simpleSim: Unconditional marker simulation

Description Usage Arguments Details Value Author(s) See Also Examples

View source: R/markerSim.R

Description

Unconditional simulation of unlinked markers

Usage

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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

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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.