comparison run_spp.R @ 11:495a6d033ca1

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10:c57381059179

	cat(paste("Detected",sum(unlist(lapply(narrow.peaks$npl,function(d) length(d$x)))),"peaks"),"\n",file=stdout())
	
	# Write to narrowPeak file
	if (!is.na(iparams$output.npeak.file)) {
		write.narrowpeak.binding(narrow.peaks,iparams$output.npeak.file,margin=round(crosscorr$whs/2),npeaks=iparams$npeak)
		system(paste('gzip -f ',iparams$output.npeak.file))
	}
	
	# Compute and write regionPeak file
	if (!is.na(iparams$output.rpeak.file)) {
		region.peaks <- add.broad.peak.regions(chip.data,control.data,narrow.peaks,window.size=max(50,round(crosscorr$whs/4)),z.thr=10)
		write.narrowpeak.binding(region.peaks,iparams$output.rpeak.file,margin=round(crosscorr$whs/2),npeaks=iparams$npeak)
		system(paste('gzip -f ',iparams$output.rpeak.file))
	}
	
	# Save Rdata file    
	if (! is.na(iparams$output.rdata.file)) {
		save(iparams,

11:495a6d033ca1

	cat(paste("Detected",sum(unlist(lapply(narrow.peaks$npl,function(d) length(d$x)))),"peaks"),"\n",file=stdout())
	
	# Write to narrowPeak file
	if (!is.na(iparams$output.npeak.file)) {
		write.narrowpeak.binding(narrow.peaks,iparams$output.npeak.file,margin=round(crosscorr$whs/2),npeaks=iparams$npeak)
		#system(paste('gzip -f ',iparams$output.npeak.file))
	}
	
	# Compute and write regionPeak file
	if (!is.na(iparams$output.rpeak.file)) {
		region.peaks <- add.broad.peak.regions(chip.data,control.data,narrow.peaks,window.size=max(50,round(crosscorr$whs/4)),z.thr=10)
		write.narrowpeak.binding(region.peaks,iparams$output.rpeak.file,margin=round(crosscorr$whs/2),npeaks=iparams$npeak)
		#system(paste('gzip -f ',iparams$output.rpeak.file))
	}
	
	# Save Rdata file    
	if (! is.na(iparams$output.rdata.file)) {
		save(iparams,