[Bioc-devel] Lack of Genomic RleList

[Hervé Pagès]

Hi Dario,

On 03/16/2016 04:00 AM, Dario Strbenac wrote:
> Hello,
>
> I have a use case for which I notice other users have already asked about https://stat.ethz.ch/pipermail/bioconductor/2013-December/056400.html and http://kasperdanielhansen.github.io/genbioconductor/html/GenomicRanges_Rle.html#rles-and-granges I'm hoping that, by mentioning it again, it could be included in the future plans for GenomicRanges. It would be nice to avoid making loops for chromosomes and strands, which improves readability.

Janet was asking about subsetting a RleList using a GRanges object.
I added this more than 2 years ago and it's documented (see last example
in ?GRanges).

Kasper's section "Rles and GRanges" could benefit from an update showing
how to subset 'rl' by 'grView' instead of trying to create views on it.

Creating views on a RleList object is not supported yet but could easily
be done in the same way that I've done it for views on a BSgenome
object (requested by Kasper 16 months ago):

   https://support.bioconductor.org/p/62749/

H.

>
> --------------------------------------
> Dario Strbenac
> PhD Student
> University of Sydney
> Camperdown NSW 2050
> Australia
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>

-- 
Hervé Pagès

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