pegas: hw.test – R documentation

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hw.test

Test of Hardy–Weinberg Equilibrium

Description

This function tests, for a series of loci, the hypothesis that genotype frequencies follow the Hardy–Weinberg equilibrium. hw.test is a generic with methods for the classes "loci" and genind. Note that the latter replaces HWE.test.genind in the adegenet package.

Usage

hw.test(x, B = 1000, ...)
## S3 method for class 'loci'
hw.test(x, B = 1000, ...)
## S3 method for class 'genind'
hw.test(x, B = 1000, ...)

Arguments

`x`	an object of class `"loci"` or genind.
`B`	the number of replicates for the Monte Carlo procedure; for the regular HW test, set B = 0 (see details).
`...`	further arguments to be passed.

Details

This test can be performed with any level of ploidy. Two versions of the test are available: the classical chi^2-test based on the expected genotype frequencies calculated from the allelic frequencies, and an exact test based on Monte Carlo permutations of alleles (Guo and Thompson 1992). For the moment, the latter version is available only for diploids. Set B = 0 if you want to skip the second test.

Value

A matrix with three or four columns with the chi^2-value, the number of degrees of freedom, the associated P-value, and possibly the P-value from the Monte Carlo test. The rows of this matrix are the different loci in x.

Author(s)

Main code by Emmanuel Paradis; wrapper for genind objects by Thibaut Jombart.

References

Guo, S. W. and Thompson, E. A. (1992) Performing the exact test of Hardy–Weinberg proportion for multiple alleles. Biometrics, 48, 361–372.

Examples

## Not run: 
require(adegenet)

## load data
data(nancycats)

## test on genind object, no permutation
hw.test(nancycats, B=0)

## test on loci object
x <- as.loci(nancycats)
hw.test(x)

## End(Not run)
data(jaguar)
hw.test(jaguar)

pegas

Population and Evolutionary Genetics Analysis System

v1.0

GPL (>= 2)

Authors

Emmanuel Paradis [aut, cre, cph] (<https://orcid.org/0000-0003-3092-2199>), Thibaut Jombart [aut, cph] (<https://orcid.org/0000-0003-2226-8692>), Zhian N. Kamvar [aut, cph] (<https://orcid.org/0000-0003-1458-7108>), Brian Knaus [aut, cph] (<https://orcid.org/0000-0003-1665-4343>), Klaus Schliep [aut, cph] (<https://orcid.org/0000-0003-2941-0161>), Alastair Potts [aut, cph] (<https://orcid.org/0000-0003-0919-7279>), David Winter [aut, cph] (<https://orcid.org/0000-0002-6165-0029>)

Initial release

2021-04-08