Fix incorrect precursor assignment in Lumos switching mode files converted to mzXML (ProteoWizard)

fixLumosMzXml.R

library(XML)
# dir <- "C:/Input_data/MassBank/20180219_Test"
# setwd(dir)
# fIn<- "01_4093_Flazasulfuron.mzXML"


# 
# fixLumosMzXml <- function(f, prefix="fix_" out = paste0(dirname(f), prefix, basename(f)))
# {
# x <- xmlParse(f)
# ns <-  c(n= xmlNamespaceDefinitions(x, simplify = TRUE)[[1]])
# #prec <- getNodeSet(x, "//n:precursorMz", ns)
# # 
# # scansPos1 <- getNodeSet(x, "//n:scan[@polarity='+'][@msLevel=1]", ns)
# # scansPos2 <- getNodeSet(x, "//n:scan[@polarity='+'][@msLevel=2]/precursorMz", ns)
# # scansNeg1 <- getNodeSet(x, "//n:scan[@polarity='-'][@msLevel=1]", ns)
# # scansNeg2 <- getNodeSet(x, "//n:scan[@polarity='-'][@msLevel=2]", ns)

fixLumosMzXml <- function(inFile, prefix="fix_", outFile=paste0(prefix, inFile), outString=FALSE)
{
  
  x <- xmlParse(inFile)
  ns <-  c(n= xmlNamespaceDefinitions(x, simplify = TRUE)[[1]])
  for(polarity in c("+", "-"))
  {
    scans1 <- as.numeric(unlist(xpathApply(x, sprintf("//n:scan[@polarity='%s'][@msLevel=1]",polarity), 
                                           function(node)
                                           {
                                             xmlAttrs(node)[["num"]]
                                           },
                                           namespaces=ns)))
    
    scans2.orig <- unlist(xpathApply(x, sprintf("//n:scan[@polarity='%s'][@msLevel=2]/n:precursorMz", polarity), 
                                     function(node){
                                       xmlAttrs(node)[["precursorScanNum"]]
                                     },
                                     namespaces = ns))
    
    scans2 <- unlist(xpathApply(x, sprintf("//n:scan[@polarity='%s'][@msLevel=2]/n:precursorMz", polarity), 
                                function(node)
                                {
                                  scanNo <- as.numeric(xmlAttrs(xmlParent(node))[["num"]])
                                  parentNo <- max(scans1[scans1 < scanNo])
                                  xmlAttrs(node)["precursorScanNum"] <- as.character(parentNo)
                                  xmlAttrs(node)[["precursorScanNum"]]
                                },
                                namespaces=ns))
    
    
    scans2.revised <- unlist(xpathApply(x, sprintf("//n:scan[@polarity='%s'][@msLevel=2]/n:precursorMz", polarity), 
                                        function(node){
                                          xmlAttrs(node)[["precursorScanNum"]]
                                        },
                                        namespaces = ns))
  }
  if(!outString)
    saveXML(x, outFile)
  else
    return(saveXML(x))
}