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Genomic relationship matrix (VanRaden)

Source: R/grm.R
Gmatrix.Rd

Builds the additive genomic relationship matrix from allele dosages using VanRaden's first method: with markers centred by twice the allele frequency, G = W W' / (2 * sum(p (1 - p))). This is the standard additive GRM used in GBLUP.

Usage

Gmatrix(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 genomic relationship matrix with the row/column names taken from rownames(geno).

References

VanRaden, P. M. (2008) "Efficient methods to compute genomic predictions." Journal of Dairy Science 91, 4414-4423. doi:10.3168/jds.2007-0980

Examples

sim <- simulate_population(n = 80, m = 400, seed = 1)
G <- Gmatrix(sim$geno)
dim(G)
#> [1] 80 80