Acid Genomics GSEA
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Documentation for package ‘AcidGSEA’ version 0.8.8
Help Pages
| alphaThreshold | Alpha threshold |
| alphaThreshold-method | Alpha threshold |
| alphaThreshold<- | Alpha threshold |
| alphaThreshold<--method | Alpha threshold |
| collectionNames | Gene set collection names |
| collectionNames-method | Gene set collection names |
| collectionNames<- | Gene set collection names |
| collectionNames<--method | Gene set collection names |
| combine | Combine multiple objects |
| combine-method | Combine multiple objects |
| contrastNames | Contrast names |
| contrastNames-method | Contrast names |
| contrastNames<- | Contrast names |
| contrastNames<--method | Contrast names |
| convertToHuman | Convert data set by mapping to human orthologs |
| convertToHuman-method | Convert data set by mapping to human orthologs |
| enrichedGeneSets | Enriched gene sets |
| enrichedGeneSets-method | Enriched gene sets |
| export | Export |
| export-method | Export |
| fgsea | FGSEAList example data |
| FGSEAList | Parameterized fast gene set enrichment analysis (GSEA) |
| FGSEAList-class | Fast GSEA list |
| FGSEAList-method | Parameterized fast gene set enrichment analysis (GSEA) |
| Gene2Symbol | Gene-to-symbol mappings |
| Gene2Symbol-method | Gene-to-symbol mappings |
| geneSet | Gene set |
| geneSet-method | Gene set |
| geneSetNames | Gene set names |
| geneSetNames-method | Gene set names |
| geneSetResults | Gene set results |
| geneSetResults-method | Gene set results |
| leadingEdge | Leading edge genes |
| leadingEdge-method | Leading edge genes |
| markdownTables | Markdown tables |
| markdownTables-method | Markdown tables |
| nesThreshold | Normalized enrichment score (NES) threshold |
| nesThreshold-method | Normalized enrichment score (NES) threshold |
| nesThreshold<- | Normalized enrichment score (NES) threshold |
| nesThreshold<--method | Normalized enrichment score (NES) threshold |
| plotEnrichedGeneSets | Plot enriched gene sets |
| plotEnrichedGeneSets-method | Plot enriched gene sets |
| plotEnrichedUpset | UpSet plot of directional enriched pathway intersections across contrasts |
| plotEnrichedUpset-method | UpSet plot of directional enriched pathway intersections across contrasts |
| plotGeneSet | Plot gene set enrichment |
| plotGeneSet-method | Plot gene set enrichment |
| plotHeatmap | Heatmap |
| plotHeatmap-method | Heatmap |
| plotLFC | Plot log2 fold change distributions |
| plotLFC-method | Plot log2 fold change distributions |
| plotNES | Plot normalized enrichment score |
| plotNES-method | Plot normalized enrichment score |
| prepareGeneSetFiles | Prepare gene set files |
| RankedList | Ranked list of genes |
| RankedList-class | Ranked list of genes |
| RankedList-method | Ranked list of genes |
| results | Results |
| results-method | Results |
| show | Show an object |
| show-method | Show an object |
| updateObject | Update object |
| updateObject-method | Update object |