>
> 2012/3/14 "Pär K. Ingvarsson" <par.ingvarsson@​emg.umu.se<par.ingvarsson@emg.umu.se>
> >

There are several packages that can handle kinship matrices for doing
> association studies in R. Of the top of my head I can come up with:
> kinship (http://cran.r-project.org/​web/packages/kinship/index.​html<http://cran.r-project.org/web/packages/kinship/index.html>
> )
> EMMA (http://mouse.cs.ucla.edu/​emma/news.html<http://mouse.cs.ucla.edu/emma/news.html>
> )
> GenABEL (http://www.genabel.org/)


I know these packages but in fact, digressions about association mapping
were all my fault and not part of the first question asked by Juliet
Hannah. As she was talking about kinship, I allowed myself to go in that
direction to illustrate my kinf od explainations (about that, thanks to
Ryan King for the mathematical explainations of what I tried to explain
with my words).

When I was saying that ASREML was the only package allowing something, it
was not association mapping but the possibility to specify a
variance/covariance matrix by directly importing the entire matrix (as in
the example of specifying an external kinship matrix for a genetic effect).

On Wed, Mar 14, 2012 at 8:28 AM, Ryan King <c.ryan.king@gmail.com> wrote:
> > You can also use MCMCglmm and R-INLA.


Ryan, have you got some links for what you talk about ? I'm quite surprised
that there are already packages for doing that because a lot of geneticists
are using ASREML even if they have to pay for it. I really hope that there
is a good reason for that !

Yves

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