makeD: Creates the dominance genetic realationship matrix

In nadiv: Functions to construct non-additive genetic relatedness matrices

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

Details

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

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.

Value

A	the A matrix in sparse matrix form
D	the D matrix in sparse matrix form
logDet	the log determinant of the D matrix
Dinv	the inverse of the D matrix in sparse matrix form
listDinv	the three column form of the non-zero elements for the inverse of the D matrix

Author(s)

[e-mail]

References

Quaas, R.L. 1995. Fx algorithms. An unpublished note.

Lynch M., & Walsh, B. 1998. Genetics and Analysis of Quantitative Traits. Sinauer, Sunderland, Massachusetts.

See Also

makeDsim

Examples

  DinvMat <- makeD(Mrode9)$Dinv

Example output

Loading required package: Matrix
starting to make D....done 
starting to invert D....done 

nadiv documentation built on May 2, 2019, 4:55 p.m.