zalpha

R package for the zalpha suite of selection statistics. This package allows the user to run a suite of selection statistics over genomic data. The aim is to identify regions of the genome which have experienced a selective sweep.

Installing

Version 0.3.0 is on CRAN.

To install this package from CRAN:

install.packages("zalpha")

To install the development version of this package from github:

1. Install the devtools package

install.packages("devtools")

2. Load the devtools package

library(devtools)

3. Install the zalpha package direct from Github using the install_github function

install_github("chorscroft/zalpha")

How to use the zalpha package

For a full explanation of how to use the zalpha package, please see the "zalpha" vignette.

browseVignettes("zalpha")
# or
vignette("zalpha")

If this does not work and you installed the packages directly from Github, try installing using the following code:

install_github("chorscroft/zalpha", build_vignettes=TRUE)  # might also have to include the option force=TRUE if the package is already installed

Dependencies

This package requires R version 2.10 or higher.

Optional packages:

• fitdistrplus

Authors

• Clare Horscroft

Acknowledgments

Guy Jacobs for the original development of the Zalpha statistics

Citation

If you use the zalpha package in your work, please cite the following paper:

Horscroft et al., (2020). zalpha: an R package for the identification of regions of the genome under selection. Journal of Open Source Software, 5(56), 2638, https://doi.org/10.21105/joss.02638

Community Guidelines

I am very open to feedback, bug reports and requests!

• If you have a bug to report or a new feature request, please create a new issue on GitHub.

• If you would like to contribute, please feel free to fork the project and create a pull request on GitHub. A guide to how this works can be found here.

• If you have any other feedback or need support, please email the author.