Flexible Phenotype Simulation from Different Genetic and Noise Models


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Documentation for package ‘PhenotypeSimulator’ version 0.2.0

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PhenotypeSimulator-package PhenotypeSimulator: A package for simulating phenotypes from different genetic and noise components
addNonNulls Add all non-NULL elements of list.
commaList2vector Comma-separated string to numeric vector.
correlatedBgEffects Simulate correlated background effects.
expGen2probGen Rewrite expected genotypes into genotype probabilities.
geneticBgEffects Simulate infinitesimal genetic effects (reflecting sample kinship).
geneticFixedEffects Simulate genetic variant effects.
getAlleleFrequencies Compute allele frequencies from genotype data.
getCausalSNPs Draw random SNPs from genotypes.
getKinship Get genetic kinship.
noiseBgEffects Simulate observational noise effects.
noiseFixedEffects Simulate noise fixed effects.
PhenotypeSimulator PhenotypeSimulator: A package for simulating phenotypes from different genetic and noise components
probGen2expGen Compute expected genotypes from genotype probabilities.
readStandardGenotypes Read genotypes from file.
read_lines Scan file for specific line numbers
rescaleVariance Scale phenotype component.
runSimulation Run phenotype simulation.
savePheno Save final phenotype and phenotype components.
setModel Set simulation model.
simulateDist Data simulation for different distributions.
simulateGenotypes Simulate bi-allelic genotypes.
simulatePhenotypes Command line execution for PhenotypeSimulator
standardiseGenotypes Standardise genotypes
vmessage Print userinfo.
writeStandardOutput Write simulated data into formats used by standard GWAS software