Nothing
PeakML.Normalization <- function(filename,ionisation="detect",Rawpath=NULL,outputfile,values=NULL)
{
PeakMLdata <- PeakML.Read(filename=filename,ionisation=ionisation,Rawpath=Rawpath)
## Append peakdata with a vector of normalisation values which should be used for every vector of intensities
## if values=NULL use TIC's of the raw data files for normalisation
if (is.null(values))
{
values <- rep(NA,length(PeakMLdata$sampleNames))
for (file in 1:length(PeakMLdata$sampleNames))
{
rawfile <- xcmsRaw(PeakMLdata$rawDataFullPaths[file])
values[file] <- sum(rawfile@tic)
}
}
normvals <- rep(NA,nrow(PeakMLdata$peakDataMtx))
for (nval in 1:length(PeakMLdata$sampleNames))
{
normvals[PeakMLdata$peakDataMtx[,9]==nval] <- values[nval]
}
## Normalize data
for (chrnum in 1:length(normvals))
{
PeakMLdata$chromDataList[[chrnum]][2,] <- PeakMLdata$chromDataList[[chrnum]][2,]/normvals[chrnum]*10^4
}
## Write all of this out
PeakML.Write(peakMLdata=PeakMLdata, outFileName=outputfile)
}
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