# Fast Gene Set Enrichment Analysis

## Documentation for package ‘fgsea’ version 1.39.2

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package NEWS
- Package README

## Help Pages

calcGseaStat | Calculates GSEA statistics for a given query gene set
calcGseaStatBatchCpp | Calculates GSEA statistic valus for all gene sets in 'selectedStats' list.
calcGseaStatCumulative | Calculates GSEA statistic values for all the prefixes of a gene set
collapsePathways | Collapse list of enriched pathways to independent ones.
collapsePathwaysGeseca | Collapse list of enriched pathways to independent ones (GESECA version, highly experimental).
collapsePathwaysORA | Collapse list of enriched pathways to independent ones. Version for ORA hypergeometric test.
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 polarization.
fgsea | Wrapper to run methods for preranked gene set enrichment analysis.
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 input data.
fora | Simple overrepresentation analysis based on hypergeometric test
geseca | Runs multilevel Monte-Carlo variant for performing gene sets co-regulation analysis
gesecaSimple | Runs simple variant for performing gene sets co-regulation analysis
gmtPathways | Returns a list of pathways from a GMT file.
mapIdsList | Effeciently converts collection of pathways using AnnotationDbi::mapIds function. Parameters are the sames as for mapIds except for keys, which is assumed to be a list of vectors.
multilevelError | Calculates the expected error for the standard deviation of the P-value logarithm.
multilevelImpl | Calculates P-values for preprocessed data.
plotCoregulationProfile | Plots expression profile of a gene set
plotCoregulationProfileImage | Spatial visualization of GESECA scores for individual cells
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' function.
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