Genotype Simulations for Rare or Common Variants Using Haplotypes from 1000 Genomes
Contains recombination model information.
Downloads a genetic map for a particular chromosome under GRCh37 coord...
Computes pairwise IBD1 for a specific pair of individuals. See functio...
Computes pairwise IBD1/2 for a specific pair of individuals
Computes pairwise IBD2 for a specific pair of individuals
Creates a regional vcf file using bcftools to extract a region from 10...
Generates a recombination vector arising from one meiotic event. The o...
Generates a fake genetic map that spans the whole genome.
Generate inter-recombination distances using a chi-square model. Note ...
Generate recombination distances using a no-interference model.
Genetates a recombination vector arising from one meiotic event. The o...
Generates a uniform genetic map.
Generates variant data for n unrelated individuals
Holds the genetic map information that is used for simulations.
Converts centimorgan position to base-pair. Return a list of centimorg...
Load some previously saved simulation data by function saveSimulation
Generates genotype data for a family of 3 generations
Simulates genotypes for 1 family with n offspring
Simulates genotypes for 1 family with 1 offspring
Holds general package options
Generates a plot of the genetic map for a specified region.
Utility function that prints a matrix. Useful for IBD12 matrices.
Reads a genetic map downloaded from the function downloadGeneticMap or...
Reads a genetic map to be used for simulations. The genetic map should...
Read a vcf file, with options to filter out low or high frequency mark...
Removes all individuals that have been simulated and resets the simula...
Retrieve a matrix of simulated genotypes for a specific set of individ...
Save the data for a simulation for later use. When simulating multiple...
Set recombination model to either poisson (no interference) or chi-squ...
Holds data necessary for a simulation.
Simulations of rare/common variants using haplotype data from 1000 gen...
Starts and initializes the data structures required for a simulation. ...
Generate a market subset of a vcf file
Writes a plink compatible PED/MAP file from the simulated genotypes
Generates realistic simulated genetic data in families or unrelated individuals.