prepareGeneSetFiles: Prepare gene set files

In steinbaugh/pfgsea: Acid Genomics GSEA

Prepare gene set files

Description

Prepare gene set files

Usage

prepareGeneSetFiles(
  dir,
  keyType = c("geneName", "ncbiGeneId"),
  ext = "gmt",
  recursive = FALSE
)

Arguments

dir	character(1). Directory name containing MSigDb release.
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).
ext	character(1). Gene set file extension. Case insensitive.
recursive	logical(1). Whether to search for gene set files recursively in dir argument.

Details

Intended primarily to match GMT files from MSigDb.

Note

Updated 2021-10-20.

See Also

• https://www.gsea-msigdb.org/gsea/msigdb/

• https://www.ncbi.nlm.nih.gov/gene/

Examples

dir <- system.file(
    "extdata",
    "msigdb",
    "7.0",
    "msigdb_v7.0_GMTs",
    package = "AcidGSEA",
    mustWork = TRUE
)
files <- prepareGeneSetFiles(dir, keyType = "geneName")
print(files)

steinbaugh/pfgsea documentation built on March 29, 2025, 5:30 a.m.