Man pages for montilab/K2Taxonomer
Creating annotated submodules of high-throughput data through recursive partitioning
| aggregateGSVAscores | Take difference of two paired GSVA scores |
| cKmeansWrapper | Wrapper for constrained K-means |
| cKmeansWrapperSubsample | Wrapper for constrained K-means on subsampled data |
| getDGETable | Extract table of differential results from 'K2' object |
| getEnrichmentTable | Extract table of enrichment results from 'K2' object |
| getGenePathways | Map features (genes) to feature list (genesets) |
| getTestsModTable | Extract table of phenotypic variable tests from 'K2' object |
| hclustWrapper | Wrapper for hierarchical clustering |
| K2-class | K2 object |
| K2dashboard | Generate interactive dashboard of K2 Taxonomer results |
| K2data | Data matrix from K2 object |
| K2dendro | Reformat K2Taxonomer results to dendrogram object |
| K2eSet | ExpressionSet object used in K2Taxonomer run |
| K2gene2Pathway | Vector of collapsed pathways for which each gene belongs |
| K2genesets | Named list of genesets used in K2Taxonomer run |
| K2genesetURL | Assign URLs to genesets included in K2Taxonomer run |
| K2geneURL | Assign URLs to genes included in K2Taxonomer run |
| K2gSet | ExpressionSet object of of GSVA output |
| K2info | Data frame of phenotypic information from K2 object |
| K2meta | Meta data defining parameters of K2Taxonomer run |
| K2preproc | Function to create K2 object for pre-processing |
| K2res | Example K2Taxonomer output |
| K2results | Annotated list of partition assignments from K2Taxonomer run |
| K2tax | Function K2 Taxonomer |
| K2visNetwork | Interactive K2 dendrogram |
| runDGEmods | Perform differential analysis of gene splits |
| runDSSEmods | Perform differential analysis of single-sample gene set... |
| runGSEmods | Perform hyperenrichment of split specific gene signatures |
| runGSVAmods | Perform ssGSVA on gene sets and get set signature hits |
| runK2Taxonomer | Wrapper function to run K2Taxonomer algorithm and annotation |
| runTestsMods | Perform tests to test for associations between subgroups and... |
