compute_GL {CodataGS}

Computes genomic relationship matrix

Description

This function computes the genomic relationship matrix, G, together with its matrix square root, L.

Usage

compute_GL(Z, w)

Arguments

Z

Scaled matrix with genotype information

w

weights

Value

L

Square root matrix of G

svdVec

Vectors in the Single Value Decomposition of G

svdD

Diagonal elements in the Single Value Decomposition of G

wZt

weights times the transpose of Z

Author(s)

Lars Ronnegard

Examples

set.seed(1234)
N <- 20 #Number of individuals
k <- 30 #Number of SNPs with all marker positions including a QTL
Z1 <- matrix(0, N, k )
Z2 <- matrix(0, N, k )
Z1[1:N, 1] <- rbinom(N, 1, 0.5) #Simulated phased SNP matrices
Z2[1:N, 1] <- rbinom(N, 1, 0.5) 
LD.par <- 0.2 #A parameter to simulate LD. 0 gives full LD, and 0.5 no LD
for (j in 2:k) {
  Z1[1:N, j] <- abs( Z1[1:N, j-1] - rbinom(N, 1, LD.par) )
  Z2[1:N, j] <- abs( Z2[1:N, j-1] - rbinom(N, 1, LD.par) )
} 
Z <- Z1 + Z2 #Genotypic SNP matrix
sim.res <- compute_GL(Z, w = rep(1,k))