R: Hardy-Weinberg Equilibrium test for multilocus data

HWE.test.genind {adegenet} | R Documentation

## Hardy-Weinberg Equilibrium test for multilocus data

### Description

The function `HWE.test` is a generic function to perform Hardy-Weinberg Equilibrium tests defined by the `genetics` package. adegenet proposes a method for `genind` objects.

The output can be of two forms:
- a list of tests (class `htest`) for each locus-population combinaison
- a population x locus matrix containing p-values of the tests

### Usage

    ## S3 method for class 'genind'
    HWE.test(x,pop=NULL,permut=FALSE,nsim=1999,hide.NA=TRUE,res.type=c("full","matrix"))

### Arguments

`x` | an object of class `genind`.
`pop` | a factor giving the population of each individual. If NULL, pop is seeked from x\$pop.
`permut` | a logical passed to `HWE.test` stating whether Monte Carlo version (TRUE) should be used or not (FALSE, default).
`nsim` | number of simulations if Monte Carlo is used (passed to `HWE.test`).
`hide.NA` | a logical stating whether non-tested loci (e.g., when an allele is fixed) should be hidden in the results (TRUE, default) or not (FALSE).
`res.type` | a character or a character vector whose only first argument is considered giving the type of result to display. If "full", then a list of complete tests is returned. If "matrix", then a matrix of p-values is returned.

### Details

Monte Carlo procedure is quiet computer-intensive when large datasets are involved. For more precision on the performed test, read `HWE.test` documentation (`genetics` package).

### Value

Returns either a list of tests or a matrix of p-values. In the first case, each test is designated by locus first and then by population. For instance if `res` is the "full" output of the function, then the test for population "PopA" at locus "Myloc" is given by res$Myloc$PopA. If `res` is a matrix of p-values, populations are in rows and loci in columns. P-values are given for the upper-tail: they correspond to the probability that an oberved chi-square statistic as high as or higher than the one observed occured under H0 (HWE).

In all cases, NA values are likely to appear in fixed loci, or entirely non-typed loci.

### Author(s)

Thibaut Jombart t.jombart@imperial.ac.uk

### See Also

`HWE.test` in the `genetics` package, `chisq.test`

### Examples

    ## Not run:
    data(nancycats)
    obj <- nancycats
    if(require(genetics)){
    obj.test <- HWE.test(obj)

    # pvalues matrix to have a preview
    HWE.test(obj,res.type="matrix")

    #more precise view to...
    obj.test$fca90$P10
    }

    ## End(Not run)

[Package adegenet version 2.1.4 Index]