How to specify user-defined matrix Z?
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 _______________________________________________ R-sig-mixed-models at r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-sig-mixed-models ________________________________ UT Southwestern Medical Center The future of medicine, today. _______________________________________________ R-sig-mixed-models at r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-sig-mixed-models