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admixr-R package for reproducible analyses using ADMIXTOOLS.

Martin Petr1, Benjamin Vernot1, Janet Kelso1

  • 1Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.

Bioinformatics (Oxford, England)
|January 23, 2019
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Summary
This summary is machine-generated.

The admixr R package streamlines population genetic analyses by automating ADMIXTOOLS workflows. This enhances reproducibility and simplifies complex analyses for researchers.

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Area of Science:

  • Population Genetics
  • Bioinformatics
  • Computational Biology

Background:

  • Traditional ADMIXTOOLS workflows require manual configuration file generation and output parsing.
  • This process is often complex, time-consuming, and prone to errors, hindering reproducibility.

Purpose of the Study:

  • To introduce admixr, an R package simplifying population genetic analyses.
  • To automate ADMIXTOOLS workflows, enhancing reproducibility and accessibility for researchers.

Main Methods:

  • Developed an R package, admixr, providing a unified interface for ADMIXTOOLS.
  • Automated configuration file generation and output parsing for population genetic analyses.
  • Included functions for processing and manipulating EIGENSTRAT format datasets.

Main Results:

  • admixr simplifies complex analyses (f3, D, f4, f4-ratio, qpWave, qpAdm) into single R commands.
  • The package automates low-level steps, reducing manual effort and potential errors.
  • Facilitates the creation of automated analytic pipelines for improved reproducibility.

Conclusions:

  • admixr significantly enhances the reproducibility of population genetic studies.
  • The package lowers the barrier to entry for complex population genetic analyses.
  • Provides a robust framework for automated, reproducible population genetic research.