[Bioc-devel] Lack of Genomic RleList

[Kasper Daniel Hansen]

Thanks for the pointer, I'll experiment and update my materials.

Kasper

On Tue, Mar 29, 2016 at 2:43 PM, Hervé Pagès <hpages at fredhutch.org> wrote:

> 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
>> _______________________________________________
>> Bioc-devel at r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>
>>
> --
> Hervé Pagès
>
> Program in Computational Biology
> Division of Public Health Sciences
> Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N, M1-B514
> P.O. Box 19024
> Seattle, WA 98109-1024
>
> E-mail: hpages at fredhutch.org
> Phone:  (206) 667-5791
> Fax:    (206) 667-1319
>
>
> _______________________________________________
> Bioc-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>

	[[alternative HTML version deleted]]