| af | Function to compute allele frequencies |
| AFtest | Exact test of equality of allele frequencies for males and... |
| afx | Function to compute X-chromosomal allele frequencies |
| agcounts | Calculate allele and genotype counts for X-chromosomal... |
| alleles | Extract alleles |
| AllelesToTriangular | Calculate triangular genotype matrix for vector(s) of... |
| Alzheimer | Genotype frequencies for 70 SNPs related to Alzheimer's... |
| CEUchr22 | Biallelic polymorphisms sampled from chromosome 22 of the CEU... |
| dgraffelmanweir.bi | Calculate Graffelman-Weir exact density for bi-allelic... |
| 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... |
| 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... |
| HardyWeinberg-package | Statistical Tests and Graphics for Hardy-Weinberg Equilibrium |
| he | Calculate expected heterozygosity (He) |
| HWABO | Estimate allele frequencies and test for Hardy-Weinberg... |
| HWAIC | Compute Akaike's Information Criterion (AIC) for HWP and EAF... |
| 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... |
| 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... |
| HWEM | Estimation of contributions of two populations to a sample of... |
| 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... |
| 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... |
| 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... |
| HWLratio | Likelihood ratio test for Hardy Weinberg equilibrium |
| HWLRtest | Perform likelihood ratio test comparing two nested scenarios... |
| HWMissing | Test a bi-allelic marker for Hardy-Weinberg equilibrium in... |
| HWNetwork | Autosomal and X-chromosomal exact tests for HWE via a Network... |
| 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... |
| 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... |
| HWStrata | Asymptotic test for HWE across strata for a single biallelic... |
| HWTernaryPlot | Ternary plot with the Hardy-Weinberg acceptance region |
| HWTriExact | Exact test for Hardy-Weinberg equilibrium and equality of... |
| ifisherz | Inverse Fisher z transformation |
| is.mono | Detects autosomal and X-chromosomal monomorphic variants |
| JPTmultiallelicsChr7 | Multi-allelic autosomal variants of the Japanese population... |
| JPTmultiallelicsChrX | Multi-allelic X-chromosomal variants of the Japanese... |
| JPTsnps | Bi-allelic SNPs from a Japanese population stratified by... |
| JPTtriallelicsChr7 | Tri-allelic variants on chromosome 7 of the Japanese (JPT)... |
| JPTtriallelicsChrX | Tri-allelic variants on the X-chromosome of the Japanese... |
| 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... |
| UniqueGenotypeCounts | Extract unique genotypic compositions from a matrix |
| vaf | Computes the sample variance of the allele frequency for a... |
