gmt2geneSet {GIGSEA} | R Documentation |
gmt2geneSet transforms a gmt format file into geneSets.
gmt2geneSet(gmt, termCol = 1, nonGeneCol = termCol, singleValue = NULL)
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) |
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)
Shijia Zhu, shijia.zhu@mssm.edu
geneSet2Net
; geneSet2sparseMatrix
;
# 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 )