R/EnsembleAnnotate.R

In Morriseylab/ExpressExtras:

#'Annotate a ExpressioSet
#' @param eset An ExpressionSet
#' @return eSet with Featuredata upadted
#'
#' @export
EnsemblAnnotate <- function(eset, transcriptdb,ensemblonly=T){
  gns <- AnnotationDbi::select(transcriptdb, keys=featureNames(eset), columns=c("SYMBOL","GENENAME",'ENTREZID','ENSEMBL'), keytype="PROBEID")
  gns_cts <- count(gns,PROBEID)
  colnames(gns_cts)[2] <- "GenestoProbe"
  gns <- gns[!duplicated(gns[,1]),]
  gnsmerg <-inner_join(gns,gns_cts,by='PROBEID')
  rownames(gnsmerg)<-gnsmerg$PROBEID
  colnames(gnsmerg)[1] ='ID'
  fData(eset) <- gnsmerg
  return(eset)
}