dartR: utils.prob.hwe – R documentation

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utils.prob.hwe

Exact SNP test of Hardy-Weinberg Equilibrium

Description

This code calculates an exact probability of departure from Hardy-Weinberg Equilibrium as described in Wigginton, JE, Cutler, DJ, and Abecasis, GR (2005) A Note on Exact Tests of Hardy-Weinberg Equilibrium. American Journal of Human Genetics. 76:887-893.

Usage

utils.prob.hwe(obs_hets, obs_hom1, obs_hom2)

Arguments

`obs_hets`	– count of heterozygotes by locus
`obs_hom1`	– count of homozygotes, reference state
`obs_hom2`	– count of homozygotes, alternate state

Details

Note: return code of -1.0 signals an error condition; return code of NA signals that all alleles are NA for a locus

Value

Exact probability of agreement with HWE

Author(s)

Arthur Georges (Post to https://groups.google.com/d/forum/dartr)

Examples

hets <- 20
hom_1 <- 5
hom_2 <- 30
#p_value <- prob.hwe(hets, hom_1, hom_2)

dartR

Importing and Analysing SNP and Silicodart Data Generated by Genome-Wide Restriction Fragment Analysis

v1.9.6

GPL-2

Authors

Bernd Gruber [aut, cre], Arthur Georges [aut], Jose L. Mijangos [aut], Peter J. Unmack [ctb], Oliver Berry [ctb], Lindsay V. Clark [ctb], Floriaan Devloo-Delva [ctb]

Initial release

2021-04-29