R/getAbnormalMark.R

In DHLab-TSENG/lab: a package for EHR laboratory data

#' @rdname abMark
#' @export
#'

getAbnormalMark <- function (labData, idColName, labItemColName, valueColName, genderColName, genderTable, referenceTable = refLOINC){
  labData <- as.data.table(labData)
  genderTable <- as.data.table(genderTable)
  referenceTable <- as.data.table(referenceTable)

  labCols <- unlist(strsplit(deparse(substitute(labItemColName))," [+] "))

  if(!labCols %in% colnames(labData)|!labCols %in% colnames(referenceTable)){
    stop("The labItemColName of labData and refLOINC have to be the same.")
  }

  idString<-deparse(substitute(idColName))
  if(!idString %in% colnames(labData)|!idString %in% colnames(genderTable)){
    stop("The idColName of labData and genderTable have to be the same.")
  }

  setnames(labData, deparse(substitute(valueColName)), "Value")
  setnames(genderTable, deparse(substitute(genderColName)), "Gender")
  setnames(labData, deparse(substitute(idColName)), "ID")
  setnames(genderTable, deparse(substitute(idColName)), "ID")


  colNameList <- colnames(labData)
  labData$Value <- as.numeric(labData$Value)
  # Write a warning msg to notify that NAs introudced because of non-numeric results
  labData <- merge(labData, genderTable, by = "ID", all.x=TRUE)
  labData <- merge(labData, referenceTable, by= labCols, all.x=TRUE)
  labData$ABMark <- NA

  labData[, ABMark := ifelse(Gender == "M",
                                 ifelse (grepl("\\(|=",labData$LowerBound_Male),
                                         ifelse(Value < as.numeric(gsub("[^0-9.,]","",labData$LowerBound_Male)), "L", ABMark),
                                         ifelse(Value <= as.numeric(gsub("[^0-9.,]","",labData$LowerBound_Male)) , "L", ABMark)),
                                 ABMark)]
  labData[, ABMark := ifelse(Gender == "M",
                                 ifelse (grepl("\\)|=", labData$UpperBound_Male),
                                         ifelse(Value > as.numeric(gsub("[^0-9.,]","",labData$UpperBound_Male)), "H", ABMark),
                                         ifelse(Value >= as.numeric(gsub("[^0-9.,]","",labData$UpperBound_Male)) , "H", ABMark)),
                                 ABMark)]
  labData[, ABMark := ifelse(Gender == "F",
                                 ifelse (grepl("\\(|=",labData$LowerBound_Female),
                                         ifelse(Value < as.numeric(gsub("[^0-9.,]","",labData$LowerBound_Female)), "L", ABMark),
                                         ifelse(Value <= as.numeric(gsub("[^0-9.,]","",labData$LowerBound_Female)) , "L", ABMark)),
                                 ABMark)]
  labData[, ABMark := ifelse(Gender == "F",
                                 ifelse (grepl("\\)|=", labData$UpperBound_Female),
                                         ifelse(Value > as.numeric(gsub("[^0-9.,]","",labData$UpperBound_Female)), "H", ABMark),
                                         ifelse(Value >= as.numeric(gsub("[^0-9.,]","",labData$UpperBound_Female)) , "H", ABMark)),
                                 ABMark)]


  labData[, c(colNameList,"ABMark"), with = FALSE]
}