PhenotypeSimulator: Flexible Phenotype Simulation from Different Genetic and Noise Models

Simulation is a critical part of method development and assessment in quantitative genetics. 'PhenotypeSimulator' allows for the flexible simulation of phenotypes under different models, including genetic variant and infinitesimal genetic effects (reflecting population structure) as well as non-genetic covariate effects, observational noise and additional correlation effects. The different phenotype components are combined into a final phenotype while controlling for the proportion of variance explained by each of the components. For each effect component, the number of variables, their distribution and the design of their effect across traits can be customised. For the simulation of the genetic effects, external genotype data from a number of standard software ('plink', 'hapgen2'/ 'impute2', 'genome', 'bimbam', simple text files) can be imported. The final simulated phenotypes and its components can be automatically saved into .rds or .csv files. In addition, they can be saved in formats compatible with commonly used genetic association software ('gemma', 'bimbam', 'plink', 'snptest', 'LiMMBo').

Version: 0.3.1
Depends: R (≥ 3.3.0)
Imports: methods, optparse, R.utils, mvtnorm, snpStats, zoo, data.table (≥ 1.11.0), Rcpp (≥ 0.12.11), ggplot2, reshape2, dplyr
LinkingTo: Rcpp
Suggests: testthat, knitr, rmarkdown
Published: 2018-10-25
Author: Hannah Meyer ORCID iD [aut, cre], Konrad Rudolph ORCID iD [ctb]
Maintainer: Hannah Meyer <hannah at>
License: MIT + file LICENSE
NeedsCompilation: yes
Materials: README NEWS
CRAN checks: PhenotypeSimulator results


Reference manual: PhenotypeSimulator.pdf
Vignettes: Flexible phenotype simulation with PhenotypeSimulator
Supported Genotype Simulation
Simulation and linear model fit
Package source: PhenotypeSimulator_0.3.1.tar.gz
Windows binaries: r-devel:, r-release:, r-oldrel:
OS X binaries: r-release: PhenotypeSimulator_0.3.1.tgz, r-oldrel: PhenotypeSimulator_0.3.1.tgz
Old sources: PhenotypeSimulator archive


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