Simulate a pedigree for generating Diversity Outbred (DO) mice (a table of individual, mom, dad, sex).
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")
)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.
Number of generations of outbreeding
Number of breeding pairs at each generation
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.
Number of offspring per pair for the last generation
How to choose crosses: either random but avoiding siblings, or completely at random
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).
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
sim_from_pedigree(),
sim_ril_pedigree(), sim_ail_pedigree(),
sim_4way_pedigree()