simpleSim: Unconditional marker simulation

Description

Unconditional simulation of unlinked markers

Usage

simpleSim(x, N, alleles, afreq, available, Xchrom=FALSE, mutmat=NULL, seed=NULL, 
          verbose=T)

Arguments

a linkdat object

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.

available

a vector containing IDs of the available individuals, i.e. those whose genotypes should be simulated.

Xchrom

a logical: X linked markers or not?

mutmat

a mutation matrix, or a list of two such matrices named "female" and "male". The matrix/matrices must be square, with the allele labels as dimnames, and each row must sum to 1 (after rounding to 3 decimals).

seed

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

verbose

a logical.

Value

a linkdat object equal to x in all respects except its markerdata 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 available are removed.

Examples

Run this code

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

y = addOffspring(cousinPed(1), father=7, mother=8, noffs=1)
simpleSim(y, N=3, alleles=LETTERS[1:10])
# }