Convert between Ensembl gene ID and Entrez gene id/symbol

entrez_ensg_conversion.R

#### Get gene annotations ####
# By Michael Love, http://www.bioconductor.org/help/workflows/rnaseqGene/

library("AnnotationDbi")
library("org.Hs.eg.db")
columns(org.Hs.eg.db)

convertIDs <- function( ids, from, to, db, ifMultiple=c("putNA", "useFirst")) {
  stopifnot( inherits( db, "AnnotationDb" ) )
  ifMultiple <- match.arg( ifMultiple )
  suppressWarnings( selRes <- AnnotationDbi::select(
    db, keys=ids, keytype=from, columns=c(from,to) ) )
  if ( ifMultiple == "putNA" ) {
    duplicatedIds <- selRes[ duplicated( selRes[,1] ), 1 ]
    selRes <- selRes[ ! selRes[,1] %in% duplicatedIds, ]
  }
  return( selRes[ match( ids, selRes[,1] ), 2 ] )
}

# Example:
#res$hgnc_symbol <- convertIDs(row.names(res), "ENSEMBL", "SYMBOL", org.Hs.eg.db)
#res$entrezgene <- convertIDs(row.names(res), "ENSEMBL", "ENTREZID", org.Hs.eg.db)