DT_halfdiallel: half diallel data for corn hybrids

In sommer: Solving Mixed Model Equations in R

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

See Also

The core functions of the package mmer and mmec

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)

A <- diag(7); colnames(A) <- rownames(A) <- 1:7;A # if you want to provide a covariance matrix
#### model using overlay
modh <- mmer(sugar~1, 
             random=~vsr(overlay(femalef,malef, sparse = FALSE), Gu=A) 
             + genof,
             data=DT)
summary(modh)$varcomp

Ai <- as(solve(A + diag(1e-4,ncol(A),ncol(A))), Class="dgCMatrix")
modhb <- mmec(sugar~1, 
             random=~vsc(isc(overlay(femalef,malef, sparse = TRUE)), Gu=Ai) 
             + genof,
             data=DT)
summary(modhb)$varcomp

sommer documentation built on Sept. 11, 2024, 6:22 p.m.