admixr—interactive R interface for ADMIXTOOLS

What is admixr?

The admixr package provides a convenient R interface to ADMIXTOOLS, a widely used software package for calculating admixture statistics and testing population admixture hypotheses.

A typical ADMIXTOOLS workflow often involves a combination of sed/awk/shell scripting and manual editing to create different configuration files. These are then passed as command-line arguments to one of ADMIXTOOLS commands, and control how to run a particular analysis. The results of such computation are then usually redirected to another file, which needs to be parsed by the user to extract values of interest, often using command-line utilities again or by manual copy-pasting, and finally analysed in R, Excel or another program.

This workflow can be a little cumbersome, especially if one wants to explore many hypotheses involving different combinations of populations or data filtering strategies. Most importantly, it makes it difficult to follow the rules of best practice for reproducible science, especially given the need for manual intervention on the command-line or custom shell scripting to orchestrate more complex pipelines.

admixr makes it possible to perform all stages of an ADMIXTOOLS analysis entirely from R. It provides a set of convenient functions that completely remove the need for "low-level" configuration of individual ADMIXTOOLS programs, allowing users to focus on the analysis itself.

How to cite

admixr is now published as an Application Note in the journal Bioinformatics. If you use it in your work, please cite the paper! You will join an excellent company of papers who have used it to do amazing research.