comparison run_spp.R @ 11:495a6d033ca1 draft

Uploaded
author modencode-dcc
date Thu, 07 Feb 2013 23:06:36 -0500
parents 86146a313b66
children
comparison
equal deleted inserted replaced
10:c57381059179 11:495a6d033ca1
858 cat(paste("Detected",sum(unlist(lapply(narrow.peaks$npl,function(d) length(d$x)))),"peaks"),"\n",file=stdout()) 858 cat(paste("Detected",sum(unlist(lapply(narrow.peaks$npl,function(d) length(d$x)))),"peaks"),"\n",file=stdout())
859 859
860 # Write to narrowPeak file 860 # Write to narrowPeak file
861 if (!is.na(iparams$output.npeak.file)) { 861 if (!is.na(iparams$output.npeak.file)) {
862 write.narrowpeak.binding(narrow.peaks,iparams$output.npeak.file,margin=round(crosscorr$whs/2),npeaks=iparams$npeak) 862 write.narrowpeak.binding(narrow.peaks,iparams$output.npeak.file,margin=round(crosscorr$whs/2),npeaks=iparams$npeak)
863 system(paste('gzip -f ',iparams$output.npeak.file)) 863 #system(paste('gzip -f ',iparams$output.npeak.file))
864 } 864 }
865 865
866 # Compute and write regionPeak file 866 # Compute and write regionPeak file
867 if (!is.na(iparams$output.rpeak.file)) { 867 if (!is.na(iparams$output.rpeak.file)) {
868 region.peaks <- add.broad.peak.regions(chip.data,control.data,narrow.peaks,window.size=max(50,round(crosscorr$whs/4)),z.thr=10) 868 region.peaks <- add.broad.peak.regions(chip.data,control.data,narrow.peaks,window.size=max(50,round(crosscorr$whs/4)),z.thr=10)
869 write.narrowpeak.binding(region.peaks,iparams$output.rpeak.file,margin=round(crosscorr$whs/2),npeaks=iparams$npeak) 869 write.narrowpeak.binding(region.peaks,iparams$output.rpeak.file,margin=round(crosscorr$whs/2),npeaks=iparams$npeak)
870 system(paste('gzip -f ',iparams$output.rpeak.file)) 870 #system(paste('gzip -f ',iparams$output.rpeak.file))
871 } 871 }
872 872
873 # Save Rdata file 873 # Save Rdata file
874 if (! is.na(iparams$output.rdata.file)) { 874 if (! is.na(iparams$output.rdata.file)) {
875 save(iparams, 875 save(iparams,