sim_dof1_pedigree {simcross}

Simulate pedigree for F1 between diversity outbreds and another inbred line

Description

Simulate a pedigree for a set of DOF1 individuals: the F1 offspring of a set of diversity outbred mice and another inbred strain (such as a mutant line).

Usage

sim_dof1_pedigree(
  ngen = 12,
  npairs = 144,
  ccgen = rep(4:12, c(21, 64, 24, 10, 5, 9, 5, 3, 3)),
  nkids_per = 5,
  design = c("nosib", "random")
)

Arguments

ngen

Number of generations of outbreeding

npairs

Number of breeding pairs at each generation

ccgen

Vector of length npairs, with the number of generations for each CC line. If length 1, it is repeated to a vector of length npairs.

nkids_per

Number of offspring per pair for the last DO generation (each will be crossed to produce one F1)

design

How to choose crosses: either random but avoiding siblings, or completely at random

Details

Diversity outbred (DO) mice are generated from a set of 8 inbred lines. We need two individuals from each line (one female and one male) as the order of the initial crosses will be randomized; for example, sometimes the individual from line 1 will be a mother and sometimes a father. The founders are numbered 1-8 for the females from the 8 lines, and 9-16 for the corresponding males.

Diversity Outbred mice are generated by first creating a panel of partially-inbred 8-way RIL (the so-called pre-CC, for pre-Collaborative Cross). The ccgen argument specifies the number of inbreeding generations for each of the CC lines. We generate a pre-CC line for each of the npairs breeding pairs, and generate a sibling pair from each as the starting material.

The subsequent ngen outbreeding generations then proceed by crossing a male and female from the preceding generation (mated completely at random, with design="random", or avoiding siblings, with design="nosib"). Each breeding pair gives a single female and a single male to the next generation, except at the last generation nkids_per offspring are mated, in equal numbers male and female. (If nkids_per is an odd number, the number of males and females in each sibship will differ by one, alternating between sibships, with one additional female and then one additional male.

The default for ccgen is taken from Figure 1 of Svenson et al. (2012).

We assume that the F1 offspring are all from a cross DO female x line 17 male, and so the last generation of the DO is taken to be all females.

Value

A data frame with seven columns: individual ID, mother ID, father ID, sex, generation, a TRUE/FALSE indicator for whether DO or pre-DO, and a TRUE/FALSE indicator for whether DOF1. Founders have 0 for mother and father ID. Sex is coded 0 for female and 1 for male.

References

Svenson KL, Gatti DM, Valdar W, Welsh CE, Cheng R, Chesler EJ, Palmer AA, McMillan L, Churchill GA (2012) High-resolution genetic mapping using the mouse Diversity Outbred population. Genetics 190:437-447

See Also

sim_from_pedigree(), sim_ril_pedigree(), sim_ail_pedigree(), sim_4way_pedigree()

Examples

tab <- sim_dof1_pedigree(8)