hw.test: Test of Hardy-Weinberg Equilibrium
| hw.test | R Documentation |
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 |
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)
