DT_halfdiallel | R Documentation |
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"
This data was generated by a corn study.
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 mmes
####=========================================####
#### 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 <- mmes(sugar~1,
random=~vsm(ism(overlay(femalef,malef, sparse = FALSE)), Gu=A)
+ genof,
data=DT)
summary(modh)$varcomp
# if ussing mmes=TRUE provide Gu with inverses
# Ai <- solve(A + diag(1e-4,ncol(A),ncol(A)))
# Ai <- as(as(as( Ai, "dMatrix"), "generalMatrix"), "CsparseMatrix")
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