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