[Bioc-devel] OrganismDb and associated TxDb

Hahne, Florian florian.hahne at novartis.com
Mon Feb 16 11:50:55 CET 2015

Hi Vince,
I haven't looked too much at the OrganismDb stuff yet. Just let me know
when you run into any major roadblocks for a Gviz patch. We could refactor
some things to make it work.

On 13/02/15 19:01, "Vincent Carey" <stvjc at channing.harvard.edu> 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
>of a mystery.
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