[BioC] GWAS with family data

[Naomi Altman]

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