sim_do_pedigree: Simulate a pedigree for Diversity Outbred mice

In kbroman/simcross: Simulate Experimental Crosses

Simulate a pedigree for Diversity Outbred mice

Description

Simulate a pedigree for generating Diversity Outbred (DO) mice (a table of individual, mom, dad, sex).

Usage

sim_do_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 generation
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).

Value

A data frame with six columns: individual ID, mother ID, father ID, sex, generation, and TRUE/FALSE indicator for whether DO or pre-DO. 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_do_pedigree(8)

kbroman/simcross documentation built on Jan. 13, 2024, 10:31 p.m.