Creates the dominance genetic relationship matrix through simulation

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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

1
makeDsim(pedigree, N, invertD = FALSE, calcSE = FALSE)

Arguments

pedigree

A pedigree with columns organized: ID, Dam, Sire

N

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

Details

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

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.

Value

A

the A matrix in sparse matrix form

D

the approximate D matrix in sparse matrix form

logDetD

the log determinant of the approximate D matrix

Dinv

the inverse of the approximate D matrix in sparse matrix form

listDinv

the three column form of the non-zero elements for the inverse of the approximate D matrix

Dsim

the simulated D matrix in sparse matrix form

logDetDsim

the log determinant of the simulated D matrix

Dsiminv

the inverse of the simulated D matrix in sparse matrix form

listDsim

the three column form of the non-zero and non-self elements for the simulated D matrix

listDsiminv

the three column form of the non-zero elements for the inverse of the simulated D matrix

Note

This simulation can take a long time for large values of N. If unsure, it is advisable to start with a lower N and gradually increase to gain a sense of the time required to execute a desired N.

Author(s)

matthewwolak@gmail.com

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.

See Also

makeD

Examples

1
  simDinvMat <- makeDsim(Mrode9, N = 1000, invertD = FALSE, calcSE = TRUE)$listDsim