R/PeakML.Write.R

In mzmatch.R: mzmatch and PeakML integration for XCMS.

PeakML.Write <- function(peakMLdata=NULL, peakDataMtx=NULL, chromDataList=NULL, sampleNames=NULL, rawDataFullPaths=NULL, phenoData=NULL, corRT=NULL, rawRT=NULL, ionisation=NULL, GroupAnnotations=NULL, outFileName){
	# PRE:
	#	peakDataMtx <- PeakML.Methods.getPeakData$peakDataMtx
	#	chromDataList <- PeaKML.Methods.getChromData or PeakML.Methods.getPeakData$chromDataList
	#	sampleName <- sample names; PeakML.Methods.getPeakData$sampleNames
	#	rawDataFullPaths <- full paths to the raw data; PeakML.Methods.getPeakData$rawDataFullPaths
	#	phenoData <- the pheno data PeakML.Methods.getPeakData$phenoData
	#	corRT <- the corrected retention time PeakML.Methods.getPeakData$correctedRTList
	#	rawRT <- the raw retention time; PeakML.Methods.getPeakData$rawRTList
	#	outFileName <- the output file name 
	#	ionisation <- the ionisation, leave it as default
	# POST:
	#	write the peakml the the file specified

	if (!is.null(peakMLdata))
	{
		peakDataMtx <- peakMLdata$peakDataMtx
		chromDataList <- peakMLdata$chromDataList
		sampleNames <- peakMLdata$sampleNames
		rawDataFullPaths <- peakMLdata$rawDataFullPaths
		phenoData <- peakMLdata$phenoData
		corRT <- peakMLdata$correctedRTList
		rawRT <- peakMLdata$rawRTList
		ionisation <- peakMLdata$massCorrection[[2]]
		GroupAnnotations <- peakMLdata$GroupAnnotations
	}

	if (length(sampleNames)>1)
	{
		project <- .jnew("peakml/util/rjava/Project", sampleNames, rawDataFullPaths, phenoData)
	} else
	{
		project <- .jnew("peakml/util/rjava/ProjectSingleMeasurement", sampleNames, rawDataFullPaths)
	}

	for (measID in 1:length(sampleNames)){
		for (scanID in 1:length(rawRT[[measID]])){
			.jcall(project, returnSig="V", method="addScanInfo", as.integer(measID-1), as.numeric(corRT[[measID]][scanID]), as.character(ionisation))
			.jcall(project, returnSig="V", method="addScanAnnotation", as.integer(measID-1), as.integer(scanID-1), as.character("RT_raw"), as.character(rawRT[[measID]][scanID]))
		}
	}

	for (peakID in 1:length(chromDataList)){
		chrom <- chromDataList[[peakID]]
		.jcall(project, returnSig="V", method="addMassChromatogram", as.integer(peakDataMtx[peakID,9]-1), as.integer(chrom[4,]), as.numeric(chrom[3,]),as.numeric(chrom[1,]), as.numeric(chrom[2,]), as.character(ionisation))
	}

	if (length(sampleNames)>1)
	{
		setIndexes <- vector("list",length(unique(peakDataMtx[,10])))
		for (sid in 1:length(setIndexes))
		{
			setIndexes[[sid]] <- which(peakDataMtx[,10]==unique(peakDataMtx[,10])[sid])
		}
	
		for (sid in 1:length(setIndexes)){
			.jcall(project, returnSig="V", method="addPeakSet", as.integer(setIndexes[[sid]]-1))
		}

		if (!is.null(GroupAnnotations))
		{
			PeakML.Methods.writeGroupAnnotations (project, GroupAnnotations)
		}
		.jcall(project, returnSig="V", method="write", outFileName)
	} else
	{
		.jcall (project,returnSig="V",method="writeMeasurements", outFileName)
	}
}