main_p3: Estimate allele frequency and double reduction in tetraploids...

In dcgerard/phwelike: Code from Jiang, Ren, and Wu (2021) in Package Form

Estimate allele frequency and double reduction in tetraploids using just homozygosity versus heterozygosity.

Description

This uses just homozygosity versus heterozygosity, as opposed to main_p2(), which uses all genotypes.

Usage

main_p3(nm, oiter = 10)

Arguments

nm	A vector of genotypes. nm[[i]] is the genotype for individual i. This is coded weird, though. You should set 0 = nullplex, 1 = heterozygous, 2 = quadriplex.
oiter	The number of EM iterations to run.

Value

A vector of length 2. The first element is the estimated allele frequency, the second element is the estimated double reduction parameter.

Author(s)

Libo Jiang

References

• Jiang, Libo, Xiangyu Ren, and Rongling Wu. 2021. "Computational Characterization of Double Reduction in Autotetraploid Natural Populations." The Plant Journal 105 (6): 1703–9. doi: 10.1111/tpj.15126

Examples

nm <- sim_p3(c(0.5, 0.1), n = 100)
main_p3(nm = nm)

dcgerard/phwelike documentation built on July 27, 2022, 8:07 a.m.