R/tools.R

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

setGeneric(name = "SXTMTmatch",
           def = 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))
  }

}