GBLUP.fit: Muti-trait GBLUP Model

Description

Built the muti-trait GBLUP model using the phenotypic and genotypic data of a training population by 'mmer' from R package 'sommer'. Then, output the fitted values of the training population.

Usage

GBLUP.fit(t1, t2, t3, t4, t5, geno = NULL, K = NULL, outcross = FALSE)

Value

fitted.value: The fitted values.
fitted.A: The additive effect part of fitted values.
fitted.D: The dominance effect part of fitted values.
mu: The average value of fitted values.

Arguments

t1: vector. The phenotype of trait1. The missing value must be coded as NA. The length of all triat must be the same.
t2: vector. The phenotype of trait2. The missing value must be coded as NA. The length of all triat must be the same.
t3: vector. The phenotype of trait3. The missing value must be coded as NA. The length of all triat must be the same.
t4: vector. The phenotype of trait4. The missing value must be coded as NA. The length of all triat must be the same.
t5: vector. The phenotype of trait5. The missing value must be coded as NA. The length of all triat must be the same.
geno: matrix. An n*p matrix with n individuals and p markers of the training population. The markers must be coded as 1, 0, or -1 for alleles AA, Aa, or aa. The missing value must have been already imputed.
K: matrix. An n*n matrix denotes the genomic relationship matrix of the training population if geno is set to be NULL.
outcross: logical. A logical variable, if outcross is set to be TRUE, the crop is regarded as an outcross crop. The kinship matrix of dominance effects are also considered in the model. The geno data must be given when outcross being TRUE.

References

Habier D, Fernando RL, Dekkers JCM. 2007. The impact of genetic relationship information on genome-assisted breeding values. Genetics 177:2389-2397.

VanRaden PM. 2008. Efficient methods to compute genomic predictions. J Dairy Sci. 91:4414-4423.

Examples

Run this code

# generate simulated data
set.seed(2000)
t1 <- rnorm(50,30,10)
t2 <- rnorm(50,10,5)
t3 <- rnorm(50,20,20)
t4 <- NULL
t5 <- NULL

# run with the marker score matrix
geno.test <- matrix(sample(c(1, -1), 5000, replace = TRUE), 50, 100)
result1 <- GBLUP.fit(t1, t2, t3, t4, t5, geno = geno.test)
result1$fitted.value

# run with the genomic relationship matrix
K.test <- geno.test%*%t(geno.test)/ncol(geno.test)
result2 <- GBLUP.fit(t1, t2, t3, t4, t5, K = K.test)
result2$fitted.value