[BioC] GWAS with family data

Paul Geeleher paulgeeleher at gmail.com
Wed Apr 16 18:43:27 CEST 2014

GenABEL will allow you to do this fairly easily. Notably, it is also
very well documented.

EMMAX may provide something a little more cutting edge when analysing
family GWAS (but not in an R environment):


On Tue, Apr 15, 2014 at 12:09 PM, Naomi Altman <naomi at stat.psu.edu> 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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Dr. Paul Geeleher, PhD
Section of Hematology-Oncology
Department of Medicine
The University of Chicago
900 E. 57th St.,
KCBD, Room 7144
Chicago, IL 60637

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