readGmt {paxtoolsr}R Documentation

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

results <- readGmt(system.file("extdata", "test_gsea.gmt", package="paxtoolsr"))
results <- readGmt(system.file("extdata", "test_gsea_1.gmt", package="paxtoolsr"))
results <- readGmt(system.file("extdata", "test_gsea.gmt", package="paxtoolsr"), removePrefix=TRUE)
results <- readGmt(system.file("extdata", "test_gsea.gmt", package="paxtoolsr"), returnInfo=TRUE)


[Package paxtoolsr version 1.16.0 Index]