# Acid Genomics GSEA

## Documentation for package ‘AcidGSEA’ version 0.8.8

- DESCRIPTION file.
- Package NEWS.

## 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