MME: Mixed Model Equations In synbreed: Framework for the Analysis of Genomic Prediction Data using R

Description

Set up Mixed Model Equations for given design matrices, i.e. variance components for random effects must be known.

Usage

 `1` ```MME(X, Z, GI, RI, y) ```

Arguments

 `X` Design matrix for fixed effects `Z` Design matrix for random effects `GI` Inverse of (estimated) variance-covariance matrix of random (genetic) effects multplied by the ratio of residual to genetic variance `RI` Inverse of (estimated) variance-covariance matrix of residuals (without multiplying with a constant, i.e. sigma2e) `y` Vector of phenotypic records

Details

The linear mixed model is given by

y = Xb + Zu +e

with u = N(0,G) and e = N(0,R). Solutions for fixed effects b and random effects u are obtained by solving the corresponding mixed model equations (Henderson, 1984)

(X'RIX,X'RIZ,Z'RIX,ZRIZ+GI)(bhat,uhat)=(X'RIy,Z'RIy)

Matrix on left hand side of mixed model equation is denoted by LHS and matrix on the right hand side of MME is denoted as RHS. Generalized Inverse of LHS equals prediction error variance matrix. Square root of diagonal values multiplied with sigma2e equals standard error of prediction. Note that variance components for fixed and random effects are not estimated by this function but have to be specified by the user, i.e. GI must be multiplied with shrinkage factor sigma2e/sigma2g.

Value

A list with the following arguments

 `b` Estimations for fixed effects vector `u` Predictions for random effects vector `LHS` left hand side of MME `RHS` right hand side of MME `C` Generalized inverse of LHS. This is the prediction error variance matrix `SEP` Standard error of prediction for fixed and random effects `SST` Sum of Squares Total `SSR` Sum of Squares due to Regression `residuals` Vector of residuals

Valentin Wimmer

References

Henderson, C. R. 1984. Applications of Linear Models in Animal Breeding. Univ. of Guelph, Guelph, ON, Canada.

`regress`, `crossVal`
 ``` 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27``` ```## Not run: library(synbreedData) data(maize) # realized kinship matrix maizeC <- codeGeno(maize) U <- kin(maizeC,ret="realized")/2 # solution with gpMod m <- gpMod(maizeC,kin=U,model="BLUP") # solution with MME diag(U) <- diag(U) + 0.000001 # to avoid singularities # determine shrinkage parameter lambda <- m\$fit\$sigma[2]/ m\$fit\$sigma[1] # multiply G with shrinkage parameter GI <- solve(U)*lambda y <- maizeC\$pheno[,1,] n <- length(y) X <- matrix(1,ncol=1,nrow=n) mme <- MME(y=y,Z=diag(n),GI=GI,X=X,RI=diag(n)) # comparison head(m\$fit\$predicted[,1]-m\$fit\$beta) head(mme\$u) ## End(Not run) ```