sim_do_pedigree_fix_n: Simulate a pedigree for Diversity Outbreds for a target...
In simcross: Simulate Experimental Crosses

sim_do_pedigree_fix_n

R Documentation

Simulate a pedigree for Diversity Outbreds for a target sample size

Description

Simulate a pedigree for Diversity Outbred (DO) mice (a table of individual, mom, dad, sex) so that the last generation reaches a desired sample size.

Usage

sim_do_pedigree_fix_n(
  ngen = 12,
  nkids_per = 5,
  nccgen = 15,
  nsample_ngen = 150,
  npairs = NULL,
  method = c("last2", "sub2", "fixcc"),
  design = c("nosib", "random"),
  selc.method = c("byfamily", "byindiv")
)

Arguments

`ngen`	Number of generations of outbreeding
`nkids_per`	Number of offspring per pair for the last generation
`nccgen`	The number of generations for each CC line, only used when `method` is not `"fixcc"`.
`nsample_ngen`	Number of individuals desired at the last generation
`npairs`	Number of breeding pairs at each generation. If missing, we use 30 when `method="last2"` and 300 when `method="sub2"`.
`method`	Method used to generate the pedigree: either expand at the last two generations or generate a pedigree with a large number of pairs and then select a subset to have the desired sample size. With `method="fixcc"`, we use the pre-CC generations as performed at the Jackson Lab.
`design`	How to choose crosses: either random but avoiding siblings, or completely at random
`selc.method`	Method used to select the individuals from last generation.

Details

The default number of breeding pairs depends on the chosen method. With method="last2", the default is npairs=30; with method="sub2", the default is npairs=300; with method="fixcc", npairs is ignored and is fixed at 144.

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.