[BioC] PFAM gene enrichment test using GOstats and Category

[Marc Carlson]

Hi Henrik,

You are correct that there isn't a PFAMFrame yet.  But the usage 
situation for PFAM should be very similar to what happens with KEGG.  So 
theoretically, you should  be able to use a KEGGFrame for this purpose.  
Have you tried this?


   Marc



On 11/25/2011 02:12 AM, Henrik De Fine Licht wrote:
> Dear List
>
> I want to do a hypergeometric testing of GO, KEGG and PFAM terms. I'm using
> the GOstats package and the method described in the vignette: "How to use
> GOstas and Category to do hypergeometric testing with unsupported model
> organisms" by M. Carlson, Oct. 31. 2011, because my organism is a non-model
> organisms.
>
> I have obtained the annotation for my gene sets from other sources and the
> method described in the vignette is working perfect for GO and KEGG. But
> now I would like to do the same for PFAM domains, but I'm having trouble
> figuring out how to do this.
>
> It seems that there is no function for creating a PFAMFrame object similar
> to the GOFrame and KEGGFrame functions, but I guess such an object could be
> constructed by other means, but I'm unsure how this is done?
>
> Many thanks for your time and help
>
> best,
> Henrik Licht
>
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>
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