read_gmt: Read in gene set information from .gmt files

In girke-lab/signatureSearch: Environment for Gene Expression Searching Combined with Functional Enrichment Analysis

Read in gene set information from .gmt files

Description

This function reads in and parses information from the MSigDB's .gmt files. Pathway information will be returned as a list of gene sets.

Usage

read_gmt(file, start = 1, end = -1)

Arguments

file	The .gmt file to be read
start	integer(1), read the gmt file from start line
end	integer(1), read the gmt file to the end line, the default -1 means read to the end

Details

The .gmt format is a tab-delimited list of gene sets, where each line is a separate gene set. The first column must specify the name of the gene set, and the second column is used for a short description (which this function discards). For complete details on the .gmt format, refer to the Broad Institute's Data Format's page http://www.broadinstitute.org/cancer/software/gsea/wiki/index.php/Data_formats.

Value

A list, where each index represents a separate gene set.

Warning

The function does not check that the file is correctly formatted, and may return incorrect or partial gene sets, e.g. if the first two columns are omitted. Please make sure that files are correctly formatted before reading them in using this function.

Examples

gmt_path <- system.file("extdata/test_gene_sets_n4.gmt", package="signatureSearch")
geneSets <- read_gmt(gmt_path)

girke-lab/signatureSearch documentation built on Feb. 21, 2024, 8:32 a.m.