# Fast Gene Set Enrichment Analysis

## Documentation for package ‘fgsea’ version 1.16.0

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

## Help Pages

calcGseaStat | Calculates GSEA statistics for a given query gene set
calcGseaStatBatchCpp | Calculates GSEA statistic valus for all gene sets in 'selectedStats' list.
collapsePathways | Collapse list of enriched pathways to independent ones.
collapsePathwaysORA | Collapse list of enriched pathways to independent ones. Version for ORA hypergeometric test.
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
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.
plotEnrichment | Plots GSEA enrichment plot.
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