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README.md

Correlated Trait Locus (CTL) mapping

Build Status CRAN_Status_Badge JOSS DOI

This repository contains the source code for the Correlated Trait Locus (CTL) mapping algorithm. CTL mapping is a novel approach to detect genetic regulation of phenotypes in natural and experimental populations. It is a method which complements classical QTL analysis, providing additional insights overlooked by the classical QTL approach.

Algorithm

Learn more about the algorithm behind CTL mapping. Alternatively, learn more about CTL mapping by following the workshop I presented at the complex traits consortium meeting in Glasgow to demonstrate CTL mapping on an example data set. The presentation and code can be found on my website

Installing the R package from CRAN

The quickest and prefered way to start mapping CTLs, is to install the package directly from CRAN, start R and issue the following command to install the package:

install.packages("ctl")

After installation, load the package by:

library("ctl")

Next thing is to map your first CTL on either example data or your own data. For this see: doc/STARTINGinR.md

Sometimes it is needed to install a develpoment version, since CRAN might take a while to update after a bug is fixed. To learn how to install a development version see: doc/DEVELOPMENT.md

Test

CTL mapping uses the build in R framework to test the package for global regressions and unit-testing of documented functions. Tests can be executed from the commandline, by using the following command:

R CMD check Rctl                    # Run the unit-tests of the R package

Make sure that when running the tests using MS Windows the Rtools package is installed. Rtools for MS Windows can be installed from here

Documentation

A short online introduction is available, or learn by doing by following the workshop on CTL mapping, which can be found here. Additionally almost all R function come with a help files with examples. In R you can access the help using:

library(ctl)                            # Load the library
?ctl                                    # Show the general help for ctl
?CTLscan                                # Show the help for the CTLscan function

Issues

Issues can be raised through the github issue tracker.

Contributing

Want to contribute? Great! We're actively looking for someone to manage the CTL website www.mapctl.org

Contribute to CTL source code by forking the Github repository, and sending us pull requests.

For a list of active developments tasks, see Rctl/inst/TODO.txt

Its also possible to just post comments on code / commits.

Or be a maintainer, and adopt a function

Cite

When this software was helpful, please cite the JOSS paper in your publication: JOSS

When (re-)using the any code or data provided by this package, please also cite: DOI

Citations are also available for import in bibtex format [TODO: bibtex with DOIs].

License

The CTL mapping source code is released under the GNU GENERAL PUBLIC LICENSE Version 3 (GPLv3). See LICENSE.txt.

This software was developed between 2012-2016 at the Groningen Bioinformatics Centre by Danny Arends, Yang Li, Pjotr Prins and Ritsert C. Jansen

Contact

Code managed by Dr. Danny Arends and the Groningen Bioinformatics Centre, Groningen, NLD.