simpleSim: Unconditional marker simulation

In forrel: Forensic Pedigree Analysis and Relatedness Inference

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 with allele labels.
afreq	a numeric vector of allele frequencies. If missing, the alleles are assumed to be equi-frequent.
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	An integer seed for the random number generator (optional).
verbose	a logical.

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.

Value

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

Author(s)

Magnus Dehli Vigeland

See Also

markerSim()

Examples

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])

forrel documentation built on March 14, 2021, 1:06 a.m.