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

---

Documentation for package ‘sim1000G’ version 1.40

• DESCRIPTION file.
• User guides, package vignettes and other documentation.

Help Pages

sim1000G-package	Simulations of rare/common variants using haplotype data from 1000 genomes
computePairIBD1	Computes pairwise IBD1 for a specific pair of individuals. See function computePairIBD12 for description.
computePairIBD12	Computes pairwise IBD1/2 for a specific pair of individuals
computePairIBD2	Computes pairwise IBD2 for a specific pair of individuals
createVCF	Creates a regional vcf file using bcftools to extract a region from 1000 genomes vcf files
crossoverCDFvector	Contains recombination model information.
downloadGeneticMap	Downloads a genetic map for a particular chromosome under GRCh37 coordinates for use with sim1000G.
generateChromosomeRecombinationPositions	Generates a recombination vector arising from one meiotic event. The origin of segments is coded as (0 - haplotype1 , 1 - haplotype2 )
generateFakeWholeGenomeGeneticMap	Generates a fake genetic map that spans the whole genome.
generateRecombinationDistances	Generate inter-recombination distances using a chi-square model. Note this are the distances between two succesive recombination events and not the absolute positions of the events. To generate the locations of the recombination events see the example below.
generateRecombinationDistances_noInterference	Generate recombination distances using a no-interference model.
generateSingleRecombinationVector	Genetates a recombination vector arising from one meiotic event. The origin of segments is coded as (0 - haplotype1 , 1 - haplotype2 )
generateUniformGeneticMap	Generates a uniform genetic map.
generateUnrelatedIndividuals	Generates variant data for n unrelated individuals
geneticMap	Holds the genetic map information that is used for simulations.
getCMfromBP	Converts centimorgan position to base-pair. Return a list of centimorgan positions that correspond to the bp vector (in basepairs).
loadSimulation	Load some previously saved simulation data by function saveSimulation
newFamily3generations	Generates genotype data for a family of 3 generations
newFamilyWithOffspring	Simulates genotypes for 1 family with n offspring
newNuclearFamily	Simulates genotypes for 1 family with 1 offspring
pkg.opts	Holds general package options
plotRegionalGeneticMap	Generates a plot of the genetic map for a specified region.
printMatrix	Utility function that prints a matrix. Useful for IBD12 matrices.
readGeneticMap	Reads a genetic map downloaded from the function downloadGeneticMap or reads a genetic map from a specified file. If the argument filename is used then the genetic map is read from the corresponding file. Otherwise, if a chromosome is specified, the genetic map is downloaded for human chromosome using grch37 coordinates.
readGeneticMapFromFile	Reads a genetic map to be used for simulations. The genetic map should be of a single chromosome and covering the extent of the region to be simulated. Whole chromosome genetic maps can also be used.
readVCF	Read a vcf file, with options to filter out low or high frequency markers.
resetSimulation	Removes all individuals that have been simulated and resets the simulator.
retrieveGenotypes	Retrieve a matrix of simulated genotypes for a specific set of individual IDs
saveSimulation	Save the data for a simulation for later use. When simulating multiple populations it allows saving and restoring of simulation data for each population.
setRecombinationModel	Set recombination model to either poisson (no interference) or chi-square.
SIM	Holds data necessary for a simulation.
sim1000G	Simulations of rare/common variants using haplotype data from 1000 genomes
startSimulation	Starts and initializes the data structures required for a simulation. A VCF file should be read beforehand with the function readVCF.
subsetVCF	Generate a market subset of a vcf file
writePED	Writes a plink compatible PED/MAP file from the simulated genotypes