R/fullDecon.R

In parasitetwin/metLab: Toolkit for metabolomics data

##Deconv full lipid set and save file##

#'Deconvolutes all lipid types present and saves them as .xslx
#'
#'Takes a .xlsx file outputed from reorgXcalArea, applies deconvLipids on all different lipid types and saves an .xlsx-document.
#'@param fileOutputName The output name of the file you want to create
#'@usage Put in the file names you want and the function will use deconvLipids() to create an .xlsx document with all of them deconvoluted inside
#'@return A list with as many items as lipid types will be returned by the function
#'@depends Rdisop MASS openxlsx
#'@export




fullDecon<-function(fileOutputName, batchCorr=FALSE){
  require(openxlsx)
  cat("##############################################################\nChoose the reference file with lipids and chemical formulas:\n#############################################################\n\n")
  flush.console()
  refFileName<-file.choose()
  
  cat("#################################################################\nChoose the file containing areas from samples and lipid species:\n#################################################################\n\n")
  flush.console()
  areaFileName<-file.choose()
  
  wb<-createWorkbook()
  lipidTypes<-as.character(getSheetNames(refFileName))
  nSheets<-length(lipidTypes)
  deconList<-list()
  
  for(i in 1:nSheets){
    deconList[[i]]<-deconLipids(i, refFileName, areaFileName)
    addWorksheet(wb,paste(lipidTypes[i]))
    writeData(wb,paste(lipidTypes[i]),deconList[[i]])
  }
  
  
  
  if(batchCorr==TRUE){
    wb2<-createWorkbook()
    allLipids<-data.frame()
    
    for(i in 1:nSheets){
      allLipids<-rbind(allLipids,deconList[[i]])
    }
    
    addWorksheet(wb2,"AllLipids")
    writeData(wb2,"AllLipids", t(allLipids), rowNames = TRUE, colNames = TRUE)
    if(substring(fileOutputName,nchar(fileOutputName)-4,nchar(fileOutputName))==".xlsx"){
      saveWorkbook(wb2,fileOutputName)
    } else {saveWorkbook(wb2,paste(fileOutputName,".xlsx",sep=""))}
    
  } else {
    if(substring(fileOutputName,nchar(fileOutputName)-4,nchar(fileOutputName))==".xlsx"){
      saveWorkbook(wb,fileOutputName)
    } else {saveWorkbook(wb,paste(fileOutputName,".xlsx",sep=""))}
  }
  
  return(deconList[[i]])
}