newFamily3generations: Generates genotype data for a family of 3 generations

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

Description

Generates genotype data for a family of 3 generations

Usage

newFamily3generations(familyid, noffspring2 = 2, noffspring3 = c(1, 1))

Arguments

familyid	What will be the family_id (for example: 100)
noffspring2	Number of offspring in generation 2
noffspring3	Number of offspring in generation 3 (vector of length noffspring2)

Value

family structure object

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)

ped_line = newFamily3generations(12, 3, c(3,3,2) )

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