R/bitrdqd.R

In LianzePuppet/GOenrich:

bitrdqd<-function (geneID, fromType, toType, OrgDb, drop = TRUE)
{
  idTypes <- idType(OrgDb)
  msg <- paste0("should be one of ", paste(idTypes, collapse = ", "),
                ".")
  if (!fromType %in% idTypes) {
    stop("'fromType' ", msg)
  }
  if (!all(toType %in% idTypes)) {
    stop("'toType' ", msg)
  }
  geneID %<>% as.character %>% unique
  db <- GOSemSim::load_OrgDb(OrgDb)
  res <- suppressWarnings(AnnotationDbi::select(db, keys = geneID,
                                                keytype = fromType, columns = c(fromType, toType)))
  ii <- which(is.na(res[, 2]))
  if (length(ii)) {
    n <- res[ii, 1] %>% unique %>% length
    if (n) {
      warning(paste0(round(n/length(geneID) * 100, 2),
                     "%"), " of input gene IDs are fail to map...")
    }
    if (drop) {
      res <- res[-ii, ]
    }
  }
  return(res)
}