[R-sig-ME] User defined variance-covariance matrix of random effects

David Duffy David.Duffy at qimr.edu.au
Tue Nov 11 22:27:53 CET 2008

On Tue, 11 Nov 2008, Marc Moragues Canela wrote:

> Dear all,
> I am trying to build a mixed model to do association mapping of QTL.
> Basically I want to know if a marker is correlated with a trait. I know
> there are some packages that do this type of analysis like GenABEL, but I
> need more flexibility to modify the model to include, for example, the
> genotype by environment interaction.

You will have to use the kinship package, which uses lme.  It is 
pretty fast, unless you have very large pedigrees.  Doug Bates and 
others are still working on a lmer based equivalent.

David Duffy.
| David Duffy (MBBS PhD)                                         ,-_|\
| email: davidD at qimr.edu.au  ph: INT+61+7+3362-0217 fax: -0101  /     *
| Epidemiology Unit, Queensland Institute of Medical Research   \_,-._/
| 300 Herston Rd, Brisbane, Queensland 4029, Australia  GPG 4D0B994A v

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