Nothing
nhppSimConstWindowGen <-
function(controlRates, filename, chromosomeN, nSpike=25, cptLen=c(3,5,8,12,20,30,50,75,100), nPair=2, nRepeat=10, minGain=1.5, maxGain=4, minLoss=0.01, maxLoss=0.5, pGain=0.6) {
nCptLen = length(cptLen)
segseqRunName = as.matrix(c(sapply(1:nCptLen, function(x) {sapply(1:nRepeat, function(y) {return(paste("SegSeq -i ", filename, "_Meta_", cptLen[x], "_", y, ".txt -s ",filename,cptLen[x],"_",y, sep=""))})}), "exit"), ncol=1)
write.table(segseqRunName, file=paste(filename, "Run.m", sep=""), row.names=FALSE, col.names=FALSE, quote=FALSE)
for(k in 1:nRepeat) {
for(i in 1:nCptLen) {
normalDataName = sapply(1:nPair, function(j) {return(paste(filename, "_Data_Normal_", j, "_", k, ".txt", sep=""))})
tumorDataName = sapply(1:nPair, function(j) {return(paste(filename, "_Data_Tumor_Spike", cptLen[i], "_", j, "_", k, ".txt", sep=""))})
dataFileName = c(normalDataName, tumorDataName)
sampleName = c(rep(paste(filename, "_N","_", k, sep=""), nPair), rep(paste(filename, "_T", cptLen[i], "_", k, sep=""), nPair))
sampleType = c(rep("Normal", nPair), rep("Tumor", nPair))
metaMat = cbind(dataFileName, sampleName, sampleType)
metaName = paste(filename, "_Meta_", cptLen[i], "_", k, ".txt", sep="")
colnames(metaMat) = c("File", "Sample", "Type")
write.table(metaMat, file=metaName, sep="\t", row.names=FALSE, col.names=TRUE, quote=FALSE)
}
for(j in 1:nPair) {
dataFileName = paste(filename, "_Data_Normal_", j, "_", k, ".txt", sep="")
controlSim = nhppSimulate(controlRates)
nLength = length(controlSim)
strandSim = sample(0:1, nLength, replace=TRUE)
chromosomeSim = rep(chromosomeN, nLength)
dataMat = cbind(chromosomeSim, controlSim, strandSim)
write.table(dataMat, file=dataFileName, sep="\t", row.names=FALSE, col.names=FALSE, quote=FALSE)
}
for(i in 1:nCptLen) {
newSpikeRate = nhppSpikeConstWindow(controlRates, nSpike, cptLen[i], minGain, maxGain, minLoss, maxLoss, pGain)
newSpikeMat = newSpikeRate$spikeMat
spikeName = paste(filename, "_spikeMat_", cptLen[i], "_", k, ".txt", sep="")
write.table(newSpikeMat, file=spikeName, sep="\t", row.names=FALSE, col.names=FALSE, quote=FALSE)
for(j in 1:nPair) {
dataFileName = paste(filename, "_Data_Tumor_Spike", cptLen[i], "_", j, "_", k, ".txt", sep="")
caseSim = nhppSimulate(newSpikeRate$caseRates)
nLength = length(caseSim)
strandSim = sample(0:1, nLength, replace=TRUE)
chromosomeSim = rep(chromosomeN, nLength)
dataMat = cbind(chromosomeSim, caseSim, strandSim)
write.table(dataMat, file=dataFileName, sep="\t", row.names=FALSE, col.names=FALSE, quote=FALSE)
#newSpikeCBSN5 = ScanCBS(controlSim, newSpikeSim, statistic="normal", takeN=5, minStat=8, maxNCut=50, timing=TRUE)
#newCBSRes = list(spikeCBSN5=newSpikeCBSN5, spikeMat=newSpikeRate$spikeMat)
#simCBSRes[[counter]] = newCBSRes
}
}
}
}
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