guokai8 / rtomahawk

R-bindings for interfacing with Tomahawk: computing and visualising linkage-disequilibrium data

rtomahawk

This package provides native R-bindings for interfacing with Tomahawk libraries and provides additional graphical functionality. This means exposing most of the features and flexibility of the C++ API while not sacrificing the usability that R provides.

GWAS plots	Dense LD data	Square LD data

Get started

• Read the documentation

Requirements

• Your processor should support SSE4.2 (It is supported by most Intel and AMD processors released since 2008.)
• C++11 compliant compiler (GCC is assumed)
• A Linux-like distribution is assumed by the makefile

Installation

For Ubuntu, Debian, and Mac systems, installation is easy: just run

git clone --recursive https://github.com/mklarqvist/rtomahawk
R CMD INSTALL rtomahawk

or in R

install.packages(path_to_rtomahawk, repos = NULL, type="source")

or alternatively

library(devtools)
install_github("mklarqvist/rtomahawk")

Check that the package can be loaded and list the built libraries (in R):

library(rtomahawk)
tomahawkVersion()

This will print a version string to the console:

rtomahawk: 0.1.1
Libraries: tomahawk-0.7.1; ZSTD-1.3.1; htslib 1.9

Contributing

Interested in contributing? Fork and submit a pull request and it will be reviewed.

Support

We are actively developing Tomahawk and are always interested in improving its quality. If you run into an issue, please report the problem on our Issue tracker. Be sure to add enough detail to your report that we can reproduce the problem and address it. We have not reached version 1.0 and as such the function names may change.

Version

This is rtomahawk 0.1.1. rtomahawk follows semantic versioning.

Author

Marcus D. R. Klarqvist ([e-mail])
Department of Genetics, University of Cambridge
Wellcome Sanger Institute

License

rtomahawk is licensed under MIT
tomahawk is licensed under MIT