admixr—R package for reproducible analyses using ADMIXTOOLS

• DOI: 10.1093/bioinformatics/btz030
• Publication Date: 2019-01-17T12:09:41Z
• Authors: Martin Petr; Benjamin Vernot; Janet Kelso
• Keywords: R package; Interface (matter); MIT License

We present a new R package admixr, which provides convenient interface for performing reproducible population genetic analyses (f3, D, f4, f4-ratio, qpWave and qpAdm), as implemented by command-line programs in the ADMIXTOOLS software suite. In traditional workflow, user must first generate set of text configuration files tailored to each individual analysis, often using combination shell scripting manual editing. The non-tabular output then need be parsed extract values interest prior further analyses. Our simplifies this process automating all low-level parsing steps, making simple running single command. Furthermore, we provide functions processing, filtering manipulating datasets EIGENSTRAT format. By unifying steps workflow under framework, enables automation analytic pipelines, significantly improving reproducibility studies.The source code is available MIT license. Installation instructions, reference tutorial can found on website at https://bioinf.eva.mpg.de/admixr.Supplementary data are Bioinformatics online.