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. FLorian
On 13/02/15 19:01, "Vincent Carey" <st...@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 >something >of a mystery. > > [[alternative HTML version deleted]] > >_______________________________________________ >Bioc-devel@r-project.org mailing list >https://stat.ethz.ch/mailman/listinfo/bioc-devel _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
