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').

Version: 0.2.0
Depends: R (≥ 3.3.0)
Imports: methods, optparse, R.utils, mvtnorm, snpStats, zoo, data.table, Rcpp (≥ 0.12.11), ggplot2, reshape2, dplyr
LinkingTo: Rcpp
Suggests: testthat, knitr, rmarkdown
Published: 2018-01-07
Author: Hannah Meyer [aut, cre], Konrad Rudolph [ctb]
Maintainer: Hannah Meyer <hannah at ebi.ac.uk>
BugReports: https://github.com/HannahVMeyer/PhenotypeSimulator/issues
License: MIT + file LICENSE
URL: https://github.com/HannahVMeyer/PhenotypeSimulator
NeedsCompilation: yes
Materials: README
CRAN checks: PhenotypeSimulator results

Downloads:

Reference manual: PhenotypeSimulator.pdf
Vignettes: Simulation and linear model fit
Flexible phenotype simulation with PhenotypeSimulator
Vignette Title
Package source: PhenotypeSimulator_0.2.0.tar.gz
Windows binaries: r-devel: PhenotypeSimulator_0.2.0.zip, r-release: PhenotypeSimulator_0.2.0.zip, r-oldrel: PhenotypeSimulator_0.2.0.zip
OS X binaries: r-release: PhenotypeSimulator_0.2.0.tgz, r-oldrel: not available
Old sources: PhenotypeSimulator archive

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