On Thu, Aug 12, 2010 at 2:14 AM, Johannes Waage <johannes.waage@bric.dk>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
>
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