Maternal Genetic Effects in MCMCglmm
Hi Jarrod, Thanks so much for your help so far. I tried your advice but I get an error message that I don't understand: Error in MCMCglmm(LRS ~ 1, random = ~dam + animal, ginverse = list(animal = invA, : animal ginverse appears but pedigree has been passed I think that this means that I have replaced my pedigree with the ginverse? Is there something that I am missing to make sure that both are included in the model? Below is some of my code. I hope that I am making a blatantly obvious mistake. data$dam<-factor(data$dam, levels=levels(data$animal)) invA<-inverseA(ped) model.LRS.a<-MCMCglmm(LRS~1, random=~dam+animal, ginverse=list(animal=invA, dam=invA), ped = ped, data=data, prior=prior.LRS.a, nitt=nitt, thin=thin, burnin=burnin, verbose=FALSE, family="poisson", pr=FALSE) Thank you for your help, Eryn
On 2011-10-11, at 4:27 PM, Jarrod Hadfield wrote:
Hi Eryn, You can now fit maternal genetic effects by using the ginverse argument: ginverse=list(animal=invA, dam=invA) invA is the inverse relationship matrix which you can get using inverseA. you need to make sure that the dam factor has the same levels as animal even if they are not represented: your_data$dam<-factor(your_data$dam, levels=levels(your_data$animal)) Two problems you may have are: i) slow speed and mixing ii) it is not yet possible to fit the covariance between maternal genetic and direct genetic effects Cheers, Jarrod On 11 Oct 2011, at 20:55, Eryn McFarlane wrote:
Dear List, I hope that you can help me. I would like to use MCMCglmm to estimate Maternal Genetic Effects. I think that what I want to do is use an A matrix for the maternal effects, and I think that I want to do this by linking my "dam" random effect to the pedigree somehow. Does anyone know if there is a way to do this that is already written into MCMCglmm? I have not seen anything previously in the list about this, so if it exists else where, then that would be excellent as well. Thank you for your help, Eryn Eryn McFarlane MSc Candidate Department of Integrative Biology University of Guelph Guelph, ON, Canada N1G 2W1
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