startSimulation: Starts and initializes the data structures required for a...

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

Description

Starts and initializes the data structures required for a simulation. A VCF file should be read beforehand with the function readVCF.

Usage

startSimulation(vcf, totalNumberOfIndividuals = 2000, subset = NA,
  randomdata = 0, typeOfGeneticMap = "download")

Arguments

vcf	Input vcf file of a region (can be .gz). Must contain phased data.
totalNumberOfIndividuals	Maximum Number of individuals to allocate memory for. Set it above the number of individuals you want to simulate.
subset	A subset of individual IDs to use for simulation
randomdata	If 1, disregards the genotypes in the vcf file and generates independent markers that are not in LD.
typeOfGeneticMap	Specify whether to download a genetic map for this chromosome

Examples

library("sim1000G")
library(gplots)

examples_dir = system.file("examples", package = "sim1000G")
vcf_file = file.path(examples_dir, "region.vcf.gz")

vcf = readVCF( vcf_file, maxNumberOfVariants = 100)


genetic_map_of_region = system.file(
   "examples",
   "chr4-geneticmap.txt",
   package = "sim1000G"
)

readGeneticMapFromFile(genetic_map_of_region)

pdf(file=tempfile())
plotRegionalGeneticMap(vcf$vcf[,2]+1)
dev.off()

startSimulation(vcf, totalNumberOfIndividuals = 200)

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