BAGS (version 2.12.0)

ReadGMT: Function that extracts the gene set definition from a .gmt file.

Description

This function reads the gene set definitions provided by a .gmt file (MSigDB annotation files) an stores the information into a list.

Usage

ReadGMT(path)

Arguments

path

The path where the .gmt file is stored..

Value

This function returns a list of the same length as gene sets in the .gmt file provided. The entries of the lists are the associated gene identifier associated to their respective gene set

Details

This function reads the gene set definitions provided by a .gmt file (MSigDB annotation files) an stores the information into a list. The .gmt file needs to have the name of the gene set in column 1. A description/properties of the gene set in column 2. And finally the gene identifiers associated to the gene set from column 3 and on. These gene identifiers can be Ensembl, Affymetrix, Gene Symbols, etc...

See Also

See the BAGS Vignette for examples on how to use function Gibbs2.

Examples

# An example on the use of this function:
# gene.sets.DB=ReadGMT("/Users/Bioinformatics/Projects/c5.mf.v3.0.symbols.gmt")
#
# #Where the path is where the gmt file from the MSigDB is stored.