HWStr: Testing a set of microsatellites (STRs) for Hardy-Weinberg...

In HardyWeinberg: Statistical Tests and Graphics for Hardy-Weinberg Equilibrium

Testing a set of microsatellites (STRs) for Hardy-Weinberg equilibrium

Description

Function HWStr is a wrapper function arount HWPerm.mult and HWChisq in order to test a set of STRs for Hardy-Weinberg equilibrium.

Usage

HWStr(X, test = "permutation", verbose = FALSE, ...)

Arguments

X	A data matrix with STRs in columns, with there two alleles coded in successive columns.
test	permutation for a permutation test, or "chisq" for a chisquare test
verbose	be silent if set to FALSE or print info for each STR if TRUE.
...	possible extra parameters to be passed on to HWPerm.mult such as nperm or eps.

Details

It is recommended to test by a permutation test. By default, 17.000 permutations are used. Exact testing is not implemented. Missing genotypes are excluded on a per STR basis.

Value

A data frame with the

strnames	STR name
N	sample size
Nt	number of alleles
MinorAF	minor allele frequency
MajorAF	major allele frequency
Ho	observed heterozygosity
He	expected heterozygosity (without bias correction)
Hp	Shannon index of allele frequencies
pval	p-value of the HWE test

Author(s)

Jan Graffelman [e-mail]

See Also

HWPerm.mult, HWChisq

Examples

data(NistSTRs)
## Not run: 
Results <- HWStr(NistSTRs,test="permutation")

## End(Not run)

HardyWeinberg documentation built on May 29, 2024, 6:17 a.m.