The kinship2 package implements a mixed model for family data. It is not
GWAS specific, but has been used in GWAS studies with family data.


On Wed, Apr 16, 2014 at 3:00 PM, NAOMI S ALTMAN <naomi@stat.psu.edu> wrote:

> 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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>>
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