Man pages for sim1000G
Genotype Simulations for Rare or Common Variants Using Haplotypes from 1000 Genomes

computePairIBD1Computes pairwise IBD1 for a specific pair of individuals....
computePairIBD12Computes pairwise IBD1/2 for a specific pair of individuals
computePairIBD2Computes pairwise IBD2 for a specific pair of individuals
createVCFCreates a regional vcf file using bcftools to extract a...
crossoverCDFvectorContains recombination model information.
downloadGeneticMapDownloads a genetic map for a particular chromosome under...
generateChromosomeRecombinationPositionsGenerates a recombination vector arising from one meiotic...
generateFakeWholeGenomeGeneticMapGenerates a fake genetic map that spans the whole genome.
generateRecombinationDistancesGenerate inter-recombination distances using a chi-square...
generateRecombinationDistances_noInterferenceGenerate recombination distances using a no-interference...
generateSingleRecombinationVectorGenetates a recombination vector arising from one meiotic...
generateUniformGeneticMapGenerates a uniform genetic map.
generateUnrelatedIndividualsGenerates variant data for n unrelated individuals
geneticMapHolds the genetic map information that is used for...
getCMfromBPConverts centimorgan position to base-pair. Return a list of...
loadSimulationLoad some previously saved simulation data by function...
newFamily3generationsGenerates genotype data for a family of 3 generations
newFamilyWithOffspringSimulates genotypes for 1 family with n offspring
newNuclearFamilySimulates genotypes for 1 family with 1 offspring
pkg.optsHolds general package options
plotRegionalGeneticMapGenerates a plot of the genetic map for a specified region.
printMatrixUtility function that prints a matrix. Useful for IBD12...
readGeneticMapReads a genetic map downloaded from the function...
readGeneticMapFromFileReads a genetic map to be used for simulations. The genetic...
readVCFRead a vcf file, with options to filter out low or high...
resetSimulationRemoves all individuals that have been simulated and resets...
retrieveGenotypesRetrieve a matrix of simulated genotypes for a specific set...
saveSimulationSave the data for a simulation for later use. When simulating...
setRecombinationModelSet recombination model to either poisson (no interference)...
SIMHolds data necessary for a simulation.
sim1000G-packageSimulations of rare/common variants using haplotype data from...
startSimulationStarts and initializes the data structures required for a...
subsetVCFGenerate a market subset of a vcf file
writePEDWrites a plink compatible PED/MAP file from the simulated...
sim1000G documentation built on March 18, 2018, 2:23 p.m.