ReadGMT: Function that extracts the gene set definition from a .gmt...
In BAGS: A Bayesian Approach for Geneset Selection

Description Usage Arguments Details Value Author(s) See Also Examples

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

1	ReadGMT(path)

path

The path where the .gmt file is stored..

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...

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

A. Quiroz-Zarate aquiroz@jimmy.harvard.edu

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

# 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.

BAGS documentation built on Nov. 8, 2020, 11:11 p.m.