readGmt: Read in gene sets from GMT files

In BioPAX/paxtoolsr: Access Pathways from Multiple Databases Through BioPAX and Pathway Commons

Read in gene sets from GMT files

Description

This function will read in gene sets in the GMT format into a named list.

Usage

readGmt(inputFile, removePrefix = FALSE, returnInfo = FALSE)

Arguments

inputFile	an inputFile
removePrefix	Pathway Commons genesets are prefixed with a NCBI organism taxonomy number (e.g. 9606 for humans); this is a boolean whether to remove the prefix (default: FALSE)
returnInfo	a boolean whether to return information on genesets; these results are returned a list of two items: 1) basic GMT results and 2) datasource, organism, and id type information for each gene set (default: FALSE)

Value

a named list where each entry corresponds to a gene set or a list described in the returnInfo parameter

Examples

f1 <- system.file("extdata", "test_PathwayCommons12.kegg.hgnc.gmt", 
  package="paxtoolsr")
f2 <- system.file("extdata", "test_PathwayCommons12.netpath.hgnc.gmt", 
  package="paxtoolsr")
  
results <- readGmt(f1)
results <- readGmt(f2)
results <- readGmt(f1, removePrefix=TRUE)
results <- readGmt(f2, returnInfo=TRUE)

BioPAX/paxtoolsr documentation built on Jan. 31, 2023, 4:22 a.m.