[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.
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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