sommer: DT_halfdiallel – R documentation

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DT_halfdiallel

half diallel data for corn hybrids

Description

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.

Usage

data("DT_halfdiallel")

Format

The format is: chr "DT_halfdiallel"

Source

This data was generated by a corn study.

References

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

Examples

####=========================================####
#### 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)

sommer

Solving Mixed Model Equations in R

v4.1.3

GPL (>= 2)

Authors

Giovanny Covarrubias-Pazaran

Initial release

2021-04-01