ABO1KG                  Predicted ABO genotypes for the Expanded 1000
                        Genomes Project cohort
AFtest                  Exact test of equality of allele frequencies
                        for males and females
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.
EAFExact                Exact test for equality of allele frequencies
                        in males and females
GenerateSamples         Generate genotypic compositions
Glyoxalase              Glyoxalase genotype data
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
HWBalance               Compositional Statistic and Test for
                        Hardy-Weinberg equilibrium
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
HWGenotypePlot          Scatter plot of the genotype frequencies
HWIlr                   Compute isometric log ratio coordinates.
HWIlrPlot               Plot bi-allelic genetic markers in isometric
                        log ratio coordinates
HWLRAllTests            Perform most relevant likelihood ratio test for
                        Hardy-Weinberg equilibrium and equality of
                        allele frequencies
HWLRtest                Perform likelihood ratio test comparing two
                        nested scenarios for a bi-allelic genetic
                        variant, distinguishing the two sexes.
HWLindley               Calculate a posteriori density for Lindley's
                        alpha
HWLindley.cri           Calculate a credible interval for Lindley's
                        alpha for HWE,
HWLratio                Likelihood ratio test for Hardy Weinberg
                        equilibrium
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
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.
HWf                     Computation of inbreeding coefficient
HapMapCHBChr1           Genotype frequencies for 225 SNPs on chromosome
                        1 of the CHB population.
HardyWeinberg-package   Statistical Tests and Graphics for
                        Hardy-Weinberg Equilibrium
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
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
NistSTRs                NIST autosomal STR data
TSIXTriAllelics         Tri-allelic polymorphisms on the X chromosome
                        of the TSI population
ThetatoF                Convert theta to an inbreeding coefficient
UniqueGenotypeCounts    Extract unique genotypic compositions from a
                        matrix
af                      Function to compute allele frequencies
afx                     Function to compute X-chromosomal allele
                        frequencies
agcounts                Calculate allele and genotype counts for
                        X-chromosomal markers
alleles                 Extract alleles
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
fisherz                 Fisher's z transformation
fold                    Fold a square matrix
genlabels               Label genotype counts of a vector or matrix
he                      Calculate expected heterozygosity (He)
ifisherz                Inverse Fisher z transformation
is.mono                 Detects autosomal and X-chromosomal monomorphic
                        variants
mac                     Compute the minor allele count.
maf                     Function to compute minor allele frequencies
n.alleles               Number of alleles
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
toTriangular            Convert a vector of genotype counts to
                        triangular format
vaf                     Computes the sample variance of the allele
                        frequency for a biallelic marker.
