Mercurial > repos > stemcellcommons > spp_tool
comparison run_spp.R @ 14:d4e99c087688
Changes for compatibility with SPP R package version 1.11.
| author | Ilya Sytchev <isytchev@hsph.harvard.edu> |
|---|---|
| date | Tue, 15 Oct 2013 15:05:49 -0400 |
| parents | 495a6d033ca1 |
| children | ea38ad1cfb62 |
comparison
equal
deleted
inserted
replaced
| 13:64f2784d471f | 14:d4e99c087688 |
|---|---|
| 857 } | 857 } |
| 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$whs/2)) |
| 863 #system(paste('gzip -f ',iparams$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)) |
| 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)) { |