Message-ID: <514CC50F.60701@fhcrc.org>
Date: 2013-03-22T20:54:39Z
From: Marc Carlson
Subject: [Bioc-devel] Mus.musculus and genome version
In-Reply-To: <CAG10-bqiesF19u_HnPn_T0=_ePkGnev4L+Fo_dD1TAnPhL4miw@mail.gmail.com>
Hi Mattia,
These packages are actually modular and are intended to be adjustable if
you need to use other TxDbs. Please see the main package vignette for
OrganismDbi for details on how this works.
http://www.bioconductor.org/packages/2.12/bioc/vignettes/OrganismDbi/inst/doc/OrganismDbi.pdf
So basically, as long as you have packages that implement a select
method, and which are relatable to each to each other via extractable
foreign keys, you should be able to make a custom package to suit your
needs pretty easily.
Marc
On 03/22/2013 07:47 AM, mattia pelizzola wrote:
> Hi,
> I find the Mus.musculus and Homo.sapiens annotation environments extremely
> useful. Still, one important limitation to me is that they are only based
> on the latest genome version available.
> For example, Mus.musculus contains the TxDB object for the mm10 genome
> version, while several TxDB are available for different genome versions.
> It would be great if one could have Mus.musculus releases corresponding to
> the different genome versions as well.
>
> Thanks,
>
> mattia
>
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>
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