Ridge regression BLUP (RRBLUP)

This example illustrates how to fit ridge regression BLUP using the rrBLUP R package.

Data

We will use the maize data available in the synbreedData R package.

rm(list = ls())
library(synbreedData)
data(maize)
`?`(maize)
names(maize)
y <- maize$pheno[, 1, 1]
W <- maize$geno
W[W == 0] = -1  # convert 0 to -1
map <- maize$map

Ridge regression BLUP

The mixed.solve() function implements ridge regression BLUP.

# install.packages('rrBLUP')
library(rrBLUP)
`?`(mixed.solve)
fit <- mixed.solve(y = y, Z = W)

Results

fit$beta  # intercept

head(fit$u)  # marker effects

fit$Vu  # marker genetic variance

fit$Ve  # residual variance

fit$Ve/fit$Vu  # lambda