knitr::opts_chunk$set(echo = TRUE,eval=FALSE,class.source = "numberLines lineAnchors")
library(BGLR) data(wheat) K<-tcrossprod(scale(wheat.X,center=TRUE)) K<-K/mean(diag(K)) Y<-wheat.Y # 4 traits # Fitting a GBLUP un-structured cov-matrices LP<-list(mar=list(K=K,model="RKHS")) set.seed(123) fmUN<-Multitrait(y=Y,ETA=LP,nIter=10000,burnIn=5000, saveAt="UN_",verbose=FALSE) # Retrieving estimates and posterior SD fmUN$resCov$R # residual co-variance matrix fmUN$resCov$SD.R fmUN$ETA$mar$Cov$Omega # genomic covariance matrix fmUN$ETA$mar$Cov$SD.Omega fmUN$ETA$mar$u # predicted random effects
#(continued from Box 1) # Genetic (co)variance recursive (not fully), Residual (co)variance diagonal # Matrix specifying loading among traits 2=>3,2=>4,3=>4 M1<-matrix(nrow = 4, ncol = 4, FALSE) M1[3,2]<-M1[4,2]<-M1[4,3]<-TRUE CovREC<-list(type="REC",M=M1) LP<-list(mar=list(K=K,model="RKHS",Cov=CovREC)) CovDIAG<-list(type="DIAG") set.seed(456) fmRD<-Multitrait(y=Y,ETA=LP,nIter=10000,burnIn=5000, resCov=CovDIAG,saveAt= "REC_DIAG_", verbose=FALSE) fmRD$resCov$R fmRD$ETA$mar$Cov$Omega # genomic covariance fmRD$ETA$mar$Cov$W # recursive genetic effects fmRD$ETA$mar$u # predicted genetic effects fmRD$ETA$mar$Cov$PSI # scaling factors # Omega-FA(2), R-diagonal M2<-matrix(nrow=4,ncol=1,FALSE) M2[2:4,1]<-TRUE CovFA<-list(type="FA",M=M2) LP<-list(mar=list(K=K,model="RKHS",Cov=CovFA)) set.seed(789) fmFAD<-Multitrait(y=Y,ETA=LP,nIter=10000,burnIn=5000, resCov=CovDIAG,saveAt= "FA_DIAG_", verbose=FALSE) fmFAD$resCov$R fmFAD$ETA$mar$Cov$Omega # genomic covariance fmFAD$ETA$mar$Cov$W # factor scores fmFAD$ETA$mar$u # predicted genetic effects fmFAD$ETA$mar$Cov$PSI # scaling factors
fmSS<-Multitrait(y=Y,ETA=list(list(X=X,model='SpikeSlab', saveEffects=TRUE)),nIter=12000,burnIn=2000)
K<-tcrossprod(X) K<-K/mean(diag(K)) LP<-list(list(K=K,model="RKHS")) #Fit multivariate GBLUP with UN-structured covariance matrixes fmG<-Multitrait(y=YNa,ETA=LP,nIter=10000,burnIn=5000,thin=10, verbose=FALSE) #Missing values for trait 3 whichNa3<-fmG$missing_records[fmG$patterns[,3]] Y[whichNa3,3] #Observed values fmG$ETAHat[whichNa3,3] #Predicted values
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