makeD: Creates the dominance genetic realationship matrix
Description
Given a pedigree, the matrix of coefficients of fraternity are returned - the D matrix. Note, no inbreeding must be assumed. Will return the inverse of the D matrix by default, otherwise this operation can be skipped if desired.
Usage
makeD(pedigree, invertD = TRUE)
Arguments
pedigree
A pedigree with columns organized: ID, Dam, Sire
invertD
A logical indicating whether or not to invert the D matrix
Value
Athe A matrix in sparse matrix form
Dthe D matrix in sparse matrix form
logDetthe log determinant of the D matrix
Dinvthe inverse of the D matrix in sparse matrix form
listDinvthe three column form of the non-zero elements for the inverse of the D matrix
Details
There exists no convenient method of obtaining the inverse of the dominance genetic relatedness matrix (or the D matrix itself) directly from a pedigree (such as for the inverse of A, i.e., Quaas (1995)). Therefore, this function computes the coefficient of fraternity (Lynch and Walsh, 1998) for every individual in the pedigree with a non-zero additive genetic relatedness. Note, the construction of the D matrix is more computationally demanding (in time and space) than is the construction of A.
References
Quaas, R.L. 1995. Fx algorithms. An unpublished note.
Lynch M., & Walsh, B. 1998. Genetics and Analysis of Quantitative Traits. Sinauer, Sunderland, Massachusetts.