sim_ail_pedigree_fix_n: Simulate AIL pedigree with fixed n

In kbroman/simcross: Simulate Experimental Crosses

Simulate AIL pedigree with fixed n

Description

Simulate a pedigree for advanced intercross lines (a table of individual, mom, dad, sex) so that the last generation reaches a desired sample size n

Usage

sim_ail_pedigree_fix_n(
  ngen = 12,
  nkids_per = 5,
  nsample_ngen = 150,
  npairs = NULL,
  method = c("last2", "sub2"),
  design = c("nosib", "random")
)

Arguments

ngen	Number of generations of outbreeding
nkids_per	Number of offspring per pair for the last generation
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 pedigree: either expand at the last two generations or generate a pedigree with a large number of pairs and select a subset to have the desired sample size.
design	How to choose crosses: either random but avoiding siblings, or completely at random

Details

The default value for npairs depends on the choice of method. For method="last2", we use a default of npairs=30; for method="sub2", we use a default of npairs=300.

Value

A data frame with five columns: individual ID, mother ID, father ID, sex, and generation. Founders have 0 for mother and father ID. Sex is coded 0 for female and 1 for male.

See Also

sim_from_pedigree(), sim_ril_pedigree(), sim_ail_pedigree(), sim_do_pedigree(), sim_4way_pedigree(), sim_do_pedigree_fix_n()

Examples

tab <- sim_ail_pedigree_fix_n(12)

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