[BioC] Using GO functions without using LocusLink mappings

[Seth Falcon]

Hi Anar,

"Khan, Anar" <Anar.Khan at agresearch.co.nz> writes:
> We have custom Affy chips based on proprietary sequences from a species
> which isn't well represented in public databases. We've assigned GO
> annotations ourselves using InterProScan and other methods, because the
> level of annotations of related species in public databases is also very
> poor.
>
> Is it possible to feed predetermined GO annotations into GOstats (or any
> other package which performs GO analyses), or are LocusLink IDs always
> required to initialise the GO mappings?

Right now, the functions in GOstats need an annotation data package
that _looks like_ the BioC annotation packages produced for Affy
chips.  

So one option is to use AnnBuilder to generate such a package using
the annotations you have.  With such a package, GOstats should Just
Work.

That said, I'm currently working on some modifications that should
make GOstats a bit more flexible in this regard.

Best,

+ seth