[R-sig-ME] How to specify user-defined matrix Z?

[Diogo Melo]

I'm pretty sure lme4qtl can handle this:

https://www.biorxiv.org/content/early/2017/05/18/139816.1
https://github.com/variani/lme4qtl

Cheers,
Diogo

On Fri, Sep 29, 2017 at 4:51 PM, Zhengyang Zhou <
Zhengyang.Zhou at utsouthwestern.edu> wrote:

> Hi Jacob,
>
> Thank you for your reply. I need to use lme4 because I want to test for
> the fixed effects (ie., beta), and the packages which can do it (eg,
> pbkrtest) is based on lme4.
>
> Sincerely,
> Zhengyang
> ________________________________________
> From: R-sig-mixed-models <r-sig-mixed-models-bounces at r-project.org> on
> behalf of Jacob Bergstedt <jacoba at control.lth.se>
> Sent: Friday, September 29, 2017 6:39 AM
> To: r-sig-mixed-models at r-project.org
> Subject: Re: [R-sig-ME] How to specify user-defined matrix Z?
>
> Hi,
>
> You can use the lmekin function in the coxme package.
>
> Best regards,
>
> Jacob
>
>
> On 2017-09-29 12:28, Crump, Ron wrote:
> > Hi Zhengyang,
> >
> >> In genetic studies, we sometimes include the genetic relatedness matrix
> as a variance component, so we have this following model:
> >> Y~Xbeta+Zb+error,
> >>
> >> where beta are the fixed effects, b~N(0,sigma^2*I) are the random
> effects, error are the random error, Z is the cholesky decomposition of the
> known genetic relatedness matrix. So how to use lme4 to fit this model if
> we know X and Z beforehand? I can use the package "nlme" to do it using the
> code like
> >>
> >> lme(y~-1+X, random=list(group=pdIdent(~-1+Z))),
> >> but how to do it using lme4?
> > I think, assuming you are using I to indicate an identity matrix, that
> > in neither case are you specifying a genetic relationship matrix, unless
> > you are somehow incorporating it into Z (in which case I'd like to see
> how).
> >
> > I don't believe that either lme4 or nlme will allow you to do what you
> > want. (Somebody might correct me on this).
> >
> > Within R you could certainly use MCMCglmm or INLA to do analysis of
> > quantitative genetics data to obtain genetic parameters (or the asremlr
> > interface to ASREML). I've not used it, but the pedigreemm package also
> > looks like it would help you and there may be others. Outside of R,
> > Karin Meyer's wombat program will also do the job.
> >
> >
> > Regards,
> > Ron.
> > _______________________________________________
> > R-sig-mixed-models at r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/r-sig-mixed-models
>
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