Statistical Tests and Graphics for Hardy-Weinberg Equilibrium
Function to compute allele frequencies
Exact test of equality of allele frequencies for males and females
Function to compute X-chromosomal allele frequencies
Calculate allele and genotype counts for X-chromosomal markers
Extract alleles
Calculate triangular genotype matrix for vector(s) of alleles.
Calculate Graffelman-Weir exact density for bi-allelic X-chromosomal v...
Calculate Levene's density for a bi-allelic variant
Calculate Levene's exact density for k alleles
Exact test for equality of allele frequencies in males and females
Fisher's z transformation
Fold a square matrix
Generate genotypic compositions
Label genotype counts of a vector or matrix
Statistical Tests and Graphics for Hardy-Weinberg Equilibrium
Calculate expected heterozygosity (He)
Estimate allele frequencies and test for Hardy-Weinberg equilibrium wi...
Compute Akaike's Information Criterion (AIC) for HWP and EAF models
Perform all tests for Hardy-Weinberg equilibrium
Compute additive log-ratio transformation
Plot genetic markers in additive log-ratio coordinates
Chi square tests for Hardy Weinberg equilibrium
Matrix version of HWChisq
Fast computation of chi-square statistics for Hardy-Weinberg equilibri...
Convert genotype counts to compositions
Compute the centred log-ratio transformation
Plot genetic markers in centred log-ratio coordinates
Compute probability of a genotypic sample
Compute disequilibrium statistic D
Generate genetic marker data in or out of Hardy-Weinberg Equilibrium
Estimation of contributions of two populations to a sample of genotype...
Exact test for Hardy-Weinberg equilibrium
Matrix version of HWExact
Exact test for Hardy-Weinberg equilibrium
Computation of Exact p-values for Hardy-Weinberg equilibrium for sets ...
Computation of inbreeding coefficient
Scatter plot of the genotype frequencies
Compute isometric log ratio coordinates.
Plot bi-allelic genetic markers in isometric log ratio coordinates
Calculate a credible interval for Lindley's alpha for HWE,
Calculate a posteriori density for Lindley's alpha
Perform most relevant likelihood ratio test for Hardy-Weinberg equilib...
Likelihood ratio test for Hardy Weinberg equilibrium
Perform likelihood ratio test comparing two nested scenarios for a bi-...
Test a bi-allelic marker for Hardy-Weinberg equilibrium in the presenc...
Autosomal and X-chromosomal exact tests for HWE via a Network algorith...
Permutation tests fo variants with multiple alleles
Permutation test for Hardy-Weinberg equilibrium
Calculation of posterior probabilities and Bayes factors for Hardy-Wei...
Compute the power of a test for Hardy-Weinberg equilibrium.
A Q-Q plot for Hardy-Weinberg equilibrium
Testing a set of microsatellites (STRs) for Hardy-Weinberg equilibrium
Asymptotic test for HWE across strata for a single biallelic marker
Ternary plot with the Hardy-Weinberg acceptance region
Exact test for Hardy-Weinberg equilibrium and equality of allele frequ...
Inverse Fisher z transformation
Detects autosomal and X-chromosomal monomorphic variants
Compute the minor allele count.
Function to compute minor allele frequencies
Create genotype counts from bi-allelic marker data
Make factors from genotyping data
Number of alleles
Reordering of autosomal genotype counts
Reordering of X-chromosomal genotype counts
Q-Q plot for a uniform distribution.
Recode genotype information
Shannon index
Sort tokens of a set of strings
Convert theta to an inbreeding coefficient
Convert a vector of genotype counts to triangular format
Extract unique genotypic compositions from a matrix
Computes the sample variance of the allele frequency for a biallelic m...
Contains tools for exploring Hardy-Weinberg equilibrium (Hardy, 1908; Weinberg, 1908) for bi and multi-allelic genetic marker data. All classical tests (chi-square, exact, likelihood-ratio and permutation tests) with bi-allelic variants are included in the package, as well as functions for power computation and for the simulation of marker data under equilibrium and disequilibrium. Routines for dealing with markers on the X-chromosome are included (Graffelman & Weir, 2016) <doi:10.1038/hdy.2016.20>, including Bayesian procedures. Some exact and permutation procedures also work with multi-allelic variants. Special test procedures that jointly address Hardy-Weinberg equilibrium and equality of allele frequencies in both sexes are supplied, for the bi and multi-allelic case. Functions for testing equilibrium in the presence of missing data by using multiple imputation are also provided. Implements several graphics for exploring the equilibrium status of a large set of bi-allelic markers: ternary plots with acceptance regions, log-ratio plots and Q-Q plots. The functionality of the package is explained in detail in a related JSS paper <doi:10.18637/jss.v064.i03>.