README.md
In segtest: Tests for Segregation Distortion in Polyploids

segtest

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:

seg_multi(): Run the likelihood ratio test for segregation distortion in parallel at many loci.
multidog_to_g: Format the genotyping output from updog::multidog() to be compatible with the input of seg_multi().
seg_lrt(): Test for segregation distortion for any even ploidy.
gamfreq(): Gamete frequencies.
gf_freq(): Genotype frequencies of an F1 population of polyploids.
drbounds(): Upper bounds on the double reduction rate(s) based on two different extreme models of meiosis.
simgl(): Simulate genotype log-likelihoods given a vector of genotype counts.

Older functions that are only applicable to tetraploids are:

multi_lrt(): Run any of the tetraploid likelihood ratio tests for segregation distortion in parallel across many SNPs.
lrt_men_g4(): Tetraploid likelihood ratio test for segregation distortion using known genotypes.
lrt_men_gl4(): Tetraploid likelihood ratio test for segregation distortion using genotype likelihoods.
offspring_gf_2(): Tetraploid offspring genotype frequencies under the two parameter model of meiosis.
offspring_gf_3(): Tetraploid offspring genotype frequencies under the three parameter model of meiosis.
simf1g(): Simulate genotypes from an F1 population of tetraploids.
simf1gl(): Simulate genotype likelihoods from an F1 population of tetraploids.

We also provide some functions from “competing” methods:

polymapr_test(): Test from polymapR.
chisq_g4(): Chi-squared test (not accounting for double reduction and preferential pairing) when genotypes are known.
chisq_gl4(): Chi-squared test (not accounting for double reduction and preferential pairing) using genotype likelihoods.

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

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")

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.

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

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