Man pages for adimitromanolakis/sim1000G
Genotype Simulations for Rare or Common Variants Using Haplotypes from 1000 Genomes
| computePairIBD1 | Computes pairwise IBD1 for a specific pair of individuals.... |
| 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... |
| crossoverCDFvector | Contains recombination model information. |
| downloadGeneticMap | Downloads a genetic map for a particular chromosome under... |
| generateChromosomeRecombinationPositions | Generates a recombination vector arising from one meiotic... |
| generateFakeWholeGenomeGeneticMap | Generates a fake genetic map that spans the whole genome. |
| generateRecombinationDistances | Generate inter-recombination distances using a chi-square... |
| generateRecombinationDistances_noInterference | Generate recombination distances using a no-interference... |
| generateSingleRecombinationVector | Genetates a recombination vector arising from one meiotic... |
| generateUniformGeneticMap | Generates a uniform genetic map. |
| generateUnrelatedIndividuals | Generates variant data for n unrelated individuals |
| geneticMap | Holds the genetic map information that is used for... |
| getCMfromBP | Converts centimorgan position to base-pair. Return a list of... |
| loadSimulation | Load some previously saved simulation data by function... |
| 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... |
| readGeneticMap | Reads a genetic map downloaded from the function... |
| readGeneticMapFromFile | Reads a genetic map to be used for simulations. The genetic... |
| readVCF | Read a vcf file, with options to filter out low or high... |
| resetSimulation | Removes all individuals that have been simulated and resets... |
| retrieveGenotypes | Retrieve a matrix of simulated genotypes for a specific set... |
| saveSimulation | Save the data for a simulation for later use. When simulating... |
| setRecombinationModel | Set recombination model to either poisson (no interference)... |
| SIM | Holds data necessary for a simulation. |
| sim1000G-package | Simulations of rare/common variants using haplotype data from... |
| startSimulation | Starts and initializes the data structures required for a... |
| subsetVCF | Generate a market subset of a vcf file |
| writePED | Writes a plink compatible PED/MAP file from the simulated... |
