[Bioc-devel] OrganismDb and associated TxDb

Marc Carlson mcarlson at fredhutch.org
Fri Feb 13 23:09:47 CET 2015

Hi Vince,

First of all thank you for using OrganismDb objects.  You raise some 
interesting points though about keeping these APIs better synchronized 
that I feel point to some deficiencies in the current design.  I spoke 
with Herve about this and we are puzzling over possibly using 
inheritance to make this a bit easier for maintenance.


On 02/13/2015 10:01 AM, Vincent Carey wrote:
> Gviz has a nice way of working with TxDb instances to derive gene models.
> It can be cumbersome to refer to a TxDb instance, and the Homo.sapiens
> OrganismDb instance is very convenient to work with.
> I do not see any straightforward way to extract a reference to a TxDb from
> Homo.sapiens.  I could traverse the graph slot but class?OrganismDb
> makes no reference to this.
> In summary, I think it would be good to document the OrganismDb API and
> to think about preferences for using OrganismDb as opposed to
> TxDb and OrgDb (org.Hs.eg.db) whenever possible.
> BTW I attempted to 'patch' Gviz by substituting OrganismDb for TxDb --
> there are only two references to TxDb in Gviz ... and it would seem that
> the necessary operations apply to OrganismDb just as well as to TxDb.
> But the APIs are not in sync ... I ran into seqlevels0 ... and that is
> something
> of a mystery.
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