[BioC] GWAS with family data

NAOMI S ALTMAN naomi at stat.psu.edu
Wed Apr 16 21:00:34 CEST 2014

Thanks, Stephanie.

This was actually to demonstrate GWAS to my course.  The only GWAS 
analysis I had done previously had no family info - most of the folks I 
talk with have nuclear families.  So even if the association is bogus, I 
am glad you did it this way - it brought up a number of issues I was not 
aware of at that time, which means that my class is now aware of the issues.

Did you notice that there was a pretty strong association between race 
and your status variable?


On 4/16/2014 11:23 AM, Stephanie M. Gogarten wrote:
> Hi Naomi,
> Just a word of caution on the GWASdata package - the case-control 
> status for those samples is not real, I made it up for the GWASTools 
> examples by randomly assigning case status to HapMap samples.
> I'm afraid I don't have any advice on family studies - when I've done 
> analyses with GWASTools I've selected only unrelated samples for the 
> association tests, which is presumably not what you want to do for a 
> family study.
> Stephanie
> On 4/15/14 1:09 PM, Naomi Altman wrote:
>> Is there software in R for doing GWAS analysis with family case-control
>> data?
>> I started with the data in GWASdata.  This is a set of 13 families of 2
>> ethnicities.  So just treating the data as a bunch of 2x3 tables is
>> clearly not correct.
>> I cannot seem to find any software that is extensible.  The workflow in
>> GWAStools seems OK (I did not do all of it) but it is a pipeline - not
>> really the same as controlling my own analysis.
>> Thanks
>> --Naomi
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