readPathwayGMT {rWikiPathways} | R Documentation

## 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"))

[Package rWikiPathways version 1.10.2 Index]