simulateGen {pedSimulate}

Simulate genotypes

Description

Simulate genotypes for a given pedigree, allele frequency and mutation rate at each marker locus.

Usage

simulateGen(ped, AF, mut.rate = 0, seed = NA)

Arguments

ped

: Pedigree data.frame with columns for animal, sire, and dam identification.

AF

: Vector of allele frequencies at different loci for the genotypes to be simulated.

mut.rate

: Vector of mutation rates at different loci for the genotypes to be simulated, default = 0 for no mutation.

seed

: A numeric variable input to the random number generator for reproducible simulations, default = 'NA' for non-reproducible simulations.

Details

Only diploid and bi-allelic situations are covered. No linkage disequilibrium is simulated.

Value

M : The simulated genotype data.frame with rows corresponding to animals (in the same order as in the pedigree) and columns corresponding to markers.

Examples

nSNP = 100
AF = runif(nSNP, 0.01, 0.99)
mut.rate = runif(nSNP, 0, 10^-5)
ped = data.frame(ID=1:5, SIRE=c(0,0,1,0,3), DAM=c(0,0,2,2,4))
gen = simulateGen(ped, AF, mut.rate, seed=684)