Nothing
PeakML.BlankFilter <- function (filename, ionisation="detect", Rawpath=NULL, outputfile, BlankSample=NULL, IgnoreIntensity=FALSE, detectedInNumOfBlanks=NULL, rtwindow=NULL)
{
st <- system.time (PeakMLdata <- PeakML.Read (filename,ionisation,Rawpath))
PeakTable <- PeakML.Methods.getCompleteTable (PeakMLdata)
numberOfpeakSets <- ncol(PeakTable[[1]])
## Check which samples are blanks
blanksamples <- which (PeakMLdata$phenoData==BlankSample)
if (length(blanksamples)<1)
{
stop ("No samples matching a given names for \"blanks\" are found. Please check if function parameter `BlankSample` is set correctly.")
}
Intensities.blank <- PeakTable[[1]][blanksamples,]
Intensities.blank[is.na(Intensities.blank)] <- 0
Intensities.blank <- rbind(Intensities.blank,NULL)
if (nrow(Intensities.blank)>1)
{
Intensities.blank <- apply(Intensities.blank,2,max)
}
Intensities.rest <- PeakTable[[1]][-c(blanksamples),]
Intensities.rest[is.na(Intensities.rest)] <- 0
Intensities.rest <- apply(Intensities.rest,2,max,na.rm=TRUE)
to.remove <- which(Intensities.blank >= Intensities.rest)
if (IgnoreIntensity==TRUE)
{
to.remove <- which(Intensities.blank!=0)
}
if (!is.null(detectedInNumOfBlanks))
{
Intensities.blank <- PeakTable[[1]][blanksamples,]
ndetect <- rep(NA, ncol(PeakTable[[1]]))
for (nd in 1:length(ndetect))
{
ndetect[nd] <- nrow(Intensities.blank)-length(which(is.na(Intensities.blank[,nd])))
}
hits <- which (ndetect >= detectedInNumOfBlanks)
to.remove <- to.remove[to.remove%in%hits]
}
if (!is.null(rtwindow))
{
rtwindow <- rtwindow*60
rt.times <- apply (PeakTable[[3]],2,median,na.rm=TRUE)
hits <- which(rt.times >= rtwindow[1] & rt.times <= rtwindow[2])
to.remove <- to.remove[to.remove%in%hits]
}
## Write no matching
if (length(to.remove)>0)
{
PeakML.Methods.extractPeakGroups (PeakMLData=PeakMLdata, outputfile=paste("blank_removed_",outputfile,sep=""), sets=c(1:numberOfpeakSets)[to.remove])
}
# Not macthed from std file
if (length(to.remove)>0)
{
PeakML.Methods.extractPeakGroups (PeakMLData=PeakMLdata, outputfile=outputfile, sets=c(1:numberOfpeakSets)[-c(to.remove)])
} else
{
PeakML.Methods.extractPeakGroups (PeakMLData=PeakMLdata, outputfile=outputfile, sets=c(1:numberOfpeakSets))
}
}
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