runGMT: Run gene set enrichement on custom gene sets
In sansomlab/gsfisher: Geneset Fisher

runGMT

R Documentation

Run gene set enrichement on custom gene sets

Description

A wrapper function to run Fisher tests for enrichement from GMT files.

Usage

runGMT(
  foreground_ids,
  background_ids,
  gene_id_type = c("entrez", "ensembl"),
  species = c("mm", "hs"),
  gmt_file,
  ...
)

Arguments

`foreground_ids`	A list of ENTREZ ids of interest (e.g. significantly differentially expressed genes).
`background_ids`	A list of background ENTREZ ids. against which enrichment will be tested (i.e., the gene universe).
`gene_id_type`	Either "entrez" (default) or "ensembl".
`species`	Species identifier (only "hs" or "mm" are supported).
`gmt_file`	path to a GMT file.

Author(s)

Steve Sansom

Examples

gmtFile <- system.file(package = "gsfisher", "extdata", "kegg_hs.gmt")
ann_gmt <- readGMT(gmtFile)
# Take 50% of the first gene set as an example list of interest
foreground <- head(ann_gmt[[1]], length(ann_gmt[[1]]) / 2)
## Not run: 
# TODO

## End(Not run)

sansomlab/gsfisher documentation built on July 7, 2022, 4:21 a.m.