On 7 March 2011 16:57, Martin Morgan <mtmorgan@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

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Matthew Pocock
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