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HardyWeinberg (version 1.7.8)

Statistical Tests and Graphics for Hardy-Weinberg Equilibrium

Description

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) , 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 .

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Version

Install

install.packages('HardyWeinberg')

Monthly Downloads

3,832

Version

1.7.8

License

GPL (>= 2)

Homepage

https://www.r-project.org

Maintainer

Jan Graffelman

Last Published

April 6th, 2024

Functions in HardyWeinberg (1.7.8)

Plot bi-allelic genetic markers in isometric log ratio coordinates

Plot genetic markers in additive log-ratio coordinates

Perform most relevant likelihood ratio test for Hardy-Weinberg equilibrium and equality of allele frequencies

HWExactPrevious

Exact test for Hardy-Weinberg equilibrium

Computation of Exact p-values for Hardy-Weinberg equilibrium for sets of SNPs

Calculation of posterior probabilities and Bayes factors for Hardy-Weinberg tests at X-chromosomal variants.

Estimation of contributions of two populations to a sample of genotype frequencies with the EM algorithm.

Test a bi-allelic marker for Hardy-Weinberg equilibrium in the presence of missing genotype information.

Autosomal and X-chromosomal exact tests for HWE via a Network algorithm

Calculate a posteriori density for Lindley's alpha

Perform likelihood ratio test comparing two nested scenarios for a bi-allelic genetic variant, distinguishing the two sexes.

Generate genetic marker data in or out of Hardy-Weinberg Equilibrium

Compute the power of a test for Hardy-Weinberg equilibrium.

Matrix version of HWExact

Compute isometric log ratio coordinates.

JPTmultiallelicsChr7

Multi-allelic autosomal variants of the Japanese population of the 1000 genomes project

Likelihood ratio test for Hardy Weinberg equilibrium

Calculate a credible interval for Lindley's alpha for HWE,

Permutation tests fo variants with multiple alleles

TSIXTriAllelics

Tri-allelic polymorphisms on the X chromosome of the TSI population

Testing a set of microsatellites (STRs) for Hardy-Weinberg equilibrium

JPTmultiallelicsChrX

Multi-allelic X-chromosomal variants of the Japanese population of the 1000 genomes project

Asymptotic test for HWE across strata for a single biallelic marker

A Q-Q plot for Hardy-Weinberg equilibrium

Computation of inbreeding coefficient

Scatter plot of the genotype frequencies

Permutation test for Hardy-Weinberg equilibrium

Genotype frequencies for blood group locus MN

Exact test for Hardy-Weinberg equilibrium

Exact test for Hardy-Weinberg equilibrium and equality of allele frequencies for tri-allelic variants.

Convert theta to an inbreeding coefficient

Calculate expected heterozygosity (He)

Calculate Levene's exact density for k alleles

Calculate Levene's density for a bi-allelic variant

Ternary plot with the Hardy-Weinberg acceptance region

Create genotype counts from bi-allelic marker data

Inverse Fisher z transformation

Label genotype counts of a vector or matrix

JPTtriallelicsChrX

Tri-allelic variants on the X-chromosome of the Japanese (JPT) sample of the 1000 genomes project

NIST autosomal STR data

Sort tokens of a set of strings

Convert a vector of genotype counts to triangular format

Detects autosomal and X-chromosomal monomorphic variants

Computes the sample variance of the allele frequency for a biallelic marker.

Make factors from genotyping data

SNP data and intensities

UniqueGenotypeCounts

Extract unique genotypic compositions from a matrix

Function to compute allele frequencies

Recode genotype information

Fisher's z transformation

Function to compute minor allele frequencies

Compute the minor allele count.

Fold a square matrix

Function to compute X-chromosomal allele frequencies

Bi-allelic SNPs from a Japanese population stratified by gender

HardyWeinberg-package

Statistical Tests and Graphics for Hardy-Weinberg Equilibrium

Reordering of X-chromosomal genotype counts

Genotype frequencies for 225 SNPs on chromosome 1 of the CHB population.

Extract alleles

dgraffelmanweir.bi

Calculate Graffelman-Weir exact density for bi-allelic X-chromosomal variant

Calculate allele and genotype counts for X-chromosomal markers

Q-Q plot for a uniform distribution.

Reordering of autosomal genotype counts

Number of alleles

JPTtriallelicsChr7

Tri-allelic variants on chromosome 7 of the Japanese (JPT) sample of the 1000 genomes project

Compute Akaike's Information Criterion (AIC) for HWP and EAF models

Compute additive log-ratio transformation

Exact test for equality of allele frequencies in males and females

Biallelic polymorphisms sampled from chromosome 22 of the CEU population of the 1000 Genomes project.

GenerateSamples

Generate genotypic compositions

Matrix version of HWChisq

Estimate allele frequencies and test for Hardy-Weinberg equilibrium with a tri-allelic ABO system.

Plot genetic markers in centred log-ratio coordinates

AllelesToTriangular

Calculate triangular genotype matrix for vector(s) of alleles.

Compute the centred log-ratio transformation

Chi square tests for Hardy Weinberg equilibrium

Perform all tests for Hardy-Weinberg equilibrium

Genotype frequencies for 70 SNPs related to Alzheimer's disease

Fast computation of chi-square statistics for Hardy-Weinberg equilibrium

Glyoxalase genotype data

Exact test of equality of allele frequencies for males and females

Compute probability of a genotypic sample

Compute disequilibrium statistic D

Convert genotype counts to compositions