Flexible Phenotype Simulation from Different Genetic and Noise Models

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Documentation for package ‘PhenotypeSimulator’ version 0.3.4

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

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.