[BioC] GWAS with family data

Stephanie M. Gogarten sdmorris at u.washington.edu
Wed Apr 16 17:23:10 CEST 2014

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.


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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