readPathwayGMT: Read Pathway GMT File

In wikipathways/rWikiPathways: rWikiPathways - R client library for the WikiPathways API

Read Pathway GMT File

Description

Reads a WikiPathways GMT file to produce a data frame of pathway-gene associations useful in enrichment analyses and other applications.

Usage

readPathwayGMT(file)

Arguments

file	Path to GMT file

Details

The returned data frame includes pathway name, version, identifier, and organism. The gene content is provided as NCBI Entrez Gene identifiers. The input file can be retrieved by using downloadPathwayArchive(organism="Homo sapiens",format="gmt").

Value

Data frame of pathway-gene associations

References

Adapted from the generic GMT reader provided by clusterProfiler, https://github.com/YuLab-SMU/clusterProfiler/blob/master/R/GMT.R

See Also

downloadPathwayArchive

Examples

#readPathwayGMT(system.file("extdata",
#  "wikipathways-20201010-gmt-Homo_sapiens.gmt", package="rWikiPathways"))

wikipathways/rWikiPathways documentation built on Nov. 1, 2024, 9 p.m.