Man pages for ctlab/fgsea
Fast Gene Set Enrichment Analysis
| calcGseaStat | Calculates GSEA statistics for a given query gene set |
| calcGseaStatBatchCpp | Calculates GSEA statistic valus for all gene sets in... |
| collapsePathways | Collapse list of enriched pathways to independent ones. |
| collapsePathwaysGeseca | Collapse list of enriched pathways to independent ones... |
| collapsePathwaysORA | Collapse list of enriched pathways to independent ones.... |
| exampleExpressionMatrix | Example of expression values obtained for GSE14308. |
| examplePathways | Example list of mouse Reactome pathways. |
| exampleRanks | Example vector of gene-level statistics obtained for Th1... |
| fgsea | Wrapper to run methods for preranked gene set enrichment... |
| fgseaLabel | Runs label-permuring gene set enrichment analysis. |
| fgseaMultilevel | Runs preranked gene set enrichment analysis. |
| fgseaSimple | Runs preranked gene set enrichment analysis. |
| fgseaSimpleImpl | Runs preranked gene set enrichment analysis for preprocessed... |
| fora | Simple overrepresentation analysis based on hypergeometric... |
| geseca | Runs multilevel Monte-Carlo variant for performing gene sets... |
| gesecaSimple | Runs simple variant for performing gene sets co-regulation... |
| gmtPathways | Returns a list of pathways from a GMT file. |
| mapIdsList | Effeciently converts collection of pathways using... |
| multilevelError | Calculates the expected error for the standard deviation of... |
| multilevelImpl | Calculates P-values for preprocessed data. |
| plotCoregulationProfile | Plots expression profile of a gene set |
| plotCoregulationProfileReduction | Plot a spatial expression profile of a gene set |
| plotCoregulationProfileSpatial | Plot a spatial expression profile of a gene set |
| plotEnrichment | Plots GSEA enrichment plot. For more flexibility use... |
| plotEnrichmentData | Returns data required for doing an enrichment plot. |
| plotGesecaTable | Plots table of gene set profiles. |
| plotGseaTable | Plots table of enrichment graphs using ggplot and gridExtra. |
| reactomePathways | Returns a list of Reactome pathways for given Entrez gene IDs |
| writeGmtPathways | Write collection of pathways (list of vectors) to a gmt file |
