Dominance genomic relationship matrix

Builds the dominance genomic relationship matrix from allele dosages using the genotypic parameterisation of Vitezica et al. (2013): homozygotes and heterozygotes are coded so the matrix captures dominance (heterozygote versus homozygote) deviations, complementing the additive relationships from Gmatrix(). Supplying it to gblup() as K fits a dominance GBLUP model, and the additive and dominance GEBVs can be compared.

Usage

Dmatrix(geno, min_maf = 0)

Arguments

geno: A numeric marker matrix (individuals x markers), coded 0/1/2, with no missing values (run qc_markers() or impute_markers() first).
min_maf: Markers with minor allele frequency below this are dropped before building the matrix. Default 0 (keep all supplied markers).

Value

An n x n symmetric dominance relationship matrix, with row/column names taken from rownames(geno).

References

Vitezica, Z. G., Varona, L. & Legarra, A. (2013) "On the additive and dominant variance and covariance of individuals within the genomic selection scope." Genetics 195, 1223-1230. doi:10.1534/genetics.113.155176

Examples

sim <- simulate_population(n = 80, m = 400, seed = 1)
D <- Dmatrix(sim$geno)
dim(D)
#> [1] 80 80
# dominance GBLUP:
fit <- gblup(sim$pheno, K = D)