simPedMCN: Middle Class Neighborhood pedigree construction

In matthewwolak/nadiv: (Non)Additive Genetic Relatedness Matrices

Middle Class Neighborhood pedigree construction

Description

Simulates a pedigree for the “middle class neighborhood” mating design (Shabalina, Yampolsky, and Kondrashov 1997).

Usage

simPedMCN(pedTemp, g, Nfam = NULL, noff = 2)

Arguments

pedTemp	A data.frame pedigree of a template pedigree from which the middle class neighborhood design should continue. If NULL, a new pedigree will be created with Nfam families.
g	Integer number of generations to produce from the middle class neighborhood design
Nfam	Integer number of families with which to start a new pedigree following the middle class neighborhood design.
noff	Integer number of full-sib offspring produced by each family (must be >=2).

Details

This creates a pedigree following a breeding design which maintains equal contributions to the next generation by each family in the design. It effectively removes the effect of natural selection which makes it amenable to quantify the contribution of mutations to phenotypic variance over the course of the breeding design.

For a starting pedigree template (pedTemp), the last generation is used as parents to begin the breeding design for the next g generations. The number of families in the last generation of the template pedigree (pedTemp) will be the number of families in each generation.

Alternatively, if no template pedigree is provided (pedTemp=NULL), Nfam number of families will be produced in the first generation from Nfam unique sire and Nfam unique dams.

Either pedTemp or Nfam must be NULL, but not both.

Value

A data.frame with columns corresponding to: id, dam, sire, sex, and generation. Sex is M for males and F for females. The first generation produced in the middle class neighborhood scheme is assigned a value of “1”, with their parents being assigned to generation 0. If pedTemp was provided, the generations from this pedigree will be denoted with negative integers.

Author(s)

[e-mail]

References

Shabalina, S.A, L.Y. Yampolsky, and A.S. Kondrashov. 1997. Rapid decline of fitness in panmictic populations of Drosophila melanogaster maintained under relaxed natural selection. Proc. Natl. Acad. Sci. USA. 94:13034-13039.

See Also

simPedHS, simPedDFC

Examples

 # No template pedigree provided - start from scrtach
  mcn1 <- simPedMCN(pedTemp = NULL, g = 3, Nfam = 4, noff = 2)

 # Provide a template pedigree (half-sib design)
  hsped <- simPedHS(s = 2, d = 2, n = 4)
  mcnHS <- simPedMCN(pedTemp = hsped, g = 3)

matthewwolak/nadiv documentation built on July 7, 2023, 1:24 p.m.