#' symbolConvert
#'
#' .
#'
#' @param x .
#' @param in.type .
#' @param out.type .
#'
#' @return value
#'
#' @export
symbolConvert <- function(x, in.type, out.type){
if(is.vector(x)==TRUE ) {
x=as.data.frame(x)
}
#manually set objects for when you are debugging, ignore otherwise
#in.type="entrezgene"
#out.type="hgnc_symbol"
#x=adhdq
mart <- useDataset("hsapiens_gene_ensembl", useMart("ensembl"))
conversions <- getBM(filters= in.type, attributes= c(in.type,out.type),values=x,mart= mart)
#conversions<-conversions[match(x,conversions[,1]),]
row1<-as.character(x[,1])
row2<-as.character(conversions[,1])
nas<-is.na(match(row1,row2))
notfound<-x[grep("TRUE",nas),]
if(length(notfound)>=1) {
warning(paste("the following entries were not found:",paste(notfound,sep=",",collapse=" , ")))
}
c<-conversions[match(row1,row2),]
c<-c[is.na(c[,1])==FALSE,]
c<-c[,2]
return(c)
}
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