**PhenotypeSimulator** allows for the flexible simulation of phenotypes
from different genetic and non-genetic (noise) components.

In quantitative genetics, genotype to phenotype mapping is commonly
realised by fitting a linear model to the genotype as the explanatory
variable and the phenotype as the response variable. Other explanatory
variable such as additional sample measures (e.g. age, height, weight)
or batch effects can also be included. For linear mixed models, in
addition to the fixed effects of the genotype and the covariates,
different random effect components can be included, accounting for
population structure in the study cohort or environmental effects. The
application of linear and linear mixed models in quantitative genetics
ranges from genetic studies in model organism such as yeast and
*Arabidopsis thaliana* to human molecular, morphological or imaging
derived traits. Developing new methods for increasing numbers of sample
cohorts, phenotypic measurements or complexity of phenotypes to analyse,
often requires the simulation of datasets with a specific underlying
phenotype structure.

**PhenotypeSimulator** allows for the simulation of complex phenotypes
under different models, including genetic variant effects and
infinitesimal genetic effects (reflecting population structure) as well
as correlated, non-genetic covariates and observational noise effects.
Different phenotypic effects can be combined into a final phenotype
while controlling for the proportion of variance explained by each of
the components. For each component, the number of variables, their
distribution and the design of their effect across traits can be
customised.

Full documentation of **PhenotypeSimulator** is available at
https://HannahVMeyer.github.io/PhenotypeSimulator/.

The current github version of *PhenotypeSimulator* is 0.3.4 and can be
installed via

```
# install.packages("devtools")
devtools::install_github("HannahVMeyer/PhenotypeSimulator")
```

The current CRAN version of *PhenotypeSimulator* is 0.3.4 and can be
installed via:

```
install.packages("PhenotypeSimulator")
```

A log of version changes can be found here.

Meyer, HV & Birney E (2018) PhenotypeSimulator: A comprehensive
framework for simulating multi-trait, multi-locus genotype to phenotype
relationships,
*Bioinformatics*, 34(17):2951–2956

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