On Thu, Aug 12, 2010 at 2:14 AM, Johannes Waage <[email protected]>wrote:
> Hi all, > > In a Chip-SEQ pipeline, I import my mapped reads in to R, calculate > coverage > with cov(), and run through a set of filters for peak selection, ending up > with a SimpleRleViewsList object. Now, I would like to visualize the file > in > UCSC GB using the bigWig format, a task I normally accomplish by using the > rtracklayer's export on SimpleRleList objects, producing a bedGraph file > (that can then be converted to a bigWig). > > The problem - when I use export() on a SimpleRleViewsList, the run-length > per-base information is lost, instead just producing ranges for each peak. > > How can I convert a View on a Rle back to a per-base Rle? > > It's just the subject() method: rleList <- subject(rleViewsList) Also, you can directly output to bigWig using export.bw(), except on Windows. Michael > Best regards, > > Johannes Waage > Biotech Research and Innovation Center, > University of Copenhagen > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioc-sig-sequencing mailing list > [email protected] > https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing > [[alternative HTML version deleted]] _______________________________________________ Bioc-sig-sequencing mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
