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.
[Bioc-devel] OrganismDb and associated TxDb
3 messages · Vincent Carey, Marc Carlson, Hahne, Florian
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. [[alternative HTML version deleted]]
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2 days later
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" <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 something of a mystery. [[alternative HTML version deleted]]
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