analyseGenesets: Wrapped to run gene set enrichement on multiple annotation...

In sansomlab/gsfisher: Geneset Fisher

Wrapped to run gene set enrichement on multiple annotation databases

Description

A wrapper function to run Fisher tests for enrichement from GO categories, KEGG pathways and GMT files

Usage

analyseGenesets(
  foreground_ids,
  background_ids,
  gene_id_type = c("entrez", "ensembl"),
  kegg_pathways = NULL,
  gmt_files = c(),
  species = c("hs", "mm")
)

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")
kegg_pathways	A list of KEGG gene sets.
gmt_files	A named list of paths to GMT files.
species	Species identifier (only "hs" or "mm" are supported).

Author(s)

Steve Sansom

See Also

runGO, runKEGG, runGMT.

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.