nadiv (version 2.11)

makeDsim: Creates the dominance genetic relationship matrix through iteration

Description

Alleles are explicitly traced through a pedigree to obtain coefficients of fraternity between pairs of individuals (the probability of sharing both alleles identical by descent). This is accomplished in an iterative process to account for the various routes by which an allele will progress through a pedigree due to Mendelian sampling. This is an implementation of the simulation approach of Ovaskainen et al. (2008).

Usage

makeDsim(pedigree, N, parallel = FALSE, ncores = getOption("mc.cores", 2L),
         invertD = TRUE, calcSE = FALSE, returnA = FALSE)

Arguments

pedigree

A pedigree with columns organized: ID, Dam, Sire

N

The number of times to iteratively trace alleles through the pedigree

parallel

A logical indicating whether or not to use parallel processing. Note, this may only be available for Mac and Linux operating systems.

ncores

The number of cpus to use when constructing the dominance relatedness matrix. Default is all available.

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

returnA

Logical, indicating if the numerator relationship matrix (A) should be stored and returned.

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

Details

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

parallel = TRUE should only be used on Linux or Mac operating systems (i.e., not Windows).

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, especially 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.

See Also

makeD

Examples

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