[Bioc-devel] seqnames as a candidate for BiocGenerics

Hervé Pagès hpages at fredhutch.org
Mon Apr 27 20:14:15 CEST 2015

Hi Nico,

On 04/26/2015 09:58 AM, Nicolas Delhomme wrote:
> Hej Hervé (I guess)!
> Could it be possible to move the generic from "seqnames" and "seqnames<-" from GenomeInfoDb to BiocGenerics? I would then deprecate the "seq_name" and "seq_name<-" functions of the genomeIntervals package and import them in the easyRNASeq package.

I guess I could.

However I want to make it clear that a generic function doesn't have
to go to BiocGenerics before it can be shared across packages. There
are situations where this kind of move actually helps to resolve
conflicts but it doesn't seem to be the case here. Any reason why
you can't just import GenomeInfoDb? This is what all the packages that
need the "seqnames" and "seqnames<-" generics currently do. Moving
these generics to BiocGenerics will likely break many of them.


> Cheers,
> Nico
> ---------------------------------------------------------------
> Nicolas Delhomme
> The Street Lab
> Department of Plant Physiology
> Umeå Plant Science Center
> Tel: +46 90 786 5478
> Email: nicolas.delhomme at umu.se
> SLU - Umeå universitet
> Umeå S-901 87 Sweden
> ---------------------------------------------------------------
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Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
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