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HybridCheck, an R package for quickly scripting scans of sequence data for recombination regions.
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README.md

HybridCheck

Introduction

HybridCheck is an R package that is intended to make it quick, simple and easy to script analyses scanning for recombination signal between haplotype sequences.

It can plot such scans:

hybridcheck-plot

It also allows you to compute ABBA BABA tests for gene flow and some variants of the ABBA BABA test.

Installation instructions

Installing HybridCheck from GitHub is easy if you have "devtools" installed. If you don't have devtools, fear not, it is easy to acquire.

install.packages("devtools")

Once you have devtools, you can use the install_github function to grab and install HybridCheck.

devtools::install_github("BenJWard/HybridCheck", build_vignettes = TRUE)

Documentation

User manual

HybridCheck comes with a user manual vignette, that you can access from an R session.

Enter:

vignette("HybridCheck-manual")

and hit return. A new window should pop up with the manual inside. It will guide you through loading your sequence data and running an analysis.

API reference documentation

The documentation of each HybridCheck class and method/function can be viewed from within R by typing:

?function_name_here

in the R console.

Test dataset

An example sequence alignment of 10 sequences as a DNAbin object is available in the package to use to test HybridCheck functionality. For more details, see the user manual.

data(MySequences)

Contact

If you would like to contribute to HybridCheck, or want to ask a question or report a bug. You can either use GitHub Issues and Pull Requests in the usual way, or you can contact either of the two maintainers below:

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