Fast Gene Set Enrichment Analysis


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Documentation for package ‘fgsea’ version 1.10.1

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.
examplePathways Example list of mouse Reactome pathways.
exampleRanks Example vector of gene-level statistics obtained for Th1 polarization.
fgsea Runs preranked gene set enrichment analysis.
fgseaLabel Runs label-permuring gene set enrichment analysis.
fgseaMultilevel Runs preranked gene set enrichment analysis.
fgseaSimpleImpl Runs preranked gene set enrichment analysis for preprocessed input data.
gmtPathways Returns a list of pathways from a GMT file.
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