Build Pedigree-Based Additive Relationship Matrix

Description

Constructs the numerator relationship matrix (A) from pedigree data following Henderson (1976). The A matrix captures additive genetic relationships based on known ancestry, and can be used in masreml() for pedigree-based BLUP (PBLUP) or combined with genomic relationship matrices.

Usage

build_A_ped(pedigree)

Arguments

pedigree

data.frame with columns id, sire, and dam. Rows must be ordered such that parents appear before offspring. IDs must be integers or convertible to integer (1-based). Use 0 for unknown parents. Example format:

  id sire dam
   1    0   0
   2    0   0
   3    1   2
   4    1   2
   5    3   4

Value

numeric matrix (n x n) of additive relationships. Diagonal elements equal 1 + inbreeding coefficient. Off-diagonal elements equal twice the coefficient of kinship between pairs.

References

Henderson (1976) A simple method for computing the inverse of a numerator relationship matrix. Biometrics 32:69-83.

Examples

library("masreml")

ped <- data.frame(
  id   = 1:5,
  sire = c(0, 0, 1, 1, 3),
  dam  = c(0, 0, 2, 2, 4)
)
A <- build_A_ped(ped)

# Use in masreml (pedigree BLUP)
fit <- masreml(y, G = list(pedigree = A))