segtest

CRAN status NSF-2132247 License: GPL v3 R-CMD-check Codecov test coverage

Provides a suite of tests for segregation distortion for F1 populations of polyploids under various models of meiosis. You can use these tests for autopolyploids that exhibit full polysomic inheritance, allopolyploids that exhibit full disomic inheritance, or segmental allopolyploids that exhibit partial preferential pairing. Double reduction is (optionally) fully accounted for in tetraploids, and (optionally) partially accounted for (only at simplex loci) for higher ploidies. Some maximum proportion of outliers can be specified, and so these methods can accommodate moderate levels of double reduction at non-simplex loci. Offspring genotypes can either be known, or genotype uncertainty can be represented through genotype likelihoods. Parent data may or may not be provided, at your option. Parents can have different (even) ploidies, at your option.

This package only contains likelihood ratio and chi-squared tests. See the menbayes package for Bayesian tests for tetraploids.

The main functions are:

Older functions that are only applicable to tetraploids are:

We also provide some functions from “competing” methods:

Details of these methods may be found in Gerard et al. (2025a) and Gerard et al. (2025b).

Installation

You can install the stable version of segtest from CRAN with:

install.packages("segtest")

You can install the development version of segtest from GitHub with:

# install.packages("pak")
pak::pak("github::dcgerard/segtest")

Code of Conduct

Please note that the segtest project is released with a Contributor Code of Conduct. By contributing to this project, you agree to abide by its terms.

References

Gerard D, Thakkar M, & Ferrão LFV (2025a). “Tests for segregation distortion in tetraploid F1 populations.” Theoretical and Applied Genetics, 138(30), p. 1–13. doi:10.1007/s00122-025-04816-z.

Gerard, D, Ambrosano, GB, Pereira, GdS, & Garcia, AAF (2025b). “Tests for segregation distortion in higher ploidy F1 populations.” bioRxiv, p. 1–20. bioRxiv:2025.06.23.661114

Acknowledgments

Part of this material is based upon work supported by the National Science Foundation under Grant No. 2132247.

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