Sounds nice but we have to be careful.  We may need a parameter:
Homo.sapiens("hg19") ... because
broad adoption of new builds may take considerable time.


On Wed, Jun 18, 2014 at 6:13 PM, Hervé Pagès <hpages@fhcrc.org> wrote:

> On 06/18/2014 05:26 AM, Michael Lawrence wrote:
>
>> Would it make sense for an OrganismDb object to have an associated
>> BSgenome? This association is implicit anyway. Or do we need an even
>> broader umbrella object? This would make some things easier. For example,
>> predictCoding(variants, Homo.sapiens). Just nice to have everything in one
>> bundle. Also, could there be a mapping between the genome(variants) ID and
>> Homo.sapiens, so predictCoding(variants) is possible? Or is that just
>> being
>> too automatic?
>>
>> At the very least, it would be nice if the various TranscriptDb methods
>> started to support OrganismDb as an alternative.
>>
>
> I know Marc has added many of them already. Which one are missing? My
> understanding is that most of them actually delegate to the method for
> TranscriptDb objects. Why not just make OrganismDb extend TranscriptDb
> so all of them would actually work out-of-the-box (then only override
> when needed).
> We could do the same with BSgenome. This looks like a place where
> multiple inheritance could maybe save us a lot of work.
>
> Cheers,
>
> H.
>
>
>> Michael
>>
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>>
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>>
> --
> Hervé Pagès
>
> Program in Computational Biology
> Division of Public Health Sciences
> Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N, M1-B514
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> Seattle, WA 98109-1024
>
> E-mail: hpages@fhcrc.org
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>
>
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