makeDsim: Create the dominance genetic relationship matrix through an...

In nadiv: (Non)Additive Genetic Relatedness Matrices

Create the dominance genetic relationship matrix through an iterative (simulation) process

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) - for either autosomes or sex chromosomes. 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 at either autosomes or sex chromosomes. The autosomal case 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,
  verbose = TRUE
)

makeSdsim(
  pedigree,
  heterogametic,
  N,
  DosageComp = c(NULL, "ngdc", "hori", "hedo", "hoha", "hopi"),
  parallel = FALSE,
  ncores = getOption("mc.cores", 2L),
  invertSd = TRUE,
  calcSE = FALSE,
  returnS = FALSE,
  verbose = TRUE
)

Arguments

pedigree	A pedigree with columns organized: ID, Dam, Sire. For use with makeSdsim, a fourth column indicates the sex of each individual in the pedigree.
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, invertSd	A logical indicating whether or not to invert the D or Sd matrix
calcSE	A logical indicating whether or not the standard errors for each coefficient of fraternity should be calculated
returnA, returnS	Logical, indicating if the numerator relationship matrix (A or S) should be stored and returned.
verbose	Logical, indicating if progress messages should be displayed.
heterogametic	Character indicating the label corresponding to the heterogametic sex used in the "Sex" column of the pedigree
DosageComp	A character indicating which model of dosage compensation. If NULL then the “ngdc” model is assumed.

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 objects listDsim and listSdsim will list both the approximate values (returned from makeD or makeSd) as well as the simulated values. If calcSE is TRUE, these values will be listed in listDsim or listSdsim.

Value

a list:

A,S

the A or S matrix in sparse matrix form

D,Sd

the approximate D or Sd matrix in sparse matrix form

logDetD,logDetSd

the log determinant of the D or Sd matrix

Dinv,Sdinv

the inverse of the approximate D or approximate Sd matrix in sparse matrix form

listDinv,listSdinv

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

Dsim,Sdsim

the simulated D or Sd matrix in sparse matrix form

logDetDsim,logDetSdsim

the log determinant of the simulated D or simulated Sd matrix

Dsiminv,Sdsiminv

the inverse of the simulated D or simulated Sd matrix in sparse matrix form

listDsim,listSdsim

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

listDsiminv,listSdsiminv

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

Note

This simulation can take a long time for large pedigrees (a few thousand and higher) and large values of N (one thousand and higher). If unsure, it is advisable to start with a lower N and gradually increase to obtain a sense of the time required to execute a desired N.

Author(s)

[e-mail]

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, makeSd

Examples

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

  simSd <- makeSdsim(FG90, heterogametic = "0", N = 1000, parallel = FALSE,
		invertSd = TRUE, calcSE = TRUE)$listSdsim

nadiv documentation built on May 29, 2024, 10:40 a.m.