[Bioc-devel] [BioC] lookUp for other terminologies
Hi Matthew, I think that you could probably do something like what you are describing by following the instructions in the Vignette titled "Hypergeometric tests for less common model organisms" which can be seen in the GOstats package: http://www.bioconductor.org/help/bioc-views/release/bioc/html/GOstats.html. It was developed for a similarly generic circumstance as this. An extension of the methods developed for this case would be one way to tackle this. In terms of DO to gene mappings. Where did you get them? I have not found these from any of the expected places. If we can just get the appropriate mappings from a reliable source then it might make sense to include them in our packages. However, if this is not practical, then an approach like what was defined for unsupported organisms is probably a good idea. Marc
On 03/07/2011 10:10 AM, Matthew Pocock wrote:
On 7 March 2011 16:57, Martin Morgan <mtmorgan at fhcrc.org> wrote:
I wonder if you could be a bit more specific about the tasks you're
trying to accomplish?
There are lots of packages in bioconductor that provide methods that run
with GO - GOstats, globaltest, GlobalAncova, ... and all of these that I've
looked at so far essentially only need an annotation Bimap, some way to get
terms, and something with the CHILDREN/OFFSPRING/... methods. I'd like to be
able to run them for DO, but I'm sure there are other interesting
terminologies out there that other people may want to use.
I've been given an entrez<->do mapping file - I can't attest to its
provenance or accuracy. From this, I've got functions that produce
${annotation}DO bimaps if there is an ${annotation}ENTREZID bimap present.
As for the algorithms themselves, so far I've been copying out bits of these
packages and hacking them about to use DO rather than GO* hierarchies.
However, it's error-prone and not pretty, and I'd prefer to be able to do
this with less hackery - or at least, by relying upon bioconductor-blessed
and encapsulated hackery.
Matthew