R/getRxCuiViaATC.R

In DHLab-CGU/pharm: pharm

#' @rdname getRxCuiViaATC
#' @export

getRxCuiViaATC <- function(df, AtcColName = ATC, cores=8){

  colnames(df)[colnames(df)==deparse(substitute(AtcColName))] <- "ATC"
  dfu <- df %>% select("ATC") %>% unique()

  cl <- makeCluster(cores)
  registerDoParallel(cl)
  RxNormIdData = foreach(i = 1:nrow(dfu),
                         .combine = "rbind",
                         .packages = "jsonlite") %dopar% {
                           rxid <- tryCatch({fromJSON(paste0("https://rxnav.nlm.nih.gov/REST/rxcui.json?idtype=ATC&id=",dfu$ATC[i]))},
                                            error = function(e){"ERROR"})
                           if(rxid == "ERROR"){
                             rxTable <- data.frame(ATC = dfu$ATC[i],
                                                   RxCui = "error",
                                                   stringsAsFactors = FALSE)
                           }else{
                           if(is.null(rxid$idGroup$rxnormId)){
                             rxTable <- data.frame(ATC = dfu$ATC[i],
                                                   RxCui = NA,
                                                   stringsAsFactors = FALSE)
                           }else{
                             rxTable <- data.frame(ATC = dfu$ATC[i],
                                                   RxCui = rxid$idGroup$rxnormId,
                                                   stringsAsFactors = FALSE)
                           }
                           }
                           rxTable
                         }
  stopCluster(cl)
  RxNormIdData <- unique(RxNormIdData)
  ATC_RXCUI <- left_join(df,RxNormIdData, by = "ATC")
  colnames(ATC_RXCUI)[colnames(ATC_RXCUI)== "ATC"] <- deparse(substitute(AtcColName))

  return (ATC_RXCUI)
}