| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| recode | Recode genotype information |
| 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. |