forrel (version 1.0.0)

simpleSim: Unconditional marker simulation

Description

Unconditional simulation of unlinked markers

Usage

simpleSim(
  x,
  N,
  alleles,
  afreq,
  ids,
  Xchrom = FALSE,
  mutmod = NULL,
  seed = NULL,
  verbose = TRUE
)

Arguments

x

a ped object

N

a positive integer: the number of markers to be simulated

alleles

a vector containing the allele names. If missing, the alleles are taken to be seq_along(afreq).

afreq

a vector of length 2 containing the population frequencies for the alleles. If missing, the alleles are assumed equifrequent.

ids

a vector containing ID labels of those pedigree members whose genotypes should be simulated.

Xchrom

a logical: X linked markers or not?

mutmod

a pedmut::mutationModel() object, i.e., list of mutation matrices named 'female' and 'male'.

seed

NULL, or a numeric seed for the random number generator.

verbose

a logical.

Value

a ped object equal to x in all respects except its MARKERS entry, which consists of the N simulated markers.

Details

This simulation is done by distributing alleles randomly to all founders, followed by unconditional gene dropping down throughout the pedigree (i.e. for each non-founder a random allele is selected from each of the parents). Finally the genotypes of any individuals not included in ids are removed.

See Also

markerSim()

Examples

# NOT RUN {
library(pedtools)
x = nuclearPed(1)
simpleSim(x, N = 3, afreq = c(0.5, 0.5))

y = cousinPed(1, child = TRUE)
simpleSim(y, N = 3, alleles = LETTERS[1:10])

# }