# Flexible Phenotype Simulation from Different Genetic and Noise Models

## Documentation for package ‘PhenotypeSimulator’ version 0.3.4

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

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.
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.
testNumerics | Test lists for different properties of numerics.
transformNonlinear | Phenotype transformation.
vmessage | Print userinfo.
writeStandardOutput | Write simulated data into formats used by standard GWAS software.