# Statistical Tests and Graphics for Hardy-Weinberg Equilibrium

## Documentation for package ‘HardyWeinberg’ version 1.7.8

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

HardyWeinberg-package | Statistical Tests and Graphics for Hardy-Weinberg Equilibrium
af | Function to compute allele frequencies
AFtest | Exact test of equality of allele frequencies for males and females
afx | Function to compute X-chromosomal allele frequencies
agcounts | Calculate allele and genotype counts for X-chromosomal markers
alleles | Extract alleles
AllelesToTriangular | Calculate triangular genotype matrix for vector(s) of alleles.
Alzheimer | Genotype frequencies for 70 SNPs related to Alzheimer's disease
CEUchr22 | Biallelic polymorphisms sampled from chromosome 22 of the CEU population of the 1000 Genomes project.
dgraffelmanweir.bi | Calculate Graffelman-Weir exact density for bi-allelic X-chromosomal variant
dlevene | Calculate Levene's exact density for k alleles
dlevene.bi | Calculate Levene's density for a bi-allelic variant
EAFExact | Exact test for equality of allele frequencies in males and females
fisherz | Fisher's z transformation
fold | Fold a square matrix
GenerateSamples | Generate genotypic compositions
genlabels | Label genotype counts of a vector or matrix
Glyoxalase | Glyoxalase genotype data
HapMapCHBChr1 | Genotype frequencies for 225 SNPs on chromosome 1 of the CHB population.
HardyWeinberg | Statistical Tests and Graphics for Hardy-Weinberg Equilibrium
he | Calculate expected heterozygosity (He)
HWABO | Estimate allele frequencies and test for Hardy-Weinberg equilibrium with a tri-allelic ABO system.
HWAIC | Compute Akaike's Information Criterion (AIC) for HWP and EAF models
HWAlltests | Perform all tests for Hardy-Weinberg equilibrium
HWAlr | Compute additive log-ratio transformation
HWAlrPlot | Plot genetic markers in additive log-ratio coordinates
HWChisq | Chi square tests for Hardy Weinberg equilibrium
HWChisqMat | Matrix version of HWChisq
HWChisqStats | Fast computation of chi-square statistics for Hardy-Weinberg equilibrium
HWClo | Convert genotype counts to compositions
HWClr | Compute the centred log-ratio transformation
HWClrPlot | Plot genetic markers in centred log-ratio coordinates
HWCondProbAB | Compute probability of a genotypic sample
HWD | Compute disequilibrium statistic D
HWData | Generate genetic marker data in or out of Hardy-Weinberg Equilibrium
HWEM | Estimation of contributions of two populations to a sample of genotype frequencies with the EM algorithm.
HWExact | Exact test for Hardy-Weinberg equilibrium
HWExactMat | Matrix version of HWExact
HWExactPrevious | Exact test for Hardy-Weinberg equilibrium
HWExactStats | Computation of Exact p-values for Hardy-Weinberg equilibrium for sets of SNPs
HWf | Computation of inbreeding coefficient
HWGenotypePlot | Scatter plot of the genotype frequencies
HWIlr | Compute isometric log ratio coordinates.
HWIlrPlot | Plot bi-allelic genetic markers in isometric log ratio coordinates
HWLindley | Calculate a posteriori density for Lindley's alpha
HWLindley.cri | Calculate a credible interval for Lindley's alpha for HWE,
HWLRAllTests | Perform most relevant likelihood ratio test for Hardy-Weinberg equilibrium and equality of allele frequencies
HWLratio | Likelihood ratio test for Hardy Weinberg equilibrium
HWLRtest | Perform likelihood ratio test comparing two nested scenarios for a bi-allelic genetic variant, distinguishing the two sexes.
HWMissing | Test a bi-allelic marker for Hardy-Weinberg equilibrium in the presence of missing genotype information.
HWNetwork | Autosomal and X-chromosomal exact tests for HWE via a Network algorithm
HWPerm | Permutation test for Hardy-Weinberg equilibrium
HWPerm.mult | Permutation tests fo variants with multiple alleles
HWPosterior | Calculation of posterior probabilities and Bayes factors for Hardy-Weinberg tests at X-chromosomal variants.
HWPower | Compute the power of a test for Hardy-Weinberg equilibrium.
HWQQplot | A Q-Q plot for Hardy-Weinberg equilibrium
HWQqplot | A Q-Q plot for Hardy-Weinberg equilibrium
HWStr | Testing a set of microsatellites (STRs) for Hardy-Weinberg equilibrium
HWStrata | Asymptotic test for HWE across strata for a single biallelic marker
HWTernaryPlot | Ternary plot with the Hardy-Weinberg acceptance region
HWTriExact | Exact test for Hardy-Weinberg equilibrium and equality of allele frequencies for tri-allelic variants.
ifisherz | Inverse Fisher z transformation
is.mono | Detects autosomal and X-chromosomal monomorphic variants
JPTmultiallelicsChr7 | Multi-allelic autosomal variants of the Japanese population of the 1000 genomes project
JPTmultiallelicsChrX | Multi-allelic X-chromosomal variants of the Japanese population of the 1000 genomes project
JPTsnps | Bi-allelic SNPs from a Japanese population stratified by gender
JPTtriallelicsChr7 | Tri-allelic variants on chromosome 7 of the Japanese (JPT) sample of the 1000 genomes project
JPTtriallelicsChrX | Tri-allelic variants on the X-chromosome of the Japanese (JPT) sample of the 1000 genomes project
mac | Compute the minor allele count.
maf | Function to compute minor allele frequencies
MakeCounts | Create genotype counts from bi-allelic marker data
MakeFactor | Make factors from genotyping data
Markers | SNP data and intensities
Mourant | Genotype frequencies for blood group locus MN
n.alleles | Number of alleles
NistSTRs | NIST autosomal STR data
order.auto | Reordering of autosomal genotype counts
order.x | Reordering of X-chromosomal genotype counts
qqunif | Q-Q plot for a uniform distribution.
recode | Recode genotype information
shannon | Shannon index
strsort | Sort tokens of a set of strings
ThetatoF | Convert theta to an inbreeding coefficient
toTriangular | Convert a vector of genotype counts to triangular format
TSIXTriAllelics | Tri-allelic polymorphisms on the X chromosome of the TSI population
UniqueGenotypeCounts | Extract unique genotypic compositions from a matrix
vaf | Computes the sample variance of the allele frequency for a biallelic marker.