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All functions

FGSEAList-class
Fast GSEA list
FGSEAList()
Parameterized fast gene set enrichment analysis (GSEA)
Gene2Symbol()
Gene-to-symbol mappings
RankedList-class
Ranked list of genes
RankedList()
Ranked list of genes
alphaThreshold() `alphaThreshold<-`()
Alpha threshold
collectionNames() `collectionNames<-`()
Gene set collection names
combine()
Combine multiple objects
contrastNames() `contrastNames<-`()
Contrast names
convertToHuman()
Convert data set by mapping to human orthologs
enrichedGeneSets()
Enriched gene sets
export()
Export
fgsea
FGSEAList example data
geneSet()
Gene set
geneSetNames()
Gene set names
geneSetResults()
Gene set results
leadingEdge()
Leading edge genes
nesThreshold() `nesThreshold<-`()
Normalized enrichment score (NES) threshold
plotEnrichedGeneSets()
Plot enriched gene sets
plotEnrichedUpset()
UpSet plot of directional enriched pathway intersections across contrasts
plotGeneSet()
Plot gene set enrichment
plotHeatmap()
Heatmap
plotLFC()
Plot log2 fold change distributions
plotNES()
Plot normalized enrichment score
prepareGeneSetFiles()
Prepare gene set files
results()
Results
show(<FGSEAList>)
Show an object
topTables()
Top tables
updateObject()
Update object