simcross (version 0.6)

sim_from_pedigree_allchr: 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
)

Value

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

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.

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)