Files in cola

A Framework for Consensus Partitioning

README.md R/correspond_rank.R R/z.register.R R/hierarchical.R R/run_all_methods.R R/RcppExports.R R/utils.R R/merge_back.R R/stat.R R/sample_by_columns.R R/report.R R/get.R R/top_rows.R R/down_sampling.R R/zzz.R R/test_with_known.R R/00_classes.R R/data.R R/cola.R R/dend_utils.R R/signatures.R R/00_S4_generic_methods.R R/z.global.R R/collect.R R/consensus_partition.R R/functional_enrichment.R R/predict.R vignettes/cola_quick.Rmd vignettes/silhouette.R vignettes/rand_jaccard.R vignettes/work_with_big_datasets.Rmd vignettes/PAC.R vignettes/cola.Rmd vignettes/test_NMF.R vignettes/functional_enrichment.Rmd vignettes/predict.Rmd vignettes/ATC.R vignettes/vignette_example.R man/membership_heatmap-ConsensusPartition-method.Rd man/ncol-dispatch.Rd man/consensus_heatmap-ConsensusPartition-method.Rd man/collect_classes-HierarchicalPartition-method.Rd man/HierarchicalPartition-class.Rd man/show-dispatch.Rd man/collect_plots-ConsensusPartition-method.Rd man/adjust_outlier.Rd man/consensus_partition.Rd man/get_param-ConsensusPartition-method.Rd man/all_partition_methods.Rd man/register_SOM.Rd man/functional_enrichment-dispatch.Rd man/get_signatures-HierarchicalPartition-method.Rd man/get_anno-dispatch.Rd man/dimension_reduction-matrix-method.Rd man/dim.DownSamplingConsensusPartition.Rd man/collect_plots-ConsensusPartitionList-method.Rd man/cola_opt.Rd man/golub_cola.Rd man/cola.Rd man/register_top_value_methods.Rd man/select_partition_number-ConsensusPartition-method.Rd man/FCC.Rd man/golub_cola_ds.Rd man/predict_classes-dispatch.Rd man/get_stats-dispatch.Rd man/dimension_reduction-DownSamplingConsensusPartition-method.Rd man/nrow-HierarchicalPartition-method.Rd man/rownames-ConsensusPartitionList-method.Rd man/test_between_factors.Rd man/test_to_known_factors-HierarchicalPartition-method.Rd man/collect_stats-ConsensusPartition-method.Rd man/nrow-ConsensusPartition-method.Rd man/suggest_best_k-ConsensusPartitionList-method.Rd man/get_anno_col-ConsensusPartition-method.Rd man/remove_top_value_methods.Rd man/test_to_known_factors-ConsensusPartitionList-method.Rd man/knitr_insert_tabs.Rd man/ncol-ConsensusPartitionList-method.Rd man/register_NMF.Rd man/colnames-DownSamplingConsensusPartition-method.Rd man/ncol-ConsensusPartition-method.Rd man/all_top_value_methods.Rd man/colnames-HierarchicalPartition-method.Rd man/get_consensus-ConsensusPartition-method.Rd man/dim.HierarchicalPartition.Rd man/hierarchical_partition.Rd man/collect_classes-ConsensusPartition-method.Rd man/cola_report-HierarchicalPartition-method.Rd man/get_signatures-DownSamplingConsensusPartition-method.Rd man/consensus_partition_by_down_sampling.Rd man/golub_cola_rh.Rd man/top_rows_heatmap-ConsensusPartitionList-method.Rd man/colnames-ConsensusPartitionList-method.Rd man/ExtractExtract.ConsensusPartitionList.Rd man/nrow-dispatch.Rd man/david_enrichment.Rd man/get_matrix-ConsensusPartition-method.Rd man/collect_classes-dispatch.Rd man/test_to_known_factors-dispatch.Rd man/get_classes-ConsensusPartition-method.Rd man/cola_report-ConsensusPartition-method.Rd man/test_to_known_factors-ConsensusPartition-method.Rd man/compare_signatures-dispatch.Rd man/aPAC.Rd man/get_matrix-ConsensusPartitionList-method.Rd man/find_best_km.Rd man/rownames-HierarchicalPartition-method.Rd man/predict_classes-matrix-method.Rd man/dimension_reduction-HierarchicalPartition-method.Rd man/dim.ConsensusPartitionList.Rd man/is_stable_k-dispatch.Rd man/relabel_class.Rd man/get_signatures-dispatch.Rd man/dimension_reduction-dispatch.Rd man/map_to_entrez_id.Rd man/concordance.Rd man/Extract.HierarchicalPartition.Rd man/suggest_best_k-HierarchicalPartition-method.Rd man/collect_stats-dispatch.Rd man/all_leaves-HierarchicalPartition-method.Rd man/top_elements_overlap.Rd man/collect_stats-ConsensusPartitionList-method.Rd man/ATC.Rd man/ConsensusPartition-class.Rd man/get_classes-DownSamplingConsensusPartition-method.Rd man/knitr_add_tab_item.Rd man/nrow-ConsensusPartitionList-method.Rd man/is_stable_k-ConsensusPartitionList-method.Rd man/rownames-ConsensusPartition-method.Rd man/PAC.Rd man/top_rows_overlap-matrix-method.Rd man/functional_enrichment-ConsensusPartition-method.Rd man/suggest_best_k-ConsensusPartition-method.Rd man/show-HierarchicalPartition-method.Rd man/register_partition_methods.Rd man/dimension_reduction-ConsensusPartition-method.Rd man/is_best_k-dispatch.Rd man/cola_report-dispatch.Rd man/correspond_between_two_rankings.Rd man/get_classes-ConsensusPartitionList-method.Rd man/get_membership-ConsensusPartitionList-method.Rd man/colnames-ConsensusPartition-method.Rd man/get_matrix-dispatch.Rd man/ncol-DownSamplingConsensusPartition-method.Rd man/is_best_k-ConsensusPartitionList-method.Rd man/Extract.ConsensusPartitionList.Rd man/get_anno_col-dispatch.Rd man/is_best_k-ConsensusPartition-method.Rd man/max_depth-HierarchicalPartition-method.Rd man/get_stats-ConsensusPartition-method.Rd man/get_signatures-ConsensusPartition-method.Rd man/run_all_consensus_partition_methods.Rd man/collect_plots-dispatch.Rd man/get_classes-HierarchicalPartition-method.Rd man/top_rows_heatmap-dispatch.Rd man/colnames-dispatch.Rd man/show-DownSamplingConsensusPartition-method.Rd man/predict_classes-ConsensusPartition-method.Rd man/cola_report-ConsensusPartitionList-method.Rd man/correspond_between_rankings.Rd man/get_anno-DownSamplingConsensusPartition-method.Rd man/collect_classes-ConsensusPartitionList-method.Rd man/compare_signatures-HierarchicalPartition-method.Rd man/suggest_best_k-dispatch.Rd man/get_matrix-HierarchicalPartition-method.Rd man/adjust_matrix.Rd man/ExtractExtract.HierarchicalPartition.Rd man/cola_rl.Rd man/ConsensusPartitionList-class.Rd man/get_stats-ConsensusPartitionList-method.Rd man/show-ConsensusPartition-method.Rd man/test_to_known_factors-DownSamplingConsensusPartition-method.Rd man/plot_ecdf-ConsensusPartition-method.Rd man/recalc_stats.Rd man/get_classes-dispatch.Rd man/dim.ConsensusPartition.Rd man/all_nodes-HierarchicalPartition-method.Rd man/ncol-HierarchicalPartition-method.Rd man/get_anno_col-HierarchicalPartition-method.Rd man/DownSamplingConsensusPartition-class.Rd man/top_rows_heatmap-matrix-method.Rd man/get_anno-HierarchicalPartition-method.Rd man/get_membership-dispatch.Rd man/compare_signatures-ConsensusPartition-method.Rd man/remove_partition_methods.Rd man/get_anno-ConsensusPartitionList-method.Rd man/rownames-dispatch.Rd man/top_rows_overlap-dispatch.Rd man/get_anno-ConsensusPartition-method.Rd man/get_anno_col-ConsensusPartitionList-method.Rd man/top_rows_overlap-ConsensusPartitionList-method.Rd man/get_membership-ConsensusPartition-method.Rd man/functional_enrichment-ANY-method.Rd man/show-ConsensusPartitionList-method.Rd man/functional_enrichment-ConsensusPartitionList-method.Rd man/is_stable_k-ConsensusPartition-method.Rd tests/test-all.R tests/testthat/test_relabel.R tests/testthat/test_pdist.R tests/testthat/test-stats.R tests/testthat/test_column_sampling.R inst/doc/cola_quick.Rmd inst/doc/work_with_big_datasets.R inst/doc/work_with_big_datasets.Rmd inst/doc/cola.Rmd inst/doc/functional_enrichment.Rmd inst/doc/predict.Rmd inst/doc/cola.R inst/doc/cola_quick.R inst/doc/functional_enrichment.R inst/doc/predict.R inst/extdata/test_cola.R