Files in adimitromanolakis/sim1000G
Genotype Simulations for Rare or Common Variants Using Haplotypes from 1000 Genomes
.Rbuildignore
.gitignore
DESCRIPTION
Makefile
Meta/vignette.rds
NAMESPACE
R/1000G-package.r
R/hapsim2-functions.R
R/readvcf.R
R/recombination.R
R/simulation.R
R/writeped.R
README.md
extra/1
extra/2
extra/20130606_g1k.ped
extra/Rplots.pdf
extra/Untitled Book1.csv
extra/Untitled Book1.xls
extra/Untitled Book1.xlsx
extra/job-sim1000g-timings.log
extra/job-sim1000g-timings.sh
extra/sim1000G-timings.log.R
extra/sim1000G-timings.log.txt
extra/time1.png
include-filelist.txt
inst/CITATION
inst/datasets/README.txt
inst/doc/ExtractingRegionsForSimulation.R
inst/doc/ExtractingRegionsForSimulation.Rmd
inst/doc/ExtractingRegionsForSimulation.html
inst/doc/SimulatingFamilyData.R
inst/doc/SimulatingFamilyData.Rmd
inst/doc/SimulatingFamilyData.html
inst/examples/20130606_g1k.ped
inst/examples/Rplot02.pdf
inst/examples/amelia/start_sim_14Nov2017_2000_Apo.R
inst/examples/chr4-geneticmap.txt
inst/examples/examine-maf-and-correlation.R
inst/examples/example1-single-population.R
inst/examples/example1x-single-population.R
inst/examples/example2-population-stratification.R
inst/examples/example2-stratification-qqplots-and-summary.R
inst/examples/example4-population-stratification.R
inst/examples/examples-from-manuscript/1
inst/examples/examples-from-manuscript/example1.R
inst/examples/examples-from-manuscript/example2.R
inst/examples/examples-from-manuscript/example3.R
inst/examples/examples-from-manuscript/example4.R
inst/examples/extract-1000genomes-genes.R
inst/examples/extracting-vcf-files/read-and-subset-vcf.R
inst/examples/family/Example_for_package.R
inst/examples/family/FamEvent_1.4.tar.gz
inst/examples/family/IBD_family44.txt
inst/examples/family/Simulations_family_survival_data.R
inst/examples/family/data1.rdata
inst/examples/family/frailtypack_3.2.tar.gz
inst/examples/family/summary_results.R
inst/examples/generate-sim-cmds.R
inst/examples/manuscript-plot-LD.R
inst/examples/plot1.R
inst/examples/region-chr4-93-TMEM156.vcf.gz
inst/examples/region.vcf.gz
inst/examples/sample_subset1.txt
inst/examples/sample_subset2.txt
inst/examples/timings.R
inst/extdata/20130606_g1k.ped
inst/extdata/chr4-geneticmap.txt
inst/extdata/region.vcf.gz
man/SIM.Rd
man/computePairIBD1.Rd
man/computePairIBD12.Rd
man/computePairIBD2.Rd
man/createVCF.Rd
man/crossoverCDFvector.Rd
man/downloadGeneticMap.Rd
man/generateChromosomeRecombinationPositions.Rd
man/generateFakeWholeGenomeGeneticMap.Rd
man/generateRecombinationDistances.Rd
man/generateRecombinationDistances_noInterference.Rd
man/generateSingleRecombinationVector.Rd
man/generateUniformGeneticMap.Rd
man/generateUnrelatedIndividuals.Rd
man/geneticMap.Rd
man/getCMfromBP.Rd
man/loadSimulation.Rd
man/newFamily3generations.Rd
man/newFamilyWithOffspring.Rd
man/newNuclearFamily.Rd
man/pkg.opts.Rd
man/plotRegionalGeneticMap.Rd
man/printMatrix.Rd
man/readGeneticMap.Rd
man/readGeneticMapFromFile.Rd
man/readVCF.Rd
man/resetSimulation.Rd
man/retrieveGenotypes.Rd
man/saveSimulation.Rd
man/setRecombinationModel.Rd
man/sim1000G-package.Rd
man/startSimulation.Rd
man/subsetVCF.Rd
man/writePED.Rd
sim1000G.Rproj
tests/tests.R
tests/testthat.R
tests/testthat/test1.geneticmap.txt
tests/testthat/test1.vcf.rdata
tests/testthat/test_2.R
vignettes/ExtractingRegionsForSimulation.Rmd
vignettes/ExtractingRegionsForSimulation.html
vignettes/SimulatingFamilyData.Rmd
vignettes/SimulatingFamilyData.html
