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

1
makeAA(pedigree)

Arguments

pedigree

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

Details

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

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).

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

Author(s)

matthewwolak@gmail.com

See Also

makeA

Examples

1
  AAoutput <- makeAA(Mrode2)