 0.60 0.40 0.00 0.00
#> TCGA.HU.A4G3.01 4 0.2706 0.325 0.08 0.00 0.02 0.90
#> TCGA.D7.A74A.01 4 0.4994 0.562 0.00 0.48 0.00 0.52
#> TCGA.BR.8372.01 4 0.0000 0.414 0.00 0.00 0.00 1.00
#> TCGA.HU.8244.01 4 0.4994 0.562 0.00 0.48 0.00 0.52
#> TCGA.IN.A6RR.01 4 0.4994 0.562 0.00 0.48 0.00 0.52
#> TCGA.VQ.A8P2.01 4 0.4994 0.562 0.00 0.48 0.00 0.52
#> TCGA.D7.8573.01 1 0.4855 0.987 0.60 0.40 0.00 0.00
#> TCGA.BR.8360.01 4 0.7021 -0.217 0.40 0.00 0.12 0.48
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> TCGA.BR.6452.01 5 0.4726 0.7083 0.00 0.40 0.02 0.00 0.58
#> TCGA.VQ.A8PO.01 2 0.2732 0.7417 0.00 0.84 0.00 0.16 0.00
#> TCGA.VQ.AA69.01 1 0.0000 0.9741 1.00 0.00 0.00 0.00 0.00
#> TCGA.BR.8589.01 1 0.0000 0.9741 1.00 0.00 0.00 0.00 0.00
#> TCGA.BR.8382.01 2 0.5979 -0.1175 0.00 0.52 0.36 0.00 0.12
#> TCGA.HU.8604.01 3 0.2516 0.8139 0.00 0.14 0.86 0.00 0.00
#> TCGA.BR.8676.01 1 0.1732 0.9177 0.92 0.00 0.00 0.00 0.08
#> TCGA.VQ.A923.01 1 0.0000 0.9741 1.00 0.00 0.00 0.00 0.00
#> TCGA.BR.8679.01 4 0.2732 0.8379 0.00 0.16 0.00 0.84 0.00
#> TCGA.VQ.A92D.01 4 0.4818 0.0787 0.00 0.46 0.00 0.52 0.02
#> TCGA.BR.6455.01 1 0.1732 0.9177 0.92 0.00 0.00 0.00 0.08
#> TCGA.BR.8591.01 2 0.2280 0.5498 0.00 0.88 0.00 0.00 0.12
#> TCGA.HU.8608.01 1 0.0000 0.9741 1.00 0.00 0.00 0.00 0.00
#> TCGA.VQ.A91D.01 5 0.4227 0.6758 0.00 0.42 0.00 0.00 0.58
#> TCGA.HU.8602.01 5 0.5727 0.4097 0.00 0.10 0.34 0.00 0.56
#> TCGA.BR.8381.01 1 0.1732 0.9177 0.92 0.00 0.00 0.00 0.08
#> TCGA.IN.8663.01 4 0.0000 0.9358 0.00 0.00 0.00 1.00 0.00
#> TCGA.VQ.A91W.01 1 0.0000 0.9741 1.00 0.00 0.00 0.00 0.00
#> TCGA.F1.6177.01 4 0.0609 0.9261 0.00 0.00 0.00 0.98 0.02
#> TCGA.VQ.AA6I.01 4 0.2732 0.8379 0.00 0.16 0.00 0.84 0.00
#> TCGA.CG.4437.01 2 0.0000 0.6620 0.00 1.00 0.00 0.00 0.00
#> TCGA.VQ.A8PP.01 2 0.0609 0.6820 0.00 0.98 0.00 0.02 0.00
#> TCGA.VQ.A8PF.01 1 0.0000 0.9741 1.00 0.00 0.00 0.00 0.00
#> TCGA.BR.8487.01 4 0.0609 0.9261 0.00 0.00 0.00 0.98 0.02
#> TCGA.VQ.A91K.01 4 0.3106 0.8461 0.00 0.14 0.00 0.84 0.02
#> TCGA.BR.8686.01 1 0.0000 0.9741 1.00 0.00 0.00 0.00 0.00
#> TCGA.IN.A6RO.01 4 0.0000 0.9358 0.00 0.00 0.00 1.00 0.00
#> TCGA.BR.A4QI.01 3 0.2516 0.8139 0.00 0.14 0.86 0.00 0.00
#> TCGA.HU.A4G2.01 1 0.0000 0.9741 1.00 0.00 0.00 0.00 0.00
#> TCGA.BR.A4IY.01 3 0.4540 0.4900 0.02 0.00 0.64 0.00 0.34
#> TCGA.BR.A4J4.01 1 0.0000 0.9741 1.00 0.00 0.00 0.00 0.00
#> TCGA.VQ.A94R.01 4 0.0000 0.9358 0.00 0.00 0.00 1.00 0.00
#> TCGA.BR.7707.01 2 0.2732 0.7417 0.00 0.84 0.00 0.16 0.00
#> TCGA.FP.7829.01 4 0.0000 0.9358 0.00 0.00 0.00 1.00 0.00
#> TCGA.HU.A4H0.01 1 0.0000 0.9741 1.00 0.00 0.00 0.00 0.00
#> TCGA.BR.A4PF.01 2 0.3291 0.5289 0.00 0.84 0.04 0.00 0.12
#> TCGA.CD.A4MJ.01 5 0.4726 0.7083 0.00 0.40 0.02 0.00 0.58
#> TCGA.HU.A4GP.01 4 0.0000 0.9358 0.00 0.00 0.00 1.00 0.00
#> TCGA.D7.A4YY.01 4 0.0000 0.9358 0.00 0.00 0.00 1.00 0.00
#> TCGA.VQ.AA6G.01 4 0.1732 0.8997 0.00 0.08 0.00 0.92 0.00
#> TCGA.CD.A4MI.01 3 0.2516 0.8139 0.00 0.14 0.86 0.00 0.00
#> TCGA.VQ.A924.01 2 0.4252 0.2107 0.00 0.70 0.02 0.00 0.28
#> TCGA.HU.A4H8.01 4 0.0000 0.9358 0.00 0.00 0.00 1.00 0.00
#> TCGA.HU.A4H3.01 2 0.2732 0.7417 0.00 0.84 0.00 0.16 0.00
#> TCGA.BR.A4PE.01 2 0.2732 0.7417 0.00 0.84 0.00 0.16 0.00
#> TCGA.BR.A4J8.01 5 0.6146 0.6796 0.00 0.24 0.20 0.00 0.56
#> TCGA.HU.A4GT.01 4 0.0000 0.9358 0.00 0.00 0.00 1.00 0.00
#> TCGA.BR.A4CQ.01 4 0.2331 0.8931 0.00 0.08 0.00 0.90 0.02
#> TCGA.HU.A4GQ.01 3 0.4890 0.5820 0.00 0.14 0.72 0.00 0.14
#> TCGA.BR.A4QM.01 2 0.3291 0.5289 0.00 0.84 0.04 0.00 0.12
#> TCGA.D7.A4YX.01 1 0.0000 0.9741 1.00 0.00 0.00 0.00 0.00
#> TCGA.VQ.A8PT.01 2 0.3690 0.6907 0.00 0.78 0.00 0.20 0.02
#> TCGA.CD.A4MG.01 2 0.2516 0.7429 0.00 0.86 0.00 0.14 0.00
#> TCGA.D7.A4YV.01 2 0.3946 0.4780 0.00 0.80 0.08 0.00 0.12
#> TCGA.BR.A4QL.01 4 0.0000 0.9358 0.00 0.00 0.00 1.00 0.00
#> TCGA.BR.7703.01 4 0.2732 0.8379 0.00 0.16 0.00 0.84 0.00
#> TCGA.D7.A6EZ.01 1 0.0000 0.9741 1.00 0.00 0.00 0.00 0.00
#> TCGA.D7.A4YU.01 2 0.5927 -0.0854 0.00 0.54 0.34 0.00 0.12
#> TCGA.IN.A6RP.01 4 0.2020 0.8870 0.00 0.10 0.00 0.90 0.00
#> TCGA.HU.A4GU.01 2 0.3690 0.6907 0.00 0.78 0.00 0.20 0.02
#> TCGA.MX.A5UJ.01 2 0.2732 0.7417 0.00 0.84 0.00 0.16 0.00
#> TCGA.HU.A4GN.01 2 0.3946 0.4780 0.00 0.80 0.08 0.00 0.12
#> TCGA.HU.A4H6.01 3 0.2516 0.8139 0.00 0.14 0.86 0.00 0.00
#> TCGA.HF.7132.01 2 0.0609 0.6820 0.00 0.98 0.00 0.02 0.00
#> TCGA.HF.7134.01 4 0.0000 0.9358 0.00 0.00 0.00 1.00 0.00
#> TCGA.BR.8370.01 5 0.5727 0.4097 0.00 0.10 0.34 0.00 0.56
#> TCGA.D7.5577.01 1 0.0000 0.9741 1.00 0.00 0.00 0.00 0.00
#> TCGA.BR.6707.01 1 0.0000 0.9741 1.00 0.00 0.00 0.00 0.00
#> TCGA.B7.5818.01 1 0.0000 0.9741 1.00 0.00 0.00 0.00 0.00
#> TCGA.CG.5733.01 2 0.3109 0.7042 0.00 0.80 0.00 0.20 0.00
#> TCGA.BR.7851.01 2 0.2873 0.5224 0.00 0.86 0.02 0.00 0.12
#> TCGA.CG.5726.01 4 0.0000 0.9358 0.00 0.00 0.00 1.00 0.00
#> TCGA.BR.8363.01 3 0.2516 0.8139 0.00 0.14 0.86 0.00 0.00
#> TCGA.CG.5720.01 2 0.3513 0.7147 0.00 0.80 0.00 0.18 0.02
#> TCGA.D7.8570.01 1 0.0000 0.9741 1.00 0.00 0.00 0.00 0.00
#> TCGA.BR.8284.01 2 0.3946 0.4780 0.00 0.80 0.08 0.00 0.12
#> TCGA.B7.A5TJ.01 4 0.0000 0.9358 0.00 0.00 0.00 1.00 0.00
#> TCGA.BR.8366.01 1 0.0000 0.9741 1.00 0.00 0.00 0.00 0.00
#> TCGA.VQ.A8E3.01 2 0.2516 0.7429 0.00 0.86 0.00 0.14 0.00
#> TCGA.CD.5801.01 1 0.0000 0.9741 1.00 0.00 0.00 0.00 0.00
#> TCGA.BR.7958.01 1 0.5425 0.3692 0.52 0.00 0.06 0.00 0.42
#> TCGA.FP.7916.01 1 0.0000 0.9741 1.00 0.00 0.00 0.00 0.00
#> TCGA.SW.A7EA.01 2 0.2732 0.7417 0.00 0.84 0.00 0.16 0.00
#> TCGA.BR.8368.01 4 0.2732 0.8379 0.00 0.16 0.00 0.84 0.00
#> TCGA.BR.8081.01 3 0.2516 0.8139 0.00 0.14 0.86 0.00 0.00
#> TCGA.CD.8535.01 4 0.0000 0.9358 0.00 0.00 0.00 1.00 0.00
#> TCGA.HF.A5NB.01 4 0.0000 0.9358 0.00 0.00 0.00 1.00 0.00
#> TCGA.CD.A48C.01 4 0.0000 0.9358 0.00 0.00 0.00 1.00 0.00
#> TCGA.BR.8285.01 1 0.0000 0.9741 1.00 0.00 0.00 0.00 0.00
#> TCGA.BR.8361.01 2 0.2732 0.7417 0.00 0.84 0.00 0.16 0.00
#> TCGA.HU.A4G9.01 4 0.0000 0.9358 0.00 0.00 0.00 1.00 0.00
#> TCGA.CD.8528.01 4 0.2732 0.8379 0.00 0.16 0.00 0.84 0.00
#> TCGA.FP.A4BE.01 5 0.6146 0.6796 0.00 0.24 0.20 0.00 0.56
#> TCGA.BR.8078.01 5 0.4767 0.6876 0.00 0.42 0.02 0.00 0.56
#> TCGA.CD.8531.01 3 0.4540 0.4900 0.02 0.00 0.64 0.00 0.34
#> TCGA.VQ.A8DT.01 4 0.0000 0.9358 0.00 0.00 0.00 1.00 0.00
#> TCGA.HU.A4G6.01 1 0.0000 0.9741 1.00 0.00 0.00 0.00 0.00
#> TCGA.HU.A4G3.01 2 0.2516 0.7429 0.00 0.86 0.00 0.14 0.00
#> TCGA.D7.A74A.01 4 0.1732 0.8997 0.00 0.08 0.00 0.92 0.00
#> TCGA.BR.8372.01 2 0.3319 0.7313 0.00 0.82 0.00 0.16 0.02
#> TCGA.HU.8244.01 4 0.0000 0.9358 0.00 0.00 0.00 1.00 0.00
#> TCGA.IN.A6RR.01 4 0.0000 0.9358 0.00 0.00 0.00 1.00 0.00
#> TCGA.VQ.A8P2.01 4 0.0000 0.9358 0.00 0.00 0.00 1.00 0.00
#> TCGA.D7.8573.01 1 0.0000 0.9741 1.00 0.00 0.00 0.00 0.00
#> TCGA.BR.8360.01 2 0.1043 0.6970 0.00 0.96 0.00 0.04 0.00
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> TCGA.BR.6452.01 5 0.3163 0.8579 0.00 0.14 0.04 0.00 0.82 0.00
#> TCGA.VQ.A8PO.01 2 0.2260 0.7553 0.00 0.86 0.00 0.14 0.00 0.00
#> TCGA.VQ.AA69.01 1 0.0000 0.9699 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BR.8589.01 1 0.0000 0.9699 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BR.8382.01 3 0.4008 0.7026 0.00 0.06 0.80 0.00 0.06 0.08
#> TCGA.HU.8604.01 3 0.0937 0.8831 0.00 0.00 0.96 0.00 0.00 0.04
#> TCGA.BR.8676.01 1 0.3746 0.7414 0.78 0.14 0.00 0.00 0.08 0.00
#> TCGA.VQ.A923.01 1 0.0000 0.9699 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BR.8679.01 4 0.3578 0.6195 0.00 0.34 0.00 0.66 0.00 0.00
#> TCGA.VQ.A92D.01 2 0.5291 0.4299 0.00 0.60 0.00 0.30 0.02 0.08
#> TCGA.BR.6455.01 1 0.3746 0.7414 0.78 0.14 0.00 0.00 0.08 0.00
#> TCGA.BR.8591.01 2 0.5580 0.6127 0.00 0.66 0.16 0.00 0.10 0.08
#> TCGA.HU.8608.01 1 0.0000 0.9699 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.VQ.A91D.01 5 0.3163 0.8579 0.00 0.14 0.04 0.00 0.82 0.00
#> TCGA.HU.8602.01 5 0.2631 0.8075 0.00 0.00 0.18 0.00 0.82 0.00
#> TCGA.BR.8381.01 1 0.3746 0.7414 0.78 0.14 0.00 0.00 0.08 0.00
#> TCGA.IN.8663.01 4 0.0000 0.8780 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.VQ.A91W.01 1 0.0547 0.9540 0.98 0.02 0.00 0.00 0.00 0.00
#> TCGA.F1.6177.01 4 0.1092 0.8561 0.00 0.00 0.00 0.96 0.02 0.02
#> TCGA.VQ.AA6I.01 4 0.3499 0.6512 0.00 0.32 0.00 0.68 0.00 0.00
#> TCGA.CG.4437.01 2 0.5327 0.6406 0.00 0.68 0.16 0.00 0.06 0.10
#> TCGA.VQ.A8PP.01 2 0.5540 0.6599 0.00 0.68 0.16 0.02 0.04 0.10
#> TCGA.VQ.A8PF.01 1 0.0000 0.9699 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BR.8487.01 4 0.3688 0.8000 0.00 0.14 0.00 0.80 0.02 0.04
#> TCGA.VQ.A91K.01 4 0.4334 0.7392 0.00 0.22 0.00 0.72 0.02 0.04
#> TCGA.BR.8686.01 1 0.0000 0.9699 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.IN.A6RO.01 4 0.0000 0.8780 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.BR.A4QI.01 3 0.1480 0.8697 0.00 0.00 0.94 0.00 0.02 0.04
#> TCGA.HU.A4G2.01 1 0.0000 0.9699 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BR.A4IY.01 6 0.2454 0.7305 0.00 0.00 0.16 0.00 0.00 0.84
#> TCGA.BR.A4J4.01 1 0.0000 0.9699 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.VQ.A94R.01 4 0.0000 0.8780 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.BR.7707.01 2 0.2260 0.7553 0.00 0.86 0.00 0.14 0.00 0.00
#> TCGA.FP.7829.01 4 0.0000 0.8780 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.HU.A4H0.01 1 0.0000 0.9699 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BR.A4PF.01 2 0.5878 0.5551 0.00 0.60 0.24 0.00 0.08 0.08
#> TCGA.CD.A4MJ.01 5 0.3163 0.8579 0.00 0.14 0.04 0.00 0.82 0.00
#> TCGA.HU.A4GP.01 4 0.0000 0.8780 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.D7.A4YY.01 4 0.2454 0.8156 0.00 0.16 0.00 0.84 0.00 0.00
#> TCGA.VQ.AA6G.01 4 0.2793 0.7890 0.00 0.20 0.00 0.80 0.00 0.00
#> TCGA.CD.A4MI.01 3 0.0937 0.8831 0.00 0.00 0.96 0.00 0.00 0.04
#> TCGA.VQ.A924.01 2 0.6492 0.0177 0.00 0.42 0.08 0.00 0.40 0.10
#> TCGA.HU.A4H8.01 4 0.0000 0.8780 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.HU.A4H3.01 2 0.3163 0.7523 0.00 0.82 0.00 0.14 0.00 0.04
#> TCGA.BR.A4PE.01 2 0.2260 0.7553 0.00 0.86 0.00 0.14 0.00 0.00
#> TCGA.BR.A4J8.01 5 0.2790 0.8343 0.00 0.02 0.14 0.00 0.84 0.00
#> TCGA.HU.A4GT.01 4 0.0000 0.8780 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.BR.A4CQ.01 4 0.4195 0.7590 0.00 0.20 0.00 0.74 0.02 0.04
#> TCGA.HU.A4GQ.01 3 0.0937 0.8612 0.00 0.00 0.96 0.00 0.04 0.00
#> TCGA.BR.A4QM.01 2 0.5256 0.6340 0.00 0.68 0.18 0.00 0.06 0.08
#> TCGA.D7.A4YX.01 1 0.0000 0.9699 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.VQ.A8PT.01 2 0.4265 0.7190 0.00 0.76 0.00 0.14 0.02 0.08
#> TCGA.CD.A4MG.01 2 0.4502 0.7424 0.00 0.74 0.02 0.14 0.00 0.10
#> TCGA.D7.A4YV.01 2 0.6237 0.3823 0.00 0.50 0.34 0.00 0.08 0.08
#> TCGA.BR.A4QL.01 4 0.0000 0.8780 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.BR.7703.01 4 0.3578 0.6195 0.00 0.34 0.00 0.66 0.00 0.00
#> TCGA.D7.A6EZ.01 1 0.0000 0.9699 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D7.A4YU.01 3 0.4008 0.7026 0.00 0.06 0.80 0.00 0.06 0.08
#> TCGA.IN.A6RP.01 4 0.2941 0.7728 0.00 0.22 0.00 0.78 0.00 0.00
#> TCGA.HU.A4GU.01 2 0.4444 0.7012 0.00 0.74 0.00 0.16 0.02 0.08
#> TCGA.MX.A5UJ.01 2 0.2260 0.7553 0.00 0.86 0.00 0.14 0.00 0.00
#> TCGA.HU.A4GN.01 2 0.6128 0.4666 0.00 0.54 0.30 0.00 0.08 0.08
#> TCGA.HU.A4H6.01 3 0.0000 0.8742 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.HF.7132.01 2 0.4444 0.6883 0.00 0.74 0.16 0.02 0.00 0.08
#> TCGA.HF.7134.01 4 0.0000 0.8780 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.BR.8370.01 5 0.2793 0.7642 0.00 0.00 0.20 0.00 0.80 0.00
#> TCGA.D7.5577.01 1 0.0000 0.9699 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BR.6707.01 1 0.0000 0.9699 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.B7.5818.01 1 0.0000 0.9699 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CG.5733.01 2 0.2454 0.7431 0.00 0.84 0.00 0.16 0.00 0.00
#> TCGA.BR.7851.01 2 0.5801 0.6119 0.00 0.64 0.16 0.00 0.10 0.10
#> TCGA.CG.5726.01 4 0.0000 0.8780 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.BR.8363.01 3 0.0937 0.8831 0.00 0.00 0.96 0.00 0.00 0.04
#> TCGA.CG.5720.01 2 0.3163 0.7420 0.00 0.82 0.00 0.14 0.00 0.04
#> TCGA.D7.8570.01 1 0.0000 0.9699 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BR.8284.01 2 0.6128 0.4666 0.00 0.54 0.30 0.00 0.08 0.08
#> TCGA.B7.A5TJ.01 4 0.0000 0.8780 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.BR.8366.01 1 0.0000 0.9699 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.VQ.A8E3.01 2 0.3163 0.7570 0.00 0.82 0.00 0.14 0.00 0.04
#> TCGA.CD.5801.01 1 0.0000 0.9699 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BR.7958.01 6 0.5863 0.5676 0.20 0.10 0.00 0.00 0.08 0.62
#> TCGA.FP.7916.01 1 0.0000 0.9699 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.SW.A7EA.01 2 0.3163 0.7523 0.00 0.82 0.00 0.14 0.00 0.04
#> TCGA.BR.8368.01 4 0.3578 0.6195 0.00 0.34 0.00 0.66 0.00 0.00
#> TCGA.BR.8081.01 3 0.0937 0.8831 0.00 0.00 0.96 0.00 0.00 0.04
#> TCGA.CD.8535.01 4 0.0000 0.8780 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.HF.A5NB.01 4 0.0000 0.8780 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.CD.A48C.01 4 0.0000 0.8780 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.BR.8285.01 1 0.0000 0.9699 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BR.8361.01 2 0.2260 0.7553 0.00 0.86 0.00 0.14 0.00 0.00
#> TCGA.HU.A4G9.01 4 0.0000 0.8780 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.CD.8528.01 4 0.3578 0.6195 0.00 0.34 0.00 0.66 0.00 0.00
#> TCGA.FP.A4BE.01 5 0.3163 0.8471 0.00 0.04 0.14 0.00 0.82 0.00
#> TCGA.BR.8078.01 5 0.3163 0.8579 0.00 0.14 0.04 0.00 0.82 0.00
#> TCGA.CD.8531.01 6 0.3660 0.7258 0.00 0.00 0.16 0.00 0.06 0.78
#> TCGA.VQ.A8DT.01 4 0.0000 0.8780 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.HU.A4G6.01 1 0.0000 0.9699 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HU.A4G3.01 2 0.3746 0.7497 0.00 0.78 0.00 0.14 0.00 0.08
#> TCGA.D7.A74A.01 4 0.4042 0.7756 0.00 0.18 0.00 0.76 0.02 0.04
#> TCGA.BR.8372.01 2 0.2790 0.7506 0.00 0.84 0.00 0.14 0.00 0.02
#> TCGA.HU.8244.01 4 0.0000 0.8780 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.IN.A6RR.01 4 0.0000 0.8780 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.VQ.A8P2.01 4 0.0000 0.8780 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.D7.8573.01 1 0.0000 0.9699 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BR.8360.01 2 0.4502 0.6925 0.00 0.74 0.14 0.02 0.00 0.10
cbind(get_classes(res, k = 7), get_membership(res, k = 7))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7
#> TCGA.BR.6452.01 5 0.1433 0.9150 0.00 0.08 0.00 0.00 0.92 0.00 0.00
#> TCGA.VQ.A8PO.01 2 0.3927 0.5034 0.00 0.66 0.00 0.04 0.00 0.00 0.30
#> TCGA.VQ.AA69.01 1 0.0000 0.9717 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BR.8589.01 1 0.0000 0.9717 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BR.8382.01 3 0.3413 0.5252 0.00 0.38 0.62 0.00 0.00 0.00 0.00
#> TCGA.HU.8604.01 3 0.1363 0.8396 0.00 0.04 0.94 0.00 0.00 0.02 0.00
#> TCGA.BR.8676.01 1 0.3052 0.7503 0.78 0.00 0.00 0.00 0.02 0.00 0.20
#> TCGA.VQ.A923.01 1 0.0000 0.9717 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BR.8679.01 4 0.5241 -0.1682 0.00 0.18 0.00 0.50 0.00 0.00 0.32
#> TCGA.VQ.A92D.01 7 0.5393 0.4964 0.00 0.26 0.00 0.12 0.00 0.04 0.58
#> TCGA.BR.6455.01 1 0.3052 0.7503 0.78 0.00 0.00 0.00 0.02 0.00 0.20
#> TCGA.BR.8591.01 2 0.1363 0.6335 0.00 0.94 0.02 0.00 0.04 0.00 0.00
#> TCGA.HU.8608.01 1 0.0000 0.9717 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.VQ.A91D.01 5 0.1433 0.9150 0.00 0.08 0.00 0.00 0.92 0.00 0.00
#> TCGA.HU.8602.01 5 0.1433 0.8730 0.00 0.00 0.08 0.00 0.92 0.00 0.00
#> TCGA.BR.8381.01 1 0.3052 0.7503 0.78 0.00 0.00 0.00 0.02 0.00 0.20
#> TCGA.IN.8663.01 4 0.0000 0.7840 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.VQ.A91W.01 1 0.0000 0.9717 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.F1.6177.01 4 0.3086 0.5610 0.00 0.00 0.00 0.80 0.00 0.04 0.16
#> TCGA.VQ.AA6I.01 4 0.5241 -0.1682 0.00 0.18 0.00 0.50 0.00 0.00 0.32
#> TCGA.CG.4437.01 2 0.0504 0.6441 0.00 0.98 0.02 0.00 0.00 0.00 0.00
#> TCGA.VQ.A8PP.01 2 0.0504 0.6441 0.00 0.98 0.02 0.00 0.00 0.00 0.00
#> TCGA.VQ.A8PF.01 1 0.0000 0.9717 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BR.8487.01 7 0.4244 0.4012 0.00 0.00 0.00 0.42 0.00 0.04 0.54
#> TCGA.VQ.A91K.01 7 0.5083 0.5842 0.00 0.06 0.00 0.34 0.00 0.04 0.56
#> TCGA.BR.8686.01 1 0.0000 0.9717 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.IN.A6RO.01 4 0.0000 0.7840 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.BR.A4QI.01 3 0.1363 0.8396 0.00 0.04 0.94 0.00 0.00 0.02 0.00
#> TCGA.HU.A4G2.01 1 0.0000 0.9717 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BR.A4IY.01 6 0.1166 0.8261 0.00 0.00 0.06 0.00 0.00 0.94 0.00
#> TCGA.BR.A4J4.01 1 0.0000 0.9717 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.VQ.A94R.01 4 0.0504 0.7791 0.00 0.00 0.00 0.98 0.00 0.00 0.02
#> TCGA.BR.7707.01 2 0.3927 0.5034 0.00 0.66 0.00 0.04 0.00 0.00 0.30
#> TCGA.FP.7829.01 4 0.0000 0.7840 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.HU.A4H0.01 1 0.0000 0.9717 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BR.A4PF.01 2 0.2278 0.5998 0.00 0.88 0.08 0.00 0.04 0.00 0.00
#> TCGA.CD.A4MJ.01 5 0.1433 0.9150 0.00 0.08 0.00 0.00 0.92 0.00 0.00
#> TCGA.HU.A4GP.01 4 0.0504 0.7791 0.00 0.00 0.00 0.98 0.00 0.00 0.02
#> TCGA.D7.A4YY.01 4 0.2832 0.4833 0.00 0.00 0.00 0.76 0.00 0.00 0.24
#> TCGA.VQ.AA6G.01 4 0.4487 0.0903 0.00 0.08 0.00 0.60 0.00 0.00 0.32
#> TCGA.CD.A4MI.01 3 0.1363 0.8396 0.00 0.04 0.94 0.00 0.00 0.02 0.00
#> TCGA.VQ.A924.01 2 0.3985 -0.1337 0.00 0.52 0.02 0.00 0.46 0.00 0.00
#> TCGA.HU.A4H8.01 4 0.0000 0.7840 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.HU.A4H3.01 2 0.4305 0.4993 0.00 0.66 0.00 0.04 0.00 0.02 0.28
#> TCGA.BR.A4PE.01 2 0.3927 0.5034 0.00 0.66 0.00 0.04 0.00 0.00 0.30
#> TCGA.BR.A4J8.01 5 0.2159 0.8906 0.00 0.02 0.06 0.00 0.90 0.00 0.02
#> TCGA.HU.A4GT.01 4 0.0000 0.7840 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.BR.A4CQ.01 7 0.4718 0.6084 0.00 0.06 0.00 0.32 0.00 0.02 0.60
#> TCGA.HU.A4GQ.01 3 0.1363 0.8254 0.00 0.04 0.94 0.00 0.02 0.00 0.00
#> TCGA.BR.A4QM.01 2 0.1363 0.6328 0.00 0.94 0.04 0.00 0.02 0.00 0.00
#> TCGA.D7.A4YX.01 1 0.0000 0.9717 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.VQ.A8PT.01 7 0.4977 0.0904 0.00 0.42 0.00 0.04 0.00 0.04 0.50
#> TCGA.CD.A4MG.01 2 0.3086 0.5898 0.00 0.80 0.00 0.04 0.00 0.00 0.16
#> TCGA.D7.A4YV.01 2 0.2512 0.5767 0.00 0.86 0.10 0.00 0.04 0.00 0.00
#> TCGA.BR.A4QL.01 4 0.0504 0.7791 0.00 0.00 0.00 0.98 0.00 0.00 0.02
#> TCGA.BR.7703.01 4 0.5241 -0.1682 0.00 0.18 0.00 0.50 0.00 0.00 0.32
#> TCGA.D7.A6EZ.01 1 0.0000 0.9717 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D7.A4YU.01 3 0.3496 0.4760 0.00 0.42 0.58 0.00 0.00 0.00 0.00
#> TCGA.IN.A6RP.01 4 0.4487 0.0903 0.00 0.08 0.00 0.60 0.00 0.00 0.32
#> TCGA.HU.A4GU.01 7 0.5083 0.2773 0.00 0.34 0.00 0.04 0.00 0.06 0.56
#> TCGA.MX.A5UJ.01 2 0.3927 0.5034 0.00 0.66 0.00 0.04 0.00 0.00 0.30
#> TCGA.HU.A4GN.01 2 0.2512 0.5767 0.00 0.86 0.10 0.00 0.04 0.00 0.00
#> TCGA.HU.A4H6.01 3 0.1433 0.8133 0.00 0.08 0.92 0.00 0.00 0.00 0.00
#> TCGA.HF.7132.01 2 0.0504 0.6453 0.00 0.98 0.00 0.02 0.00 0.00 0.00
#> TCGA.HF.7134.01 4 0.0000 0.7840 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.BR.8370.01 5 0.3058 0.8151 0.00 0.00 0.08 0.00 0.82 0.00 0.10
#> TCGA.D7.5577.01 1 0.0000 0.9717 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BR.6707.01 1 0.0000 0.9717 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.B7.5818.01 1 0.0000 0.9717 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CG.5733.01 2 0.4264 0.4238 0.00 0.62 0.00 0.06 0.00 0.00 0.32
#> TCGA.BR.7851.01 2 0.1363 0.6335 0.00 0.94 0.02 0.00 0.04 0.00 0.00
#> TCGA.CG.5726.01 4 0.0000 0.7840 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.BR.8363.01 3 0.1363 0.8396 0.00 0.04 0.94 0.00 0.00 0.02 0.00
#> TCGA.CG.5720.01 2 0.4703 0.4453 0.00 0.62 0.00 0.04 0.00 0.04 0.30
#> TCGA.D7.8570.01 1 0.0000 0.9717 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BR.8284.01 2 0.2512 0.5767 0.00 0.86 0.10 0.00 0.04 0.00 0.00
#> TCGA.B7.A5TJ.01 4 0.0504 0.7791 0.00 0.00 0.00 0.98 0.00 0.00 0.02
#> TCGA.BR.8366.01 1 0.0000 0.9717 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.VQ.A8E3.01 2 0.3841 0.5209 0.00 0.68 0.00 0.04 0.00 0.00 0.28
#> TCGA.CD.5801.01 1 0.0000 0.9717 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BR.7958.01 6 0.4092 0.7479 0.08 0.00 0.00 0.00 0.02 0.74 0.16
#> TCGA.FP.7916.01 1 0.0000 0.9717 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.SW.A7EA.01 2 0.4388 0.4725 0.00 0.64 0.00 0.04 0.00 0.02 0.30
#> TCGA.BR.8368.01 4 0.5241 -0.1682 0.00 0.18 0.00 0.50 0.00 0.00 0.32
#> TCGA.BR.8081.01 3 0.1363 0.8396 0.00 0.04 0.94 0.00 0.00 0.02 0.00
#> TCGA.CD.8535.01 4 0.0000 0.7840 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.HF.A5NB.01 4 0.0000 0.7840 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.CD.A48C.01 4 0.0504 0.7791 0.00 0.00 0.00 0.98 0.00 0.00 0.02
#> TCGA.BR.8285.01 1 0.0000 0.9717 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BR.8361.01 2 0.3927 0.5034 0.00 0.66 0.00 0.04 0.00 0.00 0.30
#> TCGA.HU.A4G9.01 4 0.0000 0.7840 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.CD.8528.01 4 0.5241 -0.1682 0.00 0.18 0.00 0.50 0.00 0.00 0.32
#> TCGA.FP.A4BE.01 5 0.1718 0.9105 0.00 0.04 0.04 0.00 0.92 0.00 0.00
#> TCGA.BR.8078.01 5 0.1433 0.9150 0.00 0.08 0.00 0.00 0.92 0.00 0.00
#> TCGA.CD.8531.01 6 0.4161 0.8114 0.00 0.00 0.10 0.00 0.06 0.76 0.08
#> TCGA.VQ.A8DT.01 4 0.0000 0.7840 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.HU.A4G6.01 1 0.0000 0.9717 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HU.A4G3.01 2 0.2016 0.6286 0.00 0.90 0.00 0.04 0.00 0.00 0.06
#> TCGA.D7.A74A.01 7 0.4718 0.6084 0.00 0.06 0.00 0.32 0.00 0.02 0.60
#> TCGA.BR.8372.01 2 0.4703 0.4453 0.00 0.62 0.00 0.04 0.00 0.04 0.30
#> TCGA.HU.8244.01 4 0.0000 0.7840 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.IN.A6RR.01 4 0.0504 0.7791 0.00 0.00 0.00 0.98 0.00 0.00 0.02
#> TCGA.VQ.A8P2.01 4 0.0000 0.7840 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.D7.8573.01 1 0.0000 0.9717 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BR.8360.01 2 0.1006 0.6442 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.BR.6452.01 5 0.1804 0.9110 0.00 0.08 0.00 0.00 0.90 0.00 0.00 0.02
#> TCGA.VQ.A8PO.01 2 0.3318 0.4089 0.00 0.54 0.00 0.00 0.00 0.00 0.00 0.46
#> TCGA.VQ.AA69.01 1 0.0000 0.9363 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BR.8589.01 1 0.0000 0.9363 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BR.8382.01 3 0.3237 0.3679 0.00 0.40 0.60 0.00 0.00 0.00 0.00 0.00
#> TCGA.HU.8604.01 3 0.0000 0.8662 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BR.8676.01 1 0.4747 0.3448 0.54 0.00 0.00 0.00 0.00 0.00 0.16 0.30
#> TCGA.VQ.A923.01 1 0.0000 0.9363 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BR.8679.01 8 0.4693 0.7887 0.00 0.12 0.00 0.42 0.00 0.00 0.00 0.46
#> TCGA.VQ.A92D.01 7 0.6147 0.5023 0.00 0.18 0.00 0.06 0.00 0.02 0.44 0.30
#> TCGA.BR.6455.01 1 0.4747 0.3448 0.54 0.00 0.00 0.00 0.00 0.00 0.16 0.30
#> TCGA.BR.8591.01 2 0.0000 0.6063 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HU.8608.01 1 0.0000 0.9363 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.VQ.A91D.01 5 0.1341 0.9141 0.00 0.08 0.00 0.00 0.92 0.00 0.00 0.00
#> TCGA.HU.8602.01 5 0.1804 0.8338 0.00 0.00 0.08 0.00 0.90 0.00 0.00 0.02
#> TCGA.BR.8381.01 1 0.4747 0.3448 0.54 0.00 0.00 0.00 0.00 0.00 0.16 0.30
#> TCGA.IN.8663.01 4 0.0000 0.8899 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.VQ.A91W.01 1 0.2132 0.8353 0.88 0.00 0.00 0.00 0.04 0.00 0.00 0.08
#> TCGA.F1.6177.01 4 0.3514 0.2727 0.00 0.00 0.00 0.64 0.00 0.00 0.34 0.02
#> TCGA.VQ.AA6I.01 8 0.4693 0.7887 0.00 0.12 0.00 0.42 0.00 0.00 0.00 0.46
#> TCGA.CG.4437.01 2 0.0000 0.6063 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.VQ.A8PP.01 2 0.0471 0.6105 0.00 0.98 0.00 0.00 0.00 0.00 0.00 0.02
#> TCGA.VQ.A8PF.01 1 0.0000 0.9363 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BR.8487.01 7 0.5116 0.6339 0.00 0.00 0.00 0.26 0.00 0.00 0.46 0.28
#> TCGA.VQ.A91K.01 7 0.5163 0.6418 0.00 0.00 0.00 0.24 0.00 0.00 0.42 0.34
#> TCGA.BR.8686.01 1 0.0000 0.9363 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.IN.A6RO.01 4 0.0000 0.8899 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.BR.A4QI.01 3 0.2407 0.7928 0.00 0.00 0.86 0.00 0.00 0.00 0.06 0.08
#> TCGA.HU.A4G2.01 1 0.0000 0.9363 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BR.A4IY.01 6 0.0471 0.7722 0.00 0.00 0.02 0.00 0.00 0.98 0.00 0.00
#> TCGA.BR.A4J4.01 1 0.0000 0.9363 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.VQ.A94R.01 4 0.0000 0.8899 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.BR.7707.01 2 0.3318 0.4089 0.00 0.54 0.00 0.00 0.00 0.00 0.00 0.46
#> TCGA.FP.7829.01 4 0.0000 0.8899 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.HU.A4H0.01 1 0.0000 0.9363 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BR.A4PF.01 2 0.1563 0.5350 0.00 0.90 0.10 0.00 0.00 0.00 0.00 0.00
#> TCGA.CD.A4MJ.01 5 0.1341 0.9141 0.00 0.08 0.00 0.00 0.92 0.00 0.00 0.00
#> TCGA.HU.A4GP.01 4 0.0000 0.8899 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.D7.A4YY.01 4 0.2756 0.2873 0.00 0.00 0.00 0.74 0.00 0.00 0.00 0.26
#> TCGA.VQ.AA6G.01 4 0.3318 -0.5487 0.00 0.00 0.00 0.54 0.00 0.00 0.00 0.46
#> TCGA.CD.A4MI.01 3 0.0000 0.8662 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.VQ.A924.01 2 0.3514 0.0791 0.00 0.64 0.00 0.00 0.34 0.00 0.00 0.02
#> TCGA.HU.A4H8.01 4 0.0000 0.8899 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.HU.A4H3.01 2 0.3714 0.4104 0.00 0.54 0.00 0.00 0.00 0.00 0.02 0.44
#> TCGA.BR.A4PE.01 2 0.3318 0.4089 0.00 0.54 0.00 0.00 0.00 0.00 0.00 0.46
#> TCGA.BR.A4J8.01 5 0.1557 0.9148 0.00 0.06 0.02 0.00 0.92 0.00 0.00 0.00
#> TCGA.HU.A4GT.01 4 0.0000 0.8899 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.BR.A4CQ.01 7 0.5497 0.6746 0.00 0.00 0.00 0.24 0.00 0.02 0.44 0.30
#> TCGA.HU.A4GQ.01 3 0.2623 0.7782 0.00 0.00 0.84 0.00 0.00 0.00 0.06 0.10
#> TCGA.BR.A4QM.01 2 0.0000 0.6063 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D7.A4YX.01 1 0.0000 0.9363 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.VQ.A8PT.01 8 0.5433 -0.1799 0.00 0.30 0.00 0.00 0.00 0.02 0.22 0.46
#> TCGA.CD.A4MG.01 2 0.2938 0.5324 0.00 0.70 0.00 0.00 0.00 0.00 0.00 0.30
#> TCGA.D7.A4YV.01 2 0.1947 0.4892 0.00 0.86 0.14 0.00 0.00 0.00 0.00 0.00
#> TCGA.BR.A4QL.01 4 0.0000 0.8899 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.BR.7703.01 8 0.4693 0.7887 0.00 0.12 0.00 0.42 0.00 0.00 0.00 0.46
#> TCGA.D7.A6EZ.01 1 0.0000 0.9363 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D7.A4YU.01 2 0.3329 -0.3555 0.00 0.52 0.48 0.00 0.00 0.00 0.00 0.00
#> TCGA.IN.A6RP.01 4 0.3318 -0.5487 0.00 0.00 0.00 0.54 0.00 0.00 0.00 0.46
#> TCGA.HU.A4GU.01 7 0.5138 0.4035 0.00 0.24 0.00 0.00 0.00 0.00 0.44 0.32
#> TCGA.MX.A5UJ.01 2 0.3318 0.4089 0.00 0.54 0.00 0.00 0.00 0.00 0.00 0.46
#> TCGA.HU.A4GN.01 2 0.1947 0.4892 0.00 0.86 0.14 0.00 0.00 0.00 0.00 0.00
#> TCGA.HU.A4H6.01 3 0.0471 0.8548 0.00 0.02 0.98 0.00 0.00 0.00 0.00 0.00
#> TCGA.HF.7132.01 2 0.0808 0.6129 0.00 0.96 0.00 0.00 0.00 0.00 0.00 0.04
#> TCGA.HF.7134.01 4 0.0000 0.8899 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.BR.8370.01 5 0.4122 0.6928 0.00 0.00 0.08 0.00 0.74 0.00 0.08 0.10
#> TCGA.D7.5577.01 1 0.0000 0.9363 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BR.6707.01 1 0.0000 0.9363 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.B7.5818.01 1 0.0000 0.9363 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CG.5733.01 2 0.3318 0.4089 0.00 0.54 0.00 0.00 0.00 0.00 0.00 0.46
#> TCGA.BR.7851.01 2 0.0000 0.6063 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CG.5726.01 4 0.0000 0.8899 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.BR.8363.01 3 0.0000 0.8662 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CG.5720.01 2 0.3329 0.3838 0.00 0.52 0.00 0.00 0.00 0.00 0.00 0.48
#> TCGA.D7.8570.01 1 0.0000 0.9363 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BR.8284.01 2 0.1947 0.4892 0.00 0.86 0.14 0.00 0.00 0.00 0.00 0.00
#> TCGA.B7.A5TJ.01 4 0.0000 0.8899 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.BR.8366.01 1 0.0000 0.9363 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.VQ.A8E3.01 2 0.3193 0.4772 0.00 0.62 0.00 0.00 0.00 0.00 0.00 0.38
#> TCGA.CD.5801.01 1 0.0000 0.9363 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BR.7958.01 6 0.5072 0.6773 0.02 0.00 0.00 0.00 0.02 0.62 0.16 0.18
#> TCGA.FP.7916.01 1 0.0000 0.9363 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.SW.A7EA.01 2 0.4137 0.3466 0.00 0.50 0.00 0.00 0.00 0.02 0.02 0.46
#> TCGA.BR.8368.01 8 0.4693 0.7887 0.00 0.12 0.00 0.42 0.00 0.00 0.00 0.46
#> TCGA.BR.8081.01 3 0.0000 0.8662 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CD.8535.01 4 0.0000 0.8899 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.HF.A5NB.01 4 0.0000 0.8899 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.CD.A48C.01 4 0.0000 0.8899 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.BR.8285.01 1 0.0000 0.9363 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BR.8361.01 2 0.3318 0.4089 0.00 0.54 0.00 0.00 0.00 0.00 0.00 0.46
#> TCGA.HU.A4G9.01 4 0.0000 0.8899 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.CD.8528.01 8 0.4693 0.7887 0.00 0.12 0.00 0.42 0.00 0.00 0.00 0.46
#> TCGA.FP.A4BE.01 5 0.1557 0.9148 0.00 0.06 0.02 0.00 0.92 0.00 0.00 0.00
#> TCGA.BR.8078.01 5 0.2025 0.8987 0.00 0.10 0.00 0.00 0.88 0.00 0.00 0.02
#> TCGA.CD.8531.01 6 0.4174 0.7445 0.00 0.00 0.02 0.00 0.02 0.70 0.22 0.04
#> TCGA.VQ.A8DT.01 4 0.0000 0.8899 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.HU.A4G6.01 1 0.0000 0.9363 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HU.A4G3.01 2 0.2406 0.5799 0.00 0.80 0.00 0.00 0.00 0.00 0.00 0.20
#> TCGA.D7.A74A.01 7 0.5102 0.6794 0.00 0.00 0.00 0.24 0.00 0.00 0.46 0.30
#> TCGA.BR.8372.01 2 0.3329 0.3838 0.00 0.52 0.00 0.00 0.00 0.00 0.00 0.48
#> TCGA.HU.8244.01 4 0.0000 0.8899 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.IN.A6RR.01 4 0.0000 0.8899 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.VQ.A8P2.01 4 0.0000 0.8899 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.D7.8573.01 1 0.0000 0.9363 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BR.8360.01 2 0.1765 0.6048 0.00 0.88 0.00 0.00 0.00 0.00 0.00 0.12
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
consensus_heatmap(res, k = 7)
consensus_heatmap(res, k = 8)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
membership_heatmap(res, k = 7)
membership_heatmap(res, k = 8)
As soon as the classes for columns are determined, the signatures that are significantly different between subgroups can be looked for. Following are the heatmaps for signatures.
get_signatures(res, k = 2)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
get_signatures(res, k = 7)
get_signatures(res, k = 8)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. To get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows (which is done by automatically selecting number of clusters).If there are too many signatures, top_signatures = ... can be set to only show the
signatures with the highest FDRs:
# code only for demonstration
# e.g. to show the top 500 most significant rows
tb = get_signature(res, k = ..., top_signatures = 500)
If the signatures are defined as these which are uniquely high in current group, diff_method argument
can be set to "uniquely_high_in_one_group":
# code only for demonstration
tb = get_signature(res, k = ..., diff_method = "uniquely_high_in_one_group")
UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
dimension_reduction(res, k = 7, method = "UMAP")
dimension_reduction(res, k = 8, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
If matrix rows can be associated to genes, consider to use functional_enrichment(res,
...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.
Parent node: Node02. Child nodes: Node0111 , Node0112 , Node0113 , Node0114-leaf , Node0121 , Node0122 , Node0123 , Node0131 , Node0132-leaf , Node0211-leaf , Node0212-leaf , Node0221-leaf , Node0222 , Node0231-leaf , Node0232-leaf , Node0233-leaf , Node0311 , Node0312-leaf , Node0313-leaf , Node0314-leaf , Node0331-leaf , Node0332-leaf , Node0333-leaf , Node0341 , Node0342-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 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 0.3895 0.611 0.611
#> 3 3 0.726 0.878 0.894 0.6465 0.709 0.524
#> 4 4 0.714 0.652 0.759 0.1144 0.899 0.705
#> 5 5 0.748 0.776 0.880 0.0816 0.878 0.603
#> 6 6 0.831 0.685 0.856 0.0404 0.968 0.864
#> 7 7 0.826 0.704 0.796 0.0294 0.923 0.642
#> 8 8 0.820 0.662 0.831 0.0263 0.947 0.688
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.VQ.AA69.01 2 0 1 0 1
#> TCGA.BR.8589.01 1 0 1 1 0
#> TCGA.BR.8676.01 2 0 1 0 1
#> TCGA.VQ.A923.01 2 0 1 0 1
#> TCGA.BR.6455.01 2 0 1 0 1
#> TCGA.HU.8608.01 1 0 1 1 0
#> TCGA.BR.8381.01 1 0 1 1 0
#> TCGA.VQ.A91W.01 2 0 1 0 1
#> TCGA.VQ.A8PF.01 1 0 1 1 0
#> TCGA.BR.8686.01 1 0 1 1 0
#> TCGA.HU.A4G2.01 1 0 1 1 0
#> TCGA.BR.A4IY.01 1 0 1 1 0
#> TCGA.BR.A4J4.01 1 0 1 1 0
#> TCGA.HU.A4H0.01 1 0 1 1 0
#> TCGA.D7.A4YX.01 1 0 1 1 0
#> TCGA.D7.A6EZ.01 1 0 1 1 0
#> TCGA.D7.5577.01 1 0 1 1 0
#> TCGA.BR.6707.01 1 0 1 1 0
#> TCGA.B7.5818.01 1 0 1 1 0
#> TCGA.D7.8570.01 1 0 1 1 0
#> TCGA.BR.8366.01 1 0 1 1 0
#> TCGA.CD.5801.01 1 0 1 1 0
#> TCGA.BR.7958.01 1 0 1 1 0
#> TCGA.FP.7916.01 1 0 1 1 0
#> TCGA.BR.8285.01 1 0 1 1 0
#> TCGA.CD.8531.01 2 0 1 0 1
#> TCGA.HU.A4G6.01 1 0 1 1 0
#> TCGA.D7.8573.01 2 0 1 0 1
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.VQ.AA69.01 2 0.334 0.916 0.12 0.88 0.00
#> TCGA.BR.8589.01 3 0.000 1.000 0.00 0.00 1.00
#> TCGA.BR.8676.01 2 0.000 0.953 0.00 1.00 0.00
#> TCGA.VQ.A923.01 2 0.480 0.830 0.22 0.78 0.00
#> TCGA.BR.6455.01 2 0.000 0.953 0.00 1.00 0.00
#> TCGA.HU.8608.01 3 0.000 1.000 0.00 0.00 1.00
#> TCGA.BR.8381.01 1 0.254 0.800 0.92 0.00 0.08
#> TCGA.VQ.A91W.01 2 0.000 0.953 0.00 1.00 0.00
#> TCGA.VQ.A8PF.01 1 0.628 0.557 0.54 0.00 0.46
#> TCGA.BR.8686.01 1 0.631 0.465 0.50 0.00 0.50
#> TCGA.HU.A4G2.01 3 0.000 1.000 0.00 0.00 1.00
#> TCGA.BR.A4IY.01 1 0.369 0.811 0.86 0.00 0.14
#> TCGA.BR.A4J4.01 1 0.502 0.803 0.76 0.00 0.24
#> TCGA.HU.A4H0.01 3 0.000 1.000 0.00 0.00 1.00
#> TCGA.D7.A4YX.01 1 0.254 0.800 0.92 0.00 0.08
#> TCGA.D7.A6EZ.01 3 0.000 1.000 0.00 0.00 1.00
#> TCGA.D7.5577.01 3 0.000 1.000 0.00 0.00 1.00
#> TCGA.BR.6707.01 1 0.254 0.800 0.92 0.00 0.08
#> TCGA.B7.5818.01 3 0.000 1.000 0.00 0.00 1.00
#> TCGA.D7.8570.01 3 0.000 1.000 0.00 0.00 1.00
#> TCGA.BR.8366.01 3 0.000 1.000 0.00 0.00 1.00
#> TCGA.CD.5801.01 3 0.000 1.000 0.00 0.00 1.00
#> TCGA.BR.7958.01 1 0.522 0.796 0.74 0.00 0.26
#> TCGA.FP.7916.01 1 0.254 0.800 0.92 0.00 0.08
#> TCGA.BR.8285.01 1 0.522 0.796 0.74 0.00 0.26
#> TCGA.CD.8531.01 2 0.207 0.941 0.06 0.94 0.00
#> TCGA.HU.A4G6.01 1 0.613 0.657 0.60 0.00 0.40
#> TCGA.D7.8573.01 2 0.000 0.953 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.VQ.AA69.01 2 0.722 0.5280 0.14 0.44 0.00 0.42
#> TCGA.BR.8589.01 3 0.000 0.9933 0.00 0.00 1.00 0.00
#> TCGA.BR.8676.01 2 0.000 0.8469 0.00 1.00 0.00 0.00
#> TCGA.VQ.A923.01 1 0.720 -0.0962 0.54 0.18 0.00 0.28
#> TCGA.BR.6455.01 2 0.000 0.8469 0.00 1.00 0.00 0.00
#> TCGA.HU.8608.01 3 0.000 0.9933 0.00 0.00 1.00 0.00
#> TCGA.BR.8381.01 1 0.000 0.5472 1.00 0.00 0.00 0.00
#> TCGA.VQ.A91W.01 2 0.000 0.8469 0.00 1.00 0.00 0.00
#> TCGA.VQ.A8PF.01 4 0.777 0.8565 0.24 0.00 0.36 0.40
#> TCGA.BR.8686.01 4 0.770 0.8441 0.22 0.00 0.38 0.40
#> TCGA.HU.A4G2.01 3 0.000 0.9933 0.00 0.00 1.00 0.00
#> TCGA.BR.A4IY.01 1 0.485 0.1517 0.60 0.00 0.00 0.40
#> TCGA.BR.A4J4.01 1 0.702 -0.2409 0.48 0.00 0.12 0.40
#> TCGA.HU.A4H0.01 3 0.000 0.9933 0.00 0.00 1.00 0.00
#> TCGA.D7.A4YX.01 1 0.000 0.5472 1.00 0.00 0.00 0.00
#> TCGA.D7.A6EZ.01 3 0.000 0.9933 0.00 0.00 1.00 0.00
#> TCGA.D7.5577.01 3 0.000 0.9933 0.00 0.00 1.00 0.00
#> TCGA.BR.6707.01 1 0.000 0.5472 1.00 0.00 0.00 0.00
#> TCGA.B7.5818.01 3 0.000 0.9933 0.00 0.00 1.00 0.00
#> TCGA.D7.8570.01 3 0.121 0.9359 0.00 0.00 0.96 0.04
#> TCGA.BR.8366.01 3 0.000 0.9933 0.00 0.00 1.00 0.00
#> TCGA.CD.5801.01 3 0.000 0.9933 0.00 0.00 1.00 0.00
#> TCGA.BR.7958.01 1 0.721 -0.3133 0.46 0.00 0.14 0.40
#> TCGA.FP.7916.01 1 0.000 0.5472 1.00 0.00 0.00 0.00
#> TCGA.BR.8285.01 1 0.721 -0.3133 0.46 0.00 0.14 0.40
#> TCGA.CD.8531.01 2 0.491 0.6685 0.00 0.58 0.00 0.42
#> TCGA.HU.A4G6.01 4 0.739 0.7100 0.24 0.00 0.24 0.52
#> TCGA.D7.8573.01 2 0.000 0.8469 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.VQ.AA69.01 1 0.6705 -0.555 0.42 0.32 0.00 0.00 0.26
#> TCGA.BR.8589.01 3 0.0000 0.935 0.00 0.00 1.00 0.00 0.00
#> TCGA.BR.8676.01 2 0.0000 1.000 0.00 1.00 0.00 0.00 0.00
#> TCGA.VQ.A923.01 1 0.0609 0.640 0.98 0.02 0.00 0.00 0.00
#> TCGA.BR.6455.01 2 0.0000 1.000 0.00 1.00 0.00 0.00 0.00
#> TCGA.HU.8608.01 3 0.2280 0.901 0.00 0.00 0.88 0.00 0.12
#> TCGA.BR.8381.01 1 0.2929 0.797 0.82 0.00 0.00 0.18 0.00
#> TCGA.VQ.A91W.01 2 0.0000 1.000 0.00 1.00 0.00 0.00 0.00
#> TCGA.VQ.A8PF.01 4 0.4676 0.720 0.00 0.00 0.12 0.74 0.14
#> TCGA.BR.8686.01 4 0.4676 0.720 0.00 0.00 0.12 0.74 0.14
#> TCGA.HU.A4G2.01 3 0.0000 0.935 0.00 0.00 1.00 0.00 0.00
#> TCGA.BR.A4IY.01 4 0.0000 0.823 0.00 0.00 0.00 1.00 0.00
#> TCGA.BR.A4J4.01 4 0.0000 0.823 0.00 0.00 0.00 1.00 0.00
#> TCGA.HU.A4H0.01 3 0.2516 0.892 0.00 0.00 0.86 0.00 0.14
#> TCGA.D7.A4YX.01 1 0.2929 0.797 0.82 0.00 0.00 0.18 0.00
#> TCGA.D7.A6EZ.01 3 0.2516 0.892 0.00 0.00 0.86 0.00 0.14
#> TCGA.D7.5577.01 3 0.0000 0.935 0.00 0.00 1.00 0.00 0.00
#> TCGA.BR.6707.01 1 0.2929 0.797 0.82 0.00 0.00 0.18 0.00
#> TCGA.B7.5818.01 3 0.0000 0.935 0.00 0.00 1.00 0.00 0.00
#> TCGA.D7.8570.01 3 0.3291 0.873 0.00 0.00 0.84 0.04 0.12
#> TCGA.BR.8366.01 3 0.0000 0.935 0.00 0.00 1.00 0.00 0.00
#> TCGA.CD.5801.01 3 0.0000 0.935 0.00 0.00 1.00 0.00 0.00
#> TCGA.BR.7958.01 4 0.0000 0.823 0.00 0.00 0.00 1.00 0.00
#> TCGA.FP.7916.01 1 0.2929 0.797 0.82 0.00 0.00 0.18 0.00
#> TCGA.BR.8285.01 4 0.0000 0.823 0.00 0.00 0.00 1.00 0.00
#> TCGA.CD.8531.01 5 0.5861 0.000 0.10 0.40 0.00 0.00 0.50
#> TCGA.HU.A4G6.01 4 0.4287 0.551 0.00 0.00 0.00 0.54 0.46
#> TCGA.D7.8573.01 2 0.0000 1.000 0.00 1.00 0.00 0.00 0.00
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> TCGA.VQ.AA69.01 6 0.6751 -0.547 0.16 0.20 0.00 0.00 0.12 0.52
#> TCGA.BR.8589.01 3 0.3198 0.810 0.00 0.00 0.74 0.00 0.26 0.00
#> TCGA.BR.8676.01 2 0.0000 1.000 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.VQ.A923.01 1 0.0000 0.937 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BR.6455.01 2 0.0000 1.000 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.HU.8608.01 3 0.0547 0.684 0.00 0.00 0.98 0.02 0.00 0.00
#> TCGA.BR.8381.01 1 0.1267 0.968 0.94 0.00 0.00 0.06 0.00 0.00
#> TCGA.VQ.A91W.01 2 0.0000 1.000 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.VQ.A8PF.01 4 0.3916 0.503 0.00 0.00 0.30 0.68 0.00 0.02
#> TCGA.BR.8686.01 4 0.3916 0.503 0.00 0.00 0.30 0.68 0.00 0.02
#> TCGA.HU.A4G2.01 3 0.3198 0.810 0.00 0.00 0.74 0.00 0.26 0.00
#> TCGA.BR.A4IY.01 4 0.1556 0.719 0.00 0.00 0.00 0.92 0.08 0.00
#> TCGA.BR.A4J4.01 4 0.1556 0.719 0.00 0.00 0.00 0.92 0.08 0.00
#> TCGA.HU.A4H0.01 3 0.3007 0.604 0.00 0.00 0.86 0.04 0.08 0.02
#> TCGA.D7.A4YX.01 1 0.0547 0.954 0.98 0.00 0.00 0.02 0.00 0.00
#> TCGA.D7.A6EZ.01 3 0.3007 0.604 0.00 0.00 0.86 0.04 0.08 0.02
#> TCGA.D7.5577.01 3 0.3198 0.810 0.00 0.00 0.74 0.00 0.26 0.00
#> TCGA.BR.6707.01 1 0.1267 0.968 0.94 0.00 0.00 0.06 0.00 0.00
#> TCGA.B7.5818.01 3 0.3198 0.810 0.00 0.00 0.74 0.00 0.26 0.00
#> TCGA.D7.8570.01 3 0.2631 0.498 0.00 0.00 0.82 0.18 0.00 0.00
#> TCGA.BR.8366.01 3 0.3198 0.810 0.00 0.00 0.74 0.00 0.26 0.00
#> TCGA.CD.5801.01 3 0.3198 0.810 0.00 0.00 0.74 0.00 0.26 0.00
#> TCGA.BR.7958.01 4 0.0000 0.745 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.FP.7916.01 1 0.1267 0.968 0.94 0.00 0.00 0.06 0.00 0.00
#> TCGA.BR.8285.01 4 0.0547 0.744 0.00 0.00 0.02 0.98 0.00 0.00
#> TCGA.CD.8531.01 5 0.5569 0.000 0.00 0.18 0.00 0.00 0.54 0.28
#> TCGA.HU.A4G6.01 6 0.6711 -0.267 0.00 0.00 0.24 0.32 0.04 0.40
#> TCGA.D7.8573.01 2 0.0000 1.000 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.VQ.AA69.01 7 0.7464 -0.568 0.06 0.18 0.00 0.00 0.22 0.14 0.40
#> TCGA.BR.8589.01 3 0.0000 1.000 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.BR.8676.01 2 0.0000 0.993 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.VQ.A923.01 1 0.1166 0.926 0.94 0.00 0.00 0.00 0.00 0.06 0.00
#> TCGA.BR.6455.01 2 0.0000 0.993 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HU.8608.01 7 0.3562 0.474 0.00 0.00 0.50 0.00 0.00 0.00 0.50
#> TCGA.BR.8381.01 1 0.0504 0.968 0.98 0.00 0.00 0.02 0.00 0.00 0.00
#> TCGA.VQ.A91W.01 2 0.0504 0.978 0.00 0.98 0.00 0.00 0.00 0.02 0.00
#> TCGA.VQ.A8PF.01 4 0.3562 0.413 0.00 0.00 0.00 0.50 0.00 0.00 0.50
#> TCGA.BR.8686.01 4 0.3562 0.413 0.00 0.00 0.00 0.50 0.00 0.00 0.50
#> TCGA.HU.A4G2.01 3 0.0000 1.000 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.BR.A4IY.01 4 0.0504 0.633 0.02 0.00 0.00 0.98 0.00 0.00 0.00
#> TCGA.BR.A4J4.01 4 0.1006 0.626 0.00 0.00 0.00 0.96 0.02 0.00 0.02
#> TCGA.HU.A4H0.01 7 0.4657 0.561 0.00 0.00 0.40 0.02 0.04 0.00 0.54
#> TCGA.D7.A4YX.01 1 0.1006 0.942 0.96 0.00 0.00 0.02 0.00 0.02 0.00
#> TCGA.D7.A6EZ.01 7 0.4244 0.552 0.00 0.00 0.42 0.00 0.04 0.00 0.54
#> TCGA.D7.5577.01 3 0.0000 1.000 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.BR.6707.01 1 0.0504 0.968 0.98 0.00 0.00 0.02 0.00 0.00 0.00
#> TCGA.B7.5818.01 3 0.0000 1.000 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.D7.8570.01 7 0.4866 0.507 0.00 0.00 0.42 0.10 0.00 0.00 0.48
#> TCGA.BR.8366.01 3 0.0000 1.000 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.CD.5801.01 3 0.0000 1.000 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.BR.7958.01 4 0.1671 0.687 0.00 0.00 0.00 0.90 0.00 0.00 0.10
#> TCGA.FP.7916.01 1 0.0504 0.968 0.98 0.00 0.00 0.02 0.00 0.00 0.00
#> TCGA.BR.8285.01 4 0.1671 0.687 0.00 0.00 0.00 0.90 0.00 0.00 0.10
#> TCGA.CD.8531.01 5 0.1433 0.000 0.00 0.08 0.00 0.00 0.92 0.00 0.00
#> TCGA.HU.A4G6.01 6 0.3449 0.000 0.00 0.00 0.00 0.08 0.00 0.78 0.14
#> TCGA.D7.8573.01 2 0.0000 0.993 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.VQ.AA69.01 8 0.1275 0.000 0.02 0.04 0.00 0.00 0.00 0.00 0.00 0.94
#> TCGA.BR.8589.01 3 0.0471 0.988 0.00 0.00 0.98 0.00 0.02 0.00 0.00 0.00
#> TCGA.BR.8676.01 2 0.0000 0.986 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.VQ.A923.01 1 0.2807 0.838 0.84 0.00 0.00 0.02 0.00 0.04 0.10 0.00
#> TCGA.BR.6455.01 2 0.0000 0.986 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HU.8608.01 7 0.5030 0.528 0.00 0.00 0.34 0.20 0.00 0.00 0.46 0.00
#> TCGA.BR.8381.01 1 0.0000 0.948 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.VQ.A91W.01 2 0.0941 0.958 0.00 0.96 0.00 0.02 0.00 0.02 0.00 0.00
#> TCGA.VQ.A8PF.01 7 0.3714 0.304 0.00 0.00 0.00 0.44 0.00 0.02 0.54 0.00
#> TCGA.BR.8686.01 7 0.3714 0.304 0.00 0.00 0.00 0.44 0.00 0.02 0.54 0.00
#> TCGA.HU.A4G2.01 3 0.0471 0.988 0.00 0.00 0.98 0.00 0.02 0.00 0.00 0.00
#> TCGA.BR.A4IY.01 4 0.3735 0.434 0.04 0.00 0.00 0.72 0.22 0.00 0.00 0.02
#> TCGA.BR.A4J4.01 4 0.4028 0.414 0.00 0.00 0.00 0.66 0.28 0.00 0.04 0.02
#> TCGA.HU.A4H0.01 7 0.2534 0.460 0.00 0.00 0.22 0.00 0.00 0.00 0.78 0.00
#> TCGA.D7.A4YX.01 1 0.1091 0.921 0.94 0.00 0.00 0.00 0.00 0.06 0.00 0.00
#> TCGA.D7.A6EZ.01 7 0.3675 0.377 0.00 0.00 0.30 0.00 0.00 0.00 0.66 0.04
#> TCGA.D7.5577.01 3 0.0000 0.988 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BR.6707.01 1 0.0000 0.948 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.B7.5818.01 3 0.0471 0.988 0.00 0.00 0.98 0.00 0.02 0.00 0.00 0.00
#> TCGA.D7.8570.01 7 0.4799 0.511 0.00 0.00 0.18 0.28 0.00 0.00 0.54 0.00
#> TCGA.BR.8366.01 3 0.0000 0.988 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CD.5801.01 3 0.0000 0.988 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BR.7958.01 4 0.2650 0.389 0.00 0.00 0.00 0.76 0.00 0.00 0.24 0.00
#> TCGA.FP.7916.01 1 0.0000 0.948 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BR.8285.01 4 0.2756 0.354 0.00 0.00 0.00 0.74 0.00 0.00 0.26 0.00
#> TCGA.CD.8531.01 5 0.3856 0.000 0.00 0.10 0.00 0.00 0.70 0.00 0.00 0.20
#> TCGA.HU.A4G6.01 6 0.2132 0.000 0.00 0.00 0.00 0.04 0.00 0.88 0.08 0.00
#> TCGA.D7.8573.01 2 0.0000 0.986 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
consensus_heatmap(res, k = 7)
consensus_heatmap(res, k = 8)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
membership_heatmap(res, k = 7)
membership_heatmap(res, k = 8)
As soon as the classes for columns are determined, the signatures that are significantly different between subgroups can be looked for. Following are the heatmaps for signatures.
get_signatures(res, k = 2)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
get_signatures(res, k = 7)
get_signatures(res, k = 8)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. To get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows (which is done by automatically selecting number of clusters).If there are too many signatures, top_signatures = ... can be set to only show the
signatures with the highest FDRs:
# code only for demonstration
# e.g. to show the top 500 most significant rows
tb = get_signature(res, k = ..., top_signatures = 500)
If the signatures are defined as these which are uniquely high in current group, diff_method argument
can be set to "uniquely_high_in_one_group":
# code only for demonstration
tb = get_signature(res, k = ..., diff_method = "uniquely_high_in_one_group")
UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
dimension_reduction(res, k = 7, method = "UMAP")
dimension_reduction(res, k = 8, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
If matrix rows can be associated to genes, consider to use functional_enrichment(res,
...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.
Parent node: Node02. Child nodes: Node0111 , Node0112 , Node0113 , Node0114-leaf , Node0121 , Node0122 , Node0123 , Node0131 , Node0132-leaf , Node0211-leaf , Node0212-leaf , Node0221-leaf , Node0222 , Node0231-leaf , Node0232-leaf , Node0233-leaf , Node0311 , Node0312-leaf , Node0313-leaf , Node0314-leaf , Node0331-leaf , Node0332-leaf , Node0333-leaf , Node0341 , Node0342-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 48 columns.
#> Top rows (1000) are extracted by 'ATC' method.
#> Subgroups are detected by 'kmeans' method.
#> Performed in total 350 partitions by row resampling.
#> Best k for subgroups seems to be 2.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_partitions"
#> [7] "compare_signatures" "consensus_heatmap" "dimension_reduction"
#> [10] "functional_enrichment" "get_anno_col" "get_anno"
#> [13] "get_classes" "get_consensus" "get_matrix"
#> [16] "get_membership" "get_param" "get_signatures"
#> [19] "get_stats" "is_best_k" "is_stable_k"
#> [22] "membership_heatmap" "ncol" "nrow"
#> [25] "plot_ecdf" "predict_classes" "rownames"
#> [28] "select_partition_number" "show" "suggest_best_k"
#> [31] "test_to_known_factors" "top_rows_heatmap"
collect_plots() function collects all the plots made from res for all k (number of subgroups)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
The plots are:
k and the heatmap of
predicted classes for each k.k.k.k.All the plots in panels can be made by individual functions and they are plotted later in this section.
select_partition_number() produces several plots showing different
statistics for choosing “optimized” k. There are following statistics:
k;k, the area increased is defined as \(A_k - A_{k-1}\).The detailed explanations of these statistics can be found in the cola vignette.
Generally speaking, higher 1-PAC score, higher mean silhouette score or higher
concordance corresponds to better partition. Rand index and Jaccard index
measure how similar the current partition is compared to partition with k-1.
If they are too similar, we won't accept k is better than k-1.
select_partition_number(res)
The numeric values for all these statistics can be obtained by get_stats().
get_stats(res)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> 2 2 1.000 0.997 0.998 0.5110 0.489 0.489
#> 3 3 0.842 0.859 0.931 0.2794 0.666 0.421
#> 4 4 0.761 0.935 0.933 0.1118 0.865 0.627
#> 5 5 0.786 0.764 0.854 0.0774 0.952 0.819
#> 6 6 0.780 0.636 0.780 0.0335 0.957 0.817
#> 7 7 0.771 0.547 0.781 0.0269 0.973 0.873
#> 8 8 0.770 0.562 0.814 0.0161 0.965 0.827
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.VQ.A8PO.01 2 0.000 1.000 0.00 1.00
#> TCGA.BR.8679.01 2 0.000 1.000 0.00 1.00
#> TCGA.VQ.A92D.01 1 0.000 0.997 1.00 0.00
#> TCGA.IN.8663.01 1 0.000 0.997 1.00 0.00
#> TCGA.F1.6177.01 1 0.000 0.997 1.00 0.00
#> TCGA.VQ.AA6I.01 2 0.000 1.000 0.00 1.00
#> TCGA.BR.8487.01 2 0.000 1.000 0.00 1.00
#> TCGA.VQ.A91K.01 1 0.000 0.997 1.00 0.00
#> TCGA.IN.A6RO.01 1 0.000 0.997 1.00 0.00
#> TCGA.VQ.A94R.01 2 0.000 1.000 0.00 1.00
#> TCGA.BR.7707.01 1 0.000 0.997 1.00 0.00
#> TCGA.FP.7829.01 2 0.000 1.000 0.00 1.00
#> TCGA.HU.A4GP.01 2 0.000 1.000 0.00 1.00
#> TCGA.D7.A4YY.01 1 0.000 0.997 1.00 0.00
#> TCGA.VQ.AA6G.01 1 0.000 0.997 1.00 0.00
#> TCGA.HU.A4H8.01 2 0.000 1.000 0.00 1.00
#> TCGA.HU.A4H3.01 2 0.000 1.000 0.00 1.00
#> TCGA.BR.A4PE.01 1 0.000 0.997 1.00 0.00
#> TCGA.HU.A4GT.01 1 0.000 0.997 1.00 0.00
#> TCGA.BR.A4CQ.01 1 0.000 0.997 1.00 0.00
#> TCGA.VQ.A8PT.01 1 0.000 0.997 1.00 0.00
#> TCGA.CD.A4MG.01 2 0.000 1.000 0.00 1.00
#> TCGA.BR.A4QL.01 1 0.000 0.997 1.00 0.00
#> TCGA.BR.7703.01 1 0.000 0.997 1.00 0.00
#> TCGA.IN.A6RP.01 1 0.000 0.997 1.00 0.00
#> TCGA.HU.A4GU.01 1 0.000 0.997 1.00 0.00
#> TCGA.MX.A5UJ.01 2 0.000 1.000 0.00 1.00
#> TCGA.HF.7134.01 2 0.000 1.000 0.00 1.00
#> TCGA.CG.5733.01 2 0.000 1.000 0.00 1.00
#> TCGA.CG.5726.01 2 0.000 1.000 0.00 1.00
#> TCGA.CG.5720.01 1 0.000 0.997 1.00 0.00
#> TCGA.B7.A5TJ.01 1 0.242 0.960 0.96 0.04
#> TCGA.VQ.A8E3.01 2 0.000 1.000 0.00 1.00
#> TCGA.SW.A7EA.01 1 0.000 0.997 1.00 0.00
#> TCGA.BR.8368.01 2 0.000 1.000 0.00 1.00
#> TCGA.CD.8535.01 2 0.000 1.000 0.00 1.00
#> TCGA.HF.A5NB.01 2 0.000 1.000 0.00 1.00
#> TCGA.CD.A48C.01 2 0.000 1.000 0.00 1.00
#> TCGA.BR.8361.01 2 0.000 1.000 0.00 1.00
#> TCGA.HU.A4G9.01 1 0.000 0.997 1.00 0.00
#> TCGA.CD.8528.01 2 0.000 1.000 0.00 1.00
#> TCGA.VQ.A8DT.01 2 0.000 1.000 0.00 1.00
#> TCGA.HU.A4G3.01 1 0.000 0.997 1.00 0.00
#> TCGA.D7.A74A.01 1 0.000 0.997 1.00 0.00
#> TCGA.BR.8372.01 1 0.242 0.960 0.96 0.04
#> TCGA.HU.8244.01 2 0.000 1.000 0.00 1.00
#> TCGA.IN.A6RR.01 2 0.000 1.000 0.00 1.00
#> TCGA.VQ.A8P2.01 1 0.000 0.997 1.00 0.00
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.VQ.A8PO.01 3 0.0000 0.913 0.00 0.00 1.00
#> TCGA.BR.8679.01 2 0.6045 0.631 0.00 0.62 0.38
#> TCGA.VQ.A92D.01 1 0.0000 1.000 1.00 0.00 0.00
#> TCGA.IN.8663.01 3 0.0000 0.913 0.00 0.00 1.00
#> TCGA.F1.6177.01 1 0.0000 1.000 1.00 0.00 0.00
#> TCGA.VQ.AA6I.01 2 0.6045 0.631 0.00 0.62 0.38
#> TCGA.BR.8487.01 3 0.0000 0.913 0.00 0.00 1.00
#> TCGA.VQ.A91K.01 1 0.0000 1.000 1.00 0.00 0.00
#> TCGA.IN.A6RO.01 1 0.0000 1.000 1.00 0.00 0.00
#> TCGA.VQ.A94R.01 2 0.0000 0.812 0.00 1.00 0.00
#> TCGA.BR.7707.01 3 0.0000 0.913 0.00 0.00 1.00
#> TCGA.FP.7829.01 3 0.0000 0.913 0.00 0.00 1.00
#> TCGA.HU.A4GP.01 2 0.0000 0.812 0.00 1.00 0.00
#> TCGA.D7.A4YY.01 1 0.0000 1.000 1.00 0.00 0.00
#> TCGA.VQ.AA6G.01 1 0.0000 1.000 1.00 0.00 0.00
#> TCGA.HU.A4H8.01 3 0.0000 0.913 0.00 0.00 1.00
#> TCGA.HU.A4H3.01 3 0.0000 0.913 0.00 0.00 1.00
#> TCGA.BR.A4PE.01 1 0.0000 1.000 1.00 0.00 0.00
#> TCGA.HU.A4GT.01 3 0.6126 0.368 0.40 0.00 0.60
#> TCGA.BR.A4CQ.01 1 0.0000 1.000 1.00 0.00 0.00
#> TCGA.VQ.A8PT.01 1 0.0000 1.000 1.00 0.00 0.00
#> TCGA.CD.A4MG.01 3 0.0000 0.913 0.00 0.00 1.00
#> TCGA.BR.A4QL.01 3 0.6126 0.368 0.40 0.00 0.60
#> TCGA.BR.7703.01 1 0.0000 1.000 1.00 0.00 0.00
#> TCGA.IN.A6RP.01 1 0.0000 1.000 1.00 0.00 0.00
#> TCGA.HU.A4GU.01 1 0.0000 1.000 1.00 0.00 0.00
#> TCGA.MX.A5UJ.01 2 0.6280 0.475 0.00 0.54 0.46
#> TCGA.HF.7134.01 2 0.5706 0.686 0.00 0.68 0.32
#> TCGA.CG.5733.01 3 0.0000 0.913 0.00 0.00 1.00
#> TCGA.CG.5726.01 2 0.0000 0.812 0.00 1.00 0.00
#> TCGA.CG.5720.01 3 0.0892 0.893 0.02 0.00 0.98
#> TCGA.B7.A5TJ.01 3 0.0000 0.913 0.00 0.00 1.00
#> TCGA.VQ.A8E3.01 2 0.6045 0.631 0.00 0.62 0.38
#> TCGA.SW.A7EA.01 3 0.5835 0.495 0.34 0.00 0.66
#> TCGA.BR.8368.01 2 0.0000 0.812 0.00 1.00 0.00
#> TCGA.CD.8535.01 2 0.4291 0.767 0.00 0.82 0.18
#> TCGA.HF.A5NB.01 3 0.0000 0.913 0.00 0.00 1.00
#> TCGA.CD.A48C.01 2 0.0000 0.812 0.00 1.00 0.00
#> TCGA.BR.8361.01 2 0.0000 0.812 0.00 1.00 0.00
#> TCGA.HU.A4G9.01 1 0.0000 1.000 1.00 0.00 0.00
#> TCGA.CD.8528.01 3 0.0000 0.913 0.00 0.00 1.00
#> TCGA.VQ.A8DT.01 3 0.0000 0.913 0.00 0.00 1.00
#> TCGA.HU.A4G3.01 3 0.0000 0.913 0.00 0.00 1.00
#> TCGA.D7.A74A.01 1 0.0000 1.000 1.00 0.00 0.00
#> TCGA.BR.8372.01 3 0.0000 0.913 0.00 0.00 1.00
#> TCGA.HU.8244.01 2 0.1529 0.808 0.00 0.96 0.04
#> TCGA.IN.A6RR.01 3 0.0000 0.913 0.00 0.00 1.00
#> TCGA.VQ.A8P2.01 1 0.0000 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.VQ.A8PO.01 3 0.0000 0.945 0.00 0.00 1.00 0.00
#> TCGA.BR.8679.01 2 0.5151 0.885 0.00 0.76 0.14 0.10
#> TCGA.VQ.A92D.01 1 0.0000 0.997 1.00 0.00 0.00 0.00
#> TCGA.IN.8663.01 3 0.0707 0.944 0.00 0.02 0.98 0.00
#> TCGA.F1.6177.01 1 0.0000 0.997 1.00 0.00 0.00 0.00
#> TCGA.VQ.AA6I.01 2 0.5383 0.883 0.00 0.74 0.16 0.10
#> TCGA.BR.8487.01 3 0.0707 0.937 0.00 0.02 0.98 0.00
#> TCGA.VQ.A91K.01 1 0.0000 0.997 1.00 0.00 0.00 0.00
#> TCGA.IN.A6RO.01 1 0.0000 0.997 1.00 0.00 0.00 0.00
#> TCGA.VQ.A94R.01 4 0.0000 1.000 0.00 0.00 0.00 1.00
#> TCGA.BR.7707.01 3 0.0000 0.945 0.00 0.00 1.00 0.00
#> TCGA.FP.7829.01 2 0.3172 0.875 0.00 0.84 0.16 0.00
#> TCGA.HU.A4GP.01 4 0.0000 1.000 0.00 0.00 0.00 1.00
#> TCGA.D7.A4YY.01 1 0.0000 0.997 1.00 0.00 0.00 0.00
#> TCGA.VQ.AA6G.01 1 0.0000 0.997 1.00 0.00 0.00 0.00
#> TCGA.HU.A4H8.01 2 0.4134 0.840 0.00 0.74 0.26 0.00
#> TCGA.HU.A4H3.01 3 0.2345 0.845 0.00 0.10 0.90 0.00
#> TCGA.BR.A4PE.01 1 0.1211 0.954 0.96 0.00 0.04 0.00
#> TCGA.HU.A4GT.01 3 0.3935 0.824 0.10 0.06 0.84 0.00
#> TCGA.BR.A4CQ.01 1 0.0000 0.997 1.00 0.00 0.00 0.00
#> TCGA.VQ.A8PT.01 1 0.0000 0.997 1.00 0.00 0.00 0.00
#> TCGA.CD.A4MG.01 3 0.0000 0.945 0.00 0.00 1.00 0.00
#> TCGA.BR.A4QL.01 3 0.3935 0.824 0.10 0.06 0.84 0.00
#> TCGA.BR.7703.01 1 0.0000 0.997 1.00 0.00 0.00 0.00
#> TCGA.IN.A6RP.01 1 0.0000 0.997 1.00 0.00 0.00 0.00
#> TCGA.HU.A4GU.01 1 0.0000 0.997 1.00 0.00 0.00 0.00
#> TCGA.MX.A5UJ.01 2 0.5077 0.889 0.00 0.76 0.16 0.08
#> TCGA.HF.7134.01 2 0.5383 0.849 0.00 0.74 0.10 0.16
#> TCGA.CG.5733.01 3 0.0707 0.937 0.00 0.02 0.98 0.00
#> TCGA.CG.5726.01 4 0.0000 1.000 0.00 0.00 0.00 1.00
#> TCGA.CG.5720.01 3 0.0707 0.942 0.02 0.00 0.98 0.00
#> TCGA.B7.A5TJ.01 3 0.0707 0.944 0.00 0.02 0.98 0.00
#> TCGA.VQ.A8E3.01 2 0.5428 0.867 0.00 0.74 0.12 0.14
#> TCGA.SW.A7EA.01 3 0.1211 0.927 0.04 0.00 0.96 0.00
#> TCGA.BR.8368.01 4 0.0000 1.000 0.00 0.00 0.00 1.00
#> TCGA.CD.8535.01 2 0.1637 0.787 0.00 0.94 0.00 0.06
#> TCGA.HF.A5NB.01 2 0.3172 0.875 0.00 0.84 0.16 0.00
#> TCGA.CD.A48C.01 4 0.0000 1.000 0.00 0.00 0.00 1.00
#> TCGA.BR.8361.01 4 0.0000 1.000 0.00 0.00 0.00 1.00
#> TCGA.HU.A4G9.01 1 0.0000 0.997 1.00 0.00 0.00 0.00
#> TCGA.CD.8528.01 3 0.0707 0.937 0.00 0.02 0.98 0.00
#> TCGA.VQ.A8DT.01 2 0.4134 0.840 0.00 0.74 0.26 0.00
#> TCGA.HU.A4G3.01 3 0.0707 0.942 0.02 0.00 0.98 0.00
#> TCGA.D7.A74A.01 1 0.0000 0.997 1.00 0.00 0.00 0.00
#> TCGA.BR.8372.01 3 0.0707 0.944 0.00 0.02 0.98 0.00
#> TCGA.HU.8244.01 2 0.4642 0.745 0.00 0.74 0.02 0.24
#> TCGA.IN.A6RR.01 2 0.3172 0.875 0.00 0.84 0.16 0.00
#> TCGA.VQ.A8P2.01 1 0.0000 0.997 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.VQ.A8PO.01 3 0.2012 0.7887 0.00 0.02 0.92 0.00 0.06
#> TCGA.BR.8679.01 2 0.1216 0.8089 0.00 0.96 0.00 0.02 0.02
#> TCGA.VQ.A92D.01 1 0.0000 0.8656 1.00 0.00 0.00 0.00 0.00
#> TCGA.IN.8663.01 3 0.0609 0.7990 0.00 0.00 0.98 0.00 0.02
#> TCGA.F1.6177.01 1 0.1043 0.8634 0.96 0.00 0.00 0.00 0.04
#> TCGA.VQ.AA6I.01 2 0.0609 0.8156 0.00 0.98 0.00 0.02 0.00
#> TCGA.BR.8487.01 3 0.5447 0.1800 0.00 0.44 0.50 0.00 0.06
#> TCGA.VQ.A91K.01 1 0.0000 0.8656 1.00 0.00 0.00 0.00 0.00
#> TCGA.IN.A6RO.01 1 0.0000 0.8656 1.00 0.00 0.00 0.00 0.00
#> TCGA.VQ.A94R.01 4 0.0000 0.9820 0.00 0.00 0.00 1.00 0.00
#> TCGA.BR.7707.01 3 0.0000 0.8040 0.00 0.00 1.00 0.00 0.00
#> TCGA.FP.7829.01 5 0.4262 0.8789 0.00 0.44 0.00 0.00 0.56
#> TCGA.HU.A4GP.01 4 0.0000 0.9820 0.00 0.00 0.00 1.00 0.00
#> TCGA.D7.A4YY.01 1 0.5341 0.7189 0.62 0.00 0.08 0.00 0.30
#> TCGA.VQ.AA6G.01 1 0.2516 0.8474 0.86 0.00 0.00 0.00 0.14
#> TCGA.HU.A4H8.01 2 0.2616 0.6597 0.00 0.88 0.02 0.00 0.10
#> TCGA.HU.A4H3.01 2 0.5828 -0.0116 0.00 0.52 0.38 0.00 0.10
#> TCGA.BR.A4PE.01 1 0.6794 0.3421 0.38 0.00 0.32 0.00 0.30
#> TCGA.HU.A4GT.01 3 0.3109 0.6828 0.00 0.00 0.80 0.00 0.20
#> TCGA.BR.A4CQ.01 1 0.0000 0.8656 1.00 0.00 0.00 0.00 0.00
#> TCGA.VQ.A8PT.01 1 0.0000 0.8656 1.00 0.00 0.00 0.00 0.00
#> TCGA.CD.A4MG.01 3 0.2616 0.7843 0.00 0.02 0.88 0.00 0.10
#> TCGA.BR.A4QL.01 3 0.3109 0.6828 0.00 0.00 0.80 0.00 0.20
#> TCGA.BR.7703.01 1 0.2732 0.8421 0.84 0.00 0.00 0.00 0.16
#> TCGA.IN.A6RP.01 1 0.4644 0.7672 0.68 0.00 0.04 0.00 0.28
#> TCGA.HU.A4GU.01 1 0.0000 0.8656 1.00 0.00 0.00 0.00 0.00
#> TCGA.MX.A5UJ.01 2 0.0609 0.8156 0.00 0.98 0.00 0.02 0.00
#> TCGA.HF.7134.01 2 0.1216 0.8089 0.00 0.96 0.00 0.02 0.02
#> TCGA.CG.5733.01 3 0.5447 0.1800 0.00 0.44 0.50 0.00 0.06
#> TCGA.CG.5726.01 4 0.1043 0.9633 0.00 0.04 0.00 0.96 0.00
#> TCGA.CG.5720.01 3 0.0000 0.8040 0.00 0.00 1.00 0.00 0.00
#> TCGA.B7.A5TJ.01 3 0.1410 0.7962 0.00 0.00 0.94 0.00 0.06
#> TCGA.VQ.A8E3.01 2 0.0609 0.8156 0.00 0.98 0.00 0.02 0.00
#> TCGA.SW.A7EA.01 3 0.0000 0.8040 0.00 0.00 1.00 0.00 0.00
#> TCGA.BR.8368.01 4 0.0000 0.9820 0.00 0.00 0.00 1.00 0.00
#> TCGA.CD.8535.01 5 0.4262 0.7527 0.00 0.44 0.00 0.00 0.56
#> TCGA.HF.A5NB.01 5 0.4262 0.8789 0.00 0.44 0.00 0.00 0.56
#> TCGA.CD.A48C.01 4 0.0000 0.9820 0.00 0.00 0.00 1.00 0.00
#> TCGA.BR.8361.01 4 0.1043 0.9633 0.00 0.04 0.00 0.96 0.00
#> TCGA.HU.A4G9.01 1 0.3690 0.8220 0.78 0.00 0.02 0.00 0.20
#> TCGA.CD.8528.01 3 0.5447 0.1800 0.00 0.44 0.50 0.00 0.06
#> TCGA.VQ.A8DT.01 2 0.0609 0.7966 0.00 0.98 0.02 0.00 0.00
#> TCGA.HU.A4G3.01 3 0.0609 0.7990 0.00 0.00 0.98 0.00 0.02
#> TCGA.D7.A74A.01 1 0.3684 0.7920 0.72 0.00 0.00 0.00 0.28
#> TCGA.BR.8372.01 3 0.1732 0.7960 0.00 0.00 0.92 0.00 0.08
#> TCGA.HU.8244.01 2 0.1216 0.8089 0.00 0.96 0.00 0.02 0.02
#> TCGA.IN.A6RR.01 5 0.4302 0.8644 0.00 0.48 0.00 0.00 0.52
#> TCGA.VQ.A8P2.01 1 0.0000 0.8656 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.VQ.A8PO.01 3 0.2794 0.677 0.00 0.08 0.86 0.00 0.00 0.06
#> TCGA.BR.8679.01 2 0.1807 0.765 0.00 0.92 0.00 0.06 0.02 0.00
#> TCGA.VQ.A92D.01 1 0.0000 0.745 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.IN.8663.01 3 0.2454 0.710 0.00 0.00 0.84 0.00 0.00 0.16
#> TCGA.F1.6177.01 1 0.0547 0.734 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.VQ.AA6I.01 2 0.2190 0.781 0.00 0.90 0.04 0.06 0.00 0.00
#> TCGA.BR.8487.01 2 0.4902 0.100 0.00 0.48 0.46 0.00 0.00 0.06
#> TCGA.VQ.A91K.01 1 0.0000 0.745 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.IN.A6RO.01 1 0.0000 0.745 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.VQ.A94R.01 4 0.0000 0.990 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.BR.7707.01 3 0.1814 0.734 0.00 0.00 0.90 0.00 0.00 0.10
#> TCGA.FP.7829.01 5 0.2631 0.892 0.00 0.18 0.00 0.00 0.82 0.00
#> TCGA.HU.A4GP.01 4 0.0000 0.990 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.D7.A4YY.01 6 0.4144 0.647 0.36 0.00 0.02 0.00 0.00 0.62
#> TCGA.VQ.AA6G.01 1 0.3578 0.298 0.66 0.00 0.00 0.00 0.00 0.34
#> TCGA.HU.A4H8.01 2 0.4860 0.639 0.00 0.72 0.14 0.00 0.04 0.10
#> TCGA.HU.A4H3.01 2 0.5199 0.477 0.00 0.58 0.30 0.00 0.00 0.12
#> TCGA.BR.A4PE.01 6 0.5102 0.718 0.24 0.00 0.14 0.00 0.00 0.62
#> TCGA.HU.A4GT.01 3 0.5756 0.453 0.00 0.04 0.58 0.00 0.10 0.28
#> TCGA.BR.A4CQ.01 1 0.0000 0.745 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.VQ.A8PT.01 1 0.0000 0.745 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CD.A4MG.01 3 0.1556 0.720 0.00 0.00 0.92 0.00 0.00 0.08
#> TCGA.BR.A4QL.01 3 0.5832 0.439 0.00 0.04 0.56 0.00 0.10 0.30
#> TCGA.BR.7703.01 1 0.3409 0.384 0.70 0.00 0.00 0.00 0.00 0.30
#> TCGA.IN.A6RP.01 1 0.3864 -0.273 0.52 0.00 0.00 0.00 0.00 0.48
#> TCGA.HU.A4GU.01 1 0.0000 0.745 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.MX.A5UJ.01 2 0.1807 0.765 0.00 0.92 0.00 0.06 0.02 0.00
#> TCGA.HF.7134.01 2 0.1556 0.766 0.00 0.92 0.00 0.08 0.00 0.00
#> TCGA.CG.5733.01 3 0.4902 -0.222 0.00 0.46 0.48 0.00 0.00 0.06
#> TCGA.CG.5726.01 4 0.0547 0.981 0.00 0.02 0.00 0.98 0.00 0.00
#> TCGA.CG.5720.01 3 0.2260 0.724 0.00 0.00 0.86 0.00 0.00 0.14
#> TCGA.B7.A5TJ.01 3 0.0000 0.735 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.VQ.A8E3.01 2 0.2725 0.780 0.00 0.88 0.04 0.06 0.00 0.02
#> TCGA.SW.A7EA.01 3 0.2260 0.724 0.00 0.00 0.86 0.00 0.00 0.14
#> TCGA.BR.8368.01 4 0.0000 0.990 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.CD.8535.01 5 0.4989 0.724 0.00 0.22 0.00 0.00 0.64 0.14
#> TCGA.HF.A5NB.01 5 0.3821 0.861 0.00 0.22 0.00 0.00 0.74 0.04
#> TCGA.CD.A48C.01 4 0.0000 0.990 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.BR.8361.01 4 0.0547 0.981 0.00 0.02 0.00 0.98 0.00 0.00
#> TCGA.HU.A4G9.01 1 0.3647 0.220 0.64 0.00 0.00 0.00 0.00 0.36
#> TCGA.CD.8528.01 3 0.4902 -0.222 0.00 0.46 0.48 0.00 0.00 0.06
#> TCGA.VQ.A8DT.01 2 0.1814 0.756 0.00 0.90 0.10 0.00 0.00 0.00
#> TCGA.HU.A4G3.01 3 0.2260 0.724 0.00 0.00 0.86 0.00 0.00 0.14
#> TCGA.D7.A74A.01 1 0.3851 -0.192 0.54 0.00 0.00 0.00 0.00 0.46
#> TCGA.BR.8372.01 3 0.1807 0.720 0.00 0.02 0.92 0.00 0.00 0.06
#> TCGA.HU.8244.01 2 0.2094 0.755 0.00 0.90 0.00 0.08 0.00 0.02
#> TCGA.IN.A6RR.01 5 0.2631 0.892 0.00 0.18 0.00 0.00 0.82 0.00
#> TCGA.VQ.A8P2.01 1 0.0000 0.745 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.VQ.A8PO.01 3 0.3494 0.4468 0.00 0.06 0.80 0.0 0.00 0.02 0.12
#> TCGA.BR.8679.01 2 0.1006 0.8388 0.00 0.96 0.00 0.0 0.02 0.00 0.02
#> TCGA.VQ.A92D.01 1 0.0000 0.7554 1.00 0.00 0.00 0.0 0.00 0.00 0.00
#> TCGA.IN.8663.01 3 0.3263 0.5448 0.00 0.00 0.80 0.0 0.00 0.12 0.08
#> TCGA.F1.6177.01 1 0.2278 0.6877 0.88 0.00 0.00 0.0 0.00 0.08 0.04
#> TCGA.VQ.AA6I.01 2 0.0504 0.8399 0.00 0.98 0.00 0.0 0.00 0.00 0.02
#> TCGA.BR.8487.01 3 0.5334 -0.0749 0.00 0.20 0.58 0.0 0.00 0.02 0.20
#> TCGA.VQ.A91K.01 1 0.0000 0.7554 1.00 0.00 0.00 0.0 0.00 0.00 0.00
#> TCGA.IN.A6RO.01 1 0.0000 0.7554 1.00 0.00 0.00 0.0 0.00 0.00 0.00
#> TCGA.VQ.A94R.01 4 0.0000 0.8797 0.00 0.00 0.00 1.0 0.00 0.00 0.00
#> TCGA.BR.7707.01 3 0.0863 0.5952 0.00 0.00 0.96 0.0 0.00 0.04 0.00
#> TCGA.FP.7829.01 5 0.0504 0.7901 0.00 0.02 0.00 0.0 0.98 0.00 0.00
#> TCGA.HU.A4GP.01 4 0.0000 0.8797 0.00 0.00 0.00 1.0 0.00 0.00 0.00
#> TCGA.D7.A4YY.01 6 0.4872 0.6413 0.30 0.00 0.08 0.0 0.00 0.60 0.02
#> TCGA.VQ.AA6G.01 1 0.3221 0.4286 0.68 0.00 0.00 0.0 0.00 0.32 0.00
#> TCGA.HU.A4H8.01 2 0.5643 -0.3084 0.00 0.54 0.08 0.0 0.08 0.00 0.30
#> TCGA.HU.A4H3.01 7 0.6179 0.0000 0.00 0.32 0.24 0.0 0.04 0.00 0.40
#> TCGA.BR.A4PE.01 6 0.4873 0.7140 0.18 0.00 0.22 0.0 0.00 0.60 0.00
#> TCGA.HU.A4GT.01 3 0.5619 0.0617 0.00 0.00 0.38 0.0 0.00 0.30 0.32
#> TCGA.BR.A4CQ.01 1 0.0000 0.7554 1.00 0.00 0.00 0.0 0.00 0.00 0.00
#> TCGA.VQ.A8PT.01 1 0.0000 0.7554 1.00 0.00 0.00 0.0 0.00 0.00 0.00
#> TCGA.CD.A4MG.01 3 0.3991 0.4186 0.00 0.00 0.72 0.0 0.04 0.02 0.22
#> TCGA.BR.A4QL.01 3 0.5619 0.0617 0.00 0.00 0.38 0.0 0.00 0.30 0.32
#> TCGA.BR.7703.01 1 0.3745 0.4999 0.70 0.00 0.00 0.0 0.00 0.26 0.04
#> TCGA.IN.A6RP.01 1 0.3994 -0.1976 0.50 0.00 0.02 0.0 0.00 0.48 0.00
#> TCGA.HU.A4GU.01 1 0.0000 0.7554 1.00 0.00 0.00 0.0 0.00 0.00 0.00
#> TCGA.MX.A5UJ.01 2 0.0504 0.8429 0.00 0.98 0.00 0.0 0.02 0.00 0.00
#> TCGA.HF.7134.01 2 0.0863 0.8335 0.00 0.96 0.00 0.0 0.00 0.00 0.04
#> TCGA.CG.5733.01 3 0.5196 -0.0234 0.00 0.22 0.60 0.0 0.00 0.02 0.16
#> TCGA.CG.5726.01 4 0.2906 0.7690 0.00 0.18 0.00 0.8 0.00 0.00 0.02
#> TCGA.CG.5720.01 3 0.1433 0.5974 0.00 0.00 0.92 0.0 0.00 0.08 0.00
#> TCGA.B7.A5TJ.01 3 0.1363 0.5812 0.00 0.00 0.94 0.0 0.02 0.00 0.04
#> TCGA.VQ.A8E3.01 2 0.1433 0.8126 0.00 0.92 0.00 0.0 0.00 0.00 0.08
#> TCGA.SW.A7EA.01 3 0.1664 0.5937 0.00 0.00 0.92 0.0 0.00 0.06 0.02
#> TCGA.BR.8368.01 4 0.0000 0.8797 0.00 0.00 0.00 1.0 0.00 0.00 0.00
#> TCGA.CD.8535.01 5 0.6267 0.4711 0.00 0.06 0.00 0.0 0.44 0.28 0.22
#> TCGA.HF.A5NB.01 5 0.2745 0.7056 0.00 0.02 0.00 0.0 0.82 0.00 0.16
#> TCGA.CD.A48C.01 4 0.0000 0.8797 0.00 0.00 0.00 1.0 0.00 0.00 0.00
#> TCGA.BR.8361.01 4 0.3517 0.6645 0.00 0.28 0.00 0.7 0.00 0.00 0.02
#> TCGA.HU.A4G9.01 1 0.4524 0.2635 0.60 0.00 0.02 0.0 0.00 0.34 0.04
#> TCGA.CD.8528.01 3 0.5293 -0.0901 0.00 0.24 0.58 0.0 0.00 0.02 0.16
#> TCGA.VQ.A8DT.01 2 0.1860 0.7953 0.00 0.92 0.04 0.0 0.02 0.00 0.02
#> TCGA.HU.A4G3.01 3 0.1433 0.5942 0.00 0.00 0.92 0.0 0.00 0.08 0.00
#> TCGA.D7.A74A.01 1 0.3546 -0.0350 0.54 0.00 0.00 0.0 0.00 0.46 0.00
#> TCGA.BR.8372.01 3 0.3661 0.4596 0.00 0.00 0.74 0.0 0.02 0.02 0.22
#> TCGA.HU.8244.01 2 0.1166 0.8200 0.00 0.94 0.00 0.0 0.00 0.00 0.06
#> TCGA.IN.A6RR.01 5 0.0504 0.7901 0.00 0.02 0.00 0.0 0.98 0.00 0.00
#> TCGA.VQ.A8P2.01 1 0.0000 0.7554 1.00 0.00 0.00 0.0 0.00 0.00 0.00
cbind(get_classes(res, k = 8), get_membership(res, k = 8))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7 p8
#> TCGA.VQ.A8PO.01 3 0.2862 0.4674 0.00 0.08 0.82 0.00 0.00 0.00 0.10 0.00
#> TCGA.BR.8679.01 2 0.1275 0.7984 0.00 0.94 0.00 0.00 0.00 0.00 0.04 0.02
#> TCGA.VQ.A92D.01 1 0.0000 0.8202 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.IN.8663.01 3 0.4337 0.5038 0.00 0.00 0.70 0.00 0.00 0.16 0.10 0.04
#> TCGA.F1.6177.01 1 0.4110 0.6054 0.76 0.00 0.00 0.00 0.02 0.06 0.10 0.06
#> TCGA.VQ.AA6I.01 2 0.0471 0.8040 0.00 0.98 0.00 0.00 0.00 0.00 0.02 0.00
#> TCGA.BR.8487.01 3 0.5386 -0.3788 0.00 0.28 0.48 0.00 0.00 0.00 0.22 0.02
#> TCGA.VQ.A91K.01 1 0.0000 0.8202 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.IN.A6RO.01 1 0.0000 0.8202 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.VQ.A94R.01 4 0.0000 0.8721 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.BR.7707.01 3 0.0808 0.6061 0.00 0.00 0.96 0.00 0.00 0.04 0.00 0.00
#> TCGA.FP.7829.01 5 0.0471 0.8438 0.00 0.02 0.00 0.00 0.98 0.00 0.00 0.00
#> TCGA.HU.A4GP.01 4 0.0000 0.8721 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.D7.A4YY.01 6 0.2114 0.8341 0.16 0.00 0.00 0.00 0.00 0.84 0.00 0.00
#> TCGA.VQ.AA6G.01 6 0.3237 0.5952 0.40 0.00 0.00 0.00 0.00 0.60 0.00 0.00
#> TCGA.HU.A4H8.01 2 0.4673 -0.3953 0.00 0.56 0.08 0.00 0.00 0.00 0.34 0.02
#> TCGA.HU.A4H3.01 7 0.5133 0.0000 0.00 0.38 0.22 0.00 0.00 0.00 0.40 0.00
#> TCGA.BR.A4PE.01 6 0.2404 0.8089 0.14 0.00 0.02 0.00 0.00 0.84 0.00 0.00
#> TCGA.HU.A4GT.01 3 0.5511 0.2265 0.00 0.00 0.46 0.00 0.00 0.16 0.34 0.04
#> TCGA.BR.A4CQ.01 1 0.0000 0.8202 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.VQ.A8PT.01 1 0.0000 0.8202 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CD.A4MG.01 3 0.1947 0.5476 0.00 0.00 0.86 0.00 0.00 0.00 0.14 0.00
#> TCGA.BR.A4QL.01 3 0.5535 0.2038 0.00 0.00 0.44 0.00 0.00 0.16 0.36 0.04
#> TCGA.BR.7703.01 1 0.5715 -0.0389 0.50 0.00 0.00 0.00 0.02 0.32 0.10 0.06
#> TCGA.IN.A6RP.01 6 0.2650 0.8480 0.24 0.00 0.00 0.00 0.00 0.76 0.00 0.00
#> TCGA.HU.A4GU.01 1 0.0000 0.8202 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.MX.A5UJ.01 2 0.1275 0.8033 0.00 0.94 0.00 0.00 0.00 0.00 0.04 0.02
#> TCGA.HF.7134.01 2 0.0471 0.8028 0.00 0.98 0.00 0.00 0.00 0.00 0.02 0.00
#> TCGA.CG.5733.01 3 0.4677 -0.2623 0.00 0.32 0.54 0.00 0.00 0.00 0.14 0.00
#> TCGA.CG.5726.01 4 0.2267 0.7591 0.00 0.18 0.00 0.82 0.00 0.00 0.00 0.00
#> TCGA.CG.5720.01 3 0.1563 0.6128 0.00 0.00 0.90 0.00 0.00 0.10 0.00 0.00
#> TCGA.B7.A5TJ.01 3 0.0471 0.5984 0.00 0.00 0.98 0.00 0.00 0.00 0.02 0.00
#> TCGA.VQ.A8E3.01 2 0.0808 0.7868 0.00 0.96 0.00 0.00 0.00 0.00 0.04 0.00
#> TCGA.SW.A7EA.01 3 0.1563 0.6128 0.00 0.00 0.90 0.00 0.00 0.10 0.00 0.00
#> TCGA.BR.8368.01 4 0.0000 0.8721 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.CD.8535.01 8 0.2856 0.0000 0.00 0.02 0.00 0.00 0.20 0.00 0.00 0.78
#> TCGA.HF.A5NB.01 5 0.3615 0.6866 0.00 0.02 0.00 0.00 0.74 0.00 0.20 0.04
#> TCGA.CD.A48C.01 4 0.0000 0.8721 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.BR.8361.01 4 0.2938 0.6193 0.00 0.30 0.00 0.70 0.00 0.00 0.00 0.00
#> TCGA.HU.A4G9.01 1 0.5782 -0.1507 0.46 0.00 0.00 0.00 0.02 0.36 0.10 0.06
#> TCGA.CD.8528.01 3 0.4677 -0.2623 0.00 0.32 0.54 0.00 0.00 0.00 0.14 0.00
#> TCGA.VQ.A8DT.01 2 0.2399 0.7059 0.00 0.88 0.04 0.00 0.00 0.00 0.04 0.04
#> TCGA.HU.A4G3.01 3 0.2224 0.6030 0.00 0.00 0.86 0.00 0.00 0.12 0.00 0.02
#> TCGA.D7.A74A.01 6 0.2756 0.8389 0.26 0.00 0.00 0.00 0.00 0.74 0.00 0.00
#> TCGA.BR.8372.01 3 0.2569 0.5204 0.00 0.00 0.82 0.00 0.00 0.00 0.16 0.02
#> TCGA.HU.8244.01 2 0.2591 0.7280 0.00 0.86 0.00 0.00 0.00 0.04 0.08 0.02
#> TCGA.IN.A6RR.01 5 0.0471 0.8438 0.00 0.02 0.00 0.00 0.98 0.00 0.00 0.00
#> TCGA.VQ.A8P2.01 1 0.0000 0.8202 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
consensus_heatmap(res, k = 7)
consensus_heatmap(res, k = 8)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
membership_heatmap(res, k = 7)
membership_heatmap(res, k = 8)
As soon as the classes for columns are determined, the signatures that are significantly different between subgroups can be looked for. Following are the heatmaps for signatures.
get_signatures(res, k = 2)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
get_signatures(res, k = 7)
get_signatures(res, k = 8)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. To get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows (which is done by automatically selecting number of clusters).If there are too many signatures, top_signatures = ... can be set to only show the
signatures with the highest FDRs:
# code only for demonstration
# e.g. to show the top 500 most significant rows
tb = get_signature(res, k = ..., top_signatures = 500)
If the signatures are defined as these which are uniquely high in current group, diff_method argument
can be set to "uniquely_high_in_one_group":
# code only for demonstration
tb = get_signature(res, k = ..., diff_method = "uniquely_high_in_one_group")
UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
dimension_reduction(res, k = 7, method = "UMAP")
dimension_reduction(res, k = 8, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
If matrix rows can be associated to genes, consider to use functional_enrichment(res,
...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.
Parent node: Node022. Child nodes: Node01111-leaf , Node01112-leaf , Node01113-leaf , Node01114-leaf , Node01115-leaf , Node01116-leaf , Node01121-leaf , Node01122-leaf , Node01123-leaf , Node01131-leaf , Node01132-leaf , Node01133-leaf , Node01134-leaf , Node01211-leaf , Node01212-leaf , Node01221-leaf , Node01222-leaf , Node01231-leaf , Node01232-leaf , Node01233-leaf , Node01311-leaf , Node01312 , Node02221-leaf , Node02222-leaf , Node02223-leaf , Node02224-leaf , Node03111-leaf , Node03112-leaf , Node03113-leaf , Node03411-leaf , Node03412-leaf , Node03413-leaf .
The object with results only for a single top-value method and a single partitioning method can be extracted as:
res = res_rh["0222"]
A summary of res and all the functions that can be applied to it:
res
#> A 'ConsensusPartition' object with k = 2, 3, 4, 5, 6, 7, 8.
#> On a matrix with 30000 rows and 24 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 0.597 0.832 0.876 0.4476 0.478 0.478
#> 3 3 0.547 0.878 0.914 0.4267 0.620 0.371
#> 4 4 0.834 0.955 0.959 0.1603 0.757 0.427
#> 5 5 0.814 0.834 0.906 0.0510 0.993 0.971
#> 6 6 0.827 0.772 0.881 0.0533 0.935 0.735
#> 7 7 0.848 0.574 0.843 0.0284 0.949 0.750
#> 8 8 0.892 0.611 0.850 0.0329 0.931 0.627
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.VQ.A8PO.01 1 0.981 0.663 0.58 0.42
#> TCGA.BR.8679.01 2 0.000 1.000 0.00 1.00
#> TCGA.VQ.AA6I.01 2 0.000 1.000 0.00 1.00
#> TCGA.BR.8487.01 1 0.000 0.682 1.00 0.00
#> TCGA.VQ.A94R.01 2 0.000 1.000 0.00 1.00
#> TCGA.FP.7829.01 2 0.000 1.000 0.00 1.00
#> TCGA.HU.A4GP.01 2 0.000 1.000 0.00 1.00
#> TCGA.HU.A4H8.01 1 0.000 0.682 1.00 0.00
#> TCGA.HU.A4H3.01 1 0.000 0.682 1.00 0.00
#> TCGA.CD.A4MG.01 1 0.000 0.682 1.00 0.00
#> TCGA.MX.A5UJ.01 1 0.981 0.663 0.58 0.42
#> TCGA.HF.7134.01 2 0.000 1.000 0.00 1.00
#> TCGA.CG.5733.01 1 0.981 0.663 0.58 0.42
#> TCGA.CG.5726.01 2 0.000 1.000 0.00 1.00
#> TCGA.VQ.A8E3.01 1 0.995 0.588 0.54 0.46
#> TCGA.BR.8368.01 1 0.981 0.663 0.58 0.42
#> TCGA.CD.8535.01 2 0.000 1.000 0.00 1.00
#> TCGA.HF.A5NB.01 1 0.000 0.682 1.00 0.00
#> TCGA.CD.A48C.01 2 0.000 1.000 0.00 1.00
#> TCGA.BR.8361.01 1 0.981 0.663 0.58 0.42
#> TCGA.CD.8528.01 1 0.981 0.663 0.58 0.42
#> TCGA.VQ.A8DT.01 2 0.000 1.000 0.00 1.00
#> TCGA.HU.8244.01 2 0.000 1.000 0.00 1.00
#> TCGA.IN.A6RR.01 2 0.000 1.000 0.00 1.00
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.VQ.A8PO.01 1 0.2959 0.840 0.90 0.00 0.10
#> TCGA.BR.8679.01 2 0.4002 0.900 0.16 0.84 0.00
#> TCGA.VQ.AA6I.01 2 0.4002 0.900 0.16 0.84 0.00
#> TCGA.BR.8487.01 3 0.0892 0.994 0.02 0.00 0.98
#> TCGA.VQ.A94R.01 1 0.4002 0.808 0.84 0.16 0.00
#> TCGA.FP.7829.01 2 0.0892 0.860 0.00 0.98 0.02
#> TCGA.HU.A4GP.01 1 0.4002 0.808 0.84 0.16 0.00
#> TCGA.HU.A4H8.01 3 0.0892 0.994 0.02 0.00 0.98
#> TCGA.HU.A4H3.01 3 0.0892 0.994 0.02 0.00 0.98
#> TCGA.CD.A4MG.01 3 0.0892 0.994 0.02 0.00 0.98
#> TCGA.MX.A5UJ.01 1 0.2959 0.840 0.90 0.00 0.10
#> TCGA.HF.7134.01 1 0.4002 0.808 0.84 0.16 0.00
#> TCGA.CG.5733.01 1 0.2959 0.840 0.90 0.00 0.10
#> TCGA.CG.5726.01 1 0.4002 0.808 0.84 0.16 0.00
#> TCGA.VQ.A8E3.01 1 0.0000 0.849 1.00 0.00 0.00
#> TCGA.BR.8368.01 1 0.2959 0.840 0.90 0.00 0.10
#> TCGA.CD.8535.01 2 0.0000 0.869 0.00 1.00 0.00
#> TCGA.HF.A5NB.01 3 0.0000 0.977 0.00 0.00 1.00
#> TCGA.CD.A48C.01 2 0.4002 0.900 0.16 0.84 0.00
#> TCGA.BR.8361.01 1 0.2959 0.840 0.90 0.00 0.10
#> TCGA.CD.8528.01 1 0.0000 0.849 1.00 0.00 0.00
#> TCGA.VQ.A8DT.01 2 0.4002 0.900 0.16 0.84 0.00
#> TCGA.HU.8244.01 1 0.4002 0.808 0.84 0.16 0.00
#> TCGA.IN.A6RR.01 2 0.0892 0.860 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.VQ.A8PO.01 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.BR.8679.01 2 0.1637 0.892 0.00 0.94 0.00 0.06
#> TCGA.VQ.AA6I.01 2 0.1637 0.892 0.00 0.94 0.00 0.06
#> TCGA.BR.8487.01 3 0.0707 0.994 0.02 0.00 0.98 0.00
#> TCGA.VQ.A94R.01 2 0.2011 0.914 0.08 0.92 0.00 0.00
#> TCGA.FP.7829.01 4 0.2335 0.962 0.00 0.06 0.02 0.92
#> TCGA.HU.A4GP.01 2 0.1637 0.916 0.06 0.94 0.00 0.00
#> TCGA.HU.A4H8.01 3 0.0707 0.994 0.02 0.00 0.98 0.00
#> TCGA.HU.A4H3.01 3 0.0707 0.994 0.02 0.00 0.98 0.00
#> TCGA.CD.A4MG.01 3 0.0707 0.994 0.02 0.00 0.98 0.00
#> TCGA.MX.A5UJ.01 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.HF.7134.01 2 0.2921 0.895 0.14 0.86 0.00 0.00
#> TCGA.CG.5733.01 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.CG.5726.01 2 0.2921 0.895 0.14 0.86 0.00 0.00
#> TCGA.VQ.A8E3.01 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.BR.8368.01 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.CD.8535.01 4 0.0000 0.941 0.00 0.00 0.00 1.00
#> TCGA.HF.A5NB.01 3 0.0000 0.974 0.00 0.00 1.00 0.00
#> TCGA.CD.A48C.01 2 0.1637 0.892 0.00 0.94 0.00 0.06
#> TCGA.BR.8361.01 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.CD.8528.01 1 0.0000 1.000 1.00 0.00 0.00 0.00
#> TCGA.VQ.A8DT.01 2 0.1637 0.892 0.00 0.94 0.00 0.06
#> TCGA.HU.8244.01 2 0.2345 0.914 0.10 0.90 0.00 0.00
#> TCGA.IN.A6RR.01 4 0.1637 0.964 0.00 0.06 0.00 0.94
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> TCGA.VQ.A8PO.01 1 0.0000 0.950 1.00 0.00 0.00 0.00 0.00
#> TCGA.BR.8679.01 2 0.1732 0.840 0.00 0.92 0.00 0.00 0.08
#> TCGA.VQ.AA6I.01 2 0.1410 0.843 0.00 0.94 0.00 0.00 0.06
#> TCGA.BR.8487.01 3 0.0000 0.995 0.00 0.00 1.00 0.00 0.00
#> TCGA.VQ.A94R.01 2 0.4182 0.554 0.00 0.60 0.00 0.00 0.40
#> TCGA.FP.7829.01 4 0.0000 0.812 0.00 0.00 0.00 1.00 0.00
#> TCGA.HU.A4GP.01 2 0.2020 0.820 0.00 0.90 0.00 0.00 0.10
#> TCGA.HU.A4H8.01 3 0.0000 0.995 0.00 0.00 1.00 0.00 0.00
#> TCGA.HU.A4H3.01 3 0.0000 0.995 0.00 0.00 1.00 0.00 0.00
#> TCGA.CD.A4MG.01 3 0.0000 0.995 0.00 0.00 1.00 0.00 0.00
#> TCGA.MX.A5UJ.01 1 0.0000 0.950 1.00 0.00 0.00 0.00 0.00
#> TCGA.HF.7134.01 2 0.3641 0.780 0.12 0.82 0.00 0.00 0.06
#> TCGA.CG.5733.01 1 0.0000 0.950 1.00 0.00 0.00 0.00 0.00
#> TCGA.CG.5726.01 2 0.3697 0.786 0.10 0.82 0.00 0.00 0.08
#> TCGA.VQ.A8E3.01 1 0.0000 0.950 1.00 0.00 0.00 0.00 0.00
#> TCGA.BR.8368.01 1 0.3796 0.642 0.70 0.00 0.00 0.00 0.30
#> TCGA.CD.8535.01 5 0.4302 0.000 0.00 0.00 0.00 0.48 0.52
#> TCGA.HF.A5NB.01 3 0.0609 0.981 0.00 0.00 0.98 0.02 0.00
#> TCGA.CD.A48C.01 2 0.2516 0.816 0.00 0.86 0.00 0.00 0.14
#> TCGA.BR.8361.01 1 0.0000 0.950 1.00 0.00 0.00 0.00 0.00
#> TCGA.CD.8528.01 1 0.0000 0.950 1.00 0.00 0.00 0.00 0.00
#> TCGA.VQ.A8DT.01 2 0.1732 0.840 0.00 0.92 0.00 0.00 0.08
#> TCGA.HU.8244.01 2 0.1732 0.827 0.00 0.92 0.00 0.00 0.08
#> TCGA.IN.A6RR.01 4 0.1732 0.796 0.00 0.00 0.00 0.92 0.08
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> TCGA.VQ.A8PO.01 1 0.0000 0.906 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BR.8679.01 2 0.3679 0.744 0.00 0.76 0.00 0.00 0.04 0.20
#> TCGA.VQ.AA6I.01 2 0.3679 0.744 0.00 0.76 0.00 0.00 0.04 0.20
#> TCGA.BR.8487.01 3 0.0000 0.973 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.VQ.A94R.01 6 0.4393 0.468 0.00 0.14 0.00 0.00 0.14 0.72
#> TCGA.FP.7829.01 4 0.0000 0.900 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.HU.A4GP.01 6 0.3499 0.645 0.00 0.32 0.00 0.00 0.00 0.68
#> TCGA.HU.A4H8.01 3 0.0000 0.973 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.HU.A4H3.01 3 0.0000 0.973 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.CD.A4MG.01 3 0.0000 0.973 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.MX.A5UJ.01 1 0.0000 0.906 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HF.7134.01 2 0.0547 0.743 0.02 0.98 0.00 0.00 0.00 0.00
#> TCGA.CG.5733.01 1 0.0000 0.906 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CG.5726.01 2 0.1092 0.732 0.02 0.96 0.00 0.00 0.00 0.02
#> TCGA.VQ.A8E3.01 1 0.0000 0.906 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BR.8368.01 1 0.6105 0.393 0.52 0.02 0.00 0.00 0.24 0.22
#> TCGA.CD.8535.01 5 0.4002 0.000 0.00 0.00 0.00 0.32 0.66 0.02
#> TCGA.HF.A5NB.01 3 0.2629 0.884 0.00 0.00 0.88 0.02 0.02 0.08
#> TCGA.CD.A48C.01 6 0.4172 0.652 0.00 0.28 0.00 0.00 0.04 0.68
#> TCGA.BR.8361.01 1 0.1814 0.845 0.90 0.00 0.00 0.00 0.10 0.00
#> TCGA.CD.8528.01 1 0.0000 0.906 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.VQ.A8DT.01 2 0.3679 0.744 0.00 0.76 0.00 0.00 0.04 0.20
#> TCGA.HU.8244.01 2 0.1807 0.709 0.00 0.92 0.00 0.00 0.06 0.02
#> TCGA.IN.A6RR.01 4 0.1267 0.897 0.00 0.00 0.00 0.94 0.06 0.00
cbind(get_classes(res, k = 7), get_membership(res, k = 7))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7
#> TCGA.VQ.A8PO.01 1 0.0000 0.924 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BR.8679.01 2 0.0000 0.603 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.VQ.AA6I.01 2 0.0000 0.603 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BR.8487.01 3 0.0000 0.950 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.VQ.A94R.01 6 0.2745 -0.318 0.00 0.02 0.00 0.00 0.00 0.82 0.16
#> TCGA.FP.7829.01 4 0.0504 0.841 0.00 0.02 0.00 0.98 0.00 0.00 0.00
#> TCGA.HU.A4GP.01 6 0.3546 -0.126 0.00 0.46 0.00 0.00 0.00 0.54 0.00
#> TCGA.HU.A4H8.01 3 0.0000 0.950 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.HU.A4H3.01 3 0.0000 0.950 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.CD.A4MG.01 3 0.0504 0.943 0.00 0.00 0.98 0.00 0.00 0.02 0.00
#> TCGA.MX.A5UJ.01 1 0.0000 0.924 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HF.7134.01 2 0.5023 0.540 0.04 0.62 0.00 0.00 0.26 0.08 0.00
#> TCGA.CG.5733.01 1 0.0000 0.924 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CG.5726.01 2 0.5220 0.527 0.04 0.60 0.00 0.00 0.26 0.10 0.00
#> TCGA.VQ.A8E3.01 1 0.0000 0.924 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BR.8368.01 7 0.5002 0.000 0.12 0.00 0.00 0.00 0.00 0.40 0.48
#> TCGA.CD.8535.01 5 0.5717 0.000 0.00 0.06 0.00 0.12 0.54 0.00 0.28
#> TCGA.HF.A5NB.01 3 0.2906 0.798 0.00 0.00 0.80 0.02 0.00 0.00 0.18
#> TCGA.CD.A48C.01 2 0.3562 -0.444 0.00 0.50 0.00 0.00 0.00 0.50 0.00
#> TCGA.BR.8361.01 1 0.3221 0.464 0.68 0.00 0.00 0.00 0.00 0.00 0.32
#> TCGA.CD.8528.01 1 0.0000 0.924 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.VQ.A8DT.01 2 0.0000 0.603 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HU.8244.01 2 0.4684 0.444 0.00 0.52 0.00 0.02 0.42 0.00 0.04
#> TCGA.IN.A6RR.01 4 0.2572 0.833 0.00 0.08 0.00 0.86 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.VQ.A8PO.01 1 0.0000 0.9864 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BR.8679.01 2 0.0000 0.6048 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.VQ.AA6I.01 2 0.0471 0.5981 0.00 0.98 0.00 0.00 0.02 0.00 0.00 0.00
#> TCGA.BR.8487.01 3 0.0000 0.8989 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.VQ.A94R.01 6 0.4383 0.3475 0.00 0.00 0.00 0.00 0.02 0.52 0.42 0.04
#> TCGA.FP.7829.01 4 0.0471 0.8793 0.00 0.02 0.00 0.98 0.00 0.00 0.00 0.00
#> TCGA.HU.A4GP.01 6 0.3198 0.6998 0.00 0.26 0.00 0.00 0.00 0.72 0.02 0.00
#> TCGA.HU.A4H8.01 3 0.0000 0.8989 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HU.A4H3.01 3 0.0000 0.8989 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CD.A4MG.01 3 0.0000 0.8989 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.MX.A5UJ.01 1 0.0000 0.9864 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HF.7134.01 2 0.6041 -0.0302 0.00 0.44 0.00 0.02 0.08 0.06 0.02 0.38
#> TCGA.CG.5733.01 1 0.0000 0.9864 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CG.5726.01 2 0.6041 -0.0302 0.00 0.44 0.00 0.02 0.08 0.06 0.02 0.38
#> TCGA.VQ.A8E3.01 1 0.0471 0.9688 0.98 0.00 0.00 0.00 0.02 0.00 0.00 0.00
#> TCGA.BR.8368.01 7 0.1091 0.2823 0.06 0.00 0.00 0.00 0.00 0.00 0.94 0.00
#> TCGA.CD.8535.01 5 0.2623 0.0000 0.00 0.06 0.00 0.10 0.84 0.00 0.00 0.00
#> TCGA.HF.A5NB.01 3 0.5440 0.4905 0.00 0.00 0.58 0.00 0.02 0.22 0.04 0.14
#> TCGA.CD.A48C.01 6 0.2938 0.6829 0.00 0.30 0.00 0.00 0.00 0.70 0.00 0.00
#> TCGA.BR.8361.01 7 0.3729 0.1747 0.46 0.00 0.00 0.00 0.02 0.00 0.52 0.00
#> TCGA.CD.8528.01 1 0.0471 0.9702 0.98 0.00 0.00 0.00 0.02 0.00 0.00 0.00
#> TCGA.VQ.A8DT.01 2 0.0000 0.6048 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HU.8244.01 8 0.2569 0.0000 0.00 0.16 0.00 0.00 0.00 0.02 0.00 0.82
#> TCGA.IN.A6RR.01 4 0.2348 0.8746 0.00 0.06 0.00 0.88 0.04 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: Node02. Child nodes: Node0111 , Node0112 , Node0113 , Node0114-leaf , Node0121 , Node0122 , Node0123 , Node0131 , Node0132-leaf , Node0211-leaf , Node0212-leaf , Node0221-leaf , Node0222 , Node0231-leaf , Node0232-leaf , Node0233-leaf , Node0311 , Node0312-leaf , Node0313-leaf , Node0314-leaf , Node0331-leaf , Node0332-leaf , Node0333-leaf , Node0341 , Node0342-leaf .
The object with results only for a single top-value method and a single partitioning method can be extracted as:
res = res_rh["023"]
A summary of res and all the functions that can be applied to it:
res
#> A 'ConsensusPartition' object with k = 2, 3, 4, 5, 6, 7, 8.
#> On a matrix with 30000 rows and 29 columns.
#> Top rows (1000) are extracted by 'SD' method.
#> Subgroups are detected by 'kmeans' method.
#> Performed in total 350 partitions by row resampling.
#> Best k for subgroups seems to be 2.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_partitions"
#> [7] "compare_signatures" "consensus_heatmap" "dimension_reduction"
#> [10] "functional_enrichment" "get_anno_col" "get_anno"
#> [13] "get_classes" "get_consensus" "get_matrix"
#> [16] "get_membership" "get_param" "get_signatures"
#> [19] "get_stats" "is_best_k" "is_stable_k"
#> [22] "membership_heatmap" "ncol" "nrow"
#> [25] "plot_ecdf" "predict_classes" "rownames"
#> [28] "select_partition_number" "show" "suggest_best_k"
#> [31] "test_to_known_factors" "top_rows_heatmap"
collect_plots() function collects all the plots made from res for all k (number of subgroups)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
The plots are:
k and the heatmap of
predicted classes for each k.k.k.k.All the plots in panels can be made by individual functions and they are plotted later in this section.
select_partition_number() produces several plots showing different
statistics for choosing “optimized” k. There are following statistics:
k;k, the area increased is defined as \(A_k - A_{k-1}\).The detailed explanations of these statistics can be found in the cola vignette.
Generally speaking, higher 1-PAC score, higher mean silhouette score or higher
concordance corresponds to better partition. Rand index and Jaccard index
measure how similar the current partition is compared to partition with k-1.
If they are too similar, we won't accept k is better than k-1.
select_partition_number(res)
The numeric values for all these statistics can be obtained by get_stats().
get_stats(res)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> 2 2 1.000 1.000 1.000 0.5030 0.498 0.498
#> 3 3 0.818 0.984 0.961 0.3006 0.837 0.673
#> 4 4 0.761 0.833 0.868 0.1047 1.000 1.000
#> 5 5 0.741 0.626 0.816 0.0873 0.877 0.632
#> 6 6 0.775 0.625 0.800 0.0502 0.948 0.767
#> 7 7 0.821 0.673 0.804 0.0265 0.882 0.442
#> 8 8 0.778 0.711 0.828 0.0265 0.970 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.BR.6452.01 1 0 1 1 0
#> TCGA.BR.8382.01 1 0 1 1 0
#> TCGA.HU.8604.01 1 0 1 1 0
#> TCGA.BR.8591.01 2 0 1 0 1
#> TCGA.VQ.A91D.01 2 0 1 0 1
#> TCGA.HU.8602.01 1 0 1 1 0
#> TCGA.CG.4437.01 2 0 1 0 1
#> TCGA.VQ.A8PP.01 2 0 1 0 1
#> TCGA.BR.A4QI.01 1 0 1 1 0
#> TCGA.BR.A4PF.01 2 0 1 0 1
#> TCGA.CD.A4MJ.01 2 0 1 0 1
#> TCGA.CD.A4MI.01 2 0 1 0 1
#> TCGA.VQ.A924.01 2 0 1 0 1
#> TCGA.BR.A4J8.01 1 0 1 1 0
#> TCGA.HU.A4GQ.01 2 0 1 0 1
#> TCGA.BR.A4QM.01 2 0 1 0 1
#> TCGA.D7.A4YV.01 1 0 1 1 0
#> TCGA.D7.A4YU.01 2 0 1 0 1
#> TCGA.HU.A4GN.01 2 0 1 0 1
#> TCGA.HU.A4H6.01 1 0 1 1 0
#> TCGA.HF.7132.01 2 0 1 0 1
#> TCGA.BR.8370.01 2 0 1 0 1
#> TCGA.BR.7851.01 2 0 1 0 1
#> TCGA.BR.8363.01 1 0 1 1 0
#> TCGA.BR.8284.01 1 0 1 1 0
#> TCGA.BR.8081.01 1 0 1 1 0
#> TCGA.FP.A4BE.01 2 0 1 0 1
#> TCGA.BR.8078.01 1 0 1 1 0
#> TCGA.BR.8360.01 2 0 1 0 1
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.BR.6452.01 1 0.000 0.970 1.00 0.00 0.00
#> TCGA.BR.8382.01 1 0.000 0.970 1.00 0.00 0.00
#> TCGA.HU.8604.01 1 0.000 0.970 1.00 0.00 0.00
#> TCGA.BR.8591.01 3 0.334 1.000 0.00 0.12 0.88
#> TCGA.VQ.A91D.01 3 0.334 1.000 0.00 0.12 0.88
#> TCGA.HU.8602.01 1 0.153 0.954 0.96 0.00 0.04
#> TCGA.CG.4437.01 2 0.000 1.000 0.00 1.00 0.00
#> TCGA.VQ.A8PP.01 2 0.000 1.000 0.00 1.00 0.00
#> TCGA.BR.A4QI.01 1 0.254 0.949 0.92 0.00 0.08
#> TCGA.BR.A4PF.01 2 0.000 1.000 0.00 1.00 0.00
#> TCGA.CD.A4MJ.01 3 0.334 1.000 0.00 0.12 0.88
#> TCGA.CD.A4MI.01 2 0.000 1.000 0.00 1.00 0.00
#> TCGA.VQ.A924.01 3 0.334 1.000 0.00 0.12 0.88
#> TCGA.BR.A4J8.01 1 0.254 0.949 0.92 0.00 0.08
#> TCGA.HU.A4GQ.01 2 0.000 1.000 0.00 1.00 0.00
#> TCGA.BR.A4QM.01 2 0.000 1.000 0.00 1.00 0.00
#> TCGA.D7.A4YV.01 1 0.000 0.970 1.00 0.00 0.00
#> TCGA.D7.A4YU.01 2 0.000 1.000 0.00 1.00 0.00
#> TCGA.HU.A4GN.01 2 0.000 1.000 0.00 1.00 0.00
#> TCGA.HU.A4H6.01 1 0.254 0.949 0.92 0.00 0.08
#> TCGA.HF.7132.01 2 0.000 1.000 0.00 1.00 0.00
#> TCGA.BR.8370.01 3 0.334 1.000 0.00 0.12 0.88
#> TCGA.BR.7851.01 2 0.000 1.000 0.00 1.00 0.00
#> TCGA.BR.8363.01 1 0.000 0.970 1.00 0.00 0.00
#> TCGA.BR.8284.01 1 0.254 0.949 0.92 0.00 0.08
#> TCGA.BR.8081.01 1 0.000 0.970 1.00 0.00 0.00
#> TCGA.FP.A4BE.01 3 0.334 1.000 0.00 0.12 0.88
#> TCGA.BR.8078.01 1 0.153 0.954 0.96 0.00 0.04
#> TCGA.BR.8360.01 2 0.000 1.000 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.BR.6452.01 1 0.0707 0.879 0.98 0.00 0.02 0.00
#> TCGA.BR.8382.01 1 0.0000 0.882 1.00 0.00 0.00 0.00
#> TCGA.HU.8604.01 1 0.0000 0.882 1.00 0.00 0.00 0.00
#> TCGA.BR.8591.01 4 0.1211 0.940 0.00 0.04 0.00 0.96
#> TCGA.VQ.A91D.01 4 0.1211 0.940 0.00 0.04 0.00 0.96
#> TCGA.HU.8602.01 1 0.4624 0.704 0.66 0.00 0.34 0.00
#> TCGA.CG.4437.01 2 0.2647 0.840 0.00 0.88 0.12 0.00
#> TCGA.VQ.A8PP.01 2 0.3801 0.824 0.00 0.78 0.22 0.00
#> TCGA.BR.A4QI.01 1 0.5512 0.745 0.66 0.00 0.30 0.04
#> TCGA.BR.A4PF.01 2 0.3801 0.824 0.00 0.78 0.22 0.00
#> TCGA.CD.A4MJ.01 4 0.1211 0.940 0.00 0.04 0.00 0.96
#> TCGA.CD.A4MI.01 2 0.0707 0.839 0.00 0.98 0.02 0.00
#> TCGA.VQ.A924.01 4 0.5256 0.700 0.00 0.26 0.04 0.70
#> TCGA.BR.A4J8.01 1 0.4755 0.816 0.76 0.00 0.20 0.04
#> TCGA.HU.A4GQ.01 2 0.4406 0.660 0.00 0.70 0.30 0.00
#> TCGA.BR.A4QM.01 2 0.3801 0.824 0.00 0.78 0.22 0.00
#> TCGA.D7.A4YV.01 1 0.0707 0.879 0.98 0.00 0.02 0.00
#> TCGA.D7.A4YU.01 2 0.3801 0.824 0.00 0.78 0.22 0.00
#> TCGA.HU.A4GN.01 2 0.0000 0.836 0.00 1.00 0.00 0.00
#> TCGA.HU.A4H6.01 1 0.2921 0.846 0.86 0.00 0.14 0.00
#> TCGA.HF.7132.01 2 0.0000 0.836 0.00 1.00 0.00 0.00
#> TCGA.BR.8370.01 4 0.2830 0.915 0.00 0.04 0.06 0.90
#> TCGA.BR.7851.01 2 0.3400 0.758 0.00 0.82 0.18 0.00
#> TCGA.BR.8363.01 1 0.0000 0.882 1.00 0.00 0.00 0.00
#> TCGA.BR.8284.01 1 0.2921 0.846 0.86 0.00 0.14 0.00
#> TCGA.BR.8081.01 1 0.0000 0.882 1.00 0.00 0.00 0.00
#> TCGA.FP.A4BE.01 4 0.1211 0.940 0.00 0.04 0.00 0.96
#> TCGA.BR.8078.01 1 0.4624 0.704 0.66 0.00 0.34 0.00
#> TCGA.BR.8360.01 2 0.3801 0.754 0.00 0.78 0.22 0.00
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> TCGA.BR.6452.01 1 0.0609 0.797 0.98 0.00 0.02 0.00 0.00
#> TCGA.BR.8382.01 1 0.0000 0.813 1.00 0.00 0.00 0.00 0.00
#> TCGA.HU.8604.01 1 0.0000 0.813 1.00 0.00 0.00 0.00 0.00
#> TCGA.BR.8591.01 4 0.0000 0.890 0.00 0.00 0.00 1.00 0.00
#> TCGA.VQ.A91D.01 4 0.0000 0.890 0.00 0.00 0.00 1.00 0.00
#> TCGA.HU.8602.01 3 0.4818 0.358 0.46 0.00 0.52 0.00 0.02
#> TCGA.CG.4437.01 2 0.0000 0.659 0.00 1.00 0.00 0.00 0.00
#> TCGA.VQ.A8PP.01 2 0.2929 0.679 0.00 0.82 0.00 0.00 0.18
#> TCGA.BR.A4QI.01 3 0.5759 0.415 0.18 0.00 0.62 0.00 0.20
#> TCGA.BR.A4PF.01 2 0.3690 0.662 0.00 0.78 0.02 0.00 0.20
#> TCGA.CD.A4MJ.01 4 0.0000 0.890 0.00 0.00 0.00 1.00 0.00
#> TCGA.CD.A4MI.01 2 0.2438 0.611 0.00 0.90 0.06 0.00 0.04
#> TCGA.VQ.A924.01 4 0.6003 0.481 0.00 0.18 0.04 0.66 0.12
#> TCGA.BR.A4J8.01 3 0.6111 0.386 0.26 0.00 0.56 0.00 0.18
#> TCGA.HU.A4GQ.01 5 0.5297 0.858 0.00 0.36 0.06 0.00 0.58
#> TCGA.BR.A4QM.01 2 0.3690 0.662 0.00 0.78 0.02 0.00 0.20
#> TCGA.D7.A4YV.01 1 0.0609 0.797 0.98 0.00 0.02 0.00 0.00
#> TCGA.D7.A4YU.01 2 0.2929 0.679 0.00 0.82 0.00 0.00 0.18
#> TCGA.HU.A4GN.01 2 0.2438 0.611 0.00 0.90 0.06 0.00 0.04
#> TCGA.HU.A4H6.01 1 0.4060 0.329 0.64 0.00 0.36 0.00 0.00
#> TCGA.HF.7132.01 2 0.2438 0.604 0.00 0.90 0.04 0.00 0.06
#> TCGA.BR.8370.01 4 0.2929 0.771 0.00 0.00 0.00 0.82 0.18
#> TCGA.BR.7851.01 2 0.4767 -0.589 0.00 0.56 0.02 0.00 0.42
#> TCGA.BR.8363.01 1 0.0000 0.813 1.00 0.00 0.00 0.00 0.00
#> TCGA.BR.8284.01 1 0.3983 0.365 0.66 0.00 0.34 0.00 0.00
#> TCGA.BR.8081.01 1 0.0000 0.813 1.00 0.00 0.00 0.00 0.00
#> TCGA.FP.A4BE.01 4 0.0000 0.890 0.00 0.00 0.00 1.00 0.00
#> TCGA.BR.8078.01 3 0.4818 0.358 0.46 0.00 0.52 0.00 0.02
#> TCGA.BR.8360.01 5 0.4182 0.849 0.00 0.40 0.00 0.00 0.60
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> TCGA.BR.6452.01 1 0.0547 0.860 0.98 0.00 0.02 0.00 0.00 0.00
#> TCGA.BR.8382.01 1 0.0000 0.870 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HU.8604.01 1 0.0000 0.870 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BR.8591.01 4 0.0000 0.894 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.VQ.A91D.01 4 0.0000 0.894 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.HU.8602.01 3 0.5490 0.380 0.26 0.00 0.56 0.00 0.00 0.18
#> TCGA.CG.4437.01 2 0.4810 0.543 0.00 0.66 0.22 0.00 0.12 0.00
#> TCGA.VQ.A8PP.01 2 0.0000 0.615 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.BR.A4QI.01 6 0.1814 0.845 0.10 0.00 0.00 0.00 0.00 0.90
#> TCGA.BR.A4PF.01 2 0.1635 0.591 0.00 0.94 0.02 0.00 0.02 0.02
#> TCGA.CD.A4MJ.01 4 0.0000 0.894 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.CD.A4MI.01 2 0.5698 0.451 0.00 0.44 0.40 0.00 0.16 0.00
#> TCGA.VQ.A924.01 3 0.5888 -0.306 0.00 0.00 0.40 0.40 0.20 0.00
#> TCGA.BR.A4J8.01 6 0.2793 0.847 0.20 0.00 0.00 0.00 0.00 0.80
#> TCGA.HU.A4GQ.01 5 0.1556 0.639 0.00 0.00 0.00 0.00 0.92 0.08
#> TCGA.BR.A4QM.01 2 0.2020 0.578 0.00 0.92 0.04 0.00 0.02 0.02
#> TCGA.D7.A4YV.01 1 0.0547 0.860 0.98 0.00 0.02 0.00 0.00 0.00
#> TCGA.D7.A4YU.01 2 0.0000 0.615 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.HU.A4GN.01 2 0.5698 0.451 0.00 0.44 0.40 0.00 0.16 0.00
#> TCGA.HU.A4H6.01 1 0.3647 0.320 0.64 0.00 0.00 0.00 0.00 0.36
#> TCGA.HF.7132.01 2 0.5698 0.451 0.00 0.44 0.40 0.00 0.16 0.00
#> TCGA.BR.8370.01 4 0.3706 0.465 0.00 0.00 0.00 0.62 0.38 0.00
#> TCGA.BR.7851.01 5 0.5083 0.298 0.00 0.10 0.32 0.00 0.58 0.00
#> TCGA.BR.8363.01 1 0.0000 0.870 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BR.8284.01 1 0.3198 0.539 0.74 0.00 0.00 0.00 0.00 0.26
#> TCGA.BR.8081.01 1 0.0000 0.870 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FP.A4BE.01 4 0.0000 0.894 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.BR.8078.01 3 0.5490 0.380 0.26 0.00 0.56 0.00 0.00 0.18
#> TCGA.BR.8360.01 5 0.1480 0.658 0.00 0.04 0.02 0.00 0.94 0.00
cbind(get_classes(res, k = 7), get_membership(res, k = 7))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7
#> TCGA.BR.6452.01 1 0.0000 1.0000 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BR.8382.01 1 0.0000 1.0000 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HU.8604.01 1 0.0000 1.0000 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BR.8591.01 4 0.0000 0.9893 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.VQ.A91D.01 4 0.0000 0.9893 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.HU.8602.01 3 0.3047 0.9855 0.28 0.00 0.72 0.00 0.00 0.00 0.00
#> TCGA.CG.4437.01 2 0.4266 -0.1714 0.00 0.52 0.04 0.00 0.00 0.00 0.44
#> TCGA.VQ.A8PP.01 2 0.1166 0.7631 0.00 0.94 0.00 0.00 0.00 0.00 0.06
#> TCGA.BR.A4QI.01 6 0.6307 0.2548 0.04 0.00 0.12 0.00 0.06 0.54 0.24
#> TCGA.BR.A4PF.01 2 0.0863 0.7548 0.00 0.96 0.04 0.00 0.00 0.00 0.00
#> TCGA.CD.A4MJ.01 4 0.0504 0.9676 0.00 0.00 0.00 0.98 0.02 0.00 0.00
#> TCGA.CD.A4MI.01 7 0.5662 0.4904 0.00 0.30 0.06 0.02 0.06 0.00 0.56
#> TCGA.VQ.A924.01 7 0.4569 0.3263 0.00 0.00 0.00 0.28 0.06 0.02 0.64
#> TCGA.BR.A4J8.01 6 0.1664 0.4802 0.06 0.00 0.02 0.00 0.00 0.92 0.00
#> TCGA.HU.A4GQ.01 5 0.0504 0.5866 0.00 0.00 0.00 0.00 0.98 0.00 0.02
#> TCGA.BR.A4QM.01 2 0.1166 0.7472 0.00 0.94 0.06 0.00 0.00 0.00 0.00
#> TCGA.D7.A4YV.01 1 0.0000 1.0000 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D7.A4YU.01 2 0.2016 0.7456 0.00 0.90 0.04 0.00 0.00 0.00 0.06
#> TCGA.HU.A4GN.01 7 0.5662 0.4904 0.00 0.30 0.06 0.02 0.06 0.00 0.56
#> TCGA.HU.A4H6.01 6 0.3413 0.4979 0.38 0.00 0.00 0.00 0.00 0.62 0.00
#> TCGA.HF.7132.01 7 0.3417 0.5249 0.00 0.26 0.00 0.02 0.00 0.00 0.72
#> TCGA.BR.8370.01 5 0.4408 0.0641 0.00 0.00 0.02 0.44 0.52 0.00 0.02
#> TCGA.BR.7851.01 7 0.6058 0.1580 0.00 0.04 0.04 0.02 0.36 0.04 0.50
#> TCGA.BR.8363.01 1 0.0000 1.0000 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BR.8284.01 6 0.3546 0.3653 0.46 0.00 0.00 0.00 0.00 0.54 0.00
#> TCGA.BR.8081.01 1 0.0000 1.0000 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FP.A4BE.01 4 0.0000 0.9893 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.BR.8078.01 3 0.3517 0.9855 0.28 0.00 0.70 0.00 0.00 0.00 0.02
#> TCGA.BR.8360.01 5 0.4311 0.5276 0.00 0.02 0.06 0.00 0.76 0.04 0.12
cbind(get_classes(res, k = 8), get_membership(res, k = 8))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7 p8
#> TCGA.BR.6452.01 1 0.0471 0.9583 0.98 0.00 0.02 0.00 0.00 0.00 0.00 0.00
#> TCGA.BR.8382.01 1 0.0000 0.9689 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HU.8604.01 1 0.0471 0.9589 0.98 0.02 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BR.8591.01 4 0.0000 0.9866 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.VQ.A91D.01 4 0.0000 0.9866 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.HU.8602.01 3 0.2114 1.0000 0.16 0.00 0.84 0.00 0.00 0.00 0.00 0.00
#> TCGA.CG.4437.01 7 0.4643 0.2370 0.00 0.12 0.12 0.00 0.00 0.02 0.70 0.04
#> TCGA.VQ.A8PP.01 2 0.5533 0.6975 0.00 0.54 0.12 0.00 0.00 0.02 0.28 0.04
#> TCGA.BR.A4QI.01 8 0.3992 0.0000 0.00 0.00 0.04 0.00 0.00 0.44 0.00 0.52
#> TCGA.BR.A4PF.01 2 0.1765 0.7286 0.00 0.88 0.00 0.00 0.00 0.00 0.12 0.00
#> TCGA.CD.A4MJ.01 4 0.0471 0.9866 0.00 0.00 0.00 0.98 0.00 0.02 0.00 0.00
#> TCGA.CD.A4MI.01 7 0.0471 0.6445 0.00 0.00 0.00 0.00 0.02 0.00 0.98 0.00
#> TCGA.VQ.A924.01 7 0.4953 0.4688 0.00 0.00 0.00 0.16 0.02 0.00 0.58 0.24
#> TCGA.BR.A4J8.01 6 0.2532 0.0604 0.02 0.04 0.04 0.00 0.02 0.88 0.00 0.00
#> TCGA.HU.A4GQ.01 5 0.0808 0.6594 0.00 0.00 0.00 0.00 0.96 0.00 0.04 0.00
#> TCGA.BR.A4QM.01 2 0.1765 0.7286 0.00 0.88 0.00 0.00 0.00 0.00 0.12 0.00
#> TCGA.D7.A4YV.01 1 0.2020 0.8940 0.90 0.06 0.02 0.00 0.02 0.00 0.00 0.00
#> TCGA.D7.A4YU.01 2 0.5639 0.6621 0.00 0.50 0.12 0.00 0.00 0.02 0.32 0.04
#> TCGA.HU.A4GN.01 7 0.0471 0.6445 0.00 0.00 0.00 0.00 0.02 0.00 0.98 0.00
#> TCGA.HU.A4H6.01 6 0.2938 0.6886 0.30 0.00 0.00 0.00 0.00 0.70 0.00 0.00
#> TCGA.HF.7132.01 7 0.1947 0.6542 0.00 0.00 0.00 0.00 0.00 0.00 0.86 0.14
#> TCGA.BR.8370.01 5 0.3404 0.5230 0.00 0.00 0.00 0.24 0.72 0.00 0.00 0.04
#> TCGA.BR.7851.01 7 0.4990 0.3030 0.00 0.00 0.00 0.00 0.18 0.00 0.44 0.38
#> TCGA.BR.8363.01 1 0.0000 0.9689 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BR.8284.01 6 0.3015 0.6794 0.32 0.00 0.00 0.00 0.00 0.68 0.00 0.00
#> TCGA.BR.8081.01 1 0.0000 0.9689 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FP.A4BE.01 4 0.0471 0.9866 0.00 0.00 0.00 0.98 0.00 0.02 0.00 0.00
#> TCGA.BR.8078.01 3 0.2114 1.0000 0.16 0.00 0.84 0.00 0.00 0.00 0.00 0.00
#> TCGA.BR.8360.01 5 0.4294 0.5717 0.00 0.00 0.04 0.00 0.68 0.00 0.06 0.22
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
consensus_heatmap(res, k = 7)
consensus_heatmap(res, k = 8)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
membership_heatmap(res, k = 7)
membership_heatmap(res, k = 8)
As soon as the classes for columns are determined, the signatures that are significantly different between subgroups can be looked for. Following are the heatmaps for signatures.
get_signatures(res, k = 2)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
get_signatures(res, k = 7)
get_signatures(res, k = 8)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. To get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows (which is done by automatically selecting number of clusters).If there are too many signatures, top_signatures = ... can be set to only show the
signatures with the highest FDRs:
# code only for demonstration
# e.g. to show the top 500 most significant rows
tb = get_signature(res, k = ..., top_signatures = 500)
If the signatures are defined as these which are uniquely high in current group, diff_method argument
can be set to "uniquely_high_in_one_group":
# code only for demonstration
tb = get_signature(res, k = ..., diff_method = "uniquely_high_in_one_group")
UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
dimension_reduction(res, k = 7, method = "UMAP")
dimension_reduction(res, k = 8, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
If matrix rows can be associated to genes, consider to use functional_enrichment(res,
...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.
Parent node: Node0. Child nodes: Node011 , Node012 , Node013 , Node021 , Node022 , Node023 , Node031 , Node032-leaf , Node033 , Node034 .
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 117 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 0.999 1.000 0.4490 0.552 0.552
#> 3 3 0.947 0.955 0.982 0.3636 0.709 0.528
#> 4 4 0.993 0.957 0.983 0.1507 0.840 0.621
#> 5 5 0.938 0.910 0.965 0.1293 0.850 0.538
#> 6 6 0.874 0.859 0.910 0.0130 0.994 0.969
#> 7 7 0.816 0.703 0.864 0.0172 0.995 0.975
#> 8 8 0.790 0.693 0.841 0.0130 0.994 0.972
suggest_best_k() suggests the best \(k\) based on these statistics. The rules are as follows:
suggest_best_k(res)
#> [1] 5
#> attr(,"optional")
#> [1] 2 3 4
There is also optional best \(k\) = 2 3 4 that is worth to check.
Following is the table of the partitions (You need to click the show/hide
code output link to see it). The membership matrix (columns with name p*)
is inferred by
clue::cl_consensus()
function with the SE method. Basically the value in the membership matrix
represents the probability to belong to a certain group. The finall subgroup
label for an item is determined with the group with highest probability it
belongs to.
In get_classes() function, the entropy is calculated from the membership
matrix and the silhouette score is calculated from the consensus matrix.
cbind(get_classes(res, k = 2), get_membership(res, k = 2))
#> class entropy silhouette p1 p2
#> TCGA.BR.8683.01 1 0.000 0.999 1.00 0.00
#> TCGA.CG.5716.01 1 0.000 0.999 1.00 0.00
#> TCGA.VQ.AA68.01 2 0.000 1.000 0.00 1.00
#> TCGA.CG.4441.01 2 0.000 1.000 0.00 1.00
#> TCGA.BR.8384.01 1 0.000 0.999 1.00 0.00
#> TCGA.BR.6453.01 1 0.000 0.999 1.00 0.00
#> TCGA.VQ.A91S.01 2 0.000 1.000 0.00 1.00
#> TCGA.D7.6528.01 2 0.000 1.000 0.00 1.00
#> TCGA.VQ.A8E7.01 2 0.000 1.000 0.00 1.00
#> TCGA.BR.8680.01 2 0.000 1.000 0.00 1.00
#> TCGA.BR.8483.01 2 0.000 1.000 0.00 1.00
#> TCGA.BR.6566.01 1 0.000 0.999 1.00 0.00
#> TCGA.VQ.A91X.01 2 0.000 1.000 0.00 1.00
#> TCGA.VQ.A94U.01 2 0.000 1.000 0.00 1.00
#> TCGA.VQ.A91A.01 1 0.000 0.999 1.00 0.00
#> TCGA.D7.6518.01 1 0.000 0.999 1.00 0.00
#> TCGA.VQ.A91E.01 1 0.000 0.999 1.00 0.00
#> TCGA.VQ.A8PY.01 1 0.000 0.999 1.00 0.00
#> TCGA.BR.6452.11 1 0.000 0.999 1.00 0.00
#> TCGA.BR.8682.01 1 0.000 0.999 1.00 0.00
#> TCGA.VQ.A91V.01 2 0.000 1.000 0.00 1.00
#> TCGA.VQ.A8PZ.01 1 0.000 0.999 1.00 0.00
#> TCGA.BR.6458.01 1 0.000 0.999 1.00 0.00
#> TCGA.BR.8592.01 1 0.000 0.999 1.00 0.00
#> TCGA.D7.6525.01 1 0.000 0.999 1.00 0.00
#> TCGA.BR.8588.01 1 0.000 0.999 1.00 0.00
#> TCGA.HU.8610.01 1 0.000 0.999 1.00 0.00
#> TCGA.VQ.A8PD.01 1 0.000 0.999 1.00 0.00
#> TCGA.D7.6524.01 1 0.000 0.999 1.00 0.00
#> TCGA.3M.AB47.01 1 0.000 0.999 1.00 0.00
#> TCGA.BR.6457.01 1 0.000 0.999 1.00 0.00
#> TCGA.D7.A6EV.01 2 0.000 1.000 0.00 1.00
#> TCGA.HU.A4H4.01 1 0.000 0.999 1.00 0.00
#> TCGA.BR.A4J5.01 1 0.000 0.999 1.00 0.00
#> TCGA.BR.7717.01 2 0.000 1.000 0.00 1.00
#> TCGA.BR.A4IU.01 1 0.000 0.999 1.00 0.00
#> TCGA.BR.7715.01 2 0.000 1.000 0.00 1.00
#> TCGA.HU.A4GJ.01 1 0.000 0.999 1.00 0.00
#> TCGA.BR.7196.01 1 0.000 0.999 1.00 0.00
#> TCGA.BR.6563.01 1 0.000 0.999 1.00 0.00
#> TCGA.IN.A6RJ.01 1 0.000 0.999 1.00 0.00
#> TCGA.HU.A4GX.01 1 0.000 0.999 1.00 0.00
#> TCGA.HU.A4G8.01 2 0.000 1.000 0.00 1.00
#> TCGA.HU.A4GC.01 2 0.000 1.000 0.00 1.00
#> TCGA.B7.A5TK.01 1 0.000 0.999 1.00 0.00
#> TCGA.D7.A4Z0.01 1 0.000 0.999 1.00 0.00
#> TCGA.R5.A7O7.01 1 0.000 0.999 1.00 0.00
#> TCGA.BR.A4J2.01 1 0.000 0.999 1.00 0.00
#> TCGA.HU.A4GD.01 2 0.000 1.000 0.00 1.00
#> TCGA.VQ.AA6B.01 2 0.000 1.000 0.00 1.00
#> TCGA.HU.A4HB.01 1 0.000 0.999 1.00 0.00
#> TCGA.HU.A4H2.01 2 0.000 1.000 0.00 1.00
#> TCGA.BR.6852.01 1 0.000 0.999 1.00 0.00
#> TCGA.IN.A7NT.01 1 0.000 0.999 1.00 0.00
#> TCGA.CG.5734.01 1 0.000 0.999 1.00 0.00
#> TCGA.VQ.A8P8.01 1 0.000 0.999 1.00 0.00
#> TCGA.BR.6705.01 1 0.000 0.999 1.00 0.00
#> TCGA.MX.A5UG.01 1 0.000 0.999 1.00 0.00
#> TCGA.CD.8533.01 2 0.000 1.000 0.00 1.00
#> TCGA.BR.7957.01 1 0.000 0.999 1.00 0.00
#> TCGA.CG.5722.01 1 0.000 0.999 1.00 0.00
#> TCGA.F1.6874.01 1 0.000 0.999 1.00 0.00
#> TCGA.CG.5730.01 2 0.000 1.000 0.00 1.00
#> TCGA.IP.7968.01 2 0.000 1.000 0.00 1.00
#> TCGA.D7.6822.01 2 0.000 1.000 0.00 1.00
#> TCGA.D7.A6EY.01 1 0.000 0.999 1.00 0.00
#> TCGA.BR.6706.01 1 0.000 0.999 1.00 0.00
#> TCGA.IN.7808.01 1 0.000 0.999 1.00 0.00
#> TCGA.KB.A93H.01 2 0.000 1.000 0.00 1.00
#> TCGA.BR.6802.01 1 0.000 0.999 1.00 0.00
#> TCGA.FP.A9TM.01 1 0.000 0.999 1.00 0.00
#> TCGA.FP.7998.01 1 0.000 0.999 1.00 0.00
#> TCGA.IN.A6RS.01 1 0.000 0.999 1.00 0.00
#> TCGA.B7.5816.01 1 0.000 0.999 1.00 0.00
#> TCGA.CG.5721.01 1 0.000 0.999 1.00 0.00
#> TCGA.RD.A8NB.01 1 0.000 0.999 1.00 0.00
#> TCGA.IN.AB1X.01 1 0.000 0.999 1.00 0.00
#> TCGA.CG.5728.01 1 0.000 0.999 1.00 0.00
#> TCGA.IN.A7NU.01 1 0.000 0.999 1.00 0.00
#> TCGA.D7.5578.01 1 0.000 0.999 1.00 0.00
#> TCGA.VQ.A8P5.01 2 0.000 1.000 0.00 1.00
#> TCGA.CG.5724.01 2 0.000 1.000 0.00 1.00
#> TCGA.VQ.A8PB.01 2 0.000 1.000 0.00 1.00
#> TCGA.CG.5727.01 2 0.000 1.000 0.00 1.00
#> TCGA.VQ.A8PC.01 1 0.000 0.999 1.00 0.00
#> TCGA.HU.8243.01 2 0.000 1.000 0.00 1.00
#> TCGA.BR.8362.01 1 0.000 0.999 1.00 0.00
#> TCGA.IN.8462.01 2 0.000 1.000 0.00 1.00
#> TCGA.CD.8524.01 1 0.000 0.999 1.00 0.00
#> TCGA.BR.A453.01 1 0.000 0.999 1.00 0.00
#> TCGA.BR.8367.01 1 0.000 0.999 1.00 0.00
#> TCGA.BR.8380.01 1 0.000 0.999 1.00 0.00
#> TCGA.HU.8238.01 2 0.000 1.000 0.00 1.00
#> TCGA.HU.8249.01 2 0.000 1.000 0.00 1.00
#> TCGA.R5.A804.01 1 0.000 0.999 1.00 0.00
#> TCGA.BR.A4CS.01 1 0.242 0.958 0.96 0.04
#> TCGA.D7.A6ET.01 1 0.000 0.999 1.00 0.00
#> TCGA.FP.8099.01 2 0.000 1.000 0.00 1.00
#> TCGA.D7.8579.01 1 0.000 0.999 1.00 0.00
#> TCGA.BR.8297.01 1 0.000 0.999 1.00 0.00
#> TCGA.RD.A7C1.01 1 0.000 0.999 1.00 0.00
#> TCGA.F1.A448.01 1 0.000 0.999 1.00 0.00
#> TCGA.D7.8575.01 2 0.000 1.000 0.00 1.00
#> TCGA.VQ.A8P3.01 2 0.000 1.000 0.00 1.00
#> TCGA.BR.8286.01 2 0.000 1.000 0.00 1.00
#> TCGA.BR.8369.01 1 0.000 0.999 1.00 0.00
#> TCGA.FP.A4BF.01 1 0.000 0.999 1.00 0.00
#> TCGA.R5.A805.01 1 0.000 0.999 1.00 0.00
#> TCGA.IN.A6RL.01 2 0.000 1.000 0.00 1.00
#> TCGA.BR.8289.01 2 0.000 1.000 0.00 1.00
#> TCGA.BR.8296.01 1 0.000 0.999 1.00 0.00
#> TCGA.CD.A48A.01 2 0.000 1.000 0.00 1.00
#> TCGA.CD.8534.01 1 0.000 0.999 1.00 0.00
#> TCGA.BR.7959.01 1 0.000 0.999 1.00 0.00
#> TCGA.RD.A8MV.01 1 0.000 0.999 1.00 0.00
#> TCGA.CD.8536.01 1 0.000 0.999 1.00 0.00
#> TCGA.BR.A44U.01 2 0.000 1.000 0.00 1.00
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.BR.8683.01 2 0.000 0.966 0.00 1.00 0.00
#> TCGA.CG.5716.01 1 0.000 0.985 1.00 0.00 0.00
#> TCGA.VQ.AA68.01 2 0.000 0.966 0.00 1.00 0.00
#> TCGA.CG.4441.01 2 0.000 0.966 0.00 1.00 0.00
#> TCGA.BR.8384.01 1 0.000 0.985 1.00 0.00 0.00
#> TCGA.BR.6453.01 1 0.000 0.985 1.00 0.00 0.00
#> TCGA.VQ.A91S.01 2 0.000 0.966 0.00 1.00 0.00
#> TCGA.D7.6528.01 3 0.000 0.986 0.00 0.00 1.00
#> TCGA.VQ.A8E7.01 2 0.455 0.743 0.00 0.80 0.20
#> TCGA.BR.8680.01 2 0.502 0.684 0.00 0.76 0.24
#> TCGA.BR.8483.01 3 0.000 0.986 0.00 0.00 1.00
#> TCGA.BR.6566.01 1 0.000 0.985 1.00 0.00 0.00
#> TCGA.VQ.A91X.01 3 0.000 0.986 0.00 0.00 1.00
#> TCGA.VQ.A94U.01 3 0.000 0.986 0.00 0.00 1.00
#> TCGA.VQ.A91A.01 2 0.000 0.966 0.00 1.00 0.00
#> TCGA.D7.6518.01 1 0.000 0.985 1.00 0.00 0.00
#> TCGA.VQ.A91E.01 2 0.000 0.966 0.00 1.00 0.00
#> TCGA.VQ.A8PY.01 2 0.000 0.966 0.00 1.00 0.00
#> TCGA.BR.6452.11 1 0.000 0.985 1.00 0.00 0.00
#> TCGA.BR.8682.01 2 0.000 0.966 0.00 1.00 0.00
#> TCGA.VQ.A91V.01 3 0.000 0.986 0.00 0.00 1.00
#> TCGA.VQ.A8PZ.01 1 0.000 0.985 1.00 0.00 0.00
#> TCGA.BR.6458.01 2 0.000 0.966 0.00 1.00 0.00
#> TCGA.BR.8592.01 1 0.000 0.985 1.00 0.00 0.00
#> TCGA.D7.6525.01 2 0.000 0.966 0.00 1.00 0.00
#> TCGA.BR.8588.01 1 0.000 0.985 1.00 0.00 0.00
#> TCGA.HU.8610.01 1 0.000 0.985 1.00 0.00 0.00
#> TCGA.VQ.A8PD.01 1 0.000 0.985 1.00 0.00 0.00
#> TCGA.D7.6524.01 1 0.000 0.985 1.00 0.00 0.00
#> TCGA.3M.AB47.01 1 0.000 0.985 1.00 0.00 0.00
#> TCGA.BR.6457.01 1 0.000 0.985 1.00 0.00 0.00
#> TCGA.D7.A6EV.01 2 0.000 0.966 0.00 1.00 0.00
#> TCGA.HU.A4H4.01 1 0.429 0.780 0.82 0.18 0.00
#> TCGA.BR.A4J5.01 1 0.000 0.985 1.00 0.00 0.00
#> TCGA.BR.7717.01 2 0.000 0.966 0.00 1.00 0.00
#> TCGA.BR.A4IU.01 1 0.000 0.985 1.00 0.00 0.00
#> TCGA.BR.7715.01 3 0.000 0.986 0.00 0.00 1.00
#> TCGA.HU.A4GJ.01 1 0.000 0.985 1.00 0.00 0.00
#> TCGA.BR.7196.01 1 0.000 0.985 1.00 0.00 0.00
#> TCGA.BR.6563.01 1 0.000 0.985 1.00 0.00 0.00
#> TCGA.IN.A6RJ.01 1 0.000 0.985 1.00 0.00 0.00
#> TCGA.HU.A4GX.01 2 0.000 0.966 0.00 1.00 0.00
#> TCGA.HU.A4G8.01 2 0.000 0.966 0.00 1.00 0.00
#> TCGA.HU.A4GC.01 3 0.480 0.705 0.00 0.22 0.78
#> TCGA.B7.A5TK.01 1 0.000 0.985 1.00 0.00 0.00
#> TCGA.D7.A4Z0.01 1 0.000 0.985 1.00 0.00 0.00
#> TCGA.R5.A7O7.01 1 0.000 0.985 1.00 0.00 0.00
#> TCGA.BR.A4J2.01 1 0.000 0.985 1.00 0.00 0.00
#> TCGA.HU.A4GD.01 3 0.000 0.986 0.00 0.00 1.00
#> TCGA.VQ.AA6B.01 3 0.000 0.986 0.00 0.00 1.00
#> TCGA.HU.A4HB.01 1 0.000 0.985 1.00 0.00 0.00
#> TCGA.HU.A4H2.01 2 0.000 0.966 0.00 1.00 0.00
#> TCGA.BR.6852.01 1 0.000 0.985 1.00 0.00 0.00
#> TCGA.IN.A7NT.01 1 0.000 0.985 1.00 0.00 0.00
#> TCGA.CG.5734.01 1 0.000 0.985 1.00 0.00 0.00
#> TCGA.VQ.A8P8.01 1 0.000 0.985 1.00 0.00 0.00
#> TCGA.BR.6705.01 1 0.000 0.985 1.00 0.00 0.00
#> TCGA.MX.A5UG.01 1 0.000 0.985 1.00 0.00 0.00
#> TCGA.CD.8533.01 3 0.000 0.986 0.00 0.00 1.00
#> TCGA.BR.7957.01 1 0.000 0.985 1.00 0.00 0.00
#> TCGA.CG.5722.01 1 0.000 0.985 1.00 0.00 0.00
#> TCGA.F1.6874.01 2 0.000 0.966 0.00 1.00 0.00
#> TCGA.CG.5730.01 3 0.000 0.986 0.00 0.00 1.00
#> TCGA.IP.7968.01 3 0.000 0.986 0.00 0.00 1.00
#> TCGA.D7.6822.01 3 0.000 0.986 0.00 0.00 1.00
#> TCGA.D7.A6EY.01 1 0.000 0.985 1.00 0.00 0.00
#> TCGA.BR.6706.01 1 0.000 0.985 1.00 0.00 0.00
#> TCGA.IN.7808.01 1 0.000 0.985 1.00 0.00 0.00
#> TCGA.KB.A93H.01 3 0.000 0.986 0.00 0.00 1.00
#> TCGA.BR.6802.01 1 0.000 0.985 1.00 0.00 0.00
#> TCGA.FP.A9TM.01 2 0.000 0.966 0.00 1.00 0.00
#> TCGA.FP.7998.01 1 0.000 0.985 1.00 0.00 0.00
#> TCGA.IN.A6RS.01 2 0.000 0.966 0.00 1.00 0.00
#> TCGA.B7.5816.01 1 0.000 0.985 1.00 0.00 0.00
#> TCGA.CG.5721.01 1 0.000 0.985 1.00 0.00 0.00
#> TCGA.RD.A8NB.01 1 0.000 0.985 1.00 0.00 0.00
#> TCGA.IN.AB1X.01 1 0.000 0.985 1.00 0.00 0.00
#> TCGA.CG.5728.01 1 0.000 0.985 1.00 0.00 0.00
#> TCGA.IN.A7NU.01 2 0.613 0.303 0.40 0.60 0.00
#> TCGA.D7.5578.01 2 0.000 0.966 0.00 1.00 0.00
#> TCGA.VQ.A8P5.01 2 0.000 0.966 0.00 1.00 0.00
#> TCGA.CG.5724.01 2 0.369 0.821 0.00 0.86 0.14
#> TCGA.VQ.A8PB.01 2 0.000 0.966 0.00 1.00 0.00
#> TCGA.CG.5727.01 2 0.000 0.966 0.00 1.00 0.00
#> TCGA.VQ.A8PC.01 1 0.000 0.985 1.00 0.00 0.00
#> TCGA.HU.8243.01 2 0.000 0.966 0.00 1.00 0.00
#> TCGA.BR.8362.01 2 0.000 0.966 0.00 1.00 0.00
#> TCGA.IN.8462.01 2 0.000 0.966 0.00 1.00 0.00
#> TCGA.CD.8524.01 2 0.000 0.966 0.00 1.00 0.00
#> TCGA.BR.A453.01 1 0.000 0.985 1.00 0.00 0.00
#> TCGA.BR.8367.01 1 0.000 0.985 1.00 0.00 0.00
#> TCGA.BR.8380.01 1 0.000 0.985 1.00 0.00 0.00
#> TCGA.HU.8238.01 2 0.000 0.966 0.00 1.00 0.00
#> TCGA.HU.8249.01 3 0.000 0.986 0.00 0.00 1.00
#> TCGA.R5.A804.01 1 0.000 0.985 1.00 0.00 0.00
#> TCGA.BR.A4CS.01 2 0.000 0.966 0.00 1.00 0.00
#> TCGA.D7.A6ET.01 1 0.000 0.985 1.00 0.00 0.00
#> TCGA.FP.8099.01 3 0.000 0.986 0.00 0.00 1.00
#> TCGA.D7.8579.01 1 0.000 0.985 1.00 0.00 0.00
#> TCGA.BR.8297.01 1 0.000 0.985 1.00 0.00 0.00
#> TCGA.RD.A7C1.01 1 0.455 0.753 0.80 0.20 0.00
#> TCGA.F1.A448.01 1 0.000 0.985 1.00 0.00 0.00
#> TCGA.D7.8575.01 2 0.000 0.966 0.00 1.00 0.00
#> TCGA.VQ.A8P3.01 2 0.000 0.966 0.00 1.00 0.00
#> TCGA.BR.8286.01 2 0.000 0.966 0.00 1.00 0.00
#> TCGA.BR.8369.01 1 0.429 0.780 0.82 0.18 0.00
#> TCGA.FP.A4BF.01 2 0.000 0.966 0.00 1.00 0.00
#> TCGA.R5.A805.01 1 0.429 0.780 0.82 0.18 0.00
#> TCGA.IN.A6RL.01 2 0.000 0.966 0.00 1.00 0.00
#> TCGA.BR.8289.01 2 0.000 0.966 0.00 1.00 0.00
#> TCGA.BR.8296.01 1 0.000 0.985 1.00 0.00 0.00
#> TCGA.CD.A48A.01 3 0.000 0.986 0.00 0.00 1.00
#> TCGA.CD.8534.01 2 0.000 0.966 0.00 1.00 0.00
#> TCGA.BR.7959.01 2 0.000 0.966 0.00 1.00 0.00
#> TCGA.RD.A8MV.01 1 0.000 0.985 1.00 0.00 0.00
#> TCGA.CD.8536.01 2 0.000 0.966 0.00 1.00 0.00
#> TCGA.BR.A44U.01 2 0.480 0.715 0.00 0.78 0.22
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> TCGA.BR.8683.01 2 0.0000 0.9468 0.00 1.00 0.00 0.00
#> TCGA.CG.5716.01 1 0.0000 0.9996 1.00 0.00 0.00 0.00
#> TCGA.VQ.AA68.01 4 0.0000 0.9716 0.00 0.00 0.00 1.00
#> TCGA.CG.4441.01 4 0.0000 0.9716 0.00 0.00 0.00 1.00
#> TCGA.BR.8384.01 1 0.0000 0.9996 1.00 0.00 0.00 0.00
#> TCGA.BR.6453.01 1 0.0000 0.9996 1.00 0.00 0.00 0.00
#> TCGA.VQ.A91S.01 2 0.4994 0.0919 0.00 0.52 0.00 0.48
#> TCGA.D7.6528.01 3 0.0000 0.9957 0.00 0.00 1.00 0.00
#> TCGA.VQ.A8E7.01 4 0.0000 0.9716 0.00 0.00 0.00 1.00
#> TCGA.BR.8680.01 4 0.0000 0.9716 0.00 0.00 0.00 1.00
#> TCGA.BR.8483.01 3 0.0000 0.9957 0.00 0.00 1.00 0.00
#> TCGA.BR.6566.01 2 0.0000 0.9468 0.00 1.00 0.00 0.00
#> TCGA.VQ.A91X.01 3 0.0000 0.9957 0.00 0.00 1.00 0.00
#> TCGA.VQ.A94U.01 3 0.0000 0.9957 0.00 0.00 1.00 0.00
#> TCGA.VQ.A91A.01 2 0.0000 0.9468 0.00 1.00 0.00 0.00
#> TCGA.D7.6518.01 1 0.0000 0.9996 1.00 0.00 0.00 0.00
#> TCGA.VQ.A91E.01 2 0.0000 0.9468 0.00 1.00 0.00 0.00
#> TCGA.VQ.A8PY.01 2 0.0000 0.9468 0.00 1.00 0.00 0.00
#> TCGA.BR.6452.11 1 0.0000 0.9996 1.00 0.00 0.00 0.00
#> TCGA.BR.8682.01 2 0.0000 0.9468 0.00 1.00 0.00 0.00
#> TCGA.VQ.A91V.01 3 0.0000 0.9957 0.00 0.00 1.00 0.00
#> TCGA.VQ.A8PZ.01 1 0.0000 0.9996 1.00 0.00 0.00 0.00
#> TCGA.BR.6458.01 2 0.0000 0.9468 0.00 1.00 0.00 0.00
#> TCGA.BR.8592.01 1 0.0000 0.9996 1.00 0.00 0.00 0.00
#> TCGA.D7.6525.01 2 0.0000 0.9468 0.00 1.00 0.00 0.00
#> TCGA.BR.8588.01 1 0.0000 0.9996 1.00 0.00 0.00 0.00
#> TCGA.HU.8610.01 1 0.0000 0.9996 1.00 0.00 0.00 0.00
#> TCGA.VQ.A8PD.01 1 0.0000 0.9996 1.00 0.00 0.00 0.00
#> TCGA.D7.6524.01 1 0.0000 0.9996 1.00 0.00 0.00 0.00
#> TCGA.3M.AB47.01 1 0.0707 0.9778 0.98 0.02 0.00 0.00
#> TCGA.BR.6457.01 1 0.0000 0.9996 1.00 0.00 0.00 0.00
#> TCGA.D7.A6EV.01 4 0.0000 0.9716 0.00 0.00 0.00 1.00
#> TCGA.HU.A4H4.01 2 0.0000 0.9468 0.00 1.00 0.00 0.00
#> TCGA.BR.A4J5.01 1 0.0000 0.9996 1.00 0.00 0.00 0.00
#> TCGA.BR.7717.01 4 0.0000 0.9716 0.00 0.00 0.00 1.00
#> TCGA.BR.A4IU.01 1 0.0000 0.9996 1.00 0.00 0.00 0.00
#> TCGA.BR.7715.01 3 0.0000 0.9957 0.00 0.00 1.00 0.00
#> TCGA.HU.A4GJ.01 1 0.0000 0.9996 1.00 0.00 0.00 0.00
#> TCGA.BR.7196.01 1 0.0000 0.9996 1.00 0.00 0.00 0.00
#> TCGA.BR.6563.01 1 0.0000 0.9996 1.00 0.00 0.00 0.00
#> TCGA.IN.A6RJ.01 1 0.0000 0.9996 1.00 0.00 0.00 0.00
#> TCGA.HU.A4GX.01 2 0.0000 0.9468 0.00 1.00 0.00 0.00
#> TCGA.HU.A4G8.01 4 0.1637 0.9126 0.00 0.06 0.00 0.94
#> TCGA.HU.A4GC.01 4 0.0000 0.9716 0.00 0.00 0.00 1.00
#> TCGA.B7.A5TK.01 1 0.0000 0.9996 1.00 0.00 0.00 0.00
#> TCGA.D7.A4Z0.01 1 0.0000 0.9996 1.00 0.00 0.00 0.00
#> TCGA.R5.A7O7.01 1 0.0000 0.9996 1.00 0.00 0.00 0.00
#> TCGA.BR.A4J2.01 1 0.0000 0.9996 1.00 0.00 0.00 0.00
#> TCGA.HU.A4GD.01 3 0.0000 0.9957 0.00 0.00 1.00 0.00
#> TCGA.VQ.AA6B.01 3 0.0000 0.9957 0.00 0.00 1.00 0.00
#> TCGA.HU.A4HB.01 1 0.0000 0.9996 1.00 0.00 0.00 0.00
#> TCGA.HU.A4H2.01 4 0.2921 0.8203 0.00 0.14 0.00 0.86
#> TCGA.BR.6852.01 1 0.0000 0.9996 1.00 0.00 0.00 0.00
#> TCGA.IN.A7NT.01 2 0.2647 0.8108 0.12 0.88 0.00 0.00
#> TCGA.CG.5734.01 1 0.0000 0.9996 1.00 0.00 0.00 0.00
#> TCGA.VQ.A8P8.01 1 0.0000 0.9996 1.00 0.00 0.00 0.00
#> TCGA.BR.6705.01 1 0.0000 0.9996 1.00 0.00 0.00 0.00
#> TCGA.MX.A5UG.01 1 0.0000 0.9996 1.00 0.00 0.00 0.00
#> TCGA.CD.8533.01 3 0.0000 0.9957 0.00 0.00 1.00 0.00
#> TCGA.BR.7957.01 1 0.0000 0.9996 1.00 0.00 0.00 0.00
#> TCGA.CG.5722.01 1 0.0000 0.9996 1.00 0.00 0.00 0.00
#> TCGA.F1.6874.01 2 0.0000 0.9468 0.00 1.00 0.00 0.00
#> TCGA.CG.5730.01 3 0.0000 0.9957 0.00 0.00 1.00 0.00
#> TCGA.IP.7968.01 3 0.1637 0.9356 0.00 0.00 0.94 0.06
#> TCGA.D7.6822.01 4 0.4522 0.5176 0.00 0.00 0.32 0.68
#> TCGA.D7.A6EY.01 1 0.0000 0.9996 1.00 0.00 0.00 0.00
#> TCGA.BR.6706.01 1 0.0000 0.9996 1.00 0.00 0.00 0.00
#> TCGA.IN.7808.01 1 0.0000 0.9996 1.00 0.00 0.00 0.00
#> TCGA.KB.A93H.01 3 0.0000 0.9957 0.00 0.00 1.00 0.00
#> TCGA.BR.6802.01 1 0.0000 0.9996 1.00 0.00 0.00 0.00
#> TCGA.FP.A9TM.01 2 0.0000 0.9468 0.00 1.00 0.00 0.00
#> TCGA.FP.7998.01 1 0.0000 0.9996 1.00 0.00 0.00 0.00
#> TCGA.IN.A6RS.01 2 0.0000 0.9468 0.00 1.00 0.00 0.00
#> TCGA.B7.5816.01 1 0.0000 0.9996 1.00 0.00 0.00 0.00
#> TCGA.CG.5721.01 1 0.0000 0.9996 1.00 0.00 0.00 0.00
#> TCGA.RD.A8NB.01 1 0.0000 0.9996 1.00 0.00 0.00 0.00
#> TCGA.IN.AB1X.01 1 0.0000 0.9996 1.00 0.00 0.00 0.00
#> TCGA.CG.5728.01 1 0.0000 0.9996 1.00 0.00 0.00 0.00
#> TCGA.IN.A7NU.01 2 0.0000 0.9468 0.00 1.00 0.00 0.00
#> TCGA.D7.5578.01 2 0.0000 0.9468 0.00 1.00 0.00 0.00
#> TCGA.VQ.A8P5.01 2 0.3400 0.7630 0.00 0.82 0.00 0.18
#> TCGA.CG.5724.01 4 0.0000 0.9716 0.00 0.00 0.00 1.00
#> TCGA.VQ.A8PB.01 4 0.0000 0.9716 0.00 0.00 0.00 1.00
#> TCGA.CG.5727.01 2 0.4277 0.6103 0.00 0.72 0.00 0.28
#> TCGA.VQ.A8PC.01 1 0.0000 0.9996 1.00 0.00 0.00 0.00
#> TCGA.HU.8243.01 4 0.0000 0.9716 0.00 0.00 0.00 1.00
#> TCGA.BR.8362.01 2 0.0000 0.9468 0.00 1.00 0.00 0.00
#> TCGA.IN.8462.01 4 0.0000 0.9716 0.00 0.00 0.00 1.00
#> TCGA.CD.8524.01 2 0.0000 0.9468 0.00 1.00 0.00 0.00
#> TCGA.BR.A453.01 1 0.0000 0.9996 1.00 0.00 0.00 0.00
#> TCGA.BR.8367.01 2 0.4277 0.5779 0.28 0.72 0.00 0.00
#> TCGA.BR.8380.01 1 0.0000 0.9996 1.00 0.00 0.00 0.00
#> TCGA.HU.8238.01 4 0.0000 0.9716 0.00 0.00 0.00 1.00
#> TCGA.HU.8249.01 3 0.0000 0.9957 0.00 0.00 1.00 0.00
#> TCGA.R5.A804.01 1 0.0000 0.9996 1.00 0.00 0.00 0.00
#> TCGA.BR.A4CS.01 2 0.0000 0.9468 0.00 1.00 0.00 0.00
#> TCGA.D7.A6ET.01 1 0.0000 0.9996 1.00 0.00 0.00 0.00
#> TCGA.FP.8099.01 3 0.0000 0.9957 0.00 0.00 1.00 0.00
#> TCGA.D7.8579.01 1 0.0000 0.9996 1.00 0.00 0.00 0.00
#> TCGA.BR.8297.01 2 0.1211 0.9052 0.04 0.96 0.00 0.00
#> TCGA.RD.A7C1.01 2 0.0000 0.9468 0.00 1.00 0.00 0.00
#> TCGA.F1.A448.01 1 0.0000 0.9996 1.00 0.00 0.00 0.00
#> TCGA.D7.8575.01 4 0.0000 0.9716 0.00 0.00 0.00 1.00
#> TCGA.VQ.A8P3.01 4 0.0000 0.9716 0.00 0.00 0.00 1.00
#> TCGA.BR.8286.01 4 0.0000 0.9716 0.00 0.00 0.00 1.00
#> TCGA.BR.8369.01 2 0.0000 0.9468 0.00 1.00 0.00 0.00
#> TCGA.FP.A4BF.01 2 0.0000 0.9468 0.00 1.00 0.00 0.00
#> TCGA.R5.A805.01 2 0.0000 0.9468 0.00 1.00 0.00 0.00
#> TCGA.IN.A6RL.01 4 0.0000 0.9716 0.00 0.00 0.00 1.00
#> TCGA.BR.8289.01 4 0.0000 0.9716 0.00 0.00 0.00 1.00
#> TCGA.BR.8296.01 1 0.0000 0.9996 1.00 0.00 0.00 0.00
#> TCGA.CD.A48A.01 3 0.0000 0.9957 0.00 0.00 1.00 0.00
#> TCGA.CD.8534.01 2 0.0000 0.9468 0.00 1.00 0.00 0.00
#> TCGA.BR.7959.01 2 0.0000 0.9468 0.00 1.00 0.00 0.00
#> TCGA.RD.A8MV.01 1 0.0000 0.9996 1.00 0.00 0.00 0.00
#> TCGA.CD.8536.01 2 0.0000 0.9468 0.00 1.00 0.00 0.00
#> TCGA.BR.A44U.01 4 0.0000 0.9716 0.00 0.00 0.00 1.00
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> TCGA.BR.8683.01 2 0.0000 0.95124 0.00 1.00 0.00 0.00 0.00
#> TCGA.CG.5716.01 1 0.0000 0.97083 1.00 0.00 0.00 0.00 0.00
#> TCGA.VQ.AA68.01 4 0.0000 0.94907 0.00 0.00 0.00 1.00 0.00
#> TCGA.CG.4441.01 4 0.0000 0.94907 0.00 0.00 0.00 1.00 0.00
#> TCGA.BR.8384.01 1 0.0000 0.97083 1.00 0.00 0.00 0.00 0.00
#> TCGA.BR.6453.01 1 0.0000 0.97083 1.00 0.00 0.00 0.00 0.00
#> TCGA.VQ.A91S.01 2 0.2516 0.80829 0.00 0.86 0.00 0.14 0.00
#> TCGA.D7.6528.01 3 0.0000 0.98813 0.00 0.00 1.00 0.00 0.00
#> TCGA.VQ.A8E7.01 4 0.0000 0.94907 0.00 0.00 0.00 1.00 0.00
#> TCGA.BR.8680.01 4 0.0000 0.94907 0.00 0.00 0.00 1.00 0.00
#> TCGA.BR.8483.01 3 0.0000 0.98813 0.00 0.00 1.00 0.00 0.00
#> TCGA.BR.6566.01 5 0.0000 0.94829 0.00 0.00 0.00 0.00 1.00
#> TCGA.VQ.A91X.01 3 0.0000 0.98813 0.00 0.00 1.00 0.00 0.00
#> TCGA.VQ.A94U.01 3 0.0000 0.98813 0.00 0.00 1.00 0.00 0.00
#> TCGA.VQ.A91A.01 2 0.0000 0.95124 0.00 1.00 0.00 0.00 0.00
#> TCGA.D7.6518.01 1 0.0000 0.97083 1.00 0.00 0.00 0.00 0.00
#> TCGA.VQ.A91E.01 2 0.0000 0.95124 0.00 1.00 0.00 0.00 0.00
#> TCGA.VQ.A8PY.01 2 0.0000 0.95124 0.00 1.00 0.00 0.00 0.00
#> TCGA.BR.6452.11 1 0.0000 0.97083 1.00 0.00 0.00 0.00 0.00
#> TCGA.BR.8682.01 2 0.0000 0.95124 0.00 1.00 0.00 0.00 0.00
#> TCGA.VQ.A91V.01 3 0.0000 0.98813 0.00 0.00 1.00 0.00 0.00
#> TCGA.VQ.A8PZ.01 5 0.0000 0.94829 0.00 0.00 0.00 0.00 1.00
#> TCGA.BR.6458.01 2 0.0000 0.95124 0.00 1.00 0.00 0.00 0.00
#> TCGA.BR.8592.01 1 0.0000 0.97083 1.00 0.00 0.00 0.00 0.00
#> TCGA.D7.6525.01 2 0.0000 0.95124 0.00 1.00 0.00 0.00 0.00
#> TCGA.BR.8588.01 5 0.2280 0.85221 0.12 0.00 0.00 0.00 0.88
#> TCGA.HU.8610.01 5 0.4060 0.45968 0.36 0.00 0.00 0.00 0.64
#> TCGA.VQ.A8PD.01 1 0.0000 0.97083 1.00 0.00 0.00 0.00 0.00
#> TCGA.D7.6524.01 1 0.0000 0.97083 1.00 0.00 0.00 0.00 0.00
#> TCGA.3M.AB47.01 5 0.0000 0.94829 0.00 0.00 0.00 0.00 1.00
#> TCGA.BR.6457.01 1 0.0000 0.97083 1.00 0.00 0.00 0.00 0.00
#> TCGA.D7.A6EV.01 4 0.0000 0.94907 0.00 0.00 0.00 1.00 0.00
#> TCGA.HU.A4H4.01 5 0.0609 0.93314 0.00 0.02 0.00 0.00 0.98
#> TCGA.BR.A4J5.01 1 0.0000 0.97083 1.00 0.00 0.00 0.00 0.00
#> TCGA.BR.7717.01 4 0.0000 0.94907 0.00 0.00 0.00 1.00 0.00
#> TCGA.BR.A4IU.01 1 0.0000 0.97083 1.00 0.00 0.00 0.00 0.00
#> TCGA.BR.7715.01 3 0.0000 0.98813 0.00 0.00 1.00 0.00 0.00
#> TCGA.HU.A4GJ.01 1 0.0000 0.97083 1.00 0.00 0.00 0.00 0.00
#> TCGA.BR.7196.01 1 0.0000 0.97083 1.00 0.00 0.00 0.00 0.00
#> TCGA.BR.6563.01 1 0.0000 0.97083 1.00 0.00 0.00 0.00 0.00
#> TCGA.IN.A6RJ.01 1 0.4302 0.00804 0.52 0.00 0.00 0.00 0.48
#> TCGA.HU.A4GX.01 2 0.0000 0.95124 0.00 1.00 0.00 0.00 0.00
#> TCGA.HU.A4G8.01 2 0.4302 0.03979 0.00 0.52 0.00 0.48 0.00
#> TCGA.HU.A4GC.01 4 0.0000 0.94907 0.00 0.00 0.00 1.00 0.00
#> TCGA.B7.A5TK.01 1 0.0000 0.97083 1.00 0.00 0.00 0.00 0.00
#> TCGA.D7.A4Z0.01 5 0.0000 0.94829 0.00 0.00 0.00 0.00 1.00
#> TCGA.R5.A7O7.01 5 0.0000 0.94829 0.00 0.00 0.00 0.00 1.00
#> TCGA.BR.A4J2.01 1 0.0000 0.97083 1.00 0.00 0.00 0.00 0.00
#> TCGA.HU.A4GD.01 3 0.0000 0.98813 0.00 0.00 1.00 0.00 0.00
#> TCGA.VQ.AA6B.01 3 0.0000 0.98813 0.00 0.00 1.00 0.00 0.00
#> TCGA.HU.A4HB.01 5 0.2929 0.78691 0.18 0.00 0.00 0.00 0.82
#> TCGA.HU.A4H2.01 4 0.4287 0.10123 0.00 0.46 0.00 0.54 0.00
#> TCGA.BR.6852.01 5 0.0000 0.94829 0.00 0.00 0.00 0.00 1.00
#> TCGA.IN.A7NT.01 5 0.0000 0.94829 0.00 0.00 0.00 0.00 1.00
#> TCGA.CG.5734.01 5 0.0000 0.94829 0.00 0.00 0.00 0.00 1.00
#> TCGA.VQ.A8P8.01 5 0.0000 0.94829 0.00 0.00 0.00 0.00 1.00
#> TCGA.BR.6705.01 1 0.0000 0.97083 1.00 0.00 0.00 0.00 0.00
#> TCGA.MX.A5UG.01 1 0.0000 0.97083 1.00 0.00 0.00 0.00 0.00
#> TCGA.CD.8533.01 3 0.0000 0.98813 0.00 0.00 1.00 0.00 0.00
#> TCGA.BR.7957.01 1 0.0000 0.97083 1.00 0.00 0.00 0.00 0.00
#> TCGA.CG.5722.01 1 0.0000 0.97083 1.00 0.00 0.00 0.00 0.00
#> TCGA.F1.6874.01 2 0.0000 0.95124 0.00 1.00 0.00 0.00 0.00
#> TCGA.CG.5730.01 3 0.0000 0.98813 0.00 0.00 1.00 0.00 0.00
#> TCGA.IP.7968.01 3 0.2732 0.80356 0.00 0.00 0.84 0.16 0.00
#> TCGA.D7.6822.01 4 0.4060 0.40621 0.00 0.00 0.36 0.64 0.00
#> TCGA.D7.A6EY.01 5 0.0000 0.94829 0.00 0.00 0.00 0.00 1.00
#> TCGA.BR.6706.01 1 0.0000 0.97083 1.00 0.00 0.00 0.00 0.00
#> TCGA.IN.7808.01 5 0.0000 0.94829 0.00 0.00 0.00 0.00 1.00
#> TCGA.KB.A93H.01 3 0.0000 0.98813 0.00 0.00 1.00 0.00 0.00
#> TCGA.BR.6802.01 5 0.0000 0.94829 0.00 0.00 0.00 0.00 1.00
#> TCGA.FP.A9TM.01 2 0.0000 0.95124 0.00 1.00 0.00 0.00 0.00
#> TCGA.FP.7998.01 1 0.0000 0.97083 1.00 0.00 0.00 0.00 0.00
#> TCGA.IN.A6RS.01 2 0.0000 0.95124 0.00 1.00 0.00 0.00 0.00
#> TCGA.B7.5816.01 5 0.0000 0.94829 0.00 0.00 0.00 0.00 1.00
#> TCGA.CG.5721.01 5 0.0000 0.94829 0.00 0.00 0.00 0.00 1.00
#> TCGA.RD.A8NB.01 1 0.0000 0.97083 1.00 0.00 0.00 0.00 0.00
#> TCGA.IN.AB1X.01 5 0.0000 0.94829 0.00 0.00 0.00 0.00 1.00
#> TCGA.CG.5728.01 5 0.0000 0.94829 0.00 0.00 0.00 0.00 1.00
#> TCGA.IN.A7NU.01 2 0.4060 0.41482 0.00 0.64 0.00 0.00 0.36
#> TCGA.D7.5578.01 2 0.0000 0.95124 0.00 1.00 0.00 0.00 0.00
#> TCGA.VQ.A8P5.01 2 0.0000 0.95124 0.00 1.00 0.00 0.00 0.00
#> TCGA.CG.5724.01 4 0.0000 0.94907 0.00 0.00 0.00 1.00 0.00
#> TCGA.VQ.A8PB.01 4 0.0000 0.94907 0.00 0.00 0.00 1.00 0.00
#> TCGA.CG.5727.01 2 0.1043 0.91650 0.00 0.96 0.00 0.04 0.00
#> TCGA.VQ.A8PC.01 5 0.2516 0.83382 0.14 0.00 0.00 0.00 0.86
#> TCGA.HU.8243.01 4 0.0000 0.94907 0.00 0.00 0.00 1.00 0.00
#> TCGA.BR.8362.01 2 0.0000 0.95124 0.00 1.00 0.00 0.00 0.00
#> TCGA.IN.8462.01 4 0.0000 0.94907 0.00 0.00 0.00 1.00 0.00
#> TCGA.CD.8524.01 2 0.0000 0.95124 0.00 1.00 0.00 0.00 0.00
#> TCGA.BR.A453.01 1 0.0000 0.97083 1.00 0.00 0.00 0.00 0.00
#> TCGA.BR.8367.01 5 0.0000 0.94829 0.00 0.00 0.00 0.00 1.00
#> TCGA.BR.8380.01 1 0.0000 0.97083 1.00 0.00 0.00 0.00 0.00
#> TCGA.HU.8238.01 4 0.0000 0.94907 0.00 0.00 0.00 1.00 0.00
#> TCGA.HU.8249.01 3 0.0000 0.98813 0.00 0.00 1.00 0.00 0.00
#> TCGA.R5.A804.01 5 0.0000 0.94829 0.00 0.00 0.00 0.00 1.00
#> TCGA.BR.A4CS.01 2 0.0000 0.95124 0.00 1.00 0.00 0.00 0.00
#> TCGA.D7.A6ET.01 1 0.0000 0.97083 1.00 0.00 0.00 0.00 0.00
#> TCGA.FP.8099.01 3 0.0000 0.98813 0.00 0.00 1.00 0.00 0.00
#> TCGA.D7.8579.01 1 0.3109 0.72719 0.80 0.00 0.00 0.00 0.20
#> TCGA.BR.8297.01 5 0.0000 0.94829 0.00 0.00 0.00 0.00 1.00
#> TCGA.RD.A7C1.01 5 0.0000 0.94829 0.00 0.00 0.00 0.00 1.00
#> TCGA.F1.A448.01 5 0.0000 0.94829 0.00 0.00 0.00 0.00 1.00
#> TCGA.D7.8575.01 4 0.0609 0.93227 0.00 0.02 0.00 0.98 0.00
#> TCGA.VQ.A8P3.01 4 0.1043 0.91418 0.00 0.04 0.00 0.96 0.00
#> TCGA.BR.8286.01 4 0.0000 0.94907 0.00 0.00 0.00 1.00 0.00
#> TCGA.BR.8369.01 5 0.1732 0.88086 0.00 0.08 0.00 0.00 0.92
#> TCGA.FP.A4BF.01 2 0.0000 0.95124 0.00 1.00 0.00 0.00 0.00
#> TCGA.R5.A805.01 5 0.3424 0.66991 0.00 0.24 0.00 0.00 0.76
#> TCGA.IN.A6RL.01 4 0.0000 0.94907 0.00 0.00 0.00 1.00 0.00
#> TCGA.BR.8289.01 4 0.0000 0.94907 0.00 0.00 0.00 1.00 0.00
#> TCGA.BR.8296.01 5 0.2929 0.78691 0.18 0.00 0.00 0.00 0.82
#> TCGA.CD.A48A.01 3 0.0000 0.98813 0.00 0.00 1.00 0.00 0.00
#> TCGA.CD.8534.01 2 0.0000 0.95124 0.00 1.00 0.00 0.00 0.00
#> TCGA.BR.7959.01 2 0.0000 0.95124 0.00 1.00 0.00 0.00 0.00
#> TCGA.RD.A8MV.01 5 0.0000 0.94829 0.00 0.00 0.00 0.00 1.00
#> TCGA.CD.8536.01 2 0.0000 0.95124 0.00 1.00 0.00 0.00 0.00
#> TCGA.BR.A44U.01 4 0.0000 0.94907 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.BR.8683.01 6 0.2790 0.8570 0.00 0.14 0.00 0.00 0.02 0.84
#> TCGA.CG.5716.01 1 0.0000 0.9735 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.VQ.AA68.01 4 0.0547 0.8906 0.00 0.00 0.00 0.98 0.00 0.02
#> TCGA.CG.4441.01 4 0.0547 0.8906 0.00 0.00 0.00 0.98 0.00 0.02
#> TCGA.BR.8384.01 1 0.0000 0.9735 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BR.6453.01 1 0.0000 0.9735 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.VQ.A91S.01 6 0.4613 0.5655 0.00 0.08 0.00 0.26 0.00 0.66
#> TCGA.D7.6528.01 3 0.1267 0.9186 0.00 0.06 0.94 0.00 0.00 0.00
#> TCGA.VQ.A8E7.01 4 0.2793 0.7835 0.00 0.20 0.00 0.80 0.00 0.00
#> TCGA.BR.8680.01 4 0.2941 0.7710 0.00 0.22 0.00 0.78 0.00 0.00
#> TCGA.BR.8483.01 3 0.0000 0.9347 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.BR.6566.01 5 0.0547 0.9127 0.00 0.00 0.00 0.00 0.98 0.02
#> TCGA.VQ.A91X.01 3 0.0000 0.9347 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.VQ.A94U.01 3 0.3315 0.8390 0.00 0.20 0.78 0.02 0.00 0.00
#> TCGA.VQ.A91A.01 6 0.0547 0.8591 0.00 0.00 0.00 0.00 0.02 0.98
#> TCGA.D7.6518.01 1 0.0000 0.9735 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.VQ.A91E.01 6 0.4576 0.7215 0.00 0.40 0.00 0.00 0.04 0.56
#> TCGA.VQ.A8PY.01 6 0.4845 0.7055 0.00 0.40 0.00 0.00 0.06 0.54
#> TCGA.BR.6452.11 1 0.0000 0.9735 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BR.8682.01 6 0.2581 0.8602 0.00 0.12 0.00 0.00 0.02 0.86
#> TCGA.VQ.A91V.01 3 0.0000 0.9347 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.VQ.A8PZ.01 5 0.0547 0.9263 0.02 0.00 0.00 0.00 0.98 0.00
#> TCGA.BR.6458.01 6 0.0000 0.8598 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.BR.8592.01 1 0.0000 0.9735 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D7.6525.01 6 0.0547 0.8628 0.00 0.02 0.00 0.00 0.00 0.98
#> TCGA.BR.8588.01 5 0.2454 0.8194 0.16 0.00 0.00 0.00 0.84 0.00
#> TCGA.HU.8610.01 5 0.3706 0.4398 0.38 0.00 0.00 0.00 0.62 0.00
#> TCGA.VQ.A8PD.01 1 0.0000 0.9735 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D7.6524.01 1 0.0000 0.9735 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.3M.AB47.01 5 0.0547 0.9263 0.02 0.00 0.00 0.00 0.98 0.00
#> TCGA.BR.6457.01 1 0.0000 0.9735 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D7.A6EV.01 4 0.0000 0.8849 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.HU.A4H4.01 5 0.0937 0.9023 0.00 0.00 0.00 0.00 0.96 0.04
#> TCGA.BR.A4J5.01 1 0.0000 0.9735 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BR.7717.01 4 0.0547 0.8906 0.00 0.00 0.00 0.98 0.00 0.02
#> TCGA.BR.A4IU.01 1 0.0000 0.9735 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BR.7715.01 3 0.1267 0.9183 0.00 0.06 0.94 0.00 0.00 0.00
#> TCGA.HU.A4GJ.01 1 0.0000 0.9735 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BR.7196.01 1 0.0000 0.9735 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BR.6563.01 1 0.0000 0.9735 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.IN.A6RJ.01 1 0.3851 0.0463 0.54 0.00 0.00 0.00 0.46 0.00
#> TCGA.HU.A4GX.01 6 0.3828 0.7010 0.00 0.44 0.00 0.00 0.00 0.56
#> TCGA.HU.A4G8.01 4 0.5618 0.3923 0.00 0.34 0.00 0.50 0.00 0.16
#> TCGA.HU.A4GC.01 4 0.1556 0.8595 0.00 0.08 0.00 0.92 0.00 0.00
#> TCGA.B7.A5TK.01 1 0.0000 0.9735 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D7.A4Z0.01 5 0.0547 0.9263 0.02 0.00 0.00 0.00 0.98 0.00
#> TCGA.R5.A7O7.01 5 0.0547 0.9263 0.02 0.00 0.00 0.00 0.98 0.00
#> TCGA.BR.A4J2.01 1 0.0000 0.9735 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HU.A4GD.01 3 0.0000 0.9347 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.VQ.AA6B.01 3 0.0000 0.9347 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.HU.A4HB.01 5 0.2631 0.8010 0.18 0.00 0.00 0.00 0.82 0.00
#> TCGA.HU.A4H2.01 4 0.4834 0.5575 0.00 0.10 0.00 0.64 0.00 0.26
#> TCGA.BR.6852.01 5 0.0547 0.9263 0.02 0.00 0.00 0.00 0.98 0.00
#> TCGA.IN.A7NT.01 5 0.2048 0.8430 0.00 0.00 0.00 0.00 0.88 0.12
#> TCGA.CG.5734.01 5 0.0547 0.9263 0.02 0.00 0.00 0.00 0.98 0.00
#> TCGA.VQ.A8P8.01 5 0.0547 0.9263 0.02 0.00 0.00 0.00 0.98 0.00
#> TCGA.BR.6705.01 1 0.0000 0.9735 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.MX.A5UG.01 1 0.0000 0.9735 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CD.8533.01 3 0.3309 0.8030 0.00 0.28 0.72 0.00 0.00 0.00
#> TCGA.BR.7957.01 1 0.0000 0.9735 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CG.5722.01 1 0.0000 0.9735 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.F1.6874.01 6 0.2941 0.8272 0.00 0.22 0.00 0.00 0.00 0.78
#> TCGA.CG.5730.01 3 0.0000 0.9347 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.IP.7968.01 3 0.3985 0.7977 0.00 0.14 0.76 0.10 0.00 0.00
#> TCGA.D7.6822.01 4 0.6376 0.1647 0.00 0.34 0.22 0.42 0.02 0.00
#> TCGA.D7.A6EY.01 5 0.0547 0.9263 0.02 0.00 0.00 0.00 0.98 0.00
#> TCGA.BR.6706.01 1 0.0000 0.9735 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.IN.7808.01 5 0.0547 0.9263 0.02 0.00 0.00 0.00 0.98 0.00
#> TCGA.KB.A93H.01 3 0.0000 0.9347 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.BR.6802.01 5 0.0937 0.9130 0.04 0.00 0.00 0.00 0.96 0.00
#> TCGA.FP.A9TM.01 6 0.2581 0.8606 0.00 0.12 0.00 0.00 0.02 0.86
#> TCGA.FP.7998.01 1 0.0000 0.9735 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.IN.A6RS.01 6 0.2094 0.8623 0.00 0.08 0.00 0.00 0.02 0.90
#> TCGA.B7.5816.01 5 0.0547 0.9263 0.02 0.00 0.00 0.00 0.98 0.00
#> TCGA.CG.5721.01 5 0.0547 0.9263 0.02 0.00 0.00 0.00 0.98 0.00
#> TCGA.RD.A8NB.01 1 0.0000 0.9735 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.IN.AB1X.01 5 0.0547 0.9263 0.02 0.00 0.00 0.00 0.98 0.00
#> TCGA.CG.5728.01 5 0.0547 0.9263 0.02 0.00 0.00 0.00 0.98 0.00
#> TCGA.IN.A7NU.01 6 0.3409 0.5412 0.00 0.00 0.00 0.00 0.30 0.70
#> TCGA.D7.5578.01 6 0.0000 0.8598 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.VQ.A8P5.01 6 0.2794 0.8451 0.00 0.08 0.00 0.06 0.00 0.86
#> TCGA.CG.5724.01 4 0.0547 0.8804 0.00 0.02 0.00 0.98 0.00 0.00
#> TCGA.VQ.A8PB.01 4 0.0547 0.8906 0.00 0.00 0.00 0.98 0.00 0.02
#> TCGA.CG.5727.01 6 0.2631 0.7182 0.00 0.00 0.00 0.18 0.00 0.82
#> TCGA.VQ.A8PC.01 5 0.2454 0.8208 0.16 0.00 0.00 0.00 0.84 0.00
#> TCGA.HU.8243.01 4 0.0547 0.8906 0.00 0.00 0.00 0.98 0.00 0.02
#> TCGA.BR.8362.01 6 0.0547 0.8607 0.00 0.02 0.00 0.00 0.00 0.98
#> TCGA.IN.8462.01 4 0.0547 0.8906 0.00 0.00 0.00 0.98 0.00 0.02
#> TCGA.CD.8524.01 6 0.0547 0.8591 0.00 0.00 0.00 0.00 0.02 0.98
#> TCGA.BR.A453.01 1 0.0000 0.9735 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BR.8367.01 5 0.0547 0.9127 0.00 0.00 0.00 0.00 0.98 0.02
#> TCGA.BR.8380.01 1 0.0547 0.9535 0.98 0.00 0.00 0.00 0.02 0.00
#> TCGA.HU.8238.01 4 0.0547 0.8824 0.00 0.02 0.00 0.98 0.00 0.00
#> TCGA.HU.8249.01 3 0.3797 0.6985 0.00 0.42 0.58 0.00 0.00 0.00
#> TCGA.R5.A804.01 5 0.0547 0.9263 0.02 0.00 0.00 0.00 0.98 0.00
#> TCGA.BR.A4CS.01 6 0.0000 0.8598 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.D7.A6ET.01 1 0.0000 0.9735 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FP.8099.01 3 0.0000 0.9347 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.D7.8579.01 1 0.2048 0.8375 0.88 0.00 0.00 0.00 0.12 0.00
#> TCGA.BR.8297.01 5 0.0547 0.9127 0.00 0.00 0.00 0.00 0.98 0.02
#> TCGA.RD.A7C1.01 5 0.2048 0.8385 0.00 0.00 0.00 0.00 0.88 0.12
#> TCGA.F1.A448.01 5 0.0547 0.9263 0.02 0.00 0.00 0.00 0.98 0.00
#> TCGA.D7.8575.01 4 0.4552 0.6440 0.00 0.30 0.00 0.64 0.00 0.06
#> TCGA.VQ.A8P3.01 4 0.0937 0.8825 0.00 0.00 0.00 0.96 0.00 0.04
#> TCGA.BR.8286.01 4 0.0547 0.8906 0.00 0.00 0.00 0.98 0.00 0.02
#> TCGA.BR.8369.01 5 0.2941 0.7187 0.00 0.00 0.00 0.00 0.78 0.22
#> TCGA.FP.A4BF.01 6 0.0547 0.8591 0.00 0.00 0.00 0.00 0.02 0.98
#> TCGA.R5.A805.01 5 0.4462 0.4829 0.00 0.06 0.00 0.00 0.66 0.28
#> TCGA.IN.A6RL.01 4 0.0547 0.8906 0.00 0.00 0.00 0.98 0.00 0.02
#> TCGA.BR.8289.01 4 0.0547 0.8906 0.00 0.00 0.00 0.98 0.00 0.02
#> TCGA.BR.8296.01 5 0.2631 0.8010 0.18 0.00 0.00 0.00 0.82 0.00
#> TCGA.CD.A48A.01 3 0.0000 0.9347 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.CD.8534.01 6 0.3409 0.7953 0.00 0.30 0.00 0.00 0.00 0.70
#> TCGA.BR.7959.01 6 0.2350 0.8611 0.00 0.10 0.00 0.00 0.02 0.88
#> TCGA.RD.A8MV.01 5 0.0547 0.9263 0.02 0.00 0.00 0.00 0.98 0.00
#> TCGA.CD.8536.01 6 0.2631 0.8359 0.00 0.18 0.00 0.00 0.00 0.82
#> TCGA.BR.A44U.01 4 0.0547 0.8807 0.00 0.02 0.00 0.98 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.BR.8683.01 6 0.3991 6.08e-01 0.00 0.22 0.00 0.00 0.02 0.72 0.04
#> TCGA.CG.5716.01 1 0.2512 8.78e-01 0.86 0.04 0.00 0.00 0.00 0.00 0.10
#> TCGA.VQ.AA68.01 4 0.0504 7.61e-01 0.00 0.00 0.00 0.98 0.00 0.00 0.02
#> TCGA.CG.4441.01 4 0.1363 7.45e-01 0.00 0.04 0.00 0.94 0.00 0.00 0.02
#> TCGA.BR.8384.01 1 0.0000 9.21e-01 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BR.6453.01 1 0.0000 9.21e-01 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.VQ.A91S.01 6 0.5083 5.14e-06 0.00 0.20 0.00 0.24 0.00 0.56 0.00
#> TCGA.D7.6528.01 3 0.2769 7.52e-01 0.00 0.04 0.86 0.02 0.00 0.00 0.08
#> TCGA.VQ.A8E7.01 4 0.3358 5.07e-01 0.00 0.00 0.00 0.64 0.00 0.00 0.36
#> TCGA.BR.8680.01 4 0.3294 5.31e-01 0.00 0.00 0.00 0.66 0.00 0.00 0.34
#> TCGA.BR.8483.01 3 0.0000 8.80e-01 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.BR.6566.01 5 0.0504 8.70e-01 0.00 0.00 0.00 0.00 0.98 0.02 0.00
#> TCGA.VQ.A91X.01 3 0.0000 8.80e-01 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.VQ.A94U.01 3 0.3517 4.51e-01 0.00 0.02 0.70 0.00 0.00 0.00 0.28
#> TCGA.VQ.A91A.01 6 0.3289 6.43e-01 0.00 0.10 0.00 0.00 0.06 0.82 0.02
#> TCGA.D7.6518.01 1 0.0000 9.21e-01 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.VQ.A91E.01 6 0.4214 3.34e-01 0.00 0.40 0.00 0.00 0.04 0.56 0.00
#> TCGA.VQ.A8PY.01 6 0.3985 3.30e-01 0.00 0.46 0.00 0.00 0.02 0.52 0.00
#> TCGA.BR.6452.11 1 0.2512 8.78e-01 0.86 0.04 0.00 0.00 0.00 0.00 0.10
#> TCGA.BR.8682.01 6 0.3863 6.22e-01 0.00 0.20 0.00 0.00 0.02 0.74 0.04
#> TCGA.VQ.A91V.01 3 0.0000 8.80e-01 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.VQ.A8PZ.01 5 0.0000 8.79e-01 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.BR.6458.01 6 0.2803 6.18e-01 0.00 0.10 0.00 0.06 0.00 0.84 0.00
#> TCGA.BR.8592.01 1 0.0000 9.21e-01 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D7.6525.01 6 0.3061 6.21e-01 0.00 0.08 0.00 0.06 0.00 0.84 0.02
#> TCGA.BR.8588.01 5 0.3047 6.02e-01 0.28 0.00 0.00 0.00 0.72 0.00 0.00
#> TCGA.HU.8610.01 5 0.3459 4.04e-01 0.40 0.00 0.00 0.00 0.60 0.00 0.00
#> TCGA.VQ.A8PD.01 1 0.0000 9.21e-01 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D7.6524.01 1 0.0000 9.21e-01 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.3M.AB47.01 5 0.0000 8.79e-01 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.BR.6457.01 1 0.0000 9.21e-01 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D7.A6EV.01 4 0.1166 7.57e-01 0.00 0.00 0.00 0.94 0.00 0.00 0.06
#> TCGA.HU.A4H4.01 5 0.0863 8.56e-01 0.00 0.00 0.00 0.00 0.96 0.04 0.00
#> TCGA.BR.A4J5.01 1 0.0000 9.21e-01 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BR.7717.01 4 0.0000 7.59e-01 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.BR.A4IU.01 1 0.0000 9.21e-01 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BR.7715.01 3 0.0863 8.52e-01 0.00 0.04 0.96 0.00 0.00 0.00 0.00
#> TCGA.HU.A4GJ.01 1 0.2512 8.78e-01 0.86 0.04 0.00 0.00 0.00 0.00 0.10
#> TCGA.BR.7196.01 1 0.2512 8.78e-01 0.86 0.04 0.00 0.00 0.00 0.00 0.10
#> TCGA.BR.6563.01 1 0.0000 9.21e-01 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.IN.A6RJ.01 1 0.3294 4.22e-01 0.66 0.00 0.00 0.00 0.34 0.00 0.00
#> TCGA.HU.A4GX.01 6 0.3968 2.85e-01 0.00 0.44 0.00 0.00 0.02 0.54 0.00
#> TCGA.HU.A4G8.01 2 0.5539 0.00e+00 0.00 0.38 0.00 0.38 0.00 0.24 0.00
#> TCGA.HU.A4GC.01 4 0.2832 6.25e-01 0.00 0.00 0.00 0.76 0.00 0.00 0.24
#> TCGA.B7.A5TK.01 1 0.2512 8.78e-01 0.86 0.04 0.00 0.00 0.00 0.00 0.10
#> TCGA.D7.A4Z0.01 5 0.0000 8.79e-01 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.R5.A7O7.01 5 0.0504 8.69e-01 0.02 0.00 0.00 0.00 0.98 0.00 0.00
#> TCGA.BR.A4J2.01 1 0.1433 8.99e-01 0.92 0.00 0.00 0.00 0.00 0.00 0.08
#> TCGA.HU.A4GD.01 3 0.0000 8.80e-01 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.VQ.AA6B.01 3 0.0000 8.80e-01 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.HU.A4HB.01 5 0.4908 5.36e-01 0.20 0.04 0.00 0.00 0.66 0.00 0.10
#> TCGA.HU.A4H2.01 4 0.4630 -4.67e-02 0.00 0.12 0.00 0.62 0.00 0.26 0.00
#> TCGA.BR.6852.01 5 0.0000 8.79e-01 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.IN.A7NT.01 5 0.3263 7.22e-01 0.00 0.08 0.00 0.00 0.80 0.12 0.00
#> TCGA.CG.5734.01 5 0.0000 8.79e-01 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.VQ.A8P8.01 5 0.0000 8.79e-01 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.BR.6705.01 1 0.0000 9.21e-01 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.MX.A5UG.01 1 0.0000 9.21e-01 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CD.8533.01 3 0.4127 2.95e-02 0.00 0.04 0.60 0.00 0.00 0.00 0.36
#> TCGA.BR.7957.01 1 0.0000 9.21e-01 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CG.5722.01 1 0.2512 8.78e-01 0.86 0.04 0.00 0.00 0.00 0.00 0.10
#> TCGA.F1.6874.01 6 0.3530 6.01e-01 0.00 0.20 0.00 0.02 0.02 0.76 0.00
#> TCGA.CG.5730.01 3 0.0000 8.80e-01 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.IP.7968.01 3 0.3879 6.26e-01 0.00 0.04 0.78 0.08 0.00 0.00 0.10
#> TCGA.D7.6822.01 4 0.5978 1.09e-01 0.00 0.08 0.10 0.42 0.00 0.00 0.40
#> TCGA.D7.A6EY.01 5 0.0000 8.79e-01 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.BR.6706.01 1 0.2512 8.78e-01 0.86 0.04 0.00 0.00 0.00 0.00 0.10
#> TCGA.IN.7808.01 5 0.0504 8.69e-01 0.02 0.00 0.00 0.00 0.98 0.00 0.00
#> TCGA.KB.A93H.01 3 0.0000 8.80e-01 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.BR.6802.01 5 0.0504 8.69e-01 0.02 0.00 0.00 0.00 0.98 0.00 0.00
#> TCGA.FP.A9TM.01 6 0.3734 6.45e-01 0.00 0.14 0.00 0.00 0.04 0.78 0.04
#> TCGA.FP.7998.01 1 0.2512 8.78e-01 0.86 0.04 0.00 0.00 0.00 0.00 0.10
#> TCGA.IN.A6RS.01 6 0.3404 6.62e-01 0.00 0.08 0.00 0.00 0.04 0.82 0.06
#> TCGA.B7.5816.01 5 0.0000 8.79e-01 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.CG.5721.01 5 0.0000 8.79e-01 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.RD.A8NB.01 1 0.0000 9.21e-01 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.IN.AB1X.01 5 0.0000 8.79e-01 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.CG.5728.01 5 0.0000 8.79e-01 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.IN.A7NU.01 6 0.5635 2.65e-01 0.00 0.12 0.00 0.00 0.34 0.50 0.04
#> TCGA.D7.5578.01 6 0.3055 6.33e-01 0.00 0.14 0.00 0.02 0.02 0.82 0.00
#> TCGA.VQ.A8P5.01 6 0.4181 5.27e-01 0.00 0.06 0.00 0.16 0.00 0.74 0.04
#> TCGA.CG.5724.01 4 0.1671 7.44e-01 0.00 0.00 0.00 0.90 0.00 0.00 0.10
#> TCGA.VQ.A8PB.01 4 0.0504 7.61e-01 0.00 0.00 0.00 0.98 0.00 0.00 0.02
#> TCGA.CG.5727.01 6 0.5065 5.15e-02 0.00 0.10 0.00 0.30 0.00 0.58 0.02
#> TCGA.VQ.A8PC.01 5 0.3047 6.02e-01 0.28 0.00 0.00 0.00 0.72 0.00 0.00
#> TCGA.HU.8243.01 4 0.1928 7.17e-01 0.00 0.08 0.00 0.90 0.00 0.00 0.02
#> TCGA.BR.8362.01 6 0.2016 6.34e-01 0.00 0.04 0.00 0.06 0.00 0.90 0.00
#> TCGA.IN.8462.01 4 0.0000 7.59e-01 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.CD.8524.01 6 0.2722 6.41e-01 0.00 0.12 0.00 0.00 0.04 0.84 0.00
#> TCGA.BR.A453.01 1 0.0000 9.21e-01 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BR.8367.01 5 0.1006 8.60e-01 0.00 0.02 0.00 0.00 0.96 0.00 0.02
#> TCGA.BR.8380.01 1 0.0504 9.06e-01 0.98 0.00 0.00 0.00 0.02 0.00 0.00
#> TCGA.HU.8238.01 4 0.0504 7.61e-01 0.00 0.00 0.00 0.98 0.00 0.00 0.02
#> TCGA.HU.8249.01 7 0.5341 0.00e+00 0.00 0.24 0.26 0.00 0.00 0.00 0.50
#> TCGA.R5.A804.01 5 0.0000 8.79e-01 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.BR.A4CS.01 6 0.2016 6.34e-01 0.00 0.04 0.00 0.06 0.00 0.90 0.00
#> TCGA.D7.A6ET.01 1 0.2512 8.78e-01 0.86 0.04 0.00 0.00 0.00 0.00 0.10
#> TCGA.FP.8099.01 3 0.0000 8.80e-01 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.D7.8579.01 1 0.2259 7.38e-01 0.84 0.00 0.00 0.00 0.16 0.00 0.00
#> TCGA.BR.8297.01 5 0.1860 8.33e-01 0.00 0.02 0.00 0.00 0.92 0.04 0.02
#> TCGA.RD.A7C1.01 5 0.1671 8.05e-01 0.00 0.00 0.00 0.00 0.90 0.10 0.00
#> TCGA.F1.A448.01 5 0.0000 8.79e-01 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.D7.8575.01 4 0.5709 -7.33e-01 0.00 0.34 0.00 0.46 0.00 0.18 0.02
#> TCGA.VQ.A8P3.01 4 0.1363 7.27e-01 0.00 0.02 0.00 0.94 0.00 0.04 0.00
#> TCGA.BR.8286.01 4 0.0863 7.59e-01 0.00 0.00 0.00 0.96 0.00 0.00 0.04
#> TCGA.BR.8369.01 5 0.3795 5.95e-01 0.00 0.06 0.00 0.00 0.72 0.22 0.00
#> TCGA.FP.A4BF.01 6 0.1718 6.64e-01 0.00 0.04 0.00 0.00 0.04 0.92 0.00
#> TCGA.R5.A805.01 5 0.4589 5.30e-01 0.00 0.06 0.00 0.00 0.68 0.22 0.04
#> TCGA.IN.A6RL.01 4 0.1363 7.33e-01 0.00 0.04 0.00 0.94 0.00 0.02 0.00
#> TCGA.BR.8289.01 4 0.0863 7.47e-01 0.00 0.04 0.00 0.96 0.00 0.00 0.00
#> TCGA.BR.8296.01 5 0.4908 5.36e-01 0.20 0.04 0.00 0.00 0.66 0.00 0.10
#> TCGA.CD.A48A.01 3 0.0000 8.80e-01 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.CD.8534.01 6 0.4107 5.79e-01 0.00 0.24 0.00 0.02 0.00 0.70 0.04
#> TCGA.BR.7959.01 6 0.3396 6.59e-01 0.00 0.14 0.00 0.00 0.02 0.80 0.04
#> TCGA.RD.A8MV.01 5 0.0504 8.69e-01 0.02 0.00 0.00 0.00 0.98 0.00 0.00
#> TCGA.CD.8536.01 6 0.3530 6.21e-01 0.00 0.20 0.00 0.02 0.02 0.76 0.00
#> TCGA.BR.A44U.01 4 0.2259 7.02e-01 0.00 0.00 0.00 0.84 0.00 0.00 0.16
cbind(get_classes(res, k = 8), get_membership(res, k = 8))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7 p8
#> TCGA.BR.8683.01 6 0.2981 0.7074 0.00 0.00 0.22 0.00 0.02 0.76 0.00 0.00
#> TCGA.CG.5716.01 1 0.2852 0.7773 0.72 0.00 0.28 0.00 0.00 0.00 0.00 0.00
#> TCGA.VQ.AA68.01 4 0.0808 0.7003 0.00 0.00 0.00 0.96 0.00 0.00 0.00 0.04
#> TCGA.CG.4441.01 4 0.3002 0.6421 0.00 0.00 0.02 0.82 0.00 0.00 0.04 0.12
#> TCGA.BR.8384.01 1 0.0000 0.8715 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BR.6453.01 1 0.0000 0.8715 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.VQ.A91S.01 6 0.6202 0.2849 0.00 0.00 0.10 0.32 0.00 0.46 0.06 0.06
#> TCGA.D7.6528.01 2 0.2719 0.6572 0.00 0.80 0.00 0.02 0.00 0.00 0.00 0.18
#> TCGA.VQ.A8E7.01 4 0.3862 0.2353 0.00 0.00 0.00 0.60 0.00 0.00 0.04 0.36
#> TCGA.BR.8680.01 4 0.4480 0.2103 0.00 0.00 0.00 0.58 0.00 0.00 0.12 0.30
#> TCGA.BR.8483.01 2 0.0000 0.8406 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BR.6566.01 5 0.1741 0.8371 0.00 0.00 0.00 0.00 0.92 0.04 0.02 0.02
#> TCGA.VQ.A91X.01 2 0.0000 0.8406 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.VQ.A94U.01 2 0.4059 0.3904 0.00 0.64 0.00 0.00 0.00 0.00 0.08 0.28
#> TCGA.VQ.A91A.01 6 0.2724 0.6786 0.00 0.00 0.02 0.00 0.08 0.86 0.02 0.02
#> TCGA.D7.6518.01 1 0.0000 0.8715 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.VQ.A91E.01 6 0.4770 0.5237 0.00 0.00 0.40 0.00 0.02 0.52 0.02 0.04
#> TCGA.VQ.A8PY.01 6 0.4383 0.5221 0.00 0.00 0.42 0.00 0.00 0.52 0.02 0.04
#> TCGA.BR.6452.11 1 0.2852 0.7773 0.72 0.00 0.28 0.00 0.00 0.00 0.00 0.00
#> TCGA.BR.8682.01 6 0.3095 0.6995 0.00 0.00 0.24 0.00 0.02 0.74 0.00 0.00
#> TCGA.VQ.A91V.01 2 0.0000 0.8406 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.VQ.A8PZ.01 5 0.0471 0.8693 0.00 0.00 0.02 0.00 0.98 0.00 0.00 0.00
#> TCGA.BR.6458.01 6 0.2071 0.7192 0.00 0.00 0.00 0.04 0.00 0.90 0.04 0.02
#> TCGA.BR.8592.01 1 0.0000 0.8715 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D7.6525.01 6 0.3554 0.6810 0.00 0.00 0.08 0.02 0.00 0.80 0.08 0.02
#> TCGA.BR.8588.01 5 0.2267 0.7201 0.18 0.00 0.00 0.00 0.82 0.00 0.00 0.00
#> TCGA.HU.8610.01 5 0.3943 0.2614 0.40 0.00 0.04 0.00 0.56 0.00 0.00 0.00
#> TCGA.VQ.A8PD.01 1 0.0471 0.8680 0.98 0.00 0.02 0.00 0.00 0.00 0.00 0.00
#> TCGA.D7.6524.01 1 0.0000 0.8715 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.3M.AB47.01 5 0.0000 0.8687 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.BR.6457.01 1 0.0000 0.8715 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D7.A6EV.01 4 0.1341 0.6826 0.00 0.00 0.00 0.92 0.00 0.00 0.00 0.08
#> TCGA.HU.A4H4.01 5 0.2025 0.8051 0.00 0.00 0.00 0.00 0.88 0.10 0.00 0.02
#> TCGA.BR.A4J5.01 1 0.0000 0.8715 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BR.7717.01 4 0.0471 0.6996 0.00 0.00 0.00 0.98 0.00 0.00 0.00 0.02
#> TCGA.BR.A4IU.01 1 0.0808 0.8635 0.96 0.00 0.04 0.00 0.00 0.00 0.00 0.00
#> TCGA.BR.7715.01 2 0.1563 0.7665 0.00 0.90 0.00 0.00 0.00 0.00 0.00 0.10
#> TCGA.HU.A4GJ.01 1 0.2852 0.7773 0.72 0.00 0.28 0.00 0.00 0.00 0.00 0.00
#> TCGA.BR.7196.01 1 0.2852 0.7773 0.72 0.00 0.28 0.00 0.00 0.00 0.00 0.00
#> TCGA.BR.6563.01 1 0.0000 0.8715 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.IN.A6RJ.01 1 0.2756 0.5605 0.74 0.00 0.00 0.00 0.26 0.00 0.00 0.00
#> TCGA.HU.A4GX.01 6 0.5448 0.5036 0.00 0.00 0.40 0.02 0.04 0.48 0.02 0.04
#> TCGA.HU.A4G8.01 4 0.6632 -0.0739 0.00 0.00 0.30 0.34 0.00 0.24 0.02 0.10
#> TCGA.HU.A4GC.01 4 0.3095 0.5126 0.00 0.00 0.00 0.74 0.00 0.00 0.02 0.24
#> TCGA.B7.A5TK.01 1 0.2852 0.7773 0.72 0.00 0.28 0.00 0.00 0.00 0.00 0.00
#> TCGA.D7.A4Z0.01 5 0.0000 0.8687 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.R5.A7O7.01 5 0.0471 0.8654 0.02 0.00 0.00 0.00 0.98 0.00 0.00 0.00
#> TCGA.BR.A4J2.01 1 0.2114 0.8265 0.84 0.00 0.16 0.00 0.00 0.00 0.00 0.00
#> TCGA.HU.A4GD.01 2 0.0471 0.8284 0.00 0.98 0.00 0.00 0.00 0.00 0.02 0.00
#> TCGA.VQ.AA6B.01 2 0.0000 0.8406 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HU.A4HB.01 5 0.3880 0.5725 0.08 0.00 0.24 0.00 0.68 0.00 0.00 0.00
#> TCGA.HU.A4H2.01 4 0.5880 0.2069 0.00 0.00 0.06 0.54 0.00 0.26 0.06 0.08
#> TCGA.BR.6852.01 5 0.0471 0.8693 0.00 0.00 0.02 0.00 0.98 0.00 0.00 0.00
#> TCGA.IN.A7NT.01 5 0.4734 0.6325 0.00 0.00 0.04 0.00 0.70 0.14 0.08 0.04
#> TCGA.CG.5734.01 5 0.0471 0.8693 0.00 0.00 0.02 0.00 0.98 0.00 0.00 0.00
#> TCGA.VQ.A8P8.01 5 0.0471 0.8693 0.00 0.00 0.02 0.00 0.98 0.00 0.00 0.00
#> TCGA.BR.6705.01 1 0.0000 0.8715 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.MX.A5UG.01 1 0.0000 0.8715 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CD.8533.01 2 0.4559 0.0979 0.00 0.60 0.02 0.00 0.00 0.00 0.30 0.08
#> TCGA.BR.7957.01 1 0.0000 0.8715 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CG.5722.01 1 0.2852 0.7773 0.72 0.00 0.28 0.00 0.00 0.00 0.00 0.00
#> TCGA.F1.6874.01 6 0.3483 0.7068 0.00 0.00 0.18 0.04 0.00 0.76 0.02 0.00
#> TCGA.CG.5730.01 2 0.0000 0.8406 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.IP.7968.01 2 0.5306 0.2825 0.00 0.58 0.02 0.10 0.00 0.00 0.04 0.26
#> TCGA.D7.6822.01 8 0.4492 0.0000 0.00 0.02 0.04 0.18 0.00 0.00 0.06 0.70
#> TCGA.D7.A6EY.01 5 0.0000 0.8687 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.BR.6706.01 1 0.2852 0.7773 0.72 0.00 0.28 0.00 0.00 0.00 0.00 0.00
#> TCGA.IN.7808.01 5 0.0000 0.8687 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.KB.A93H.01 2 0.0000 0.8406 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BR.6802.01 5 0.0471 0.8654 0.02 0.00 0.00 0.00 0.98 0.00 0.00 0.00
#> TCGA.FP.A9TM.01 6 0.3078 0.7086 0.00 0.00 0.10 0.00 0.06 0.82 0.00 0.02
#> TCGA.FP.7998.01 1 0.2852 0.7773 0.72 0.00 0.28 0.00 0.00 0.00 0.00 0.00
#> TCGA.IN.A6RS.01 6 0.2807 0.7139 0.00 0.00 0.10 0.00 0.04 0.84 0.00 0.02
#> TCGA.B7.5816.01 5 0.0471 0.8693 0.00 0.00 0.02 0.00 0.98 0.00 0.00 0.00
#> TCGA.CG.5721.01 5 0.0471 0.8693 0.00 0.00 0.02 0.00 0.98 0.00 0.00 0.00
#> TCGA.RD.A8NB.01 1 0.0000 0.8715 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.IN.AB1X.01 5 0.0941 0.8637 0.00 0.00 0.02 0.00 0.96 0.00 0.02 0.00
#> TCGA.CG.5728.01 5 0.0471 0.8693 0.00 0.00 0.02 0.00 0.98 0.00 0.00 0.00
#> TCGA.IN.A7NU.01 6 0.4702 0.2987 0.00 0.00 0.04 0.00 0.36 0.56 0.02 0.02
#> TCGA.D7.5578.01 6 0.2674 0.7093 0.00 0.00 0.04 0.04 0.00 0.86 0.06 0.00
#> TCGA.VQ.A8P5.01 6 0.4073 0.5849 0.00 0.00 0.10 0.24 0.00 0.66 0.00 0.00
#> TCGA.CG.5724.01 4 0.2856 0.5942 0.00 0.00 0.02 0.78 0.00 0.00 0.00 0.20
#> TCGA.VQ.A8PB.01 4 0.0471 0.7005 0.00 0.00 0.00 0.98 0.00 0.00 0.00 0.02
#> TCGA.CG.5727.01 6 0.5040 0.4654 0.00 0.00 0.04 0.24 0.00 0.62 0.02 0.08
#> TCGA.VQ.A8PC.01 5 0.2224 0.7692 0.12 0.00 0.02 0.00 0.86 0.00 0.00 0.00
#> TCGA.HU.8243.01 4 0.3128 0.6351 0.00 0.00 0.04 0.82 0.00 0.00 0.04 0.10
#> TCGA.BR.8362.01 6 0.3402 0.7210 0.00 0.00 0.06 0.06 0.00 0.82 0.04 0.02
#> TCGA.IN.8462.01 4 0.0000 0.6997 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.CD.8524.01 6 0.2204 0.7047 0.00 0.00 0.02 0.00 0.04 0.90 0.02 0.02
#> TCGA.BR.A453.01 1 0.0000 0.8715 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BR.8367.01 5 0.2020 0.8225 0.00 0.00 0.02 0.00 0.90 0.06 0.00 0.02
#> TCGA.BR.8380.01 1 0.0000 0.8715 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HU.8238.01 4 0.1341 0.6810 0.00 0.00 0.00 0.92 0.00 0.00 0.00 0.08
#> TCGA.HU.8249.01 7 0.2981 0.0000 0.00 0.22 0.00 0.00 0.00 0.00 0.76 0.02
#> TCGA.R5.A804.01 5 0.0471 0.8693 0.00 0.00 0.02 0.00 0.98 0.00 0.00 0.00
#> TCGA.BR.A4CS.01 6 0.3048 0.7011 0.00 0.00 0.04 0.08 0.00 0.84 0.02 0.02
#> TCGA.D7.A6ET.01 1 0.2852 0.7773 0.72 0.00 0.28 0.00 0.00 0.00 0.00 0.00
#> TCGA.FP.8099.01 2 0.0000 0.8406 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D7.8579.01 1 0.1947 0.7242 0.86 0.00 0.00 0.00 0.14 0.00 0.00 0.00
#> TCGA.BR.8297.01 5 0.2265 0.8089 0.00 0.00 0.02 0.00 0.88 0.08 0.00 0.02
#> TCGA.RD.A7C1.01 5 0.2856 0.7182 0.00 0.00 0.00 0.00 0.78 0.20 0.00 0.02
#> TCGA.F1.A448.01 5 0.0000 0.8687 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.D7.8575.01 4 0.5740 0.1838 0.00 0.00 0.26 0.54 0.00 0.10 0.02 0.08
#> TCGA.VQ.A8P3.01 4 0.1557 0.6766 0.00 0.00 0.02 0.92 0.00 0.06 0.00 0.00
#> TCGA.BR.8286.01 4 0.0471 0.6994 0.00 0.00 0.00 0.98 0.00 0.00 0.00 0.02
#> TCGA.BR.8369.01 5 0.3748 0.6754 0.00 0.00 0.02 0.00 0.74 0.20 0.02 0.02
#> TCGA.FP.A4BF.01 6 0.1741 0.7215 0.00 0.00 0.00 0.00 0.02 0.92 0.04 0.02
#> TCGA.R5.A805.01 5 0.4593 0.4756 0.00 0.00 0.10 0.00 0.62 0.26 0.00 0.02
#> TCGA.IN.A6RL.01 4 0.2624 0.6632 0.00 0.00 0.02 0.86 0.00 0.00 0.06 0.06
#> TCGA.BR.8289.01 4 0.2914 0.6508 0.00 0.00 0.04 0.84 0.00 0.00 0.04 0.08
#> TCGA.BR.8296.01 5 0.4165 0.5136 0.10 0.00 0.26 0.00 0.64 0.00 0.00 0.00
#> TCGA.CD.A48A.01 2 0.0471 0.8302 0.00 0.98 0.02 0.00 0.00 0.00 0.00 0.00
#> TCGA.CD.8534.01 6 0.4622 0.6546 0.00 0.00 0.26 0.06 0.00 0.64 0.02 0.02
#> TCGA.BR.7959.01 6 0.3021 0.7072 0.00 0.00 0.16 0.00 0.02 0.80 0.00 0.02
#> TCGA.RD.A8MV.01 5 0.0471 0.8654 0.02 0.00 0.00 0.00 0.98 0.00 0.00 0.00
#> TCGA.CD.8536.01 6 0.4034 0.7101 0.00 0.00 0.12 0.04 0.00 0.76 0.06 0.02
#> TCGA.BR.A44U.01 4 0.2938 0.4542 0.00 0.00 0.00 0.70 0.00 0.00 0.00 0.30
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
consensus_heatmap(res, k = 7)
consensus_heatmap(res, k = 8)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
membership_heatmap(res, k = 7)
membership_heatmap(res, k = 8)
As soon as the classes for columns are determined, the signatures that are significantly different between subgroups can be looked for. Following are the heatmaps for signatures.
get_signatures(res, k = 2)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
get_signatures(res, k = 7)
get_signatures(res, k = 8)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. To get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows (which is done by automatically selecting number of clusters).If there are too many signatures, top_signatures = ... can be set to only show the
signatures with the highest FDRs:
# code only for demonstration
# e.g. to show the top 500 most significant rows
tb = get_signature(res, k = ..., top_signatures = 500)
If the signatures are defined as these which are uniquely high in current group, diff_method argument
can be set to "uniquely_high_in_one_group":
# code only for demonstration
tb = get_signature(res, k = ..., diff_method = "uniquely_high_in_one_group")
UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
dimension_reduction(res, k = 7, method = "UMAP")
dimension_reduction(res, k = 8, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
If matrix rows can be associated to genes, consider to use functional_enrichment(res,
...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.
Parent node: Node03. Child nodes: Node0111 , Node0112 , Node0113 , Node0114-leaf , Node0121 , Node0122 , Node0123 , Node0131 , Node0132-leaf , Node0211-leaf , Node0212-leaf , Node0221-leaf , Node0222 , Node0231-leaf , Node0232-leaf , Node0233-leaf , Node0311 , Node0312-leaf , Node0313-leaf , Node0314-leaf , Node0331-leaf , Node0332-leaf , Node0333-leaf , Node0341 , Node0342-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 50 columns.
#> Top rows (1000) are extracted by 'ATC' method.
#> Subgroups are detected by 'skmeans' method.
#> Performed in total 350 partitions by row resampling.
#> Best k for subgroups seems to be 4.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_partitions"
#> [7] "compare_signatures" "consensus_heatmap" "dimension_reduction"
#> [10] "functional_enrichment" "get_anno_col" "get_anno"
#> [13] "get_classes" "get_consensus" "get_matrix"
#> [16] "get_membership" "get_param" "get_signatures"
#> [19] "get_stats" "is_best_k" "is_stable_k"
#> [22] "membership_heatmap" "ncol" "nrow"
#> [25] "plot_ecdf" "predict_classes" "rownames"
#> [28] "select_partition_number" "show" "suggest_best_k"
#> [31] "test_to_known_factors" "top_rows_heatmap"
collect_plots() function collects all the plots made from res for all k (number of subgroups)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
The plots are:
k and the heatmap of
predicted classes for each k.k.k.k.All the plots in panels can be made by individual functions and they are plotted later in this section.
select_partition_number() produces several plots showing different
statistics for choosing “optimized” k. There are following statistics:
k;k, the area increased is defined as \(A_k - A_{k-1}\).The detailed explanations of these statistics can be found in the cola vignette.
Generally speaking, higher 1-PAC score, higher mean silhouette score or higher
concordance corresponds to better partition. Rand index and Jaccard index
measure how similar the current partition is compared to partition with k-1.
If they are too similar, we won't accept k is better than k-1.
select_partition_number(res)
The numeric values for all these statistics can be obtained by get_stats().
get_stats(res)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> 2 2 1.000 0.991 0.994 0.4589 0.542 0.542
#> 3 3 1.000 0.983 0.992 0.4031 0.695 0.493
#> 4 4 1.000 1.000 1.000 0.0869 0.887 0.707
#> 5 5 0.924 0.927 0.961 0.0340 0.992 0.973
#> 6 6 0.761 0.816 0.876 0.0602 1.000 1.000
#> 7 7 0.758 0.546 0.812 0.0363 0.936 0.782
#> 8 8 0.747 0.511 0.795 0.0292 0.966 0.860
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.CG.5716.01 2 0.000 0.995 0.00 1.00
#> TCGA.BR.8384.01 1 0.000 0.994 1.00 0.00
#> TCGA.BR.6453.01 1 0.000 0.994 1.00 0.00
#> TCGA.D7.6518.01 1 0.000 0.994 1.00 0.00
#> TCGA.BR.6452.11 2 0.000 0.995 0.00 1.00
#> TCGA.VQ.A8PZ.01 2 0.000 0.995 0.00 1.00
#> TCGA.BR.8592.01 1 0.141 0.985 0.98 0.02
#> TCGA.BR.8588.01 1 0.141 0.985 0.98 0.02
#> TCGA.HU.8610.01 1 0.000 0.994 1.00 0.00
#> TCGA.VQ.A8PD.01 1 0.000 0.994 1.00 0.00
#> TCGA.D7.6524.01 2 0.327 0.943 0.06 0.94
#> TCGA.3M.AB47.01 1 0.000 0.994 1.00 0.00
#> TCGA.BR.6457.01 1 0.000 0.994 1.00 0.00
#> TCGA.BR.A4J5.01 1 0.000 0.994 1.00 0.00
#> TCGA.BR.A4IU.01 1 0.141 0.985 0.98 0.02
#> TCGA.HU.A4GJ.01 2 0.000 0.995 0.00 1.00
#> TCGA.BR.7196.01 2 0.000 0.995 0.00 1.00
#> TCGA.BR.6563.01 1 0.000 0.994 1.00 0.00
#> TCGA.IN.A6RJ.01 1 0.000 0.994 1.00 0.00
#> TCGA.B7.A5TK.01 2 0.000 0.995 0.00 1.00
#> TCGA.D7.A4Z0.01 1 0.141 0.985 0.98 0.02
#> TCGA.R5.A7O7.01 1 0.000 0.994 1.00 0.00
#> TCGA.BR.A4J2.01 1 0.000 0.994 1.00 0.00
#> TCGA.HU.A4HB.01 1 0.000 0.994 1.00 0.00
#> TCGA.BR.6852.01 2 0.000 0.995 0.00 1.00
#> TCGA.CG.5734.01 1 0.000 0.994 1.00 0.00
#> TCGA.VQ.A8P8.01 2 0.000 0.995 0.00 1.00
#> TCGA.BR.6705.01 1 0.141 0.985 0.98 0.02
#> TCGA.MX.A5UG.01 1 0.000 0.994 1.00 0.00
#> TCGA.BR.7957.01 1 0.141 0.985 0.98 0.02
#> TCGA.CG.5722.01 2 0.000 0.995 0.00 1.00
#> TCGA.D7.A6EY.01 1 0.141 0.985 0.98 0.02
#> TCGA.BR.6706.01 2 0.000 0.995 0.00 1.00
#> TCGA.IN.7808.01 1 0.000 0.994 1.00 0.00
#> TCGA.BR.6802.01 1 0.000 0.994 1.00 0.00
#> TCGA.FP.7998.01 2 0.000 0.995 0.00 1.00
#> TCGA.B7.5816.01 2 0.000 0.995 0.00 1.00
#> TCGA.CG.5721.01 1 0.000 0.994 1.00 0.00
#> TCGA.RD.A8NB.01 1 0.141 0.985 0.98 0.02
#> TCGA.IN.AB1X.01 2 0.000 0.995 0.00 1.00
#> TCGA.CG.5728.01 1 0.141 0.985 0.98 0.02
#> TCGA.VQ.A8PC.01 1 0.000 0.994 1.00 0.00
#> TCGA.BR.A453.01 1 0.000 0.994 1.00 0.00
#> TCGA.BR.8380.01 1 0.000 0.994 1.00 0.00
#> TCGA.R5.A804.01 2 0.141 0.978 0.02 0.98
#> TCGA.D7.A6ET.01 2 0.000 0.995 0.00 1.00
#> TCGA.D7.8579.01 1 0.141 0.985 0.98 0.02
#> TCGA.F1.A448.01 1 0.000 0.994 1.00 0.00
#> TCGA.BR.8296.01 2 0.000 0.995 0.00 1.00
#> TCGA.RD.A8MV.01 1 0.000 0.994 1.00 0.00
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.CG.5716.01 2 0.000 0.973 0.00 1.00 0.00
#> TCGA.BR.8384.01 1 0.000 0.993 1.00 0.00 0.00
#> TCGA.BR.6453.01 1 0.000 0.993 1.00 0.00 0.00
#> TCGA.D7.6518.01 1 0.000 0.993 1.00 0.00 0.00
#> TCGA.BR.6452.11 2 0.254 0.919 0.00 0.92 0.08
#> TCGA.VQ.A8PZ.01 3 0.000 1.000 0.00 0.00 1.00
#> TCGA.BR.8592.01 3 0.000 1.000 0.00 0.00 1.00
#> TCGA.BR.8588.01 3 0.000 1.000 0.00 0.00 1.00
#> TCGA.HU.8610.01 1 0.000 0.993 1.00 0.00 0.00
#> TCGA.VQ.A8PD.01 1 0.000 0.993 1.00 0.00 0.00
#> TCGA.D7.6524.01 1 0.400 0.805 0.84 0.16 0.00
#> TCGA.3M.AB47.01 1 0.000 0.993 1.00 0.00 0.00
#> TCGA.BR.6457.01 1 0.000 0.993 1.00 0.00 0.00
#> TCGA.BR.A4J5.01 1 0.000 0.993 1.00 0.00 0.00
#> TCGA.BR.A4IU.01 3 0.000 1.000 0.00 0.00 1.00
#> TCGA.HU.A4GJ.01 2 0.254 0.919 0.00 0.92 0.08
#> TCGA.BR.7196.01 2 0.000 0.973 0.00 1.00 0.00
#> TCGA.BR.6563.01 1 0.000 0.993 1.00 0.00 0.00
#> TCGA.IN.A6RJ.01 1 0.000 0.993 1.00 0.00 0.00
#> TCGA.B7.A5TK.01 2 0.000 0.973 0.00 1.00 0.00
#> TCGA.D7.A4Z0.01 3 0.000 1.000 0.00 0.00 1.00
#> TCGA.R5.A7O7.01 1 0.000 0.993 1.00 0.00 0.00
#> TCGA.BR.A4J2.01 1 0.000 0.993 1.00 0.00 0.00
#> TCGA.HU.A4HB.01 1 0.000 0.993 1.00 0.00 0.00
#> TCGA.BR.6852.01 3 0.000 1.000 0.00 0.00 1.00
#> TCGA.CG.5734.01 1 0.000 0.993 1.00 0.00 0.00
#> TCGA.VQ.A8P8.01 3 0.000 1.000 0.00 0.00 1.00
#> TCGA.BR.6705.01 3 0.000 1.000 0.00 0.00 1.00
#> TCGA.MX.A5UG.01 1 0.000 0.993 1.00 0.00 0.00
#> TCGA.BR.7957.01 3 0.000 1.000 0.00 0.00 1.00
#> TCGA.CG.5722.01 2 0.000 0.973 0.00 1.00 0.00
#> TCGA.D7.A6EY.01 3 0.000 1.000 0.00 0.00 1.00
#> TCGA.BR.6706.01 2 0.000 0.973 0.00 1.00 0.00
#> TCGA.IN.7808.01 1 0.000 0.993 1.00 0.00 0.00
#> TCGA.BR.6802.01 1 0.000 0.993 1.00 0.00 0.00
#> TCGA.FP.7998.01 2 0.000 0.973 0.00 1.00 0.00
#> TCGA.B7.5816.01 3 0.000 1.000 0.00 0.00 1.00
#> TCGA.CG.5721.01 1 0.000 0.993 1.00 0.00 0.00
#> TCGA.RD.A8NB.01 3 0.000 1.000 0.00 0.00 1.00
#> TCGA.IN.AB1X.01 3 0.000 1.000 0.00 0.00 1.00
#> TCGA.CG.5728.01 3 0.000 1.000 0.00 0.00 1.00
#> TCGA.VQ.A8PC.01 1 0.000 0.993 1.00 0.00 0.00
#> TCGA.BR.A453.01 1 0.000 0.993 1.00 0.00 0.00
#> TCGA.BR.8380.01 1 0.000 0.993 1.00 0.00 0.00
#> TCGA.R5.A804.01 2 0.296 0.882 0.10 0.90 0.00
#> TCGA.D7.A6ET.01 2 0.000 0.973 0.00 1.00 0.00
#> TCGA.D7.8579.01 3 0.000 1.000 0.00 0.00 1.00
#> TCGA.F1.A448.01 1 0.000 0.993 1.00 0.00 0.00
#> TCGA.BR.8296.01 2 0.000 0.973 0.00 1.00 0.00
#> TCGA.RD.A8MV.01 1 0.000 0.993 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.CG.5716.01 4 0 1 0 0 0 1
#> TCGA.BR.8384.01 1 0 1 1 0 0 0
#> TCGA.BR.6453.01 1 0 1 1 0 0 0
#> TCGA.D7.6518.01 1 0 1 1 0 0 0
#> TCGA.BR.6452.11 4 0 1 0 0 0 1
#> TCGA.VQ.A8PZ.01 4 0 1 0 0 0 1
#> TCGA.BR.8592.01 3 0 1 0 0 1 0
#> TCGA.BR.8588.01 3 0 1 0 0 1 0
#> TCGA.HU.8610.01 1 0 1 1 0 0 0
#> TCGA.VQ.A8PD.01 1 0 1 1 0 0 0
#> TCGA.D7.6524.01 4 0 1 0 0 0 1
#> TCGA.3M.AB47.01 1 0 1 1 0 0 0
#> TCGA.BR.6457.01 1 0 1 1 0 0 0
#> TCGA.BR.A4J5.01 1 0 1 1 0 0 0
#> TCGA.BR.A4IU.01 3 0 1 0 0 1 0
#> TCGA.HU.A4GJ.01 4 0 1 0 0 0 1
#> TCGA.BR.7196.01 2 0 1 0 1 0 0
#> TCGA.BR.6563.01 1 0 1 1 0 0 0
#> TCGA.IN.A6RJ.01 1 0 1 1 0 0 0
#> TCGA.B7.A5TK.01 2 0 1 0 1 0 0
#> TCGA.D7.A4Z0.01 3 0 1 0 0 1 0
#> TCGA.R5.A7O7.01 1 0 1 1 0 0 0
#> TCGA.BR.A4J2.01 1 0 1 1 0 0 0
#> TCGA.HU.A4HB.01 1 0 1 1 0 0 0
#> TCGA.BR.6852.01 4 0 1 0 0 0 1
#> TCGA.CG.5734.01 1 0 1 1 0 0 0
#> TCGA.VQ.A8P8.01 4 0 1 0 0 0 1
#> TCGA.BR.6705.01 3 0 1 0 0 1 0
#> TCGA.MX.A5UG.01 1 0 1 1 0 0 0
#> TCGA.BR.7957.01 3 0 1 0 0 1 0
#> TCGA.CG.5722.01 2 0 1 0 1 0 0
#> TCGA.D7.A6EY.01 3 0 1 0 0 1 0
#> TCGA.BR.6706.01 2 0 1 0 1 0 0
#> TCGA.IN.7808.01 1 0 1 1 0 0 0
#> TCGA.BR.6802.01 1 0 1 1 0 0 0
#> TCGA.FP.7998.01 2 0 1 0 1 0 0
#> TCGA.B7.5816.01 4 0 1 0 0 0 1
#> TCGA.CG.5721.01 1 0 1 1 0 0 0
#> TCGA.RD.A8NB.01 3 0 1 0 0 1 0
#> TCGA.IN.AB1X.01 4 0 1 0 0 0 1
#> TCGA.CG.5728.01 3 0 1 0 0 1 0
#> TCGA.VQ.A8PC.01 1 0 1 1 0 0 0
#> TCGA.BR.A453.01 1 0 1 1 0 0 0
#> TCGA.BR.8380.01 1 0 1 1 0 0 0
#> TCGA.R5.A804.01 4 0 1 0 0 0 1
#> TCGA.D7.A6ET.01 2 0 1 0 1 0 0
#> TCGA.D7.8579.01 3 0 1 0 0 1 0
#> TCGA.F1.A448.01 1 0 1 1 0 0 0
#> TCGA.BR.8296.01 4 0 1 0 0 0 1
#> TCGA.RD.A8MV.01 1 0 1 1 0 0 0
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> TCGA.CG.5716.01 4 0.1732 0.905 0.00 0.00 0.00 0.92 0.08
#> TCGA.BR.8384.01 1 0.0609 0.957 0.98 0.00 0.00 0.00 0.02
#> TCGA.BR.6453.01 1 0.2516 0.902 0.86 0.00 0.00 0.00 0.14
#> TCGA.D7.6518.01 1 0.1410 0.950 0.94 0.00 0.00 0.00 0.06
#> TCGA.BR.6452.11 4 0.1043 0.923 0.00 0.00 0.00 0.96 0.04
#> TCGA.VQ.A8PZ.01 4 0.0609 0.928 0.00 0.00 0.00 0.98 0.02
#> TCGA.BR.8592.01 3 0.1216 0.946 0.00 0.00 0.96 0.02 0.02
#> TCGA.BR.8588.01 3 0.0000 0.973 0.00 0.00 1.00 0.00 0.00
#> TCGA.HU.8610.01 1 0.0000 0.959 1.00 0.00 0.00 0.00 0.00
#> TCGA.VQ.A8PD.01 1 0.1732 0.936 0.92 0.00 0.00 0.00 0.08
#> TCGA.D7.6524.01 5 0.2020 0.000 0.00 0.00 0.00 0.10 0.90
#> TCGA.3M.AB47.01 1 0.1043 0.953 0.96 0.00 0.00 0.00 0.04
#> TCGA.BR.6457.01 1 0.1410 0.950 0.94 0.00 0.00 0.00 0.06
#> TCGA.BR.A4J5.01 1 0.1043 0.953 0.96 0.00 0.00 0.00 0.04
#> TCGA.BR.A4IU.01 3 0.0000 0.973 0.00 0.00 1.00 0.00 0.00
#> TCGA.HU.A4GJ.01 4 0.1043 0.923 0.00 0.00 0.00 0.96 0.04
#> TCGA.BR.7196.01 2 0.0000 1.000 0.00 1.00 0.00 0.00 0.00
#> TCGA.BR.6563.01 1 0.1043 0.953 0.96 0.00 0.00 0.00 0.04
#> TCGA.IN.A6RJ.01 1 0.0000 0.959 1.00 0.00 0.00 0.00 0.00
#> TCGA.B7.A5TK.01 2 0.0000 1.000 0.00 1.00 0.00 0.00 0.00
#> TCGA.D7.A4Z0.01 3 0.0000 0.973 0.00 0.00 1.00 0.00 0.00
#> TCGA.R5.A7O7.01 1 0.0000 0.959 1.00 0.00 0.00 0.00 0.00
#> TCGA.BR.A4J2.01 1 0.0000 0.959 1.00 0.00 0.00 0.00 0.00
#> TCGA.HU.A4HB.01 1 0.1043 0.937 0.96 0.00 0.00 0.00 0.04
#> TCGA.BR.6852.01 4 0.2280 0.873 0.00 0.00 0.00 0.88 0.12
#> TCGA.CG.5734.01 1 0.0000 0.959 1.00 0.00 0.00 0.00 0.00
#> TCGA.VQ.A8P8.01 4 0.1043 0.925 0.00 0.00 0.00 0.96 0.04
#> TCGA.BR.6705.01 3 0.2732 0.821 0.00 0.00 0.84 0.00 0.16
#> TCGA.MX.A5UG.01 1 0.0000 0.959 1.00 0.00 0.00 0.00 0.00
#> TCGA.BR.7957.01 3 0.0000 0.973 0.00 0.00 1.00 0.00 0.00
#> TCGA.CG.5722.01 2 0.0000 1.000 0.00 1.00 0.00 0.00 0.00
#> TCGA.D7.A6EY.01 3 0.0000 0.973 0.00 0.00 1.00 0.00 0.00
#> TCGA.BR.6706.01 2 0.0000 1.000 0.00 1.00 0.00 0.00 0.00
#> TCGA.IN.7808.01 1 0.0000 0.959 1.00 0.00 0.00 0.00 0.00
#> TCGA.BR.6802.01 1 0.1732 0.942 0.92 0.00 0.00 0.00 0.08
#> TCGA.FP.7998.01 2 0.0000 1.000 0.00 1.00 0.00 0.00 0.00
#> TCGA.B7.5816.01 4 0.2280 0.874 0.00 0.00 0.00 0.88 0.12
#> TCGA.CG.5721.01 1 0.0000 0.959 1.00 0.00 0.00 0.00 0.00
#> TCGA.RD.A8NB.01 3 0.0000 0.973 0.00 0.00 1.00 0.00 0.00
#> TCGA.IN.AB1X.01 4 0.1043 0.925 0.00 0.00 0.00 0.96 0.04
#> TCGA.CG.5728.01 3 0.1043 0.951 0.00 0.00 0.96 0.00 0.04
#> TCGA.VQ.A8PC.01 1 0.0609 0.957 0.98 0.00 0.00 0.00 0.02
#> TCGA.BR.A453.01 1 0.2020 0.931 0.90 0.00 0.00 0.00 0.10
#> TCGA.BR.8380.01 1 0.2732 0.884 0.84 0.00 0.00 0.00 0.16
#> TCGA.R5.A804.01 4 0.1732 0.905 0.00 0.00 0.00 0.92 0.08
#> TCGA.D7.A6ET.01 2 0.0000 1.000 0.00 1.00 0.00 0.00 0.00
#> TCGA.D7.8579.01 3 0.0000 0.973 0.00 0.00 1.00 0.00 0.00
#> TCGA.F1.A448.01 1 0.2516 0.902 0.86 0.00 0.00 0.00 0.14
#> TCGA.BR.8296.01 4 0.0609 0.924 0.00 0.02 0.00 0.98 0.00
#> TCGA.RD.A8MV.01 1 0.0000 0.959 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.CG.5716.01 4 0.3409 0.722 0.00 0.30 0.00 0.70 0.00 0.00
#> TCGA.BR.8384.01 1 0.2048 0.840 0.88 0.12 0.00 0.00 0.00 0.00
#> TCGA.BR.6453.01 1 0.4265 0.703 0.66 0.30 0.00 0.00 0.04 0.00
#> TCGA.D7.6518.01 1 0.2790 0.827 0.84 0.14 0.00 0.00 0.02 0.00
#> TCGA.BR.6452.11 4 0.3076 0.761 0.00 0.24 0.00 0.76 0.00 0.00
#> TCGA.VQ.A8PZ.01 4 0.0547 0.801 0.00 0.02 0.00 0.98 0.00 0.00
#> TCGA.BR.8592.01 3 0.3997 0.746 0.00 0.06 0.78 0.14 0.02 0.00
#> TCGA.BR.8588.01 3 0.0000 0.923 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.HU.8610.01 1 0.1267 0.845 0.94 0.06 0.00 0.00 0.00 0.00
#> TCGA.VQ.A8PD.01 1 0.2260 0.825 0.86 0.14 0.00 0.00 0.00 0.00
#> TCGA.D7.6524.01 5 0.0547 0.000 0.00 0.02 0.00 0.00 0.98 0.00
#> TCGA.3M.AB47.01 1 0.2631 0.815 0.82 0.18 0.00 0.00 0.00 0.00
#> TCGA.BR.6457.01 1 0.2454 0.834 0.84 0.16 0.00 0.00 0.00 0.00
#> TCGA.BR.A4J5.01 1 0.2941 0.819 0.78 0.22 0.00 0.00 0.00 0.00
#> TCGA.BR.A4IU.01 3 0.0000 0.923 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.HU.A4GJ.01 4 0.3076 0.761 0.00 0.24 0.00 0.76 0.00 0.00
#> TCGA.BR.7196.01 6 0.0000 1.000 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.BR.6563.01 1 0.2260 0.836 0.86 0.14 0.00 0.00 0.00 0.00
#> TCGA.IN.A6RJ.01 1 0.1556 0.843 0.92 0.08 0.00 0.00 0.00 0.00
#> TCGA.B7.A5TK.01 6 0.0000 1.000 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.D7.A4Z0.01 3 0.0000 0.923 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.R5.A7O7.01 1 0.1814 0.832 0.90 0.10 0.00 0.00 0.00 0.00
#> TCGA.BR.A4J2.01 1 0.1556 0.836 0.92 0.08 0.00 0.00 0.00 0.00
#> TCGA.HU.A4HB.01 1 0.2941 0.734 0.78 0.22 0.00 0.00 0.00 0.00
#> TCGA.BR.6852.01 4 0.3321 0.717 0.00 0.10 0.00 0.82 0.08 0.00
#> TCGA.CG.5734.01 1 0.1556 0.844 0.92 0.08 0.00 0.00 0.00 0.00
#> TCGA.VQ.A8P8.01 4 0.1267 0.789 0.00 0.06 0.00 0.94 0.00 0.00
#> TCGA.BR.6705.01 3 0.5018 0.692 0.00 0.08 0.72 0.10 0.10 0.00
#> TCGA.MX.A5UG.01 1 0.1556 0.836 0.92 0.08 0.00 0.00 0.00 0.00
#> TCGA.BR.7957.01 3 0.0000 0.923 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.CG.5722.01 6 0.0000 1.000 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.D7.A6EY.01 3 0.0000 0.923 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.BR.6706.01 6 0.0000 1.000 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.IN.7808.01 1 0.1556 0.838 0.92 0.08 0.00 0.00 0.00 0.00
#> TCGA.BR.6802.01 1 0.3592 0.764 0.74 0.24 0.00 0.00 0.02 0.00
#> TCGA.FP.7998.01 6 0.0000 1.000 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.B7.5816.01 4 0.3045 0.735 0.00 0.10 0.00 0.84 0.06 0.00
#> TCGA.CG.5721.01 1 0.2793 0.800 0.80 0.20 0.00 0.00 0.00 0.00
#> TCGA.RD.A8NB.01 3 0.0000 0.923 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.IN.AB1X.01 4 0.1814 0.778 0.00 0.10 0.00 0.90 0.00 0.00
#> TCGA.CG.5728.01 3 0.3045 0.824 0.00 0.10 0.84 0.00 0.06 0.00
#> TCGA.VQ.A8PC.01 1 0.1556 0.846 0.92 0.08 0.00 0.00 0.00 0.00
#> TCGA.BR.A453.01 1 0.3156 0.812 0.80 0.18 0.00 0.00 0.02 0.00
#> TCGA.BR.8380.01 1 0.4700 0.644 0.60 0.34 0.00 0.00 0.06 0.00
#> TCGA.R5.A804.01 4 0.3499 0.706 0.00 0.32 0.00 0.68 0.00 0.00
#> TCGA.D7.A6ET.01 6 0.0000 1.000 0.00 0.00 0.00 0.00 0.00 1.00
#> TCGA.D7.8579.01 3 0.0000 0.923 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.F1.A448.01 1 0.4348 0.692 0.64 0.32 0.00 0.00 0.04 0.00
#> TCGA.BR.8296.01 4 0.2190 0.779 0.00 0.04 0.00 0.90 0.00 0.06
#> TCGA.RD.A8MV.01 1 0.1267 0.843 0.94 0.06 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.CG.5716.01 4 0.0000 0.7547 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.BR.8384.01 1 0.3052 0.4093 0.78 0.02 0.00 0.00 0.00 0.00 0.20
#> TCGA.BR.6453.01 1 0.3985 -0.6787 0.52 0.02 0.00 0.00 0.00 0.00 0.46
#> TCGA.D7.6518.01 1 0.3517 0.2101 0.70 0.02 0.00 0.00 0.00 0.00 0.28
#> TCGA.BR.6452.11 4 0.0504 0.7602 0.00 0.02 0.00 0.98 0.00 0.00 0.00
#> TCGA.VQ.A8PZ.01 4 0.3413 0.1101 0.00 0.38 0.00 0.62 0.00 0.00 0.00
#> TCGA.BR.8592.01 3 0.3909 0.2990 0.00 0.40 0.58 0.02 0.00 0.00 0.00
#> TCGA.BR.8588.01 3 0.0000 0.8945 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.HU.8610.01 1 0.0863 0.5996 0.96 0.00 0.00 0.00 0.00 0.00 0.04
#> TCGA.VQ.A8PD.01 1 0.3991 0.4433 0.72 0.04 0.00 0.02 0.00 0.00 0.22
#> TCGA.D7.6524.01 5 0.0000 0.0000 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.3M.AB47.01 1 0.2572 0.4851 0.80 0.00 0.00 0.00 0.00 0.00 0.20
#> TCGA.BR.6457.01 1 0.3685 0.1728 0.66 0.02 0.00 0.00 0.00 0.00 0.32
#> TCGA.BR.A4J5.01 1 0.3139 0.3258 0.70 0.00 0.00 0.00 0.00 0.00 0.30
#> TCGA.BR.A4IU.01 3 0.0000 0.8945 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.HU.A4GJ.01 4 0.0504 0.7602 0.00 0.02 0.00 0.98 0.00 0.00 0.00
#> TCGA.BR.7196.01 6 0.0000 1.0000 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.BR.6563.01 1 0.3417 0.4426 0.72 0.00 0.00 0.02 0.00 0.00 0.26
#> TCGA.IN.A6RJ.01 1 0.1671 0.5892 0.90 0.00 0.00 0.00 0.00 0.00 0.10
#> TCGA.B7.A5TK.01 6 0.0000 1.0000 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.D7.A4Z0.01 3 0.0000 0.8945 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.R5.A7O7.01 1 0.0863 0.5953 0.96 0.00 0.00 0.00 0.00 0.00 0.04
#> TCGA.BR.A4J2.01 1 0.2081 0.5680 0.86 0.00 0.00 0.00 0.00 0.00 0.14
#> TCGA.HU.A4HB.01 1 0.3617 0.4604 0.76 0.00 0.00 0.08 0.00 0.00 0.16
#> TCGA.BR.6852.01 2 0.3417 0.5739 0.00 0.72 0.00 0.26 0.02 0.00 0.00
#> TCGA.CG.5734.01 1 0.1928 0.5671 0.90 0.02 0.00 0.00 0.00 0.00 0.08
#> TCGA.VQ.A8P8.01 2 0.3558 0.1888 0.00 0.52 0.00 0.48 0.00 0.00 0.00
#> TCGA.BR.6705.01 2 0.3909 -0.1085 0.00 0.58 0.40 0.00 0.00 0.00 0.02
#> TCGA.MX.A5UG.01 1 0.1886 0.5781 0.88 0.00 0.00 0.00 0.00 0.00 0.12
#> TCGA.BR.7957.01 3 0.0000 0.8945 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.CG.5722.01 6 0.0000 1.0000 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.D7.A6EY.01 3 0.0000 0.8945 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.BR.6706.01 6 0.0000 1.0000 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.IN.7808.01 1 0.0000 0.6054 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BR.6802.01 1 0.3867 -0.0408 0.60 0.02 0.00 0.00 0.00 0.00 0.38
#> TCGA.FP.7998.01 6 0.0000 1.0000 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.B7.5816.01 2 0.3637 0.5611 0.00 0.72 0.00 0.24 0.00 0.00 0.04
#> TCGA.CG.5721.01 1 0.4945 -0.0944 0.52 0.12 0.00 0.00 0.00 0.00 0.36
#> TCGA.RD.A8NB.01 3 0.0000 0.8945 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.IN.AB1X.01 2 0.3294 0.5244 0.00 0.66 0.00 0.34 0.00 0.00 0.00
#> TCGA.CG.5728.01 3 0.4451 0.5632 0.00 0.26 0.64 0.00 0.00 0.00 0.10
#> TCGA.VQ.A8PC.01 1 0.1664 0.6024 0.92 0.02 0.00 0.00 0.00 0.00 0.06
#> TCGA.BR.A453.01 1 0.3606 0.1434 0.68 0.02 0.00 0.00 0.00 0.00 0.30
#> TCGA.BR.8380.01 7 0.3459 0.7340 0.40 0.00 0.00 0.00 0.00 0.00 0.60
#> TCGA.R5.A804.01 4 0.0504 0.7388 0.00 0.00 0.00 0.98 0.00 0.00 0.02
#> TCGA.D7.A6ET.01 6 0.0000 1.0000 0.00 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.D7.8579.01 3 0.0000 0.8945 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.F1.A448.01 7 0.3985 0.7012 0.46 0.02 0.00 0.00 0.00 0.00 0.52
#> TCGA.BR.8296.01 4 0.4718 0.2719 0.00 0.32 0.00 0.60 0.00 0.06 0.02
#> TCGA.RD.A8MV.01 1 0.0504 0.6034 0.98 0.00 0.00 0.00 0.00 0.00 0.02
cbind(get_classes(res, k = 8), get_membership(res, k = 8))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7 p8
#> TCGA.CG.5716.01 4 0.0471 0.6982 0.00 0.00 0.00 0.98 0 0.00 0.02 0.00
#> TCGA.BR.8384.01 1 0.2569 0.4075 0.82 0.00 0.00 0.00 0 0.00 0.16 0.02
#> TCGA.BR.6453.01 1 0.4004 -0.6966 0.50 0.00 0.00 0.00 0 0.00 0.46 0.04
#> TCGA.D7.6518.01 1 0.3943 -0.1082 0.56 0.00 0.00 0.00 0 0.00 0.40 0.04
#> TCGA.BR.6452.11 4 0.1563 0.7061 0.00 0.10 0.00 0.90 0 0.00 0.00 0.00
#> TCGA.VQ.A8PZ.01 4 0.3318 -0.3389 0.00 0.46 0.00 0.54 0 0.00 0.00 0.00
#> TCGA.BR.8592.01 3 0.3374 0.5801 0.00 0.30 0.68 0.02 0 0.00 0.00 0.00
#> TCGA.BR.8588.01 3 0.0000 0.8536 0.00 0.00 1.00 0.00 0 0.00 0.00 0.00
#> TCGA.HU.8610.01 1 0.1557 0.5198 0.92 0.00 0.00 0.00 0 0.00 0.02 0.06
#> TCGA.VQ.A8PD.01 1 0.4943 0.3952 0.64 0.02 0.00 0.04 0 0.00 0.22 0.08
#> TCGA.D7.6524.01 5 0.0000 0.0000 0.00 0.00 0.00 0.00 1 0.00 0.00 0.00
#> TCGA.3M.AB47.01 1 0.3426 0.2505 0.74 0.02 0.00 0.00 0 0.00 0.22 0.02
#> TCGA.BR.6457.01 1 0.3551 0.3682 0.72 0.00 0.00 0.00 0 0.00 0.22 0.06
#> TCGA.BR.A4J5.01 1 0.4106 0.1807 0.64 0.02 0.00 0.00 0 0.00 0.30 0.04
#> TCGA.BR.A4IU.01 3 0.1275 0.8395 0.00 0.04 0.94 0.00 0 0.00 0.00 0.02
#> TCGA.HU.A4GJ.01 4 0.1563 0.7061 0.00 0.10 0.00 0.90 0 0.00 0.00 0.00
#> TCGA.BR.7196.01 6 0.0000 1.0000 0.00 0.00 0.00 0.00 0 1.00 0.00 0.00
#> TCGA.BR.6563.01 1 0.5081 0.3522 0.64 0.02 0.00 0.06 0 0.00 0.20 0.08
#> TCGA.IN.A6RJ.01 1 0.2224 0.5036 0.86 0.00 0.00 0.00 0 0.00 0.12 0.02
#> TCGA.B7.A5TK.01 6 0.0000 1.0000 0.00 0.00 0.00 0.00 0 1.00 0.00 0.00
#> TCGA.D7.A4Z0.01 3 0.1275 0.8395 0.00 0.04 0.94 0.00 0 0.00 0.00 0.02
#> TCGA.R5.A7O7.01 1 0.2648 0.5318 0.84 0.00 0.00 0.00 0 0.00 0.08 0.08
#> TCGA.BR.A4J2.01 1 0.4119 0.4868 0.74 0.02 0.00 0.02 0 0.00 0.14 0.08
#> TCGA.HU.A4HB.01 1 0.5049 0.4103 0.66 0.02 0.00 0.08 0 0.00 0.16 0.08
#> TCGA.BR.6852.01 2 0.3601 0.6024 0.00 0.76 0.00 0.16 0 0.00 0.02 0.06
#> TCGA.CG.5734.01 1 0.1275 0.5296 0.94 0.00 0.00 0.00 0 0.00 0.02 0.04
#> TCGA.VQ.A8P8.01 2 0.3272 0.3803 0.00 0.58 0.00 0.42 0 0.00 0.00 0.00
#> TCGA.BR.6705.01 3 0.4798 0.4589 0.00 0.32 0.56 0.00 0 0.00 0.02 0.10
#> TCGA.MX.A5UG.01 1 0.3503 0.5065 0.78 0.02 0.00 0.00 0 0.00 0.12 0.08
#> TCGA.BR.7957.01 3 0.0471 0.8530 0.00 0.02 0.98 0.00 0 0.00 0.00 0.00
#> TCGA.CG.5722.01 6 0.0000 1.0000 0.00 0.00 0.00 0.00 0 1.00 0.00 0.00
#> TCGA.D7.A6EY.01 3 0.0000 0.8536 0.00 0.00 1.00 0.00 0 0.00 0.00 0.00
#> TCGA.BR.6706.01 6 0.0000 1.0000 0.00 0.00 0.00 0.00 0 1.00 0.00 0.00
#> TCGA.IN.7808.01 1 0.1091 0.5326 0.94 0.00 0.00 0.00 0 0.00 0.00 0.06
#> TCGA.BR.6802.01 1 0.3991 -0.0658 0.62 0.00 0.00 0.00 0 0.00 0.32 0.06
#> TCGA.FP.7998.01 6 0.0000 1.0000 0.00 0.00 0.00 0.00 0 1.00 0.00 0.00
#> TCGA.B7.5816.01 2 0.3817 0.5739 0.00 0.76 0.00 0.12 0 0.00 0.04 0.08
#> TCGA.CG.5721.01 8 0.4559 0.0000 0.30 0.02 0.00 0.00 0 0.00 0.08 0.60
#> TCGA.RD.A8NB.01 3 0.0000 0.8536 0.00 0.00 1.00 0.00 0 0.00 0.00 0.00
#> TCGA.IN.AB1X.01 2 0.4350 0.5446 0.00 0.62 0.00 0.30 0 0.00 0.02 0.06
#> TCGA.CG.5728.01 3 0.4512 0.5850 0.00 0.08 0.66 0.00 0 0.00 0.04 0.22
#> TCGA.VQ.A8PC.01 1 0.2862 0.5248 0.82 0.00 0.00 0.00 0 0.00 0.10 0.08
#> TCGA.BR.A453.01 1 0.3272 -0.2830 0.58 0.00 0.00 0.00 0 0.00 0.42 0.00
#> TCGA.BR.8380.01 7 0.4751 0.6459 0.38 0.02 0.00 0.00 0 0.00 0.52 0.08
#> TCGA.R5.A804.01 4 0.0471 0.6982 0.00 0.00 0.00 0.98 0 0.00 0.02 0.00
#> TCGA.D7.A6ET.01 6 0.0000 1.0000 0.00 0.00 0.00 0.00 0 1.00 0.00 0.00
#> TCGA.D7.8579.01 3 0.0471 0.8530 0.00 0.02 0.98 0.00 0 0.00 0.00 0.00
#> TCGA.F1.A448.01 7 0.4008 0.6059 0.48 0.00 0.00 0.00 0 0.00 0.48 0.04
#> TCGA.BR.8296.01 2 0.6262 0.2796 0.00 0.40 0.00 0.38 0 0.06 0.06 0.10
#> TCGA.RD.A8MV.01 1 0.1557 0.5198 0.92 0.00 0.00 0.00 0 0.00 0.02 0.06
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
consensus_heatmap(res, k = 7)
consensus_heatmap(res, k = 8)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
membership_heatmap(res, k = 7)
membership_heatmap(res, k = 8)
As soon as the classes for columns are determined, the signatures that are significantly different between subgroups can be looked for. Following are the heatmaps for signatures.
get_signatures(res, k = 2)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
get_signatures(res, k = 7)
get_signatures(res, k = 8)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. To get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows (which is done by automatically selecting number of clusters).If there are too many signatures, top_signatures = ... can be set to only show the
signatures with the highest FDRs:
# code only for demonstration
# e.g. to show the top 500 most significant rows
tb = get_signature(res, k = ..., top_signatures = 500)
If the signatures are defined as these which are uniquely high in current group, diff_method argument
can be set to "uniquely_high_in_one_group":
# code only for demonstration
tb = get_signature(res, k = ..., diff_method = "uniquely_high_in_one_group")
UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
dimension_reduction(res, k = 7, method = "UMAP")
dimension_reduction(res, k = 8, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
If matrix rows can be associated to genes, consider to use functional_enrichment(res,
...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.
Parent node: Node031. Child nodes: Node01111-leaf , Node01112-leaf , Node01113-leaf , Node01114-leaf , Node01115-leaf , Node01116-leaf , Node01121-leaf , Node01122-leaf , Node01123-leaf , Node01131-leaf , Node01132-leaf , Node01133-leaf , Node01134-leaf , Node01211-leaf , Node01212-leaf , Node01221-leaf , Node01222-leaf , Node01231-leaf , Node01232-leaf , Node01233-leaf , Node01311-leaf , Node01312 , Node02221-leaf , Node02222-leaf , Node02223-leaf , Node02224-leaf , Node03111-leaf , Node03112-leaf , Node03113-leaf , Node03411-leaf , Node03412-leaf , Node03413-leaf .
The object with results only for a single top-value method and a single partitioning method can be extracted as:
res = res_rh["0311"]
A summary of res and all the functions that can be applied to it:
res
#> A 'ConsensusPartition' object with k = 2, 3, 4, 5, 6, 7, 8.
#> On a matrix with 30000 rows and 23 columns.
#> Top rows (1000) are extracted by '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 0.595 0.781 0.873 0.4957 0.478 0.478
#> 3 3 0.971 0.968 0.966 0.3157 0.862 0.711
#> 4 4 0.784 0.618 0.846 0.1257 0.960 0.884
#> 5 5 0.819 0.708 0.881 0.0603 0.874 0.600
#> 6 6 0.779 0.698 0.876 0.0557 0.960 0.818
#> 7 7 0.776 0.665 0.840 0.0248 0.921 0.615
#> 8 8 0.819 0.689 0.754 0.0309 0.929 0.571
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.BR.8384.01 1 0.141 0.952 0.98 0.02
#> TCGA.BR.6453.01 2 0.925 0.648 0.34 0.66
#> TCGA.D7.6518.01 1 0.000 0.953 1.00 0.00
#> TCGA.HU.8610.01 1 0.327 0.923 0.94 0.06
#> TCGA.VQ.A8PD.01 2 0.000 0.720 0.00 1.00
#> TCGA.3M.AB47.01 2 0.925 0.648 0.34 0.66
#> TCGA.BR.6457.01 1 0.141 0.952 0.98 0.02
#> TCGA.BR.A4J5.01 2 0.141 0.718 0.02 0.98
#> TCGA.BR.6563.01 1 0.141 0.952 0.98 0.02
#> TCGA.IN.A6RJ.01 2 0.402 0.702 0.08 0.92
#> TCGA.R5.A7O7.01 2 0.141 0.718 0.02 0.98
#> TCGA.BR.A4J2.01 2 0.943 0.385 0.36 0.64
#> TCGA.HU.A4HB.01 2 0.943 0.385 0.36 0.64
#> TCGA.CG.5734.01 1 0.000 0.953 1.00 0.00
#> TCGA.MX.A5UG.01 1 0.327 0.923 0.94 0.06
#> TCGA.IN.7808.01 2 0.925 0.648 0.34 0.66
#> TCGA.BR.6802.01 2 0.925 0.648 0.34 0.66
#> TCGA.CG.5721.01 1 0.141 0.952 0.98 0.02
#> TCGA.VQ.A8PC.01 1 0.327 0.923 0.94 0.06
#> TCGA.BR.A453.01 1 0.141 0.952 0.98 0.02
#> TCGA.BR.8380.01 2 0.327 0.718 0.06 0.94
#> TCGA.F1.A448.01 2 0.925 0.648 0.34 0.66
#> TCGA.RD.A8MV.01 1 0.242 0.937 0.96 0.04
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.BR.8384.01 1 0.0000 0.985 1.00 0.00 0.00
#> TCGA.BR.6453.01 2 0.0000 0.997 0.00 1.00 0.00
#> TCGA.D7.6518.01 1 0.0000 0.985 1.00 0.00 0.00
#> TCGA.HU.8610.01 1 0.1529 0.966 0.96 0.00 0.04
#> TCGA.VQ.A8PD.01 2 0.0000 0.997 0.00 1.00 0.00
#> TCGA.3M.AB47.01 2 0.0000 0.997 0.00 1.00 0.00
#> TCGA.BR.6457.01 1 0.0000 0.985 1.00 0.00 0.00
#> TCGA.BR.A4J5.01 3 0.2959 0.926 0.00 0.10 0.90
#> TCGA.BR.6563.01 1 0.0000 0.985 1.00 0.00 0.00
#> TCGA.IN.A6RJ.01 3 0.3415 0.935 0.02 0.08 0.90
#> TCGA.R5.A7O7.01 3 0.4291 0.861 0.00 0.18 0.82
#> TCGA.BR.A4J2.01 3 0.3572 0.926 0.06 0.04 0.90
#> TCGA.HU.A4HB.01 3 0.3572 0.926 0.06 0.04 0.90
#> TCGA.CG.5734.01 1 0.0000 0.985 1.00 0.00 0.00
#> TCGA.MX.A5UG.01 1 0.0000 0.985 1.00 0.00 0.00
#> TCGA.IN.7808.01 2 0.0892 0.979 0.00 0.98 0.02
#> TCGA.BR.6802.01 2 0.0000 0.997 0.00 1.00 0.00
#> TCGA.CG.5721.01 1 0.2959 0.919 0.90 0.00 0.10
#> TCGA.VQ.A8PC.01 1 0.0000 0.985 1.00 0.00 0.00
#> TCGA.BR.A453.01 1 0.0000 0.985 1.00 0.00 0.00
#> TCGA.BR.8380.01 2 0.0000 0.997 0.00 1.00 0.00
#> TCGA.F1.A448.01 2 0.0000 0.997 0.00 1.00 0.00
#> TCGA.RD.A8MV.01 1 0.1529 0.966 0.96 0.00 0.04
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> TCGA.BR.8384.01 1 0.0000 0.660 1.00 0.00 0.00 0.00
#> TCGA.BR.6453.01 2 0.1913 0.873 0.04 0.94 0.00 0.02
#> TCGA.D7.6518.01 1 0.2647 0.586 0.88 0.00 0.00 0.12
#> TCGA.HU.8610.01 1 0.4855 0.138 0.60 0.00 0.00 0.40
#> TCGA.VQ.A8PD.01 2 0.3853 0.775 0.00 0.82 0.02 0.16
#> TCGA.3M.AB47.01 2 0.0707 0.875 0.00 0.98 0.00 0.02
#> TCGA.BR.6457.01 1 0.0000 0.660 1.00 0.00 0.00 0.00
#> TCGA.BR.A4J5.01 3 0.1211 0.816 0.00 0.00 0.96 0.04
#> TCGA.BR.6563.01 1 0.0000 0.660 1.00 0.00 0.00 0.00
#> TCGA.IN.A6RJ.01 3 0.5512 0.748 0.00 0.04 0.66 0.30
#> TCGA.R5.A7O7.01 3 0.5883 0.733 0.00 0.06 0.64 0.30
#> TCGA.BR.A4J2.01 3 0.0000 0.831 0.00 0.00 1.00 0.00
#> TCGA.HU.A4HB.01 3 0.0000 0.831 0.00 0.00 1.00 0.00
#> TCGA.CG.5734.01 1 0.4790 0.204 0.62 0.00 0.00 0.38
#> TCGA.MX.A5UG.01 1 0.0000 0.660 1.00 0.00 0.00 0.00
#> TCGA.IN.7808.01 2 0.4907 0.527 0.00 0.58 0.00 0.42
#> TCGA.BR.6802.01 2 0.1211 0.878 0.04 0.96 0.00 0.00
#> TCGA.CG.5721.01 4 0.5173 0.000 0.32 0.02 0.00 0.66
#> TCGA.VQ.A8PC.01 1 0.4790 0.204 0.62 0.00 0.00 0.38
#> TCGA.BR.A453.01 1 0.0000 0.660 1.00 0.00 0.00 0.00
#> TCGA.BR.8380.01 2 0.0707 0.872 0.00 0.98 0.00 0.02
#> TCGA.F1.A448.01 2 0.1211 0.878 0.04 0.96 0.00 0.00
#> TCGA.RD.A8MV.01 1 0.4855 0.138 0.60 0.00 0.00 0.40
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> TCGA.BR.8384.01 1 0.0000 0.8390 1.00 0.00 0.00 0.00 0.00
#> TCGA.BR.6453.01 2 0.0609 0.8732 0.00 0.98 0.00 0.00 0.02
#> TCGA.D7.6518.01 1 0.1410 0.7927 0.94 0.00 0.00 0.06 0.00
#> TCGA.HU.8610.01 4 0.4302 0.3383 0.48 0.00 0.00 0.52 0.00
#> TCGA.VQ.A8PD.01 2 0.4302 -0.0205 0.00 0.52 0.00 0.00 0.48
#> TCGA.3M.AB47.01 2 0.0609 0.8732 0.00 0.98 0.00 0.00 0.02
#> TCGA.BR.6457.01 1 0.0000 0.8390 1.00 0.00 0.00 0.00 0.00
#> TCGA.BR.A4J5.01 3 0.0609 0.9423 0.00 0.00 0.98 0.02 0.00
#> TCGA.BR.6563.01 1 0.0000 0.8390 1.00 0.00 0.00 0.00 0.00
#> TCGA.IN.A6RJ.01 5 0.2280 0.8761 0.00 0.00 0.12 0.00 0.88
#> TCGA.R5.A7O7.01 5 0.2020 0.8844 0.00 0.00 0.10 0.00 0.90
#> TCGA.BR.A4J2.01 3 0.1043 0.9711 0.00 0.00 0.96 0.00 0.04
#> TCGA.HU.A4HB.01 3 0.1043 0.9711 0.00 0.00 0.96 0.00 0.04
#> TCGA.CG.5734.01 1 0.3895 0.2762 0.68 0.00 0.00 0.32 0.00
#> TCGA.MX.A5UG.01 1 0.0000 0.8390 1.00 0.00 0.00 0.00 0.00
#> TCGA.IN.7808.01 5 0.3037 0.7983 0.00 0.10 0.00 0.04 0.86
#> TCGA.BR.6802.01 2 0.0000 0.8752 0.00 1.00 0.00 0.00 0.00
#> TCGA.CG.5721.01 4 0.2331 0.2092 0.00 0.02 0.00 0.90 0.08
#> TCGA.VQ.A8PC.01 1 0.3796 0.3180 0.70 0.00 0.00 0.30 0.00
#> TCGA.BR.A453.01 1 0.0000 0.8390 1.00 0.00 0.00 0.00 0.00
#> TCGA.BR.8380.01 2 0.1216 0.8573 0.00 0.96 0.02 0.02 0.00
#> TCGA.F1.A448.01 2 0.0000 0.8752 0.00 1.00 0.00 0.00 0.00
#> TCGA.RD.A8MV.01 4 0.4287 0.3664 0.46 0.00 0.00 0.54 0.00
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> TCGA.BR.8384.01 1 0.0000 0.7494 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BR.6453.01 2 0.0547 0.9499 0.00 0.98 0.00 0.00 0.00 0.02
#> TCGA.D7.6518.01 1 0.4502 0.5673 0.74 0.00 0.00 0.10 0.02 0.14
#> TCGA.HU.8610.01 4 0.2260 1.0000 0.14 0.00 0.00 0.86 0.00 0.00
#> TCGA.VQ.A8PD.01 5 0.4310 0.1779 0.00 0.44 0.00 0.00 0.54 0.02
#> TCGA.3M.AB47.01 2 0.2048 0.8859 0.00 0.88 0.00 0.00 0.00 0.12
#> TCGA.BR.6457.01 1 0.0000 0.7494 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BR.A4J5.01 3 0.2474 0.8672 0.00 0.00 0.88 0.08 0.00 0.04
#> TCGA.BR.6563.01 1 0.0000 0.7494 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.IN.A6RJ.01 5 0.1556 0.7128 0.00 0.00 0.08 0.00 0.92 0.00
#> TCGA.R5.A7O7.01 5 0.0547 0.7270 0.00 0.00 0.02 0.00 0.98 0.00
#> TCGA.BR.A4J2.01 3 0.0547 0.9359 0.00 0.00 0.98 0.00 0.02 0.00
#> TCGA.HU.A4HB.01 3 0.0547 0.9359 0.00 0.00 0.98 0.00 0.02 0.00
#> TCGA.CG.5734.01 1 0.6228 0.0138 0.44 0.00 0.00 0.36 0.02 0.18
#> TCGA.MX.A5UG.01 1 0.0547 0.7424 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.IN.7808.01 5 0.2725 0.6958 0.00 0.02 0.00 0.06 0.88 0.04
#> TCGA.BR.6802.01 2 0.0547 0.9462 0.00 0.98 0.00 0.00 0.00 0.02
#> TCGA.CG.5721.01 6 0.2048 0.0000 0.00 0.00 0.00 0.12 0.00 0.88
#> TCGA.VQ.A8PC.01 1 0.6228 0.0138 0.44 0.00 0.00 0.36 0.02 0.18
#> TCGA.BR.A453.01 1 0.0547 0.7424 0.98 0.00 0.00 0.00 0.00 0.02
#> TCGA.BR.8380.01 2 0.1092 0.9372 0.00 0.96 0.02 0.02 0.00 0.00
#> TCGA.F1.A448.01 2 0.0000 0.9511 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.RD.A8MV.01 4 0.2260 1.0000 0.14 0.00 0.00 0.86 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.BR.8384.01 1 0.0000 0.895 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BR.6453.01 2 0.1886 0.808 0.00 0.88 0.00 0.00 0.00 0.00 0.12
#> TCGA.D7.6518.01 1 0.3867 0.152 0.60 0.00 0.00 0.38 0.00 0.00 0.02
#> TCGA.HU.8610.01 4 0.5007 0.633 0.16 0.00 0.00 0.56 0.00 0.28 0.00
#> TCGA.VQ.A8PD.01 5 0.3459 0.220 0.00 0.40 0.00 0.00 0.60 0.00 0.00
#> TCGA.3M.AB47.01 7 0.3943 0.000 0.00 0.42 0.00 0.00 0.02 0.00 0.56
#> TCGA.BR.6457.01 1 0.0000 0.895 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BR.A4J5.01 3 0.2769 0.870 0.00 0.00 0.86 0.04 0.00 0.08 0.02
#> TCGA.BR.6563.01 1 0.0000 0.895 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.IN.A6RJ.01 5 0.0504 0.663 0.00 0.00 0.02 0.00 0.98 0.00 0.00
#> TCGA.R5.A7O7.01 5 0.0000 0.666 0.00 0.00 0.00 0.00 1.00 0.00 0.00
#> TCGA.BR.A4J2.01 3 0.0000 0.937 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.HU.A4HB.01 3 0.0000 0.937 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.CG.5734.01 4 0.3047 0.646 0.28 0.00 0.00 0.72 0.00 0.00 0.00
#> TCGA.MX.A5UG.01 1 0.0000 0.895 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.IN.7808.01 5 0.6087 0.422 0.00 0.02 0.00 0.12 0.54 0.06 0.26
#> TCGA.BR.6802.01 2 0.0000 0.866 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CG.5721.01 6 0.4990 0.000 0.00 0.00 0.00 0.20 0.00 0.58 0.22
#> TCGA.VQ.A8PC.01 4 0.3047 0.646 0.28 0.00 0.00 0.72 0.00 0.00 0.00
#> TCGA.BR.A453.01 1 0.0000 0.895 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BR.8380.01 2 0.1006 0.852 0.00 0.96 0.00 0.02 0.00 0.02 0.00
#> TCGA.F1.A448.01 2 0.1166 0.863 0.00 0.94 0.00 0.00 0.00 0.00 0.06
#> TCGA.RD.A8MV.01 4 0.5007 0.633 0.16 0.00 0.00 0.56 0.00 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.BR.8384.01 1 0.0000 1.000 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BR.6453.01 2 0.3131 0.755 0.00 0.84 0.00 0.06 0.00 0.04 0.04 0.02
#> TCGA.D7.6518.01 4 0.4370 0.535 0.40 0.00 0.00 0.52 0.00 0.00 0.00 0.08
#> TCGA.HU.8610.01 8 0.3015 1.000 0.00 0.00 0.00 0.32 0.00 0.00 0.00 0.68
#> TCGA.VQ.A8PD.01 5 0.3299 0.162 0.00 0.44 0.00 0.00 0.56 0.00 0.00 0.00
#> TCGA.3M.AB47.01 2 0.7579 0.197 0.00 0.34 0.00 0.14 0.02 0.10 0.26 0.14
#> TCGA.BR.6457.01 1 0.0000 1.000 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BR.A4J5.01 3 0.4871 0.701 0.00 0.00 0.70 0.04 0.00 0.08 0.10 0.08
#> TCGA.BR.6563.01 1 0.0000 1.000 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.IN.A6RJ.01 5 0.0471 0.529 0.00 0.00 0.02 0.00 0.98 0.00 0.00 0.00
#> TCGA.R5.A7O7.01 5 0.0471 0.524 0.00 0.00 0.00 0.00 0.98 0.00 0.00 0.02
#> TCGA.BR.A4J2.01 3 0.0000 0.862 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HU.A4HB.01 3 0.0000 0.862 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CG.5734.01 4 0.2406 0.727 0.20 0.00 0.00 0.80 0.00 0.00 0.00 0.00
#> TCGA.MX.A5UG.01 1 0.0000 1.000 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.IN.7808.01 7 0.3449 0.000 0.00 0.02 0.00 0.00 0.32 0.00 0.66 0.00
#> TCGA.BR.6802.01 2 0.0000 0.758 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CG.5721.01 6 0.2114 0.000 0.00 0.00 0.00 0.16 0.00 0.84 0.00 0.00
#> TCGA.VQ.A8PC.01 4 0.2981 0.720 0.22 0.00 0.00 0.76 0.00 0.00 0.00 0.02
#> TCGA.BR.A453.01 1 0.0000 1.000 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BR.8380.01 2 0.0808 0.741 0.00 0.96 0.00 0.00 0.00 0.00 0.04 0.00
#> TCGA.F1.A448.01 2 0.2020 0.769 0.00 0.90 0.00 0.06 0.00 0.02 0.02 0.00
#> TCGA.RD.A8MV.01 8 0.3015 1.000 0.00 0.00 0.00 0.32 0.00 0.00 0.00 0.68
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 , Node0113 , Node0114-leaf , Node0121 , Node0122 , Node0123 , Node0131 , Node0132-leaf , Node0211-leaf , Node0212-leaf , Node0221-leaf , Node0222 , Node0231-leaf , Node0232-leaf , Node0233-leaf , Node0311 , Node0312-leaf , Node0313-leaf , Node0314-leaf , Node0331-leaf , Node0332-leaf , Node0333-leaf , Node0341 , Node0342-leaf .
The object with results only for a single top-value method and a single partitioning method can be extracted as:
res = res_rh["033"]
A summary of res and all the functions that can be applied to it:
res
#> A 'ConsensusPartition' object with k = 2, 3, 4, 5, 6, 7, 8.
#> On a matrix with 30000 rows and 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 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 0.752 0.976 0.987 0.5319 0.467 0.467
#> 3 3 1.000 1.000 1.000 0.2719 0.857 0.694
#> 4 4 0.781 0.590 0.807 0.1145 0.857 0.595
#> 5 5 0.800 0.946 0.940 0.0801 0.876 0.536
#> 6 6 0.924 0.772 0.920 0.0316 0.990 0.944
#> 7 7 0.886 0.685 0.905 0.0318 0.981 0.882
#> 8 8 0.867 0.524 0.819 0.0274 0.952 0.688
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.D7.6528.01 2 0.000 0.971 0.0 1.0
#> TCGA.BR.8483.01 1 0.000 1.000 1.0 0.0
#> TCGA.VQ.A91X.01 2 0.000 0.971 0.0 1.0
#> TCGA.VQ.A94U.01 2 0.469 0.905 0.1 0.9
#> TCGA.VQ.A91V.01 2 0.469 0.905 0.1 0.9
#> TCGA.BR.7715.01 2 0.000 0.971 0.0 1.0
#> TCGA.HU.A4GD.01 1 0.000 1.000 1.0 0.0
#> TCGA.VQ.AA6B.01 2 0.000 0.971 0.0 1.0
#> TCGA.CD.8533.01 1 0.000 1.000 1.0 0.0
#> TCGA.CG.5730.01 1 0.000 1.000 1.0 0.0
#> TCGA.IP.7968.01 1 0.000 1.000 1.0 0.0
#> TCGA.KB.A93H.01 2 0.000 0.971 0.0 1.0
#> TCGA.HU.8249.01 1 0.000 1.000 1.0 0.0
#> TCGA.FP.8099.01 2 0.000 0.971 0.0 1.0
#> TCGA.CD.A48A.01 1 0.000 1.000 1.0 0.0
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.D7.6528.01 2 0 1 0 1 0
#> TCGA.BR.8483.01 1 0 1 1 0 0
#> TCGA.VQ.A91X.01 2 0 1 0 1 0
#> TCGA.VQ.A94U.01 3 0 1 0 0 1
#> TCGA.VQ.A91V.01 3 0 1 0 0 1
#> TCGA.BR.7715.01 2 0 1 0 1 0
#> TCGA.HU.A4GD.01 1 0 1 1 0 0
#> TCGA.VQ.AA6B.01 2 0 1 0 1 0
#> TCGA.CD.8533.01 1 0 1 1 0 0
#> TCGA.CG.5730.01 1 0 1 1 0 0
#> TCGA.IP.7968.01 1 0 1 1 0 0
#> TCGA.KB.A93H.01 2 0 1 0 1 0
#> TCGA.HU.8249.01 1 0 1 1 0 0
#> TCGA.FP.8099.01 3 0 1 0 0 1
#> TCGA.CD.A48A.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.D7.6528.01 2 0.498 0.271 0.00 0.54 0.00 0.46
#> TCGA.BR.8483.01 1 0.000 0.907 1.00 0.00 0.00 0.00
#> TCGA.VQ.A91X.01 2 0.498 0.271 0.00 0.54 0.00 0.46
#> TCGA.VQ.A94U.01 3 0.000 0.782 0.00 0.00 1.00 0.00
#> TCGA.VQ.A91V.01 3 0.000 0.782 0.00 0.00 1.00 0.00
#> TCGA.BR.7715.01 4 0.000 0.833 0.00 0.00 0.00 1.00
#> TCGA.HU.A4GD.01 2 0.684 -0.506 0.44 0.46 0.00 0.10
#> TCGA.VQ.AA6B.01 4 0.234 0.824 0.00 0.10 0.00 0.90
#> TCGA.CD.8533.01 1 0.000 0.907 1.00 0.00 0.00 0.00
#> TCGA.CG.5730.01 1 0.498 0.399 0.54 0.46 0.00 0.00
#> TCGA.IP.7968.01 1 0.000 0.907 1.00 0.00 0.00 0.00
#> TCGA.KB.A93H.01 2 0.498 0.271 0.00 0.54 0.00 0.46
#> TCGA.HU.8249.01 1 0.000 0.907 1.00 0.00 0.00 0.00
#> TCGA.FP.8099.01 3 0.491 0.390 0.00 0.00 0.58 0.42
#> TCGA.CD.A48A.01 1 0.000 0.907 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.D7.6528.01 2 0.0000 1.000 0.00 1.00 0.00 0.00 0.00
#> TCGA.BR.8483.01 1 0.0000 0.995 1.00 0.00 0.00 0.00 0.00
#> TCGA.VQ.A91X.01 2 0.0000 1.000 0.00 1.00 0.00 0.00 0.00
#> TCGA.VQ.A94U.01 3 0.0000 1.000 0.00 0.00 1.00 0.00 0.00
#> TCGA.VQ.A91V.01 3 0.0000 1.000 0.00 0.00 1.00 0.00 0.00
#> TCGA.BR.7715.01 4 0.2280 0.860 0.00 0.12 0.00 0.88 0.00
#> TCGA.HU.A4GD.01 5 0.2280 0.913 0.12 0.00 0.00 0.00 0.88
#> TCGA.VQ.AA6B.01 4 0.2516 0.852 0.00 0.14 0.00 0.86 0.00
#> TCGA.CD.8533.01 1 0.0000 0.995 1.00 0.00 0.00 0.00 0.00
#> TCGA.CG.5730.01 5 0.4458 0.913 0.12 0.00 0.00 0.12 0.76
#> TCGA.IP.7968.01 1 0.0609 0.978 0.98 0.00 0.00 0.02 0.00
#> TCGA.KB.A93H.01 2 0.0000 1.000 0.00 1.00 0.00 0.00 0.00
#> TCGA.HU.8249.01 1 0.0000 0.995 1.00 0.00 0.00 0.00 0.00
#> TCGA.FP.8099.01 4 0.4676 0.698 0.00 0.00 0.14 0.74 0.12
#> TCGA.CD.A48A.01 1 0.0000 0.995 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.D7.6528.01 2 0.0000 1.000 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.BR.8483.01 1 0.0547 0.915 0.98 0.00 0.00 0.02 0.00 0.00
#> TCGA.VQ.A91X.01 2 0.0000 1.000 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.VQ.A94U.01 3 0.0000 1.000 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.VQ.A91V.01 3 0.0000 1.000 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.BR.7715.01 4 0.0937 0.799 0.00 0.04 0.00 0.96 0.00 0.00
#> TCGA.HU.A4GD.01 5 0.1556 0.000 0.08 0.00 0.00 0.00 0.92 0.00
#> TCGA.VQ.AA6B.01 4 0.2474 0.799 0.00 0.04 0.00 0.88 0.08 0.00
#> TCGA.CD.8533.01 1 0.0000 0.926 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CG.5730.01 6 0.4503 0.000 0.08 0.00 0.00 0.00 0.24 0.68
#> TCGA.IP.7968.01 1 0.3460 0.658 0.76 0.00 0.00 0.02 0.00 0.22
#> TCGA.KB.A93H.01 2 0.0000 1.000 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.HU.8249.01 1 0.0000 0.926 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FP.8099.01 4 0.4631 0.634 0.00 0.00 0.06 0.62 0.00 0.32
#> TCGA.CD.A48A.01 1 0.0000 0.926 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.D7.6528.01 2 0.0000 1.000 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BR.8483.01 1 0.3139 0.635 0.70 0.00 0.00 0.00 0.00 0.00 0.30
#> TCGA.VQ.A91X.01 2 0.0000 1.000 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.VQ.A94U.01 3 0.0000 0.949 0.00 0.00 1.00 0.00 0.00 0.00 0.00
#> TCGA.VQ.A91V.01 3 0.1363 0.949 0.00 0.00 0.94 0.00 0.02 0.04 0.00
#> TCGA.BR.7715.01 4 0.3052 0.753 0.00 0.02 0.00 0.78 0.00 0.20 0.00
#> TCGA.HU.A4GD.01 5 0.0504 0.000 0.02 0.00 0.00 0.00 0.98 0.00 0.00
#> TCGA.VQ.AA6B.01 4 0.0504 0.753 0.00 0.02 0.00 0.98 0.00 0.00 0.00
#> TCGA.CD.8533.01 1 0.0000 0.860 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CG.5730.01 6 0.3186 0.000 0.02 0.00 0.00 0.00 0.22 0.76 0.00
#> TCGA.IP.7968.01 1 0.3530 0.659 0.76 0.00 0.00 0.02 0.00 0.20 0.02
#> TCGA.KB.A93H.01 2 0.0000 1.000 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HU.8249.01 1 0.0000 0.860 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FP.8099.01 7 0.3841 0.000 0.00 0.00 0.04 0.28 0.00 0.00 0.68
#> TCGA.CD.A48A.01 1 0.0000 0.860 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.D7.6528.01 2 0.0471 0.951 0.00 0.98 0.00 0.00 0.02 0.00 0.00 0.00
#> TCGA.BR.8483.01 7 0.3318 -0.366 0.46 0.00 0.00 0.00 0.00 0.00 0.54 0.00
#> TCGA.VQ.A91X.01 2 0.1563 0.915 0.00 0.90 0.00 0.00 0.00 0.10 0.00 0.00
#> TCGA.VQ.A94U.01 3 0.1275 0.950 0.00 0.00 0.94 0.04 0.00 0.02 0.00 0.00
#> TCGA.VQ.A91V.01 3 0.0000 0.950 0.00 0.00 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BR.7715.01 8 0.3514 0.671 0.00 0.02 0.00 0.34 0.00 0.00 0.00 0.64
#> TCGA.HU.A4GD.01 5 0.0471 0.000 0.02 0.00 0.00 0.00 0.98 0.00 0.00 0.00
#> TCGA.VQ.AA6B.01 8 0.0471 0.672 0.00 0.02 0.00 0.00 0.00 0.00 0.00 0.98
#> TCGA.CD.8533.01 1 0.0000 0.765 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CG.5730.01 6 0.2025 0.000 0.02 0.00 0.00 0.00 0.10 0.88 0.00 0.00
#> TCGA.IP.7968.01 1 0.5273 0.197 0.46 0.00 0.00 0.36 0.00 0.16 0.02 0.00
#> TCGA.KB.A93H.01 2 0.0000 0.951 0.00 1.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.HU.8249.01 1 0.0000 0.765 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.FP.8099.01 7 0.5455 -0.325 0.00 0.00 0.02 0.28 0.00 0.00 0.46 0.24
#> TCGA.CD.A48A.01 1 0.0471 0.758 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.
Parent node: Node03. Child nodes: Node0111 , Node0112 , Node0113 , Node0114-leaf , Node0121 , Node0122 , Node0123 , Node0131 , Node0132-leaf , Node0211-leaf , Node0212-leaf , Node0221-leaf , Node0222 , Node0231-leaf , Node0232-leaf , Node0233-leaf , Node0311 , Node0312-leaf , Node0313-leaf , Node0314-leaf , Node0331-leaf , Node0332-leaf , Node0333-leaf , Node0341 , Node0342-leaf .
The object with results only for a single top-value method and a single partitioning method can be extracted as:
res = res_rh["034"]
A summary of res and all the functions that can be applied to it:
res
#> A 'ConsensusPartition' object with k = 2, 3, 4, 5, 6, 7, 8.
#> On a matrix with 30000 rows and 21 columns.
#> Top rows (1000) are extracted by 'ATC' method.
#> Subgroups are detected by '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 0.968 0.987 0.3656 0.619 0.619
#> 3 3 0.568 0.845 0.919 0.1020 0.890 0.842
#> 4 4 0.521 0.834 0.910 0.5332 0.686 0.525
#> 5 5 0.662 0.798 0.926 0.0654 0.952 0.863
#> 6 6 0.705 0.691 0.917 0.0706 0.976 0.921
#> 7 7 0.733 0.601 0.900 0.0650 0.981 0.931
#> 8 8 0.724 0.516 0.870 0.0404 0.986 0.944
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.VQ.AA68.01 1 0.000 1.000 1.00 0.00
#> TCGA.CG.4441.01 2 0.855 0.611 0.28 0.72
#> TCGA.VQ.A8E7.01 1 0.000 1.000 1.00 0.00
#> TCGA.BR.8680.01 1 0.000 1.000 1.00 0.00
#> TCGA.D7.A6EV.01 1 0.000 1.000 1.00 0.00
#> TCGA.BR.7717.01 1 0.000 1.000 1.00 0.00
#> TCGA.HU.A4G8.01 1 0.000 1.000 1.00 0.00
#> TCGA.HU.A4GC.01 1 0.000 1.000 1.00 0.00
#> TCGA.HU.A4H2.01 2 0.000 0.929 0.00 1.00
#> TCGA.D7.6822.01 1 0.000 1.000 1.00 0.00
#> TCGA.CG.5724.01 1 0.000 1.000 1.00 0.00
#> TCGA.VQ.A8PB.01 1 0.000 1.000 1.00 0.00
#> TCGA.HU.8243.01 2 0.000 0.929 0.00 1.00
#> TCGA.IN.8462.01 1 0.000 1.000 1.00 0.00
#> TCGA.HU.8238.01 1 0.000 1.000 1.00 0.00
#> TCGA.D7.8575.01 1 0.000 1.000 1.00 0.00
#> TCGA.VQ.A8P3.01 1 0.000 1.000 1.00 0.00
#> TCGA.BR.8286.01 1 0.000 1.000 1.00 0.00
#> TCGA.IN.A6RL.01 2 0.000 0.929 0.00 1.00
#> TCGA.BR.8289.01 2 0.000 0.929 0.00 1.00
#> TCGA.BR.A44U.01 1 0.000 1.000 1.00 0.00
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.VQ.AA68.01 1 0.4291 0.855 0.82 0.00 0.18
#> TCGA.CG.4441.01 1 0.4449 0.781 0.86 0.10 0.04
#> TCGA.VQ.A8E7.01 1 0.0892 0.887 0.98 0.02 0.00
#> TCGA.BR.8680.01 1 0.0892 0.887 0.98 0.02 0.00
#> TCGA.D7.A6EV.01 1 0.0892 0.888 0.98 0.00 0.02
#> TCGA.BR.7717.01 1 0.4291 0.855 0.82 0.00 0.18
#> TCGA.HU.A4G8.01 1 0.0892 0.887 0.98 0.02 0.00
#> TCGA.HU.A4GC.01 1 0.0892 0.888 0.98 0.00 0.02
#> TCGA.HU.A4H2.01 2 0.0000 1.000 0.00 1.00 0.00
#> TCGA.D7.6822.01 1 0.0892 0.887 0.98 0.02 0.00
#> TCGA.CG.5724.01 1 0.4291 0.855 0.82 0.00 0.18
#> TCGA.VQ.A8PB.01 1 0.5147 0.841 0.80 0.02 0.18
#> TCGA.HU.8243.01 2 0.0000 1.000 0.00 1.00 0.00
#> TCGA.IN.8462.01 1 0.4291 0.855 0.82 0.00 0.18
#> TCGA.HU.8238.01 1 0.0892 0.887 0.98 0.02 0.00
#> TCGA.D7.8575.01 1 0.0892 0.887 0.98 0.02 0.00
#> TCGA.VQ.A8P3.01 1 0.3686 0.868 0.86 0.00 0.14
#> TCGA.BR.8286.01 1 0.4291 0.855 0.82 0.00 0.18
#> TCGA.IN.A6RL.01 2 0.0000 1.000 0.00 1.00 0.00
#> TCGA.BR.8289.01 3 0.4862 0.000 0.16 0.02 0.82
#> TCGA.BR.A44U.01 1 0.0892 0.887 0.98 0.02 0.00
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> TCGA.VQ.AA68.01 4 0.441 0.816 0.30 0.00 0.00 0.70
#> TCGA.CG.4441.01 1 0.626 0.478 0.62 0.04 0.02 0.32
#> TCGA.VQ.A8E7.01 1 0.000 0.920 1.00 0.00 0.00 0.00
#> TCGA.BR.8680.01 1 0.000 0.920 1.00 0.00 0.00 0.00
#> TCGA.D7.A6EV.01 1 0.000 0.920 1.00 0.00 0.00 0.00
#> TCGA.BR.7717.01 4 0.340 0.920 0.18 0.00 0.00 0.82
#> TCGA.HU.A4G8.01 1 0.000 0.920 1.00 0.00 0.00 0.00
#> TCGA.HU.A4GC.01 1 0.000 0.920 1.00 0.00 0.00 0.00
#> TCGA.HU.A4H2.01 2 0.000 1.000 0.00 1.00 0.00 0.00
#> TCGA.D7.6822.01 1 0.000 0.920 1.00 0.00 0.00 0.00
#> TCGA.CG.5724.01 4 0.292 0.895 0.14 0.00 0.00 0.86
#> TCGA.VQ.A8PB.01 4 0.317 0.905 0.16 0.00 0.00 0.84
#> TCGA.HU.8243.01 2 0.000 1.000 0.00 1.00 0.00 0.00
#> TCGA.IN.8462.01 4 0.380 0.912 0.22 0.00 0.00 0.78
#> TCGA.HU.8238.01 1 0.000 0.920 1.00 0.00 0.00 0.00
#> TCGA.D7.8575.01 1 0.000 0.920 1.00 0.00 0.00 0.00
#> TCGA.VQ.A8P3.01 1 0.441 0.388 0.70 0.00 0.00 0.30
#> TCGA.BR.8286.01 4 0.361 0.919 0.20 0.00 0.00 0.80
#> TCGA.IN.A6RL.01 2 0.000 1.000 0.00 1.00 0.00 0.00
#> TCGA.BR.8289.01 3 0.000 0.000 0.00 0.00 1.00 0.00
#> TCGA.BR.A44U.01 1 0.000 0.920 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.VQ.AA68.01 4 0.423 0.579 0.42 0 0 0.58 0.00
#> TCGA.CG.4441.01 5 0.104 0.000 0.04 0 0 0.00 0.96
#> TCGA.VQ.A8E7.01 1 0.000 0.971 1.00 0 0 0.00 0.00
#> TCGA.BR.8680.01 1 0.000 0.971 1.00 0 0 0.00 0.00
#> TCGA.D7.A6EV.01 1 0.000 0.971 1.00 0 0 0.00 0.00
#> TCGA.BR.7717.01 4 0.293 0.812 0.18 0 0 0.82 0.00
#> TCGA.HU.A4G8.01 1 0.000 0.971 1.00 0 0 0.00 0.00
#> TCGA.HU.A4GC.01 1 0.000 0.971 1.00 0 0 0.00 0.00
#> TCGA.HU.A4H2.01 2 0.000 1.000 0.00 1 0 0.00 0.00
#> TCGA.D7.6822.01 1 0.000 0.971 1.00 0 0 0.00 0.00
#> TCGA.CG.5724.01 4 0.252 0.790 0.14 0 0 0.86 0.00
#> TCGA.VQ.A8PB.01 4 0.275 0.539 0.04 0 0 0.88 0.08
#> TCGA.HU.8243.01 2 0.000 1.000 0.00 1 0 0.00 0.00
#> TCGA.IN.8462.01 4 0.327 0.820 0.22 0 0 0.78 0.00
#> TCGA.HU.8238.01 1 0.000 0.971 1.00 0 0 0.00 0.00
#> TCGA.D7.8575.01 1 0.000 0.971 1.00 0 0 0.00 0.00
#> TCGA.VQ.A8P3.01 1 0.311 0.667 0.80 0 0 0.20 0.00
#> TCGA.BR.8286.01 4 0.342 0.811 0.24 0 0 0.76 0.00
#> TCGA.IN.A6RL.01 2 0.000 1.000 0.00 1 0 0.00 0.00
#> TCGA.BR.8289.01 3 0.000 0.000 0.00 0 1 0.00 0.00
#> TCGA.BR.A44U.01 1 0.000 0.971 1.00 0 0 0.00 0.00
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> TCGA.VQ.AA68.01 4 0.4310 0.341 0.44 0.00 0 0.54 0.00 0.02
#> TCGA.CG.4441.01 5 0.0000 0.000 0.00 0.00 0 0.00 1.00 0.00
#> TCGA.VQ.A8E7.01 1 0.0000 0.937 1.00 0.00 0 0.00 0.00 0.00
#> TCGA.BR.8680.01 1 0.0000 0.937 1.00 0.00 0 0.00 0.00 0.00
#> TCGA.D7.A6EV.01 1 0.1267 0.903 0.94 0.00 0 0.06 0.00 0.00
#> TCGA.BR.7717.01 4 0.3787 0.608 0.10 0.00 0 0.78 0.00 0.12
#> TCGA.HU.A4G8.01 1 0.0937 0.919 0.96 0.00 0 0.04 0.00 0.00
#> TCGA.HU.A4GC.01 1 0.1267 0.903 0.94 0.00 0 0.06 0.00 0.00
#> TCGA.HU.A4H2.01 2 0.0000 0.990 0.00 1.00 0 0.00 0.00 0.00
#> TCGA.D7.6822.01 1 0.0000 0.937 1.00 0.00 0 0.00 0.00 0.00
#> TCGA.CG.5724.01 4 0.2350 0.450 0.00 0.00 0 0.88 0.02 0.10
#> TCGA.VQ.A8PB.01 6 0.0937 0.000 0.00 0.00 0 0.04 0.00 0.96
#> TCGA.HU.8243.01 2 0.0000 0.990 0.00 1.00 0 0.00 0.00 0.00
#> TCGA.IN.8462.01 4 0.3460 0.668 0.22 0.00 0 0.76 0.00 0.02
#> TCGA.HU.8238.01 1 0.0000 0.937 1.00 0.00 0 0.00 0.00 0.00
#> TCGA.D7.8575.01 1 0.0000 0.937 1.00 0.00 0 0.00 0.00 0.00
#> TCGA.VQ.A8P3.01 1 0.3409 0.475 0.70 0.00 0 0.30 0.00 0.00
#> TCGA.BR.8286.01 4 0.3270 0.651 0.12 0.00 0 0.82 0.00 0.06
#> TCGA.IN.A6RL.01 2 0.0547 0.980 0.00 0.98 0 0.00 0.02 0.00
#> TCGA.BR.8289.01 3 0.0000 0.000 0.00 0.00 1 0.00 0.00 0.00
#> TCGA.BR.A44U.01 1 0.0000 0.937 1.00 0.00 0 0.00 0.00 0.00
cbind(get_classes(res, k = 7), get_membership(res, k = 7))
#> class entropy silhouette p1 p2 p3 p4 p5 p6 p7
#> TCGA.VQ.AA68.01 4 0.4461 0.330 0.32 0.00 0 0.62 0 0.02 0.04
#> TCGA.CG.4441.01 5 0.0000 0.000 0.00 0.00 0 0.00 1 0.00 0.00
#> TCGA.VQ.A8E7.01 1 0.0000 0.908 1.00 0.00 0 0.00 0 0.00 0.00
#> TCGA.BR.8680.01 1 0.0000 0.908 1.00 0.00 0 0.00 0 0.00 0.00
#> TCGA.D7.A6EV.01 1 0.2829 0.813 0.84 0.00 0 0.08 0 0.00 0.08
#> TCGA.BR.7717.01 4 0.3086 0.310 0.00 0.00 0 0.80 0 0.04 0.16
#> TCGA.HU.A4G8.01 1 0.1006 0.891 0.96 0.00 0 0.02 0 0.02 0.00
#> TCGA.HU.A4GC.01 1 0.2016 0.853 0.90 0.00 0 0.06 0 0.00 0.04
#> TCGA.HU.A4H2.01 2 0.0863 0.965 0.00 0.96 0 0.00 0 0.00 0.04
#> TCGA.D7.6822.01 1 0.0000 0.908 1.00 0.00 0 0.00 0 0.00 0.00
#> TCGA.CG.5724.01 7 0.3047 0.000 0.00 0.00 0 0.28 0 0.00 0.72
#> TCGA.VQ.A8PB.01 6 0.0000 0.000 0.00 0.00 0 0.00 0 1.00 0.00
#> TCGA.HU.8243.01 2 0.0000 0.983 0.00 1.00 0 0.00 0 0.00 0.00
#> TCGA.IN.8462.01 4 0.3487 0.470 0.10 0.00 0 0.78 0 0.00 0.12
#> TCGA.HU.8238.01 1 0.0000 0.908 1.00 0.00 0 0.00 0 0.00 0.00
#> TCGA.D7.8575.01 1 0.0000 0.908 1.00 0.00 0 0.00 0 0.00 0.00
#> TCGA.VQ.A8P3.01 1 0.5182 0.210 0.54 0.00 0 0.24 0 0.00 0.22
#> TCGA.BR.8286.01 4 0.3086 0.384 0.04 0.00 0 0.80 0 0.00 0.16
#> TCGA.IN.A6RL.01 2 0.0000 0.983 0.00 1.00 0 0.00 0 0.00 0.00
#> TCGA.BR.8289.01 3 0.0000 0.000 0.00 0.00 1 0.00 0 0.00 0.00
#> TCGA.BR.A44U.01 1 0.0504 0.899 0.98 0.00 0 0.00 0 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.VQ.AA68.01 4 0.5088 0.139 0.20 0.00 0 0.56 0 0.00 0.02 0.22
#> TCGA.CG.4441.01 5 0.0000 0.000 0.00 0.00 0 0.00 1 0.00 0.00 0.00
#> TCGA.VQ.A8E7.01 1 0.0000 0.846 1.00 0.00 0 0.00 0 0.00 0.00 0.00
#> TCGA.BR.8680.01 1 0.0000 0.846 1.00 0.00 0 0.00 0 0.00 0.00 0.00
#> TCGA.D7.A6EV.01 1 0.3299 0.721 0.76 0.00 0 0.06 0 0.00 0.00 0.18
#> TCGA.BR.7717.01 8 0.4655 0.000 0.02 0.00 0 0.34 0 0.02 0.04 0.58
#> TCGA.HU.A4G8.01 1 0.3397 0.757 0.80 0.00 0 0.06 0 0.00 0.04 0.10
#> TCGA.HU.A4GC.01 1 0.3774 0.661 0.70 0.00 0 0.08 0 0.00 0.00 0.22
#> TCGA.HU.A4H2.01 2 0.1557 0.876 0.00 0.92 0 0.00 0 0.00 0.02 0.06
#> TCGA.D7.6822.01 1 0.0000 0.846 1.00 0.00 0 0.00 0 0.00 0.00 0.00
#> TCGA.CG.5724.01 7 0.1563 0.000 0.00 0.00 0 0.10 0 0.00 0.90 0.00
#> TCGA.VQ.A8PB.01 6 0.0000 0.000 0.00 0.00 0 0.00 0 1.00 0.00 0.00
#> TCGA.HU.8243.01 2 0.0808 0.889 0.00 0.96 0 0.00 0 0.00 0.00 0.04
#> TCGA.IN.8462.01 4 0.2591 0.407 0.04 0.00 0 0.86 0 0.00 0.02 0.08
#> TCGA.HU.8238.01 1 0.0471 0.841 0.98 0.00 0 0.00 0 0.00 0.00 0.02
#> TCGA.D7.8575.01 1 0.0000 0.846 1.00 0.00 0 0.00 0 0.00 0.00 0.00
#> TCGA.VQ.A8P3.01 1 0.5668 0.149 0.46 0.00 0 0.24 0 0.00 0.04 0.26
#> TCGA.BR.8286.01 4 0.0808 0.323 0.00 0.00 0 0.96 0 0.00 0.04 0.00
#> TCGA.IN.A6RL.01 2 0.2025 0.856 0.00 0.88 0 0.00 0 0.00 0.02 0.10
#> TCGA.BR.8289.01 3 0.0000 0.000 0.00 0.00 1 0.00 0 0.00 0.00 0.00
#> TCGA.BR.A44U.01 1 0.0808 0.833 0.96 0.00 0 0.04 0 0.00 0.00 0.00
Heatmaps for the consensus matrix. It visualizes the probability of two samples to be in a same group.
consensus_heatmap(res, k = 2)
consensus_heatmap(res, k = 3)
consensus_heatmap(res, k = 4)
consensus_heatmap(res, k = 5)
consensus_heatmap(res, k = 6)
consensus_heatmap(res, k = 7)
consensus_heatmap(res, k = 8)
Heatmaps for the membership of samples in all partitions to see how consistent they are:
membership_heatmap(res, k = 2)
membership_heatmap(res, k = 3)
membership_heatmap(res, k = 4)
membership_heatmap(res, k = 5)
membership_heatmap(res, k = 6)
membership_heatmap(res, k = 7)
membership_heatmap(res, k = 8)
As soon as the classes for columns are determined, the signatures that are significantly different between subgroups can be looked for. Following are the heatmaps for signatures.
get_signatures(res, k = 2)
get_signatures(res, k = 3)
get_signatures(res, k = 4)
get_signatures(res, k = 5)
get_signatures(res, k = 6)
get_signatures(res, k = 7)
get_signatures(res, k = 8)
Compare the overlap of signatures from different k:
compare_signatures(res)
get_signature() returns a data frame invisibly. To get the list of signatures, the function
call should be assigned to a variable explicitly. In following code, if plot argument is set
to FALSE, no heatmap is plotted while only the differential analysis is performed.
# code only for demonstration
tb = get_signature(res, k = ..., plot = FALSE)
An example of the output of tb is:
#> which_row fdr mean_1 mean_2 scaled_mean_1 scaled_mean_2 km
#> 1 38 0.042760348 8.373488 9.131774 -0.5533452 0.5164555 1
#> 2 40 0.018707592 7.106213 8.469186 -0.6173731 0.5762149 1
#> 3 55 0.019134737 10.221463 11.207825 -0.6159697 0.5749050 1
#> 4 59 0.006059896 5.921854 7.869574 -0.6899429 0.6439467 1
#> 5 60 0.018055526 8.928898 10.211722 -0.6204761 0.5791110 1
#> 6 98 0.009384629 15.714769 14.887706 0.6635654 -0.6193277 2
...
The columns in tb are:
which_row: row indices corresponding to the input matrix.fdr: FDR for the differential test. mean_x: The mean value in group x.scaled_mean_x: The mean value in group x after rows are scaled.km: Row groups if k-means clustering is applied to rows (which is done by automatically selecting number of clusters).If there are too many signatures, top_signatures = ... can be set to only show the
signatures with the highest FDRs:
# code only for demonstration
# e.g. to show the top 500 most significant rows
tb = get_signature(res, k = ..., top_signatures = 500)
If the signatures are defined as these which are uniquely high in current group, diff_method argument
can be set to "uniquely_high_in_one_group":
# code only for demonstration
tb = get_signature(res, k = ..., diff_method = "uniquely_high_in_one_group")
UMAP plot which shows how samples are separated.
dimension_reduction(res, k = 2, method = "UMAP")
dimension_reduction(res, k = 3, method = "UMAP")
dimension_reduction(res, k = 4, method = "UMAP")
dimension_reduction(res, k = 5, method = "UMAP")
dimension_reduction(res, k = 6, method = "UMAP")
dimension_reduction(res, k = 7, method = "UMAP")
dimension_reduction(res, k = 8, method = "UMAP")
Following heatmap shows how subgroups are split when increasing k:
collect_classes(res)
If matrix rows can be associated to genes, consider to use functional_enrichment(res,
...) to perform function enrichment for the signature genes. See this vignette for more detailed explanations.
Parent node: Node034. Child nodes: Node01111-leaf , Node01112-leaf , Node01113-leaf , Node01114-leaf , Node01115-leaf , Node01116-leaf , Node01121-leaf , Node01122-leaf , Node01123-leaf , Node01131-leaf , Node01132-leaf , Node01133-leaf , Node01134-leaf , Node01211-leaf , Node01212-leaf , Node01221-leaf , Node01222-leaf , Node01231-leaf , Node01232-leaf , Node01233-leaf , Node01311-leaf , Node01312 , Node02221-leaf , Node02222-leaf , Node02223-leaf , Node02224-leaf , Node03111-leaf , Node03112-leaf , Node03113-leaf , Node03411-leaf , Node03412-leaf , Node03413-leaf .
The object with results only for a single top-value method and a single partitioning method can be extracted as:
res = res_rh["0341"]
A summary of res and all the functions that can be applied to it:
res
#> A 'ConsensusPartition' object with k = 2, 3, 4, 5, 6, 7, 8.
#> On a matrix with 30000 rows and 16 columns.
#> Top rows (1000) are extracted by 'ATC' method.
#> Subgroups are detected by 'kmeans' method.
#> Performed in total 350 partitions by row resampling.
#> Best k for subgroups seems to be 3.
#>
#> Following methods can be applied to this 'ConsensusPartition' object:
#> [1] "cola_report" "collect_classes" "collect_plots"
#> [4] "collect_stats" "colnames" "compare_partitions"
#> [7] "compare_signatures" "consensus_heatmap" "dimension_reduction"
#> [10] "functional_enrichment" "get_anno_col" "get_anno"
#> [13] "get_classes" "get_consensus" "get_matrix"
#> [16] "get_membership" "get_param" "get_signatures"
#> [19] "get_stats" "is_best_k" "is_stable_k"
#> [22] "membership_heatmap" "ncol" "nrow"
#> [25] "plot_ecdf" "predict_classes" "rownames"
#> [28] "select_partition_number" "show" "suggest_best_k"
#> [31] "test_to_known_factors" "top_rows_heatmap"
collect_plots() function collects all the plots made from res for all k (number of subgroups)
into one single page to provide an easy and fast comparison between different k.
collect_plots(res)
The plots are:
k and the heatmap of
predicted classes for each k.k.k.k.All the plots in panels can be made by individual functions and they are plotted later in this section.
select_partition_number() produces several plots showing different
statistics for choosing “optimized” k. There are following statistics:
k;k, the area increased is defined as \(A_k - A_{k-1}\).The detailed explanations of these statistics can be found in the cola vignette.
Generally speaking, higher 1-PAC score, higher mean silhouette score or higher
concordance corresponds to better partition. Rand index and Jaccard index
measure how similar the current partition is compared to partition with k-1.
If they are too similar, we won't accept k is better than k-1.
select_partition_number(res)
The numeric values for all these statistics can be obtained by get_stats().
get_stats(res)
#> k 1-PAC mean_silhouette concordance area_increased Rand Jaccard
#> 2 2 0.567 0.653 0.863 0.5015 0.542 0.542
#> 3 3 0.933 0.954 0.981 0.3799 0.700 0.478
#> 4 4 0.800 0.741 0.873 0.0810 0.908 0.732
#> 5 5 0.783 0.719 0.825 0.0643 0.833 0.474
#> 6 6 0.783 0.755 0.887 0.0532 0.950 0.727
#> 7 7 0.800 0.699 0.900 0.0316 0.992 0.938
#> 8 8 0.825 0.463 0.820 0.0221 0.950 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.VQ.AA68.01 2 0.995 0.755 0.46 0.54
#> TCGA.VQ.A8E7.01 1 0.995 1.000 0.54 0.46
#> TCGA.BR.8680.01 1 0.995 1.000 0.54 0.46
#> TCGA.D7.A6EV.01 2 0.000 0.297 0.00 1.00
#> TCGA.BR.7717.01 2 0.995 0.755 0.46 0.54
#> TCGA.HU.A4G8.01 1 0.995 1.000 0.54 0.46
#> TCGA.HU.A4GC.01 2 0.000 0.297 0.00 1.00
#> TCGA.D7.6822.01 1 0.995 1.000 0.54 0.46
#> TCGA.CG.5724.01 2 0.995 0.755 0.46 0.54
#> TCGA.VQ.A8PB.01 2 0.995 0.755 0.46 0.54
#> TCGA.IN.8462.01 2 0.995 0.755 0.46 0.54
#> TCGA.HU.8238.01 2 0.680 -0.219 0.18 0.82
#> TCGA.D7.8575.01 1 0.995 1.000 0.54 0.46
#> TCGA.VQ.A8P3.01 2 0.995 0.755 0.46 0.54
#> TCGA.BR.8286.01 2 0.995 0.755 0.46 0.54
#> TCGA.BR.A44U.01 2 0.680 -0.219 0.18 0.82
cbind(get_classes(res, k = 3), get_membership(res, k = 3))
#> class entropy silhouette p1 p2 p3
#> TCGA.VQ.AA68.01 2 0.000 1.000 0.0 1 0.0
#> TCGA.VQ.A8E7.01 1 0.000 1.000 1.0 0 0.0
#> TCGA.BR.8680.01 1 0.000 1.000 1.0 0 0.0
#> TCGA.D7.A6EV.01 3 0.000 0.921 0.0 0 1.0
#> TCGA.BR.7717.01 2 0.000 1.000 0.0 1 0.0
#> TCGA.HU.A4G8.01 3 0.556 0.571 0.3 0 0.7
#> TCGA.HU.A4GC.01 3 0.000 0.921 0.0 0 1.0
#> TCGA.D7.6822.01 1 0.000 1.000 1.0 0 0.0
#> TCGA.CG.5724.01 2 0.000 1.000 0.0 1 0.0
#> TCGA.VQ.A8PB.01 2 0.000 1.000 0.0 1 0.0
#> TCGA.IN.8462.01 2 0.000 1.000 0.0 1 0.0
#> TCGA.HU.8238.01 3 0.000 0.921 0.0 0 1.0
#> TCGA.D7.8575.01 1 0.000 1.000 1.0 0 0.0
#> TCGA.VQ.A8P3.01 2 0.000 1.000 0.0 1 0.0
#> TCGA.BR.8286.01 2 0.000 1.000 0.0 1 0.0
#> TCGA.BR.A44U.01 3 0.000 0.921 0.0 0 1.0
cbind(get_classes(res, k = 4), get_membership(res, k = 4))
#> class entropy silhouette p1 p2 p3 p4
#> TCGA.VQ.AA68.01 2 0.1637 0.7818 0.00 0.94 0.00 0.06
#> TCGA.VQ.A8E7.01 1 0.0000 0.8447 1.00 0.00 0.00 0.00
#> TCGA.BR.8680.01 1 0.0000 0.8447 1.00 0.00 0.00 0.00
#> TCGA.D7.A6EV.01 3 0.0000 1.0000 0.00 0.00 1.00 0.00
#> TCGA.BR.7717.01 2 0.4624 0.7719 0.00 0.66 0.00 0.34
#> TCGA.HU.A4G8.01 1 0.6831 -0.0563 0.48 0.00 0.42 0.10
#> TCGA.HU.A4GC.01 3 0.0000 1.0000 0.00 0.00 1.00 0.00
#> TCGA.D7.6822.01 1 0.0707 0.8346 0.98 0.00 0.00 0.02
#> TCGA.CG.5724.01 2 0.4624 0.7719 0.00 0.66 0.00 0.34
#> TCGA.VQ.A8PB.01 2 0.4624 0.7719 0.00 0.66 0.00 0.34
#> TCGA.IN.8462.01 2 0.0000 0.8152 0.00 1.00 0.00 0.00
#> TCGA.HU.8238.01 3 0.0000 1.0000 0.00 0.00 1.00 0.00
#> TCGA.D7.8575.01 1 0.0000 0.8447 1.00 0.00 0.00 0.00
#> TCGA.VQ.A8P3.01 2 0.1211 0.8195 0.00 0.96 0.00 0.04
#> TCGA.BR.8286.01 2 0.0000 0.8152 0.00 1.00 0.00 0.00
#> TCGA.BR.A44U.01 4 0.4907 0.0000 0.00 0.00 0.42 0.58
cbind(get_classes(res, k = 5), get_membership(res, k = 5))
#> class entropy silhouette p1 p2 p3 p4 p5
#> TCGA.VQ.AA68.01 2 0.586 0.421 0.0 0.56 0.00 0.12 0.32
#> TCGA.VQ.A8E7.01 1 0.000 1.000 1.0 0.00 0.00 0.00 0.00
#> TCGA.BR.8680.01 1 0.000 1.000 1.0 0.00 0.00 0.00 0.00
#> TCGA.D7.A6EV.01 3 0.000 1.000 0.0 0.00 1.00 0.00 0.00
#> TCGA.BR.7717.01 5 0.000 1.000 0.0 0.00 0.00 0.00 1.00
#> TCGA.HU.A4G8.01 2 0.827 -0.440 0.3 0.32 0.26 0.12 0.00
#> TCGA.HU.A4GC.01 3 0.000 1.000 0.0 0.00 1.00 0.00 0.00
#> TCGA.D7.6822.01 1 0.000 1.000 1.0 0.00 0.00 0.00 0.00
#> TCGA.CG.5724.01 5 0.000 1.000 0.0 0.00 0.00 0.00 1.00
#> TCGA.VQ.A8PB.01 5 0.000 1.000 0.0 0.00 0.00 0.00 1.00
#> TCGA.IN.8462.01 2 0.418 0.521 0.0 0.60 0.00 0.00 0.40
#> TCGA.HU.8238.01 3 0.000 1.000 0.0 0.00 1.00 0.00 0.00
#> TCGA.D7.8575.01 1 0.000 1.000 1.0 0.00 0.00 0.00 0.00
#> TCGA.VQ.A8P3.01 2 0.426 0.473 0.0 0.56 0.00 0.00 0.44
#> TCGA.BR.8286.01 2 0.418 0.521 0.0 0.60 0.00 0.00 0.40
#> TCGA.BR.A44U.01 4 0.228 0.000 0.0 0.00 0.12 0.88 0.00
cbind(get_classes(res, k = 6), get_membership(res, k = 6))
#> class entropy silhouette p1 p2 p3 p4 p5 p6
#> TCGA.VQ.AA68.01 6 0.5012 -0.291 0.00 0.30 0.00 0.00 0.10 0.60
#> TCGA.VQ.A8E7.01 1 0.0000 0.967 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.BR.8680.01 1 0.0000 0.967 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.D7.A6EV.01 3 0.0000 0.991 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.BR.7717.01 5 0.0000 1.000 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.HU.A4G8.01 6 0.8255 -0.195 0.22 0.08 0.20 0.12 0.00 0.38
#> TCGA.HU.A4GC.01 3 0.0000 0.991 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.D7.6822.01 1 0.2094 0.897 0.90 0.08 0.00 0.00 0.00 0.02
#> TCGA.CG.5724.01 5 0.0000 1.000 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.VQ.A8PB.01 5 0.0000 1.000 0.00 0.00 0.00 0.00 1.00 0.00
#> TCGA.IN.8462.01 2 0.2631 0.951 0.00 0.82 0.00 0.00 0.18 0.00
#> TCGA.HU.8238.01 3 0.0547 0.982 0.00 0.02 0.98 0.00 0.00 0.00
#> TCGA.D7.8575.01 1 0.0000 0.967 1.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.VQ.A8P3.01 2 0.3821 0.902 0.00 0.74 0.00 0.04 0.22 0.00
#> TCGA.BR.8286.01 2 0.2631 0.951 0.00 0.82 0.00 0.00 0.18 0.00
#> TCGA.BR.A44U.01 4 0.0937 0.000 0.00 0.00 0.04 0.96 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.VQ.AA68.01 6 0.331 0.000 0.00 0.24 0.00 0 0.02 0.74 0.00
#> TCGA.VQ.A8E7.01 1 0.000 0.893 1.00 0.00 0.00 0 0.00 0.00 0.00
#> TCGA.BR.8680.01 1 0.000 0.893 1.00 0.00 0.00 0 0.00 0.00 0.00
#> TCGA.D7.A6EV.01 3 0.000 0.960 0.00 0.00 1.00 0 0.00 0.00 0.00
#> TCGA.BR.7717.01 5 0.000 1.000 0.00 0.00 0.00 0 1.00 0.00 0.00
#> TCGA.HU.A4G8.01 7 0.662 0.000 0.18 0.00 0.14 0 0.00 0.24 0.44
#> TCGA.HU.A4GC.01 3 0.000 0.960 0.00 0.00 1.00 0 0.00 0.00 0.00
#> TCGA.D7.6822.01 1 0.364 0.629 0.72 0.04 0.00 0 0.00 0.00 0.24
#> TCGA.CG.5724.01 5 0.000 1.000 0.00 0.00 0.00 0 1.00 0.00 0.00
#> TCGA.VQ.A8PB.01 5 0.000 1.000 0.00 0.00 0.00 0 1.00 0.00 0.00
#> TCGA.IN.8462.01 2 0.167 0.768 0.00 0.90 0.00 0 0.10 0.00 0.00
#> TCGA.HU.8238.01 3 0.166 0.918 0.00 0.06 0.92 0 0.00 0.02 0.00
#> TCGA.D7.8575.01 1 0.000 0.893 1.00 0.00 0.00 0 0.00 0.00 0.00
#> TCGA.VQ.A8P3.01 2 0.500 0.495 0.00 0.54 0.00 0 0.14 0.00 0.32
#> TCGA.BR.8286.01 2 0.167 0.768 0.00 0.90 0.00 0 0.10 0.00 0.00
#> TCGA.BR.A44U.01 4 0.000 0.000 0.00 0.00 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.VQ.AA68.01 6 0.1765 0.000 0.00 0.12 0.00 0.00 0.00 0.88 0.00 0.00
#> TCGA.VQ.A8E7.01 1 0.5499 0.517 0.50 0.10 0.00 0.00 0.00 0.08 0.00 0.32
#> TCGA.BR.8680.01 1 0.3333 0.425 0.50 0.00 0.00 0.00 0.00 0.00 0.00 0.50
#> TCGA.D7.A6EV.01 3 0.1091 0.939 0.00 0.00 0.94 0.00 0.00 0.00 0.00 0.06
#> TCGA.BR.7717.01 5 0.0000 1.000 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.HU.A4G8.01 7 0.2265 0.000 0.08 0.00 0.02 0.02 0.00 0.00 0.88 0.00
#> TCGA.HU.A4GC.01 3 0.1275 0.939 0.00 0.02 0.94 0.00 0.00 0.04 0.00 0.00
#> TCGA.D7.6822.01 1 0.0000 0.366 1.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
#> TCGA.CG.5724.01 5 0.0000 1.000 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.VQ.A8PB.01 5 0.0000 1.000 0.00 0.00 0.00 0.00 1.00 0.00 0.00 0.00
#> TCGA.IN.8462.01 2 0.1947 0.886 0.00 0.86 0.00 0.00 0.14 0.00 0.00 0.00
#> TCGA.HU.8238.01 3 0.0941 0.921 0.00 0.02 0.96 0.00 0.00 0.00 0.00 0.02
#> TCGA.D7.8575.01 8 0.3333 -0.808 0.50 0.00 0.00 0.00 0.00 0.00 0.00 0.50
#> TCGA.VQ.A8P3.01 8 0.4999 -0.656 0.00 0.40 0.00 0.00 0.18 0.00 0.00 0.42
#> TCGA.BR.8286.01 2 0.3619 0.886 0.00 0.74 0.00 0.00 0.14 0.00 0.12 0.00
#> TCGA.BR.A44U.01 4 0.0000 0.000 0.00 0.00 0.00 1.00 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.
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
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#> [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
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#> [81] gtable_0.3.0 openssl_1.4.4 assertthat_0.2.1 clue_0.3-59
#> [85] cachem_1.0.5 ggplot2_3.3.5 xfun_0.24 eulerr_6.1.0
#> [89] xtable_1.8-4 skmeans_0.2-13 RSpectra_0.16-0 viridisLite_0.4.0
#> [93] survival_3.2-11 tibble_3.1.2 Polychrome_1.3.1 iterators_1.0.13
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