appendGen {pedSimulate}

Simulate genotypes for an appended pedigree

Description

Simulate genotypes for an appended pedigree to an existing pedigree with genotypes.

Usage

appendGen(ped, M, AF = c(), mut.rate = 0, seed = NA)

Arguments

ped

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

M

: Genotype data.frame with rows corresponding to the initial rows of the pedigree and columns corresponding to markers.

AF

: Vector of allele frequencies at different loci for the genotypes to be simulated. If no value is provided, it will be estimated from M.

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

M2 : New simulated genotypes appended to M.

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)
ped = rbind(ped, data.frame(ID=6:8, SIRE=c(3,6,6), DAM=c(0,4,5)))
gen = appendGen(ped, M=gen, AF, seed=34)