SIM                     Holds data necessary for a simulation.
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.
sim1000G-package        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
