Introduction | Graphical representations of a within-set correlation matrix | 1. The corrgram | 2. The correlogram | 3. The PCA biplot of the correlation matrix | 4. The MDS map of a correlation matrix | 5. The PFA biplot of a correlation matrix | 6. The WALS biplot of a correlation matrix | 7. The WALS biplot using a scalar adjustment of the correlation matrix | 8. The WALS biplot using column adjustment of the correlation matrix | Graphical representations of a between-set correlation matrix | References

Introduction | 1. Installation | 2. Logratio principal component analysis (LR-PCA) | 3. Logratio canonical correlation analysys (LR-CCO) | 3.1 Artificial data | 3.2 Canonical analysis of bentonites | 4. Logratio discriminant analysis (LR-LDA) | References

Introduction | 1. Installation | 2. Estimation of Jacquard the coefficients | 3. Estimation of derived relatedness parameters | 4. Alternative estimation procedures | 5. References

Introduction | 1. Installation<a name="introduction"></a> | 2. A single biallelic marker<a name="single"></a> | 2.1. Genotype and allele counts<a name="counts"></a> | 2.2. Testing for Hardy-Weinberg equilibrium<a name="testing"></a> | 2.2.1. Autosomal markers<a name="autosomal"></a> | Chi-square test | LRT test | Exact test | Permutation test | Bayesian procedure | 2.2.2. X-chromosomal markers<a name="xchromosome"></a> | Likelihood ratio test | 2.3. Special topics<a name="special"></a> | 2.3.1. Missing genotype data<a name="missing"></a> | 2.3.2. Power computation<a name="power"></a> | 2.3.3. Population substructure<a name="substructure"></a> | Testing across strata | Contributions in mixed samples | 2.3.4 Scenario testing under stratification by gender<a name="scenario"></a> | 3. Sets of biallelic markers<a name="setsbiallelic"></a> | 3.1. Genotype count patterns<a name="patterns"></a> | 3.2. Testing HWE with many variants<a name="manybiallelics"></a> | 3.3. Visualising HWE test results<a name="visualising"></a> | 3.3.1. Ternary diagrams<a name="ternary"></a> | 3.3.2. QQ plots<a name="qqplot"></a> | 3.4. Simulating biallelic marker data<a name="simulating"></a> | 4. Multiallelic markers<a name="multiallelic"></a> | 4.1. Triallelic variants<a name="triallelic"></a> | The ABO locus | Triallelic variants | 4.2. Microsatellites (STRs)<a name="microsatellites"></a> | References

Introduction | Installation | Calibration of Scatterplot axes | Calibration of Biplot axes | Online documentation | Version history