[Bioc-devel] Lack of Genomic RleList

Hervé Pagès hpages at fredhutch.org
Tue Mar 29 20:43:53 CEST 2016

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):



> --------------------------------------
> 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

More information about the Bioc-devel mailing list