[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?
--Naomi
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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