R/MSexport.R

In xdomingoal/erah-devel: Automated Spectral Deconvolution, Alignment, and Metabolite Identification in GC/MS-Based Untargeted Metabolomics

#' @name export2MSP
#' @aliases export2MSP
#' @title Export spectra to MSP
#' @description Export spectra to MSP format for comparison with the NIST library.
#' @param Experiment A 'MetaboSet' S4 object containing the experiment.
#' @param export.id If NULL, all the spectra in the experiment will be exported. Otherwise, only the AlignID in export.id will be exported
#' @param id.database The mass-spectra library used in the experiment.
#' @param store.path The path where the converted files are to be exported.
#' @param alg.version Different algorithm implementations. Users have to chose what version works with their NIST MSearch or other software version. By default, alg.version is set to 1. If it not works, try setting alg.version to 2 ;).
#' @export 

export2MSP <- function(Experiment, export.id=NULL, id.database = mslib, store.path=getwd(), alg.version=1)
{
  
  if(is.null(nrow(Experiment@Results@Identification)) | nrow(Experiment@Results@Identification)==0)
  {
    if(!is.null(export.id)) Experiment@Results@Alignment <- Experiment@Results@Alignment[which(Experiment@Results@Alignment$AlignID %in% export.id),]
    
    SpectList <- sapply(Experiment@Results@Alignment$Spectra, function(x) {
      splitted.spectra.list <- strsplit(as.character(x), split = " ")[[1]]
      splitted.spectra.list <- gsub(",", " ", splitted.spectra.list)
      if(alg.version==1){		
        splitted.spectra.list <- as.character(as.vector(sapply(splitted.spectra.list, function(x) paste(c(x,";"), collapse=""))))
        Npeaks <- length(splitted.spectra.list)
        if(Npeaks>=6)
        {
          sequ <- seq(1, Npeaks, 5)
          if(sequ[length(sequ)]!=Npeaks) sequ <- c(sequ, Npeaks)
          splitted.spectra.list <- paste(unlist(sapply(1:(length(sequ)-1), function(x) paste(c(splitted.spectra.list[sequ[x]:sequ[(x+1)]], "\n")))), collapse=" ")
        }else{
          splitted.spectra.list <- paste(splitted.spectra.list, collapse=" ")
        }
        PeakChar <- paste(gsub(",", " ", splitted.spectra.list), collapse="; ")
      }
      if(alg.version==2) {
        splitted.spectra.list <- as.character(as.vector(sapply(splitted.spectra.list, function(x) paste(c(x,"\n"), collapse=""))))
        Npeaks <- length(splitted.spectra.list)
        PeakChar <-  paste(splitted.spectra.list, collapse="")
      }		
      return(list(Npeaks=Npeaks, PeakChar=PeakChar))
    })
    SpectList <- split(SpectList,seq(NROW(SpectList)))
    
    SpectString <- as.vector(unlist(SpectList[[2]]))
    Npeaks <- as.vector(unlist(SpectList[[1]]))
    
    SpectNames.2 <- as.character(as.vector(Experiment@Results@Alignment$Factor))
    SpectNames.3 <- sapply(as.numeric(as.vector(Experiment@Results@Alignment$tmean)), function(x) paste("Rt:", x))
    
    SpectNames <- apply(cbind(SpectNames.3,SpectNames.2), 1, function(x) paste(x, collapse=" @ "))
  }else{
    
    if(Experiment@Results@Parameters@Identification$database.name != id.database@name) {
      error.msg <- paste("This experiment was not processed with the database selected. Please use ", 
                         Experiment@Results@Parameters@Identification$database.name, 
                         sep = "")
      stop(error.msg)
    }
    
    if(!is.null(export.id)) Experiment@Results@Identification<- Experiment@Results@Identification[which(Experiment@Results@Identification$AlignID %in% export.id),]
    
    SpectList <- sapply(Experiment@Results@Identification$Spectra, function(x) {
      splitted.spectra.list <- strsplit(as.character(x), split = " ")[[1]]
      splitted.spectra.list <- gsub(",", " ", splitted.spectra.list)
      if(alg.version==1){
        splitted.spectra.list <- as.character(as.vector(sapply(splitted.spectra.list, function(x) paste(c(x,";"), collapse=""))))
        Npeaks <- length(splitted.spectra.list)
        if(Npeaks>=6)
        {
          sequ <- seq(1, Npeaks, 5)
          if(sequ[length(sequ)]!=Npeaks) sequ <- c(sequ, Npeaks)
          splitted.spectra.list <- paste(unlist(sapply(1:(length(sequ)-1), function(x) paste(c(splitted.spectra.list[sequ[x]:sequ[(x+1)]], "\n")))), collapse=" ")
        }else{
          splitted.spectra.list <- paste(splitted.spectra.list, collapse=" ")
        }
        PeakChar <- paste(gsub(",", " ", splitted.spectra.list), collapse="; ")	
      }
      if(alg.version==2) {
        splitted.spectra.list <- as.character(as.vector(sapply(splitted.spectra.list, function(x) paste(c(x,"\n"), collapse=""))))
        Npeaks <- length(splitted.spectra.list)
        PeakChar <-  paste(splitted.spectra.list, collapse="")
      }
      return(list(Npeaks=Npeaks, PeakChar=PeakChar))
    })
    SpectList <- split(SpectList,seq(NROW(SpectList)))
    
    SpectString <- as.vector(unlist(SpectList[[2]]))
    Npeaks <- as.vector(unlist(SpectList[[1]]))
    
    id.found <- as.numeric(as.vector(Experiment@Results@Identification[, "DB.Id.1"]))
    met.name <- unlist(lapply(id.database@database[c(id.found)], function(x) x$Name))
    
    SpectNames.1 <- sapply(as.character(as.vector(Experiment@Results@Identification$AlignID)), function(x) paste("(Align ID: ", x, ")", sep=""))
    SpectNames.2 <- sapply(as.numeric(as.vector(Experiment@Results@Identification$tmean)), function(x) paste("Rt:", x))
    SpectNames.3 <- apply(cbind(SpectNames.2,SpectNames.1), 1, function(x) paste(x, collapse=" "))
    SpectNames <- as.character(as.vector(apply(cbind(SpectNames.3,met.name), 1, function(x) paste(x, collapse=" @ "))))
  }
  
  dir.create(file.path(store.path, "ExportMSP") , showWarnings = FALSE)
  filename <- paste(c(store.path, "/ExportMSP/", "ExportedMSP", ".msp"), collapse="")
  
  fileTag <- character()	
  for(i in 1:length(SpectString))
  { 
    fileTag[i] <- paste(c("Name: ", SpectNames[i], "\n", "Comments: MSP spectra exported by eRah \n", "Num Peaks: ", Npeaks[i], "\n",SpectString[i]), collapse="")
  }
  fileTagGen <- paste(fileTag, collapse="\n")
  
  writeLines(fileTagGen, filename)	
  cat("Spectra saved at: ", store.path, "/ExportMSP", sep="")
}

#' @name export2CEF
#' @aliases export2CEF
#' @title Export spectra to CEF
#' @description Export spectra to CEF format for comparison with the NIST library through MassHunter interface.
#' @usage export2CEF(Experiment, export.id = NULL, 
#' id.database = mslib, store.path = getwd())
#' @param Experiment A 'MetaboSet' S4 object containing the experiment.
#' @param export.id If NULL, all the spectra in the experiment will be exported. Otherwise, only the AlignID in export.id will be exported
#' @param id.database The mass-spectra library used in the experiment.
#' @param store.path The path where the converted files are to be exported.
#' @export

export2CEF <- function (Experiment, export.id = NULL, id.database = mslib, store.path = getwd()) 
{
  if (!is.null(export.id)) Experiment@Results@Alignment <- Experiment@Results@Alignment[which(Experiment@Results@Alignment$AlignID %in% export.id), ]
  SpectList <- sapply(Experiment@Results@Alignment$Spectra, function(x) {
    splitted.spectra.list <- strsplit(as.character(x), split = " ")[[1]]
    
    as.vector(sapply(splitted.spectra.list, function(y){
      y.split <- strsplit(y, ",")[[1]]
      x.cor <- y.split[1]
      y.cor <- y.split[2]
      paste("<p x=", '"', as.numeric(x.cor), '" y="', y.cor, '" />', sep="")
    }))
  })
  
  SpectNames.2 <- as.character(as.vector(Experiment@Results@Alignment$Factor))
  SpectRT <- as.numeric(as.vector(Experiment@Results@Alignment$tmean))
  SpectNames.3 <- sapply(as.numeric(as.vector(Experiment@Results@Alignment$tmean)), function(x) paste("Rt:", x))
  SpectNames <- apply(cbind(SpectNames.2, SpectNames.3), 1, function(x) paste(x, collapse = " @ "))
  
  dir.create(file.path(store.path, "ExportCEF"), showWarnings = FALSE)
  filename <- paste(c(store.path, "/ExportCEF/", "ExportedCEF", ".cef"), collapse = "")
  fileTag <- character()
  fileTag[1] <- paste("<?xml version=", '"', "1.0", '"' , "encoding=", '"', "utf-8",'"', "?><CEF version=",'"',"1.0.0.0",'"',"><CompoundList>", sep="")
  for (i in 1:length(SpectList)) {
    fileTag[length(fileTag) + 1] <- ""
    fileTag[length(fileTag) + 1] <- paste("<Compound mppid=", '"',SpectNames[i], '"'," algo=", '"',"FindByAMDIS", '"'," >", sep="")
    fileTag[length(fileTag) + 1] <- paste("<Location  rt=", '"',SpectRT[i], '"'," />", sep="")
    fileTag[length(fileTag) + 1] <- ""
    
    fileTag[length(fileTag) + 1] <- paste("<Spectrum type=", '"',"AMDIS", '"'," cpdAlgo=", '"',"FindByAMDIS", '"',">", sep="")
    fileTag[length(fileTag) + 1] <- paste("<MSDetails  p=", '"',"+", '"',"  />", sep="")
    fileTag[length(fileTag) + 1] <- "<MSPeaks>" 
    srtI <- (length(fileTag) + 1)
    srtE <- (length(fileTag) + 1) + length(SpectList[[i]]) - 1
    fileTag[srtI:srtE] <- SpectList[[i]]
    fileTag[length(fileTag) + 1] <- "</MSPeaks>" 
    fileTag[length(fileTag) + 1] <- "</Spectrum>" 
    fileTag[length(fileTag) + 1] <- "</Compound>" 
    
  }
  fileTag[length(fileTag) + 1] <- ""
  fileTag[length(fileTag) + 1] <- "</CompoundList></CEF>"
  
  #fileTagGen <- paste(fileTag, collapse = "\n \n")
  writeLines(fileTag, filename)
  cat("Spectra saved at: ", store.path, "/ExportCEF", sep = "")
}