geno.d: Generate the Genetic Design Matrix with dominance Effect

In IPLGP: Identification of Parental Lines via Genomic Prediction

Generate the Genetic Design Matrix with dominance Effect

Description

Input the commonly used additive effect genetic design matrix to generate the design matrix and kinship matrix of additive and dominance effects respectively.

Usage

geno.d(geno, AA = 1, Aa = 0, aa = -1)

Arguments

geno	matrix. An n*p matrix denotes the commonly used additive effect genetic design matrix of the training population.
AA	number or character. The code denote alleles AA in the geno data.
Aa	number or character. The code denote alleles Aa in the geno data.
aa	number or character. The code denote alleles aa in the geno data.

Value

genoA	An n*p matrix denote additive effects, and the markers are coded as 1, 0, or -1 for alleles AA, Aa, or aa.
genoD	An n*p matrix denote dominance effects, and the markers are coded as 0.5, -0.5, or 0.5 for alleles AA, Aa, or aa.
KA	An n*n matrix denote the kinship matrix of individuals with additive effects. Whitch is caculated by genoA.
KD	An n*n matrix denote the kinship matrix of individuals with dominance effects. Whitch is caculated by genoD.

References

Cockerham, C. C., 1954. An extension of the concept of partitioning hereditary variance for analysis of covariances among relatives When epistasis is present. Genetics 39: 859–882.

Examples

geno <- rbind(rep(1,10),rep(0,10),rep(-1,10),c(rep(1,5),rep(-1,5)),c(rep(-1,5),rep(1,5)))
geno

geno2 <- geno.d(geno)

geno2$genoD
geno2$KD

IPLGP documentation built on Sept. 11, 2024, 7:35 p.m.