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.
Marc
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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