Files in sim1000G

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

inst/doc/SimulatingFamilyData.R inst/doc/ExtractingRegionsForSimulation.R inst/doc/SimulatingFamilyData.Rmd inst/doc/ExtractingRegionsForSimulation.Rmd inst/examples/examine-maf-and-correlation.R inst/examples/Rplot02.pdf inst/examples/extract-1000genomes-genes.R inst/examples/example2-population-stratification.R inst/examples/example1-single-population.R inst/examples/example4-population-stratification.R inst/examples/example1x-single-population.R inst/examples/generate-sim-cmds.R inst/examples/manuscript-plot-LD.R inst/examples/plot1.R inst/examples/example2-stratification-qqplots-and-summary.R inst/examples/timings.R inst/examples/amelia/start_sim_14Nov2017_2000_Apo.R inst/examples/family/Example_for_package.R inst/examples/family/Simulations_family_survival_data.R inst/examples/family/summary_results.R inst/examples/extracting-vcf-files/read-and-subset-vcf.R inst/examples/examples-from-manuscript/example1.R inst/examples/examples-from-manuscript/example2.R inst/examples/examples-from-manuscript/example4.R inst/examples/examples-from-manuscript/example3.R vignettes/SimulatingFamilyData.Rmd vignettes/ExtractingRegionsForSimulation.Rmd R/recombination.R R/1000G-package.r R/readvcf.R R/hapsim2-functions.R R/simulation.R R/writeped.R man/generateFakeWholeGenomeGeneticMap.Rd man/pkg.opts.Rd man/downloadGeneticMap.Rd man/generateChromosomeRecombinationPositions.Rd man/saveSimulation.Rd man/newNuclearFamily.Rd man/computePairIBD2.Rd man/generateSingleRecombinationVector.Rd man/readGeneticMap.Rd man/printMatrix.Rd man/computePairIBD12.Rd man/generateRecombinationDistances_noInterference.Rd man/generateRecombinationDistances.Rd man/readVCF.Rd man/resetSimulation.Rd man/writePED.Rd man/loadSimulation.Rd man/startSimulation.Rd man/subsetVCF.Rd man/retrieveGenotypes.Rd man/crossoverCDFvector.Rd man/newFamily3generations.Rd man/getCMfromBP.Rd man/sim1000G-package.Rd man/readGeneticMapFromFile.Rd man/newFamilyWithOffspring.Rd man/computePairIBD1.Rd man/setRecombinationModel.Rd man/geneticMap.Rd man/plotRegionalGeneticMap.Rd man/SIM.Rd man/generateUniformGeneticMap.Rd man/generateUnrelatedIndividuals.Rd man/createVCF.Rd tests/testthat.R tests/tests.R tests/testthat/test_2.R