helpers.R

map_entrez_ids <- function(entrez.ids, tech = "h19"){
  
  genes = entrez.ids
  
  mapping = AnnotationDbi::select(org.Hs.eg.db,
                                  key=genes,
                                  columns=c("SYMBOL"), 
                                  keytype="ENTREZID")
  
  mapping = as.data.table(mapping)
  colnames(mapping) = c("entrez.id", "hgnc.symbol") 
  
  not.found = mapping[which(is.na(mapping$hgnc.symbol)), ]$entrez.id
  mapping = mapping[which(!(is.na(mapping$hgnc.symbol))), ] 
  
  if(length(not.found) > 0){
    if(tech == "h19"){
      x = grch37
    } else {
      x = grch38
    }
    
    x = as.data.table(x)
    x = x[,c(2,3)] 
    colnames(x) = c("entrez.id", "hgnc.symbol") 
    
    merge = x[which(x$entrez.id %in% not.found), ]
    
    mapping = rbind(mapping, merge)
    
    not.found = not.found[which(!(not.found %in% merge$entrez.id))]
  }
  
  mapping = rbind(mapping, data.table("entrez.id" = not.found, "hgnc.symbol" = NA)) 
  mapping = mapping[order(mapping$hgnc.symbol), ]
  
  mapping = unique(mapping)
  
  return(mapping)
}