[BioC] how to build a GOstats-compatible annotation package for plasmodium falciparum?

[Paul Shannon]

Hi Marc,

If (as seems quite possible) no one has time right now to do a proper  
malaria annotation package,
can you tell me how I can get started with creating the minimal data  
needed for
GOstats?

I hope that if I were to emulate the YEASTGO environment from the  
YEAST package -- creating
a PFALCIPARUMGO environment, for instance -- that that might be all  
that GOstats needs.

Would that indeed work?  If so, and assuming I could build a properly  
structured environment,
a puzzle remains:  one constructs a GOHyperGParams object specifying

          annotation = 'YEAST'

What would the equivalent argument be for a home-brewed (and minimal)  
annoation
object?  I imagine that hyperGTest does some magic to map from  
"YEAST" to the
YEASTGO environment.


      params = new ("GOHyperGParams", geneIds = unique (deleted),
                    universeGeneIds = universe,
                    annotation = "YEAST",
                    ontology = "BP", pvalueCutoff = 0.01, conditional  
= TRUE,
                    testDirection = "over")


Got any sugeestions?  Cautions?

  Thanks!

  - Paul

On Nov 5, 2007, at 2:07 PM, Marc Carlson wrote:

> Paul Shannon wrote:
>> I'm familiar with the YEAST data package, and the many chip-specific
>> annotation packages --
>> all of which work very nicely with GOstats.
>>
>> GO offers annotation for p.falciparum, the malaria parasite.  What
>> would it take to
>> put that into an R data package which will work with GOstats?
>>
>> Thanks!
>>
>>   - Paul
>>
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>>
> This is a good question.  The short answer is that it is entirely
> possible to do it, but that it's not supported by the new annotation
> pipeline at the moment.
>
> The long answer is that I would be delighted to add this organism if
> there is a strong desire for it by the community.  We are always  
> looking
> for feedback to help us know which things we should be supporting, and
> this includes indications about which organisms are being studied  
> enough
> to merit an annotation package.  For me it's not a question of whether
> or not I will add new stuff to the annotation packages.  It's really a
> question of which stuff I should be working on first.
>
> But because we want the annotation packages to be maximally helpful to
> the largest possible group of people, we are always need information
> about what you guys need.
>
>
> So my question for you is this:  Is it in fact a high priority for the
> community to collate a set of annotation packages about p.falciparum?
>
>
>     Marc