R/reorgXcalConc.R

In parasitetwin/metLab: Toolkit for metabolomics data

#Importing .csv output-files from Xcalibur quantifications and deconvoluting Lipids for lipidomics method#
#Anton Ribbenstedt, May 2016#
#' Reorganizing XCalibur-files
#'
#' Takes an output file from XCalibur (resaved as .xlsx), grabs the calculated conc. and reorganizes it into a one worksheet column and row ".xlsx" file
#' @param saveName String with name of the reorganized output-file saved to your homefolder ending with ".xlsx"; default = "ReorgResults.xslx"
#' @param saveFile Boolean parameter, deciding whether you want to save a file to your homefolder with the reorganized data or not; default = FALSE
#' @usage Function will ask for an input file (short report XCalibur output file). Then you have to choose whether to save an ".xlsx" file and the name of the saved file.
#' @return The data reorganized into columns and rows will be returned as a data frame (and saved to homefolder as ".xlsx" file if chosen)
#' @export

reorgXcalConc<-function(saveFile, saveName){
  ####Loading packages needed for import and analysis of data####
  if(is.na(saveName)==TRUE){saveName="ReorgResults.xlsx"}
  if(is.na(saveFile)==TRUE){saveFile=FALSE}
  require(openxlsx)
  #require(dplyr)
  #require(reshape)
  options(java.parameters = "-Xmx4g" )
  fileName<-file.choose()
  
  ####xlsx and xlconnect operations before requiring openxlsx####
  wbList<-list()
  wholeFile<-read.xlsx(fileName, 1)
  
  
  ##Getting analyte names from document##
  sheetNames<- getSheetNames(fileName)
  n_comp<- length(sheetNames)-2
  
  
  #Loop counting number of samples and making a list of sample names
  nSamples<-0
  sampleNames<-list()
  
  for(i in 4:1000){                     #####3:1000 if LongReport
    if(wholeFile[i,1]=="Created By:")
      break
    
    nSamples<-nSamples+1
    sampleNames[nSamples]<-wholeFile[i,1]
  }
  
  expDF<-data.frame(matrix(NA,nrow=(length(sampleNames)+1),ncol=(n_comp+1)))
  
  ####Importing any specified column from all compounds in the Xcalibur export document####
  ## To change what data you want to extract simply look in the document in which column the data you want is present, and put it into the # in "cols=c(#)" below ##
  
  xlsxFile<-system.file(fileName, package = "openxlsx")
  sampleLength<-length(sampleNames)+6
  
  for(i in 1:n_comp){
    wbList[[i]]<-read.xlsx(fileName, i, rows=c(6:sampleLength), cols=c(9), colNames=FALSE, rowNames=FALSE) ###cols=c(15) if LongReport (This is for Area)
    if(length(wbList)<i){
      wbList[[i]]=matrix(rep("NF",(sampleLength-6)),nrow=(sampleLength-6), ncol=1)
    }
    if(length(wbList[[i]][,1])<(sampleLength-6)){
      wbList[[i]]=matrix(rep("NF",(sampleLength-6)),nrow=(sampleLength-6), ncol=1)
    }
    wbList[[i]][(grep("NF",wbList[[i]][,1])),1]<-0
  }
  
  names(wbList[[i]])<-c("Conc")
  
  ####Restructuring data into rows of samples and columns of compounds####
  for(i in 2:(length(sampleNames)+1)){
    expDF[i,1]<-sampleNames[i-1]
  }
  expDF[1,-1]<-sheetNames[1:n_comp]
  
  
  #Loop for areas and export
  for(i in 1:(n_comp)){
    expDF[-1,i+1]<-as.numeric(unlist(wbList[[i]]))
  }
  
  ## Replacing peaks Not found (NF) with 0 for future mathematical applications ##
  expDF[expDF=="NF"]<-0
  
  ##Exporting data to the filename specified and the sheet-name specified##
  if(saveFile==TRUE){
    if(substring(saveName,nchar(saveName)-4,nchar(saveName))==".xlsx" || substring(saveName,nchar(saveName)-5,nchar(saveName))==".XLSX"){
      write.xlsx(expDF,saveName,col.names=FALSE)
    }else{write.xlsx(expDF,paste(saveName,".xlsx",sep=""),col.names=FALSE)}
  }
  return(expDF)
}