runKEGG: Run gene set enrichement on KEGG pathways

In sansomlab/gsfisher: Geneset Fisher

Run gene set enrichement on KEGG pathways

Description

A wrapper function to run Fisher tests for enrichement of KEGG Pathways.

Usage

runKEGG(
  foreground_ids,
  background_ids,
  gene_id_type = c("entrez", "ensembl"),
  species = c("hs", "mm"),
  keggData = NULL,
  ...
)

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).
keggData	Object retrieved with fetchKEGG(). Obtained automatically if not specified.

Author(s)

Steve Sansom

See Also

readGMT, fetchKEGG, runFisherTests.

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.