| 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 |
pop |
a factor giving the population of each individual. If NULL, pop is seeked from x$pop. |
permut |
a logical passed to |
nsim |
number of simulations if Monte Carlo is used (passed to |
hide.NA |
a logical stating whether non-tested loci (e.g., when an allele is fixed) should be hidden in the results (TRUE, default) or not (FALSE). |
res.type |
a character or a character vector whose only first argument is considered giving the type of result to display. If "full", then a list of complete tests is returned. If "matrix", then a matrix of p-values is returned. |
Details
Monte Carlo procedure is quiet computer-intensive when large
datasets are involved. For more precision on the performed test, read
HWE.test documentation (genetics package).
Value
Returns either a list of tests or a matrix of p-values. In the
first case, each test is designated by locus first and then by
population. For instance if res is the "full" output of the
function, then the test for population "PopA" at locus "Myloc" is
given by res$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)