makeDsim: Creates the dominance genetic relationship matrix through simulation

Description

Given a pedigree, the matrix of coefficients of fraternity are returned - the D matrix - as well as a simulated set of coefficients of fraternity (Ovaskainen et al. 2008).

Usage

makeDsim(pedigree, N, invertD = FALSE, calcSE = FALSE)

Arguments

pedigree

A pedigree with columns organized: ID, Dam, Sire

The number of times to simulate genotypes for the pedigree

invertD

A logical indicating whether or not to invert the D matrix

calcSE

A logical indicating whether or not the standard errors for each coefficient of fraternity should be calculated

Value

Athe A matrix in sparse matrix form
Dthe approximate D matrix in sparse matrix form
logDetDthe log determinant of the approximate D matrix
Dinvthe inverse of the approximate D matrix in sparse matrix form
listDinvthe three column form of the non-zero elements for the inverse of the approximate D matrix
Dsimthe simulated D matrix in sparse matrix form
logDetDsimthe log determinant of the simulated D matrix
Dsiminvthe inverse of the simulated D matrix in sparse matrix form
listDsimthe three column form of the non-zero and non-self elements for the simulated D matrix
listDsiminvthe three column form of the non-zero elements for the inverse of the simulated D matrix

Details

Ovaskainen et al. (2008) indicated that the method of calculating the D matrix (see makeD) is only an approximation. They proposed a simulation method that is implemented here. This should be more appropriate when inbreeding occurs in the pedigree.

The value, listDsim will list both the approximate values (returned from makeD) as well as the simulated values. If calcSE is TRUE, these values will be listed in listDsim.

References

Ovaskainen, O., Cano, J.M., & Merila, J. 2008. A Bayesian framework for comparative quantitative genetics. Proceedings of the Royal Society B 275, 669-678.

Examples

Run this code

simDinvMat <- makeDsim(Mrode9, N = 1000, invertD = FALSE, calcSE = TRUE)$listDsim

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