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HardyWeinberg (version 1.6.1)

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.

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Version

Install

install.packages('HardyWeinberg')

Monthly Downloads

3,798

Version

1.6.1

License

GPL (>= 2)

Homepage

https://www.r-project.org

Maintainer

Jan Graffelman

Last Published

May 29th, 2018

Functions in HardyWeinberg (1.6.1)

Plot bi-allelic genetic markers in isometric log ratio coordinates

HardyWeinberg-package

Statistical Tests and Graphics for Hardy-Weinberg Equilibrium

Matrix version of HWExact

Likelihood ratio test for Hardy Weinberg equilibrium

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

Ternary plot with the Hardy-Weinberg acceptance region

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

JPTtriallelicsChrX

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

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

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

Permutation test for Hardy-Weinberg equilibrium

Calculate allele and genotype counts for X-chromosomal markers

SNP data and intensities

Computation of inbreeding coefficient

Make factors from genotyping data

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

A Q-Q plot for Hardy-Weinberg equilibrium

Extract alleles

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

UniqueGenotypeCounts

Extract unique genotypic compositions from a matrix

Scatter plot of the genotype frequencies

Create genotype counts from bi-allelic marker data

Function to compute allele frequencies

Convert a vector of genotype counts to triangular format

Label genotype counts of a vector or matrix

JPTmultiallelicsChrX

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

Compute isometric log ratio coordinates.

Inverse Fisher z transformation

Genotype frequencies for blood group locus MN

Convert theta to an inbreeding coefficient

JPTmultiallelicsChr7

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

Sort tokens of a set of strings

Calculate Levene's exact density for k alleles

HWExactPrevious

Exact test for Hardy-Weinberg equilibrium

dgraffelmanweir.bi

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

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

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

Permutation tests fo variants with multiple alleles

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

JPTtriallelicsChr7

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

Calculate Levene's density for a bi-allelic variant

Fisher's z transformation

Compute the minor allele count.

Number of alleles

Function to compute minor allele frequencies

Recode genotype information

GenerateSamples

Generate genotypic compositions

Perform all tests for Hardy-Weinberg equilibrium

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

Chi square tests for Hardy Weinberg equilibrium

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

Plot genetic markers in additive log-ratio coordinates

Exact test of equality of allele frequencies for males and females

Genotype frequencies for 70 SNPs related to Alzheimer's disease

Compute additive log-ratio transformation

Exact test for Hardy-Weinberg equilibrium

Compute disequilibrium statistic D

Convert genotype counts to compositions

Exact test for equality of allele frequencies in males and females

Compute the centred log-ratio transformation

Plot genetic markers in centred log-ratio coordinates

Matrix version of HWChisq

Compute probability of a genotypic sample

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

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