Fast Gene Set Enrichment Analysis

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Documentation for package ‘fgsea’ version 1.26.0

• 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.
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
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