sim_from_pedigree_allchr: Simulate genotypes for pedigree for multiple chromosomes

In simcross: Simulate Experimental Crosses

Simulate genotypes for pedigree for multiple chromosomes

Description

Simulate genotypes along all chromosomes for a pedigree. This is a wrap up of sim_from_pedigree.

Usage

sim_from_pedigree_allchr(
  pedigree,
  map,
  m = 10,
  p = 0,
  obligate_chiasma = FALSE
)

Arguments

pedigree	Matrix or data frame describing a pedigree, with first four columns being individual ID, mom ID, dad ID, and sex (female as 0, male as 1).
map	marker locations, a list with elements for each chromosome
m	Crossover interference parameter, for chi-square model (m=0 corresponds to no interference).
p	proportion of crossovers coming from no-interference process
obligate_chiasma	If TRUE, require an obligate chiasma on the 4-strand bundle at meiosis.

Value

A list with each component being the result from sim_from_pedigree, of length same as map.

See Also

check_pedigree(), sim_ril_pedigree(), sim_ail_pedigree() sim_from_pedigree()

Examples

library(qtl)
# marker map
map <- sim.map(len=rep(100, 19), n.mar=10, include.x=FALSE)
# simulate AIL pedigree
tab <- sim_ail_pedigree(12, 30)
# simulate data from that pedigree
dat <- sim_from_pedigree_allchr(tab, map)

simcross documentation built on May 29, 2024, 2:41 a.m.