makeDomEpi: Creates the additive by dominance and dominance by dominance...

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

Description

Given a pedigree, the matrix of additive by dominance (AD) genetic relatedness, dominance by dominance (DD) genetic relatedness, or both are returned.

Usage

makeDomEpi(pedigree, output = c("AD", "DD", "both"), Dinverse=FALSE)

Arguments

pedigree	A pedigree where the columns are ordered ID, Dam, Sire
output	Character(s) denoting which matrix and its inverse is to be constructed.
Dinverse	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'.

Because of the computational demands of constructing the D matrix (see makeD), this function allows for the inverses that are derived from the D matrix (i.e., D-inverse, AD-inverse, and DD-inverse)to be constructed at the same time. This way, the D matrix will only have to be constructed once for use in the three seperate genetic relatedness inverse matrices that depend upon it. However, using the output and Dinverse options in different combinations will ensure that only the desired matrix inverses are constructed.

Both the AD and DD matrix are computed from the Hadamard product of the respective matrices (see also, makeAA).

Value

All of the following will be returned. However, the values of the output and Dinverse options passed to the function will determine which of the following are not NULL objects within the list:

D	the D matrix in sparse matrix form
logDetD	the log determinant of the D matrix
AD	the AD matrix in sparse matrix form
logDetAD	the log determinant of the AD matrix
DD	the DD matrix in sparse matrix form
logDetDD	the log determinant of the DD matrix
Dinv	the inverse of the D matrix in sparse matrix form
ADinv	the inverse of the AD matrix in sparse matrix form
DDinv	the inverse of the DD matrix in sparse matrix form
listDinv	the three column form of the non-zero elements for the inverse of the D matrix
listADinv	the three column form of the non-zero elements for the inverse of the AD matrix
listDDinv	the three column form of the non-zero elements for the inverse of the DD matrix

Author(s)

[e-mail]

See Also

makeA, makeD, makeAA

Examples

  Boutput <- makeDomEpi(Mrode9, output = "b", Dinverse = FALSE)
  str(Boutput)
	
  DADoutput <- makeDomEpi(Mrode9, output = "AD", Dinverse = TRUE)
  str(DADoutput)

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