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PeakML.Methods.getRawSignals <- function(mzXMLSrc, sampleName, rtWindow, massWindow, massCorrection){
# PRE:
# Return the raw signals for the given sample in the rt and mass window specified
# mzXMLSrc -> mzXML raw data source path
# sampleName -> Name of the sample
# rtWindow -> the retention time window as list [min, max]
# massWindow -> the mass window as list [min, max]
# massCorrection -> PeakML.Methods.getMassCorrection
# POST:
# a table with masses,intensities,retentiontimes,scanids along the rows.
curDir <- mzXMLSrc
if (is.null(curDir)){
curDir <- getwd()
}
curFile <- list.files(path=curDir, pattern=paste("^", sampleName, ".mzXML", sep=""), full.names=TRUE, recursive=TRUE)
rawFile <- xcmsRaw(curFile)
rtStart <- rtWindow[[1]]
rtEnd <- rtWindow[[2]]
if (rtEnd > max(rawFile@scantime)){
rtEnd <- max(rawFile@scantime)
}
if (rtStart > max(rawFile@scantime)){
rtStart <- max(rawFile@scantime)
}
if (rtEnd < min(rawFile@scantime)){
rtEnd <- min(rawFile@scantime)
}
if (rtStart < min(rawFile@scantime)){
rtStart <- min(rawFile@scantime)
}
massStart <- as.numeric(massWindow[[1]])+massCorrection
massEnd <- as.numeric(massWindow[[2]])+massCorrection
# Extract data form raw data files
if ((rtEnd-rtStart)<5){
rData <- c(1,1,1)
} else{
rData <- rawMat (rawFile,mzrange=cbind(massStart, massEnd),rtrange=c(rtStart,rtEnd))
}
rData <- rbind (rData,NULL)
## Removing values with repeating RT's
## Row with largest intensity are selected
rtRepeats <- as.numeric(names(which(table(rData[,1])>=2)))
if (length(rtRepeats!=0)){
for (z in 1:length(rtRepeats)){
Csub <- which(round(rData[,1],5)==round(rtRepeats[z],5))
Csub <- Csub[-c(which(rData[Csub,3]==max(rData[Csub,3]))[1])]
rData <- rData[-c(Csub),]
rData <- rbind(rData,NULL)
}
}
scanids <- which(rawFile@scantime%in%rData[,1])
## if RT correction was applied, scans should be extracted from raw RT's
if (length(scanids)<3){
scanids <- c(-1,-1,-1)
retentiontimes <- c(-1,-1,-1)
masses <- c(-1,-1,-1)
intensities <- c(-1,-1,-1)
} else {
retentiontimes <- rData[,1]
masses <- rData[,2]
intensities <- rData[,3]
}
rm(rawFile, rData)
rv <- rbind(masses,intensities,retentiontimes,scanids-1)
rv
}
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