[Bioc-devel] OrganismDb and associated TxDb

Vincent Carey stvjc at channing.harvard.edu
Fri Feb 13 19:01:47 CET 2015

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.

	[[alternative HTML version deleted]]

More information about the Bioc-devel mailing list