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