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