On Thu, Jan 17, 2013 at 8:50 AM, Samuel Younkin <syounkin@jhsph.edu> wrote:

> BioC,
>
> I have been using snpStats to analyze case-parent sequence data, and I
> have found that it would be useful to have a method for the class snpMatrix
> (along with a pedigree object of some sort) that computed the minor allele
> frequency in the parents only.
>
> Does anyone know if that method exists somewhere for snpMatrix objects?
>
>
(correct spelling is "SnpMatrix", must avoid confusion with legacy
terminology.)  I don't know of any immediate solution, but
SnpMatrix instances obey X[sample,feature] subscripting, so by indexing to
the rows of the parents with P, MAF(X[P,]) should
do what you want


> Thanks,
>
> Sam
>
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