##
PhenotypeSimulator

**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.

##
Installation

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 0.3.3 and
can be installed via:

`install.packages("PhenotypeSimulator")`

A log of version changes can be found here.

##
Citation

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