R/utils.R

In jaspershen/metID: Metabolite identification based on MS1 and MS2 spectra

SXTMTmatch = function(data1,
                      data2,
                      mz.tol,
                      #rt.tol is relative
                      rt.tol = 30,
                      rt.error.type = c("relative", "abs")){
  rt.error.type <- match.arg(rt.error.type)
  #
  if (nrow(data1) == 0 | nrow(data2) == 0) {
    result <- NULL
    return(result)
  }
  
  info1 <- data1[, c(1, 2), drop = FALSE]
  info1 <- apply(info1, 1, list)
  
  mz2 <- as.numeric(data2[, 1])
  rt2 <- as.numeric(data2[, 2])
  
  result <- pbapply::pblapply(info1, function(x) {
    temp.mz1 <- x[[1]][[1]]
    temp.rt1 <- x[[1]][[2]]
    mz.error <- abs(temp.mz1 - mz2) * 10 ^ 6 / temp.mz1
    if (rt.error.type == "relative") {
      rt.error <- abs(temp.rt1 - rt2) * 100 / temp.rt1
    } else{
      rt.error <- abs(temp.rt1 - rt2)
    }
    
    j <- which(mz.error <= mz.tol & rt.error <= rt.tol)
    if (length(j) == 0) {
      matrix(NA, ncol = 7)
    } else{
      cbind(j, temp.mz1, mz2[j], mz.error[j], temp.rt1, rt2[j], rt.error[j])
    }
  })
  
  if (length(result) == 1) {
    result <- cbind(1, result[[1]])
  } else{
    result <- mapply(function(x, y) {
      list(cbind(x, y))
    },
    x <- 1:length(info1),
    y = result)
    result <- do.call(rbind, result)
  }
  
  result <-
    matrix(result[which(!apply(result, 1, function(x)
      any(is.na(x)))), ], ncol = 8)
  if (nrow(result) == 0)
    return(NULL)
  colnames(result) <-
    c("Index1",
      "Index2",
      "mz1",
      "mz2",
      "mz error",
      "rt1",
      "rt2",
      "rt error")
  result <- result
}



getExtension = function(file){
  tail(stringr::str_split(string = file, pattern = "\\.")[[1]], 1)
}

readTable = function(file, ...){
  extension <- getExtension(file = file)
  if (extension == "csv") {
    return(readr::read_csv(file = file, ...))
  }
  
  if (extension == 'xlsx') {
    return(readxl::read_xlsx(path = file, ...))
  }
  
  if (extension == "xls") {
    return(readxl::read_xls(path = file, ...))
  }
  
  if (extenstion != "csv" &
      extenstion != "xlsx" &
      extenstion != "xls") {
    cat(crayon::red("file are not csv, xlsx or xls.\n"))
  }
}