[BioC] hyperGTest on proteomics data

[Seth Falcon]

"Kimpel, Mark William" <mkimpel at iupui.edu> writes:
> I would like to use the hyperGTest in package "GOstats" on some
> proteomics data that I have. It is LCMS data and I have a list of all
> Entrez Gene identifiers of all identified proteins (the universe) and of
> the significant proteins. 

> I imagine this is because hyperGTest relies on the Bioc metadata
> packages to map EntrezGene to GO categories. It seems to me that there
> should be a work around to this problem using biomaRt or some direct
> calls to the GO website.

Your assessment is correct.  The code in Category and GOstats relies
upon environments from an annotation data package to retrieve the
required mappings.

It should be possible to obtain the mappings required for the test
using just the GO package, but it will require some work...

> Suggestions?

I think the way to go is to add either a new parameter class and/or a
new class for representing the annotation data (in devel there is
already code along these lines to make use of SQLite-based annotation
packages).

Then one would need to define methods for universeBuilder and
categoryToEntrezBuilder that extract the required info just using the
GO package.

At that point, things should plug into the rest of the code and Just
Work (yeah, sure).

It is something that is on my TODO list, but I don't have an ETA for
when it will be done.

+ seth