Files in HannahVMeyer/PhenotypeSimulator
Flexible Phenotype Simulation from Different Genetic and Noise Models

DESCRIPTION
INDEX.Rmd INDEX.md
LICENSE
NAMESPACE
NEWS.md R/PhenotypeSimulator.R R/RcppExports.R R/commandlineFunctions.R R/createphenotypeFunctions.R R/genotypeFunctions.R R/outputFunctions.R R/pkg.R R/utilityFunctions.R R/variancecomponentFunctions.R README.Rmd README.md
build/vignette.rds
docs/LICENSE-text.html
docs/LOG.html
docs/_config.yml
docs/articles/PhenotypeSimulator.html
docs/articles/PhenotypeSimulator_files/figure-html/unnamed-chunk-14-1.png
docs/articles/PhenotypeSimulator_files/figure-html/unnamed-chunk-14-2.png
docs/articles/PhenotypeSimulator_files/figure-html/unnamed-chunk-16-1.png
docs/articles/PhenotypeSimulator_files/figure-html/unnamed-chunk-16-2.png
docs/articles/PhenotypeSimulator_files/figure-html/unnamed-chunk-18-1.png
docs/articles/PhenotypeSimulator_files/figure-html/unnamed-chunk-18-2.png
docs/articles/PhenotypeSimulator_files/figure-html/unnamed-chunk-18-3.png
docs/articles/PhenotypeSimulator_files/figure-html/unnamed-chunk-18-4.png
docs/articles/PhenotypeSimulator_files/figure-html/unnamed-chunk-19-1.png
docs/articles/PhenotypeSimulator_files/figure-html/unnamed-chunk-19-2.png
docs/articles/PhenotypeSimulator_files/figure-html/unnamed-chunk-21-1.png
docs/articles/PhenotypeSimulator_files/figure-html/unnamed-chunk-21-2.png
docs/articles/PhenotypeSimulator_files/figure-html/unnamed-chunk-7-1.png
docs/articles/PhenotypeSimulator_files/figure-html/unnamed-chunk-7-2.png
docs/articles/Sample-scripts-external-genotype-simulation.html
docs/articles/Simulation-and-LinearModel.html
docs/articles/Simulation-and-LinearModel_files/figure-html/freq-beta-1.png
docs/articles/Simulation-and-LinearModel_files/figure-html/heatmaps-1.png
docs/articles/SimulationBasedOnExampleData.html
docs/articles/SimulationBasedOnExampleData_files/figure-html/distribution simulated data-1.png
docs/articles/SimulationBasedOnExampleData_files/figure-html/distribution-1.png
docs/articles/UsagePhenotypeSimulator.html
docs/articles/UsagePhenotypeSimulator_files/figure-html/unnamed-chunk-14-1.png
docs/articles/UsagePhenotypeSimulator_files/figure-html/unnamed-chunk-14-2.png
docs/articles/UsagePhenotypeSimulator_files/figure-html/unnamed-chunk-16-1.png
docs/articles/UsagePhenotypeSimulator_files/figure-html/unnamed-chunk-16-2.png
docs/articles/UsagePhenotypeSimulator_files/figure-html/unnamed-chunk-18-1.png
docs/articles/UsagePhenotypeSimulator_files/figure-html/unnamed-chunk-18-2.png
docs/articles/UsagePhenotypeSimulator_files/figure-html/unnamed-chunk-18-3.png
docs/articles/UsagePhenotypeSimulator_files/figure-html/unnamed-chunk-18-4.png
docs/articles/UsagePhenotypeSimulator_files/figure-html/unnamed-chunk-19-1.png
docs/articles/UsagePhenotypeSimulator_files/figure-html/unnamed-chunk-19-2.png
docs/articles/UsagePhenotypeSimulator_files/figure-html/unnamed-chunk-21-1.png
docs/articles/UsagePhenotypeSimulator_files/figure-html/unnamed-chunk-21-2.png
docs/articles/UsagePhenotypeSimulator_files/figure-html/unnamed-chunk-7-1.png
docs/articles/UsagePhenotypeSimulator_files/figure-html/unnamed-chunk-7-2.png
docs/articles/cor_pheno.png
docs/articles/cor_simulated.png
docs/articles/index.html
docs/articles/wallthickness.png
docs/authors.html
docs/docsearch.css
docs/docsearch.js
docs/favicon.ico
docs/index.html
docs/link.svg
docs/news/index.html
docs/pkgdown.css
docs/pkgdown.js
docs/pkgdown.yml
docs/reference/PhenotypeSimulator.html
docs/reference/addNonNulls.html
docs/reference/commaList2vector.html
docs/reference/correlatedBgEffects.html
docs/reference/expGen2probGen.html
docs/reference/geneticBgEffects.html
docs/reference/geneticFixedEffects.html
docs/reference/getAlleleFrequencies.html
docs/reference/getCausalSNPs.html
docs/reference/getKinship.html
docs/reference/index.html
docs/reference/noiseBgEffects.html
docs/reference/noiseFixedEffects.html
docs/reference/probGen2expGen.html
docs/reference/readStandardGenotypes.html
docs/reference/read_lines.html
docs/reference/rescaleVariance.html
docs/reference/runSimulation.html
docs/reference/savePheno.html
docs/reference/setModel.html
docs/reference/simulateDist.html
docs/reference/simulateGenotypes.html
docs/reference/simulatePhenotypes.html
docs/reference/standardiseGenotypes.html
docs/reference/testNumerics.html
docs/reference/transformNonlinear.html
docs/reference/vmessage.html
docs/reference/writeStandardOutput.html
docs/simulatedPhenotypes.png
inst/doc/Simulation-and-LinearModel.R inst/doc/Simulation-and-LinearModel.Rmd inst/doc/Simulation-and-LinearModel.pdf inst/doc/UsagePhenotypeSimulator.R inst/doc/UsagePhenotypeSimulator.Rmd inst/doc/UsagePhenotypeSimulator.pdf inst/doc/sample-scripts-external-genotype-simulation.R inst/doc/sample-scripts-external-genotype-simulation.Rmd inst/doc/sample-scripts-external-genotype-simulation.pdf
inst/extdata/genotypes/genome/genotypes_genome.txt
inst/extdata/genotypes/genome/simulate_genotypes_genome.sh
inst/extdata/genotypes/genotypes_chr22.csv
inst/extdata/genotypes/hapgen/genotypes_hapgen.cases.gen
inst/extdata/genotypes/hapgen/genotypes_hapgen.cases.sample
inst/extdata/genotypes/hapgen/genotypes_hapgen.controls.gen
inst/extdata/genotypes/hapgen/genotypes_hapgen.controls.sample
inst/extdata/genotypes/hapgen/genotypes_hapgen.summary
inst/extdata/genotypes/hapgen/legend_file
inst/extdata/genotypes/hapgen/simulate_genotypes_hapgen2.sh
inst/extdata/genotypes/plink/genotypes_plink.bed
inst/extdata/genotypes/plink/genotypes_plink.bim
inst/extdata/genotypes/plink/genotypes_plink.fam
inst/extdata/genotypes/plink/genotypes_plink.log
inst/extdata/genotypes/plink/genotypes_plink.simfreq
inst/extdata/genotypes/plink/plink_sim_par.txt
inst/extdata/genotypes/plink/simulate_genotypes_plink.sh
inst/extdata/kinship/kinship.csv
inst/extdata/resultsSimulationAndLinearModel/SNP_NrSNP10.csv
inst/extdata/resultsSimulationAndLinearModel/SNP_effects_NrSNP10.csv
inst/extdata/resultsSimulationAndLinearModel/correlation_phenotype.pdf
inst/extdata/resultsSimulationAndLinearModel/gwas_results_gemma_qqplot.png
inst/extdata/resultsSimulationAndLinearModel/sigSNPs.csv
inst/extdata/resultsSimulationAndLinearModel/simulated_withEffect.csv
inst/extdata/resultsSimulationAndLinearModel/simulation_phenoComponentsFinal.rds
man/PhenotypeSimulator.Rd man/addNonNulls.Rd man/commaList2vector.Rd man/correlatedBgEffects.Rd man/expGen2probGen.Rd man/geneticBgEffects.Rd man/geneticFixedEffects.Rd man/getAlleleFrequencies.Rd man/getCausalSNPs.Rd man/getKinship.Rd man/noiseBgEffects.Rd man/noiseFixedEffects.Rd man/probGen2expGen.Rd man/readStandardGenotypes.Rd man/read_lines.Rd man/rescaleVariance.Rd man/runSimulation.Rd man/savePheno.Rd man/setModel.Rd man/simulateDist.Rd man/simulateGenotypes.Rd man/simulatePhenotypes.Rd man/standardiseGenotypes.Rd man/testNumerics.Rd man/transformNonlinear.Rd man/vmessage.Rd man/writeStandardOutput.Rd
src/Makevars
src/RcppExports.cpp
src/read_lines.cpp
tests/testthat.R tests/testthat/test-components.R tests/testthat/test-createphenotypeFunctions.r tests/testthat/test-genotype.r tests/testthat/test-output.R tests/testthat/test-utility.r vignettes/PhenotypeSimulator.Rmd
vignettes/PhenotypeSimulator.html
vignettes/Simulation-and-LinearModel.Rmd
vignettes/SimulationAndLinearModel.bib
vignettes/SimulationBasedOnExampleData.Rmd
vignettes/Vignette-example-data.bib
vignettes/cor_pheno.png
vignettes/cor_simulated.png
vignettes/covs.rds
vignettes/genotype-simulation.bib
vignettes/pheno_small.rds
vignettes/plos-genetics.csl
vignettes/sample-scripts-external-genotype-simulation.Rmd
vignettes/sample-scripts-external-genotype-simulation.html
vignettes/wallthickness.png
HannahVMeyer/PhenotypeSimulator documentation built on Nov. 7, 2018, 10:13 a.m.