[BioC] hyperG over chromosome position...?

[Robert Gentleman]

Hi,
   Just a couple of notes,
1) chromosomal location is typically not biologically relevant in higher 
organisms, AFAIK. Since I work at a cancer center, and since some (but 
by no means all) genomic abnormalities in cancer induce an effect that 
can be detected by chromosomal location these sorts of things are 
interesting to me. Anyone using this approach should, IMHO, have a sound 
biological reason for doing so.

2) Chromosome bands are probably not ideal (as Francois so correctly 
points out), but they have the advantage of being easily obtained. Other 
options will require more effort.

3) the code that does this in the Category package and is called 
MAPAmat, but it is flawed in a number of ways. Seth and I will put 
something up that is better in a week or two.

4) any other contributions are welcome, particularly well implemented 
and documented functions.

  best wishes
    Robert

Francois Pepin wrote:
> Hi Dario,
> 
> It is possible to do it with the chromosomal band using Category. That
> was the last part of Robert Gentleman's Category tutorial at BioC2006
> (http://www.bioconductor.org/workshops/2006/BioC2006/labs/rgentleman/).
> 
> I'm not convinced if the chromosomal bands are the best partition to use
> in that case, but it's a good starting point.
> 
> Francois
> 
> On Tue, 2007-01-16 at 07:43 -0800, Seth Falcon wrote:
>> Hi Dario,
>>
>>>> Dario Greco wrote:
>>>>> hi all,
>>>>> i would like to perform hyperGTest using the chromosome position   
>>>>> (stored usually in pkgMAP environment).
>>>>> how could it be possible?
>> Actually, this is on my list of things to add to the Category
>> package.  If you, or anyone, wants to do some programming, take a look
>> at how the KEGG and PFAM tests are implemented.  A first pass for
>> chromosome position will be quite similar.
>>
>> + seth
>>
>> --
>> Seth Falcon | Computational Biology | Fred Hutchinson Cancer Research Center
>> http://bioconductor.org
>>
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> 
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-- 
Robert Gentleman, PhD
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M2-B876
PO Box 19024
Seattle, Washington 98109-1024
206-667-7700
rgentlem at fhcrc.org