Prepare gene set files

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")
#> ℹ Detected 1 GMT file of `keyType` "geneName" in /private/var/folders/l1/8y8sjzmn15v49jgrqglghcfr0000gn/T/RtmpKetMc1/temp_libpath16fef37658ca8/AcidGSEA/extdata/msigdb/7.0/msigdb_v7.0_GMTs.
print(files)
#>                                                                                                                                                  h_all_v7_0_symbols 
#> "/private/var/folders/l1/8y8sjzmn15v49jgrqglghcfr0000gn/T/RtmpKetMc1/temp_libpath16fef37658ca8/AcidGSEA/extdata/msigdb/7.0/msigdb_v7.0_GMTs/h.all.v7.0.symbols.gmt"