library("masreml")
# Create example genotype matrix (5 individuals, 4 SNPs)
W <- matrix(
c(0, 1, 2, 1,
1, 0, 1, 2,
2, 1, 0, 1,
0, 2, 1, 0,
1, 1, 2, 1),
nrow = 5, ncol = 4, byrow = TRUE
)
rownames(W) <- paste0("ind", 1:5)
colnames(W) <- paste0("SNP", 1:4)
# Build G matrix
G <- build_G_snp(W)
# Check diagonal — should be ~1
round(diag(G), 3)
# Use pre-built G in masreml
fit <- masreml(y, G = list(snp_add = G))Build SNP Additive Genomic Relationship Matrix
Build SNP Additive Genomic Relationship Matrix
Description
Constructs the SNP additive genomic relationship matrix (G) following VanRaden (2008) Method 1. The resulting matrix captures additive genetic relationships among individuals based on SNP marker data, and can be used directly in masreml() or gwablup() via the G argument.
Usage
build_G_snp(W, ref_W = NULL)
Arguments
W
|
numeric matrix (n x m) of raw genotype codes, where n is the number of individuals and m is the number of SNP markers. Values must be 0, 1, or 2 representing the number of copies of the reference allele. Row names are used as individual IDs. Example format: SNP1 SNP2 SNP3 ind1 0 1 2 ind2 1 0 1 ind3 2 1 0 |
Value
numeric matrix (n x n) of genomic relationships. Diagonal elements approximate 1 + inbreeding coefficient. Off-diagonal elements represent genomic relationships between pairs of individuals.
References
VanRaden (2008) Efficient methods to compute genomic predictions. J. Dairy Sci. 91:4414-4423.
See Also
build_G_mh, build_D_snp, masreml