Hi Marc

Thank you very much for your answer, and I'm really sorry for my much belated reply.

I have tried your suggestion, but if  I use KEGGFrame directly it gives me an error that the pfam ID's are not valid KEGG ID's (See below).

I suspect that what you have in mind is not what I have attempted here, but instead to create my data object manually by specifying a two column data.frame and the organism in a separate slot. I'm however unsure how to do this. Is there a "quick" way to do this or should I look into R object oriented programming syntax?

All the best, and many many thanks in advance for your reply
Henrik

Rcode snippets:
> pfamframedata<-read.table("IsogroupAll_pfam.mysqlout", header=TRUE, colClasses = "character")
> head(pfamframedata)
     pfam        isogid
1 PF00978 isogroup00001
2 PF05381 isogroup00001
3 PF01660 isogroup00001
4 PF05381 isogroup00001
5 PF01443 isogroup00001
6 PF01660 isogroup00001

> pfamFrame=KEGGFrame(pfamframedata, organism="XXXX")
Error in .testKEGGFrame(x, organism) :
  None of elements in the 1st column of your data.frame object are legitimate KEGG IDs.





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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Henrik Hjarvard de Fine Licht, PhD, Post Doctoral Researcher
Centre for Genomic Ecology, Microbial Ecology
Department of Biology, Lund University,
SE-223 62 Lund, Sweden
Email: henrik.de_fine_licht@biol.lu.se<mailto:henrik.de_fine_licht@biol.lu.se>
Website:  http://www.lu.se/henrik-de-fine-licht

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