Last chance! 50% off unlimited learning
Sale ends in
This dataset contains phenotpic data for 21 corn hybrids, with 2 technical repetitions, coming from a half diallel design and evaluated for sugar content. The column geno indicates the hybrid and male and female origin columns are included as well.
data("DT_halfdiallel")
The format is: chr "DT_halfdiallel"
Covarrubias-Pazaran G (2016) Genome assisted prediction of quantitative traits using the R package sommer. PLoS ONE 11(6): doi:10.1371/journal.pone.0156744
The core functions of the package mmer
# NOT RUN {
####=========================================####
#### For CRAN time limitations most lines in the
#### examples are silenced with one '#' mark,
#### remove them and run the examples
####=========================================####
data(DT_halfdiallel)
DT <- DT_halfdiallel
head(DT)
####=========================================####
####=========================================####
DT$femalef <- as.factor(DT$female)
DT$malef <- as.factor(DT$male)
DT$genof <- as.factor(DT$geno)
#### model using overlay
modh <- mmer(sugar~1,
random=~vs(overlay(femalef,malef)) + genof,
rcov=~units,
data=DT)
summary(modh)
#### model using overlay and covariance structures
A <- diag(7); A[1,2] <- 0.5; A[2,1] <- 0.5 # fake covariance structure
colnames(A) <- as.character(1:7); rownames(A) <- colnames(A);A
modh2 <- mmer(sugar~1,
random=~ vs(overlay(female,male),Gu=A) + geno,
data=DT)
summary(modh2)
# }
Run the code above in your browser using DataLab