computePairIBD2 {sim1000G}

Computes pairwise IBD2 for a specific pair of individuals

Description

Computes pairwise IBD2 for a specific pair of individuals

Usage

computePairIBD2(i, j)

Arguments

i

Index of first individual

j

Index of second individual

Value

Mean IBD2 as computed from shared haplotypes

Examples

library("sim1000G")

examples_dir = system.file("examples", package = "sim1000G")
vcf_file = file.path(examples_dir, "region.vcf.gz")
vcf = readVCF( vcf_file, maxNumberOfVariants = 100 ,
               min_maf = 0.12 ,max_maf = NA)

# For realistic data use the function downloadGeneticMap
generateUniformGeneticMap()

startSimulation(vcf, totalNumberOfIndividuals = 200)

ped1 = newNuclearFamily(1)

v = computePairIBD2(1, 3)

cat("IBD2 of pair = ", v, "\n");