FgseaList: Parameterized fast gene set enrichment analysis (GSEA)

In steinbaugh/pfgsea: Acid Genomics GSEA

Parameterized fast gene set enrichment analysis (GSEA)

Description

Extends the functionality of fgsea::fgsea().

Usage

FgseaList(object, ...)

## S4 method for signature 'DESeqAnalysis'
FgseaList(
  object,
  keyType = c("geneName", "ensemblGeneId", "ncbiGeneId"),
  value = c("stat", "log2FoldChange"),
  proteinCodingOnly = FALSE,
  ...
)

## S4 method for signature 'DESeqResults'
FgseaList(
  object,
  keyType = c("geneName", "ensemblGeneId", "ncbiGeneId"),
  value = c("stat", "log2FoldChange"),
  rowRanges,
  proteinCodingOnly = FALSE,
  ...
)

## S4 method for signature 'RankedList'
FgseaList(object, geneSetFiles)

Arguments

object	Object.
...	Additional arguments.
keyType	'character(1). Gene identifier format: "geneName": Gene names (a.k.a. symbols; e.g. "TP53"). ⁠"ensemblGeneId⁠: Ensembl gene identifiers (e.g. "ENSG00000000003"). "ncbiGeneId": NCBI (Entrez) gene identifiers (e.g. 7157).
value	character(1). Value type to use for GSEA ranked list. Currently supported: stat: Wald test statistic. This column is returned by results() but is removed in DESeq2::lfcShrink() return, currently. log2FoldChange: Shrunken log2 fold change. Note that this option requires DESeq2::lfcShrink() return to be slotted. padj: Adjusted P value. This don't provide directional ranks, but is offered as a legacy option. Not generally recommended.
proteinCodingOnly	logical(1). Restrict to protein coding genes only.
rowRanges	GenomicRanges or GenomicRangesList. Genomic ranges (e.g. genome annotations). Metadata describing the assay rows.
geneSetFiles	character. Gene set file paths (i.e. GMT files). MSigDB files are recommended by default.

Value

FgseaList.

Note

Updated 2023-10-04.

Examples

data(deseq, package = "DESeqAnalysis")

## DESeqAnalysis ====
object <- deseq
geneSetFiles <- prepareGeneSetFiles(
    dir = system.file(
        "extdata",
        "msigdb",
        "7.0",
        "msigdb_v7.0_GMTs",
        package = "AcidGSEA"
    )
)
fgsea <- FgseaList(
    object = object,
    geneSetFiles = geneSetFiles
)
print(fgsea)

steinbaugh/pfgsea documentation built on Oct. 17, 2023, 11:24 a.m.