hwep-package: Hardy-Weinberg Equilibrium in Polyploids
In hwep: Hardy-Weinberg Equilibrium in Polyploids

hwep-package

R Documentation

Hardy-Weinberg Equilibrium in Polyploids

Description

Inference concerning equilibrium and random mating in autopolyploids. Methods are available to test for equilibrium and random mating at any even ploidy level (>2) in the presence of double reduction. For autopolyploid populations in equilibrium, methods are available to estimate the degree of double reduction. We also provide functions to calculate genotype frequencies at equilibrium, or after one or several rounds of random mating, given rates of double reduction. This material is based upon work supported by the National Science Foundation under Grant No. 2132247. The opinions, findings, and conclusions or recommendations expressed are those of the author and do not necessarily reflect the views of the National Science Foundation. For details of these methods, see see Gerard (2022a) \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1111/biom.13722")} and Gerard (2022b) \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1101/2022.08.11.503635")}.

Main Functions

hwefit(): Fit either hwelike(), rmlike(), hweustat(), or hwenodr() across many loci. Parallelization is supported through the future package.
hwelike(): Likelihood inference for equilibrium. This function estimates the rate of double reduction given equilibrium, and tests for at most small deviations from equilibrium.
rmlike(): Likelihood inference for random mating in polyploids. This function tests for random mating and estimates gametic frequencies given random mating. This function does not assume a model for meiosis.
hweustat(): U-statistic approach for equilibrium and double reduction. This function tests for equilibrium given double reduction rates and estimates these rates given equilibrium.
hwenodr(): Implements a likelihood ratio test that tests for equilibrium in autopolyploids given no double reduction.
hweboot(): Implements a bootstrap approach to test for equilibrium which is more appropriate for small samples and uncertain genotypes.

Other Functions

dgamete(): Gamete dosage probability given parental dosage.
drbounds(): Upper bounds on the rates of double reduction given the complete equational segregation model.
freqnext(): Update genotype frequencies after one generation of random mating.
gsegmat(): Gamete dosage probabilities for all possible parental dosages.
hwefreq(): Generate equilibrium genotype frequencies.
p_from_alpha(): Obtain gamete frequencies from the major allele frequency and double reduction rates.
zsegarray(): All zygote dosage distributions given all possible parental dosages.
zygdist(): Zygote dosage distribution given one pair of parental dosages.