Questions about MCMCglmm and marker data

Hello,

I'm not familiar with this kind of genomic problems, but if the
columns are the number of a given SNP for a given individual and can
be only 0, 1 and 2, is this really possible to consider they follow a
normal distribution?

? Hi,
? 
? I use the MCMCglmm function in the genomic selection context in the 
? univariate case. In fact I have for each trait one marker matrix 
? constituted of 0,1 and 2. The rows are the individuals and the columns 
? the SNPs. In a first time, we consider that each SNP follow a normal 
? distribution with the *same *variance. So I use the following model:
? 
? prior.1.1 <- list(G=list(G1=list(V=diag(x = as.numeric(scale), nrow=1, 
? ncol=1),nu=ddl),
?                            R=list(V=matrix(scale),nu=ddl))
? 
? mcmc.fit.1.1 <- MCMCglmm(P~ 1,random=~idv(SNP),prior=prior.1.1,
?                    data=data1.1,
?                    nitt=5000, burnin=1000,verbose=FALSE,
?                    thin=10,pr=TRUE)
? 
? So, I obtained a common variance associated to my SNPs.
? 
? 
? The second step is a bivariate analysis. I would like to obtain a 
? (co)variance matrix 2*2  associated to the trait1 and trait 2 and the 
? correlation between both. (one variance for the SNPs for the trait 1 and 
? one for the trait 2). But I don't know how i can do. The following model 
? give me only one variance for all SNPs and both traits.
? 
?      prior.3<- list(G=list(G1=list(V=diag(x = as.numeric(scale), nrow=1,
?                            ncol=1),n=1)),
?                R=list(V=diag(x=as.numeric(0.1),nrow=2,ncol=2),n=2))
? 
?      mcmc.fit.3 <- MCMCglmm(cbind(P1,P2)~ trait-1,random=~idv(trait:SNP),
?                    rcov=~idh(trait):units,
?                    prior=prior.3,
?                    data=data1.3,family=c("gaussian","gaussian"),
?                    nitt=2000, burnin=500,verbose=FALSE,
?                    thin=10,pr=TRUE)
? 
? 
? 
? thanks for your help,
? 
? 
? 
? 
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Emmanuel CURIS
                                emmanuel.curis at univ-paris5.fr

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