mzmatch.ipeak.sort.MetAssign <- function(JHeapSize=1425,i=NULL, o=NULL, basepeaks=NULL, ppm=NULL, p1=NULL, p0=NULL, alpha=NULL, alpha0=NULL, alpha1=NULL, numDraws=NULL, burnIn=NULL, databases=NULL, adducts=NULL, minDistributionValue=NULL, maxValues=NULL, rho=NULL, retentionTimeSD=NULL, retentionTimePredSD=NULL, identificationPeaks=NULL, filterPPM=NULL, rtClustering=NULL, seed=NULL, debug=NULL, debugOut=NULL, dbIdentOut=NULL, test=NULL, h=NULL, v=NULL)
{
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)
{
stop ("This tool can't be used with mzmatch version belw 2.0")
} else
{
mzmatch <- paste(java, " ", find.package("mzmatch.R"), "/java/mzmatch_2.0.jar", sep="")
}
## setup the tool
tool <- paste(mzmatch, "mzmatch.ipeak.sort.MetAssign")
if (!is.null(i))
tool <- paste(tool, "-i", i)
if (!is.null(o))
tool <- paste(tool, "-o", o)
if (!is.null(basepeaks))
tool <- paste(tool, "-basepeaks", basepeaks)
if (!is.null(ppm))
tool <- paste(tool, "-ppm", ppm)
if (!is.null(p1))
tool <- paste(tool, "-p1", p1)
if (!is.null(p0))
tool <- paste(tool, "-p0", p0)
if (!is.null(alpha))
tool <- paste(tool, "-alpha", alpha)
if (!is.null(alpha0))
tool <- paste(tool, "-alpha0", alpha0)
if (!is.null(alpha1))
tool <- paste(tool, "-alpha1", alpha1)
if (!is.null(numDraws))
tool <- paste(tool, "-numDraws", numDraws)
if (!is.null(burnIn))
tool <- paste(tool, "-burnIn", burnIn)
if (!is.null(databases))
tool <- paste(tool, "-databases", databases)
if (!is.null(adducts))
tool <- paste(tool, "-adducts", adducts)
if (!is.null(minDistributionValue))
tool <- paste(tool, "-minDistributionValue", minDistributionValue)
if (!is.null(maxValues))
tool <- paste(tool, "-maxValues", maxValues)
if (!is.null(rho))
tool <- paste(tool, "-rho", rho)
if (!is.null(retentionTimeSD))
tool <- paste(tool, "-retentionTimeSD", retentionTimeSD)
if (!is.null(retentionTimePredSD))
tool <- paste(tool, "-retentionTimePredSD", retentionTimePredSD)
if (!is.null(identificationPeaks))
tool <- paste(tool, "-identificationPeaks", identificationPeaks)
if (!is.null(filterPPM))
tool <- paste(tool, "-filterPPM", filterPPM)
if (!is.null(rtClustering))
tool <- paste(tool, "-rtClustering", rtClustering)
if (!is.null(seed))
tool <- paste(tool, "-seed", seed)
if (!is.null(debug))
tool <- paste(tool, "-debug", debug)
if (!is.null(debugOut))
tool <- paste(tool, "-debugOut", debugOut)
if (!is.null(dbIdentOut))
tool <- paste(tool, "-dbIdentOut", dbIdentOut)
if (!is.null(test))
tool <- paste(tool, "-test", test)
if (!is.null(h) && h==T)
tool <- paste(tool, "-h")
if (!is.null(v) && v==T)
tool <- paste(tool, "-v")
system(tool)
}
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