Nothing
mzmatch.R.Setup <- function (projectFolder=NULL, samplelist=NULL, outputfolder="peakml", sampleClassFromFolderNames=FALSE, extractMeasurentDate=FALSE)
{
if (is.null(projectFolder))
{
projectFolder <- tclvalue (tkchooseDirectory())
}
setwd (projectFolder)
## supported MS data formats
extensions <- c("\\.mzXML$", "\\.mzML$", "\\.mzData$", "\\.cdf$", "\\.CDF$")
if (is.null(samplelist))
{
mzXMLfiles.fullnames <- NULL
outputfilenames <- NULL
for (ext in extensions)
{
HIT <- dir(full.names=TRUE,pattern=ext,recursive=TRUE)
mzXMLfiles.fullnames <- append(mzXMLfiles.fullnames, HIT)
outputfilenames <- append(outputfilenames,sub(ext,".peakml", HIT))
}
for (i in 1:length(mzXMLfiles.fullnames))
{
outputfilenames[i] <- PeakML.Methods.extractFileName(outputfilenames[i])
}
outputfilenames <- paste(outputfolder,"/",outputfilenames, sep="")
duplicate <- table (outputfilenames)
duplicate <- duplicate[duplicate>1]
if (length(duplicate)!=0)
{
cat ("Oh no! Output file names:", names(duplicate)," have duplicates. Please check that input files doesn't have a duplicate file names. \n")
stop()
}
sampleList <- data.frame (filenames=mzXMLfiles.fullnames, sampleClass=rep("",length(mzXMLfiles.fullnames)), globalClass=rep("",length(mzXMLfiles.fullnames)), measurementTimeStamp=rep("", length(mzXMLfiles.fullnames)))
if (sampleClassFromFolderNames==FALSE)
{
fix (sampleList)
## fix writes edited object to the .GlobalEnv, we have to read it back into fucntion environmnet.
sampleList <- get ("sampleList", envir=.GlobalEnv)
} else
{
#create sample classes, supports subfolders.
foldernames <- do.call(rbind,strsplit (mzXMLfiles.fullnames,"/"))
cnames <- apply(foldernames,2, function(x) (length(unique(x))))
hits <- which(cnames>1)
if (length(hits)>0)
{
sampleList$sampleClass <- foldernames[,hits[1]]
}
}
if (extractMeasurentDate==TRUE)
{
sampleList$measurementTimeStamp <- sapply (mzXMLfiles.fullnames,PeakML.Methods.mzML.startTimeStamp)
}
sampleList[,1] <- as.character(sampleList[,1])
write.table (sampleList,file="sample_setup.tsv",sep="\t",row.names=FALSE)
}
else
{
sampleList <- read.table (samplelist, sep="\t", header=TRUE)
mzXMLfiles.shortnames <- rep(NA,nrow(sampleList))
sampleList[,1] <- as.character(sampleList[,1])
for (i in 1:nrow(sampleList))
{
mzXMLfiles.shortnames[i] <- PeakML.Methods.extractFileName(sampleList$filenames[i])
}
outputfilenames <- paste(outputfolder,"/", mzXMLfiles.shortnames, sep="")
for (ext in extensions)
{
outputfilenames <- sub(ext, ".peakml", outputfilenames)
}
if (extractMeasurentDate==TRUE)
{
sampleList$measurementTimeStamp <- sapply (mzXMLfiles.fullnames,PeakML.Methods.mzML.startTimeStamp)
}
}
if (!file.exists(outputfolder))
{
dir.create (outputfolder)
}
sampleList$outputfilenames <- outputfilenames
assign("sampleList", sampleList, envir=.GlobalEnv)
}
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