Man pages for steinbaugh/pfgsea
Acid Genomics GSEA
| 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 |
