Nothing
mzmatch.ipeak.filter.RSDFilter <- function(JHeapSize=1425,i=NULL, o=NULL, rejected=NULL, rsd=NULL, h=NULL, v=NULL, sampleList=NULL, nSlaves=1, inputfolder="combined")
{
version.1 <- get("version.1",envir=.GlobalEnv)
## define the java runtime parameters
java <- "java -da -dsa -Xmn1g -Xss228k -XX:+UseParallelGC -XX:ParallelGCThreads=10"
## locate the mzmatch.jar file (it's included in the peakmlR package)
## JHeapSize - define amount of RAM availiable for java VM
JHeapSize <- paste(JHeapSize,"m",sep="")
java <- paste(java," -Xms",JHeapSize," -Xmx",JHeapSize," -cp",sep="")
if (version.1==TRUE)
{
mzmatch <- paste(java, " ", find.package("mzmatch.R"), "/java/mzmatch.jar", sep="")
## setup the tool
tool <- paste(mzmatch, "mzmatch.ipeak.filter.RSDFilter")
if (!is.null(i))
tool <- paste(tool, "-i", i)
if (!is.null(o))
tool <- paste(tool, "-o", o)
if (!is.null(rejected))
tool <- paste(tool, "-rejected", rejected)
if (!is.null(rsd))
tool <- paste(tool, "-rsd", rsd)
if (!is.null(h) && h==T)
tool <- paste(tool, "-h")
if (!is.null(v) && v==T)
tool <- paste(tool, "-v")
system(tool)
} else
{
MainClasses <- levels(sampleList$sampleClass)
outputfiltered <- paste(inputfolder,"_RSD_filtered", sep="")
outputrejected<- paste(inputfolder,"_RSD_rejected", sep="")
if (!file.exists(outputfiltered))
{
dir.create (outputfiltered)
}
if (!file.exists(outputrejected))
{
dir.create (outputrejected)
}
RSDfunction <- function (fnum)
{
FILESf <- sampleList$outputfilenames[which(sampleList$sampleClass==MainClasses[fnum])]
if (length(FILESf)>1)
{
i <- paste(inputfolder,"/",MainClasses[fnum],".peakml",sep="")
o <- paste(outputfiltered,"/",MainClasses[fnum],".peakml",sep="")
rejected <- paste(outputrejected,"/",MainClasses[fnum],".peakml",sep="")
mzmatch <- paste(java, " ", find.package("mzmatch.R"), "/java/mzmatch_2.0.jar", sep="")
## setup the tool
tool <- paste(mzmatch, "mzmatch.ipeak.filter.RSDFilter")
if (!is.null(i))
tool <- paste(tool, "-i", i)
if (!is.null(o))
tool <- paste(tool, "-o", o)
if (!is.null(rejected))
tool <- paste(tool, "-rejected", rejected)
if (!is.null(rsd))
tool <- paste(tool, "-rsd", rsd)
if (!is.null(h) && h==T)
tool <- paste(tool, "-h")
if (!is.null(v) && v==T)
tool <- paste(tool, "-v")
system(tool)
} else
{
i <- paste(inputfolder,"/",MainClasses[fnum],".peakml",sep="")
o <- paste(outputfiltered,"/",MainClasses[fnum],".peakml",sep="")
file.copy (i,o)
}
}
if (nSlaves>1)
{
cl <- makeCluster (nSlaves)
envname <- environment()
clusterExport (cl, list=c("RSDfunction","MainClasses","sampleList","rsd","java","h","v"), envir=envname)
system.time(clusterApply(cl,1:length(MainClasses),RSDfunction))
stopCluster(cl)
} else
{
for (fnum in 1:length(MainClasses))
{
RSDfunction(fnum)
}
}
}
}
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