readList {gage} | R Documentation

## 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.

### Author(s)

Weijun Luo <luo_weijun@yahoo.com>

### 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]

[Package gage version 2.38.3 Index]