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fgsea

Fast Gene Set Enrichment Analysis

The package implements an algorithm for fast gene set enrichment analysis. Using the fast algorithm allows to make more permutations and get more fine grained p-values, which allows to use accurate stantard approaches to multiple hypothesis correction.

Functions (20)

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