gmt2geneSet {GIGSEA} | R Documentation

## gmt2geneSet

### Description

gmt2geneSet transforms a gmt format file into geneSets.

### Usage

    gmt2geneSet(gmt, termCol = 1, nonGeneCol = termCol, singleValue = NULL)

### Arguments

`gmt` | a vector of character values. Each item is a list of words comprising a term and its corresponding gene set, which are separated by tab.
`termCol` | an integer value indicating in each item of gmt, which word is the term , by default, 1.
`nonGeneCol` | an integer value indicating in each item of gmt, which words are not the gene set, by default, termCol.
`singleValue` | a numeric value, which assigns the same value to all genes in a given gene set. This is useful when combining together the up-regulated gene sets (regularly, singleValue=1) and the down-regulated gene sets (regularly, singleValue=-1)

### Value

a data frame, comprising three vectors: term (like pathway names), geneset (a gene symbol list separate by comma), and value (either discrete or continuous separated by comma)

### Author(s)

Shijia Zhu, shijia.zhu@mssm.edu

### See Also

`geneSet2Net`; `geneSet2sparseMatrix`;

### Examples

    # download the gmt file
    gmt <- readLines( paste0('http://amp.pharm.mssm.edu/CREEDS/download/',
    'single_drug_perturbations-v1.0.gmt') )

    # obtain the index of up-regulated and down-regulated gene sets
    index_up <- grep('-up',gmt)
    index_down <- grep('-dn',gmt)

    # transform the gmt file into gene sets. The gene set is a data frame,
    # comprising three vectors:
    # term (here is drug), geneset (a gene symbol list separate by comma),
    # and value (1 and -1 separate by comma)
    gff_up <- gmt2geneSet( gmt[index_up], termCol=c(1,2), singleValue = 1 )
    gff_down <- gmt2geneSet( gmt[index_down], termCol=c(1,2), singleValue = -1 )

[Package GIGSEA version 1.0.0 Index]