hwep

Hardy-Weinberg Equilibrium in Polyploids

https://github.com/dcgerard/hwep

Repository

Hardy-Weinberg Equilibrium in Polyploids

README.Rmd

---
output: github_document
---



```{r, include = FALSE}
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.path = "man/figures/README-",
  out.width = "100%"
)
```

# hwep 


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Inference concerning equilibrium and random mating in autopolyploids. Methods are available to test for equilibrium and random mating at any even ploidy level (>2) in the presence of double reduction at biallelic loci. For autopolyploid populations in equilibrium, methods are available to estimate the degree of double reduction. We also provide functions to calculate genotype frequencies at equilibrium, or after one or several rounds of random mating, given rates of double reduction. For details of these methods, see Gerard (2023a) \<[doi:10.1111/biom.13722](https://doi.org/10.1111/biom.13722)\> and Gerard (2023b) \<[doi:10.1111/1755-0998.13856](https://doi.org/10.1111/1755-0998.13856)\>.

The main functions for inference are:

- `hwefit()`: Fit either `hwelike()`,`rmlike()`, `hweustat()`, 
  `hwenodr()`, or `hweboot()` across many loci. Parallelization is supported through the 
  [future](https://cran.r-project.org/package=future) package.
  
- `hwelike()`: Likelihood inference for equilibrium.
  This function estimates the rate of double reduction given
  equilibrium, and tests for at most small deviations from
  equilibrium.
  
- `rmlike()`: Likelihood inference for random mating in polyploids. 
  This function tests for random mating and estimates gametic frequencies 
  given random mating. This function does not assume a model for meiosis.
  
- `hweustat()`: U-statistic approach for equilibrium and double reduction. 
   This function tests for equilibrium given double reduction rates and 
   estimates these rates given equilibrium.
   
- `hwenodr()`: Implements a likelihood ratio test that tests for Hardy-Weinberg 
  equilibrium in autopolyploids given no double reduction.

- `hweboot()`: Implements a bootstrap approach to test for equilibrium
  which is more appropriate for small samples and uncertain genotypes.
  
- `rmbayes()`: Implements a Bayesian test for random mating in autopolyploids
  for any ploidy level.
  
- `rmbayesgl()`: Bayesian test for random mating, accounting for genotype
  uncertainty using genotype likelihoods.
  
- `menbayesgl()`: Bayesian test for Mendelian segregation frequencies in
  S1 or F1 populations using genotype likelihoods.

Functions are provided for calculating genotype frequencies for individuals and gametes:

- `gsegmat()`: Produces the segregation probabilities for gamete dosages given parental dosages and the double reduction rate.

- `gsegmat_symb()`: Provides a symbolic representation of the output of `gsegmat()`.

- `zsegarray()`: Obtains offspring genotype probabilities given parental probabilities, the ploidy of the species, and the overdispersion parameter, for all possible parental genotypes.

- `freqnext()`: Updates the genotype frequencies after one generation of random mating.

- `hwefreq()`: Calculate genotype frequencies at equilibrium.

The bounds on the double reduction rate under the complete equational segregation model are provided by `drbounds()`.

Functions for evaluating the uniformity of p-values are provided in `ts_bands()` and `qqpvalue()`.

## Installation

You can install the released version of hwep from [CRAN](https://cran.r-project.org/package=hwep) with:

```{r, eval = FALSE}
install.packages("hwep")
```

You can install the development version from [GitHub](https://github.com/dcgerard/hwep) with:

```{r, eval = FALSE}
# install.packages("devtools")
devtools::install_github("dcgerard/hwep")
```

## Citation

To cite hwep in publications use:

> Gerard D (2023). "Double reduction estimation and equilibrium tests in natural autopolyploid populations." _Biometrics_, *79*(3), 2143--2156. [doi:10.1111/biom.13722](https://doi.org/10.1111/biom.13722).

A BibTeX entry for LaTeX users is

``` tex
@Article{,
  title = {Double reduction estimation and equilibrium tests in natural autopolyploid populations},
  author = {David Gerard},
  journal = {Biometrics},
  year = {2023},
  doi = {10.1111/biom.13722},
  volume = {79},
  number = {3},
  pages = {2143--2156},
}
```

If you use `rmbayes()`, `rmbayesgl()`, or `menbayeslg()`, then please also cite

> Gerard D (2023). "Bayesian tests for random mating in polyploids." _Molecular Ecology Resources_, *23*(8), 1812--1822. [doi:10.1111/1755-0998.13856](https://doi.org/10.1111/1755-0998.13856).

A BibTeX entry for LaTeX users is

``` tex
@Article{,
  title = {Bayesian Tests for Random Mating in Polyploids},
  author = {David Gerard},
  journal = {Molecular Ecology Resources},
  year = {2023},
  doi = {10.1111/1755-0998.13856},
  volume = {23},
  number = {8},
  pages = {1812--1822}
}
```

## Acknowledgments

This material is based upon work supported by the National Science Foundation under Grant No. [2132247](https://www.nsf.gov/awardsearch/showAward?AWD_ID=2132247). The opinions, findings, and conclusions or recommendations expressed are those of the author and do not necessarily reflect the views of the National Science Foundation.

## Code of Conduct

Please note that the hwep project is released with a [Contributor Code of Conduct](https://contributor-covenant.org/version/2/0/CODE_OF_CONDUCT.html). By contributing to this project, you agree to abide by its terms.

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