nadiv (version 2.9)

makeAA: Creates the additive by additive epistatic genetic relationship matrix

Description

Given a pedigree, the matrix of additive by additive genetic relatedness (AA) among all individuals in the pedigree is returned.

Usage

makeAA(pedigree)

Arguments

pedigree

A pedigree where the columns are ordered ID, Dam, Sire

Value

• AA
  the AA matrix in sparse matrix form
• logDet
  the log determinant of the AA matrix
• AAinv
  the inverse of the AA matrix in sparse matrix form
• listAAinv
  the three column form of the non-zero elements for the inverse of the AA matrix

Details

Missing parents (e.g., base population) should be denoted by either 'NA', '0', or '*'.

The function first estimates the A matrix using makeA, then it calculates the Hadamard (element-wise) product of the A matrix with itself (A # A).

See Also

makeA

Examples

AAoutput <- makeAA(Mrode2)