computePairIBD12: Computes pairwise IBD1/2 for a specific pair of individuals

In sim1000G: Genotype Simulations for Rare or Common Variants Using Haplotypes from 1000 Genomes

Description

Computes pairwise IBD1/2 for a specific pair of individuals

Usage

computePairIBD12(i, j)

Arguments

i	Index of first individual
j	Index of second individual

Value

Mean IBD1 and 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)

generateUniformGeneticMap()

startSimulation(vcf, totalNumberOfIndividuals = 200)

ped1 = newNuclearFamily(1)

v = computePairIBD12(1, 3)

cat("IBD1 of pair = ", v[1], "\n");
cat("IBD2 of pair = ", v[2], "\n");

sim1000G documentation built on June 10, 2019, 1:01 a.m.