R/writeGMT.R

In lwaldron/LeviRmisc: Levi's miscellaneous handy R functions

writeGMT <- function #Create a gmt (gene matrix transposed) file
### Createss a gmt (gene matrix transposed) file such as those
### provided by mSigDB or geneSigDB, from an R list object.
### Function by Levi Waldron.
(object,
### R list object that will be converted to GMT file.  Each element
### should contain a vector of gene names, and the names of the
### elements will used for the gene set names
 fname
### Output file name for .gmt file
 ){
  if (class(object) != "list") stop("object should be of class 'list'")
  if(file.exists(fname)) unlink(fname)
  for (iElement in 1:length(object)){
    write.table(t(c(make.names(rep(names(object)[iElement],2)),object[[iElement]])),
                sep="\t",quote=FALSE,
                file=fname,append=TRUE,col.names=FALSE,row.names=FALSE)
  }
### Called for the effect of writing a .gmt file
}