gage (version 2.22.0)

readList: Read in gene set data as a named list

Description

This function reads in gene set data in GMT (.gmt) format as a named list. GMT is defined originally by GSEA program. The code may be slightly revised for reading in gene set data in other tab-delimited formats too.

Usage

readList(file)

Arguments

file
character string, the full path name to the gene set data file in GMT format.

Value

A named list, each element is a character vector giving the gene IDs of a gene set.

References

Luo, W., Friedman, M., Shedden K., Hankenson, K. and Woolf, P GAGE: Generally Applicable Gene Set Enrichment for Pathways Analysis. BMC Bioinformatics 2009, 10:161

See Also

readExpData read in gene expression data

Examples

#an example GMT gene set data derived from MSigDB data
filename=system.file("extdata/c2.demo.gmt", package = "gage")
demo.gs=readList(filename)
demo.gs[1:3]
#to use these gene sets with gse16873, need to convert the gene symbols
#to Entrez IDs first
data(egSymb)
demo.gs.sym<-lapply(demo.gs, sym2eg)
demo.gs.sym[1:3]