readList {gage} | R Documentation |
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.
readList(file)
file |
character string, the full path name to the gene set data file in GMT format. |
A named list, each element is a character vector giving the gene IDs of a gene set.
Weijun Luo <luo_weijun@yahoo.com>
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
readExpData
read in gene expression data
#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]