Journal
BIOINFORMATICS
Volume 35, Issue 17, Pages 3194-3195Publisher
OXFORD UNIV PRESS
DOI: 10.1093/bioinformatics/btz030
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Funding
- Max Planck Society
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A Summary: We present a new R package admixr, which provides a convenient interface for performing reproducible population genetic analyses (f(3), D, f(4), f(4)-ratio, qpWave and qpAdm), as implemented by command-line programs in the ADMIXTOOLS software suite. In a traditional ADMIXTOOLS workflow, the user must first generate a set of text configuration files tailored to each individual analysis, often using a combination of shell scripting and manual text editing. The non-tabular output files then need to be parsed to extract values of interest prior to further analyses. Our package simplifies this process by automating all low-level configuration and parsing steps, making analyses as simple as running a single R command. Furthermore, we provide a set of R functions for processing, filtering and manipulating datasets in the EIGENSTRAT format. By unifying all steps of the workflow under a single R framework, this package enables the automation of analytic pipelines, significantly improving the reproducibility of population genetic studies.
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