HardyWeinberg: Statistical Tests and Graphics for Hardy-Weinberg Equilibrium
Version 1.5.8

Contains tools for exploring Hardy-Weinberg equilibrium for diallelic genetic marker data. All classical tests (chi-square, exact, likelihood-ratio and permutation tests) for Hardy-Weinberg equilibrium 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. 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 diallelic markers: ternary plots with acceptance regions, log-ratio plots and Q-Q plots.

AuthorJan Graffelman <jan.graffelman@upc.edu>
Date of publication2017-05-17 07:18:25 UTC
MaintainerJan Graffelman <jan.graffelman@upc.edu>
LicenseGPL (>= 2)
Version1.5.8
URL https://www.r-project.org http://www-eio.upc.edu/~jan
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("HardyWeinberg")

Getting started

Package overview

Popular man pages

HardyWeinberg-package: Graphical tests for Hardy-Weinberg equilibrium
HWAlrPlot: Plot genetic markers in additive log-ratio coordinates
HWChisq: Chi square tests for Hardy Weinberg equilibrium
HWGenotypePlot: Scatter plot of the genotype frequencies
HWLratio: Likelihood ratio test for Hardy Weinberg equilibrium
HWQqplot: A Q-Q plot for Hardy-Weinberg equilibrium
mac: Compute the minor allele count.
See all...

All man pages Function index File listing

Man pages

af: Function to compute allele frequencies
AFtest: Exact test of equality of allele frequencies for males and...
agcounts: Calculate allele and genotype counts for X-chromosomal...
Alzheimer: Genotype frequencies for 70 SNPs related to Alzheimer's...
fisherz: Fisher's z transformation
GenerateSamples: Generate genotypic compositions
genlabels: Label genotype counts of a vector or matrix
HapMapCHBChr1: Genotype frequencies for 225 SNPs on chromosome 1 of the CHB...
HardyWeinberg-package: Graphical tests for Hardy-Weinberg equilibrium
HWABO: Estimate allele frequencies and test for Hardy-Weinberg...
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...
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...
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...
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...
HWLratio: Likelihood ratio test for Hardy Weinberg equilibrium
HWMissing: Test a bi-allelic marker for Hardy-Weinberg equilibrium in...
HWPerm: Permutation test for Hardy-Weinberg equilibrium
HWPosterior: Calculation of posterior probabilities and Bayes factors for...
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
ifisherz: Inverse Fisher z transformation
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
recode: Recode genotype information
ThetatoF: Convert theta to an inbreeding coefficient
UniqueGenotypeCounts: Extract unique genotypic compositions from a matrix
vaf: Computes the sample variance of the allele frequency for a...

Functions

AFtest Man page Source code
Alzheimer Man page
Chisquare Source code
Chisquare.x Source code Source code
CombineChisquare Source code
CombineExact Source code
CompProbDown Source code
CompProbDownPower Source code
CompProbUp Source code
CompProbUpPower Source code
FtoTheta Source code
GenerateSamples Man page
H0 Source code
H1 Source code
H2 Source code
H3 Source code
HW.chi.mat Source code
HWABO Man page Source code
HWAlltests Man page Source code
HWAlr Man page Source code
HWAlrPlot Man page Source code
HWChisq Man page Source code
HWChisqMat Man page Source code
HWChisqStats Man page Source code
HWClo Man page Source code
HWClr Man page Source code
HWClrPlot Man page Source code
HWCondProbAB Man page
HWD Man page Source code
HWData Man page Source code
HWExact Man page Source code
HWExactMat Man page Source code
HWExactPower Source code
HWExactPrevious Man page Source code
HWExactStats Man page Source code
HWGenotypePlot Man page Source code
HWIlr Man page Source code
HWIlrPlot Man page Source code
HWLratio Man page Source code
HWMissing Man page Source code
HWPerm Man page Source code
HWPosterior Man page Source code
HWPower Man page Source code
HWQqplot Man page Man page Source code
HWTernaryPlot Man page
HWf Man page Source code
HapMapCHBChr1 Man page
HardyWeinberg Man page
HardyWeinberg-package Man page
MakeCounts Man page Source code
MakeFactor Man page Source code
Markers Man page
Mourant Man page
SNPHWE2 Source code
SNPHWEX Source code
ThetatoF Man page Source code
UniqueGenotypeCounts Man page Source code
af Man page
agcounts Man page Source code
allele.name Source code
auxiliartable Source code
combineC Source code
cutoff Source code
ddir Source code
fisherz Man page Source code
generate.outcomes Source code
genlabels Man page Source code
getpvals Source code
gmeanrow Source code
heterozyg Source code
homozyg Source code
ifisherz Man page Source code
is.wholenumber Source code
mac Man page Source code
maf Man page
make.outcomes Source code
mipvalue Source code
missingentirerow Source code
n.outcomes Source code
recode Man page Source code
sample.prob Source code
sample.prob.last Source code
subsamples.prob Source code
support Source code
vaf Man page Source code

Files

inst
inst/CITATION
inst/doc
inst/doc/HardyWeinberg.Rnw
inst/doc/HardyWeinberg.pdf
inst/doc/HardyWeinberg.R
src
src/support.cpp
src/SNPHWEX.cpp
src/RcppExports.cpp
NAMESPACE
data
data/HapMapCHBChr1.rda
data/Mourant.rda
data/Markers.rda
data/Alzheimer.rda
R
R/HWClrPlot.R
R/auxiliartable.R
R/Chisquare.R
R/HWPerm.R
R/cutoff.R
R/HWExact.R
R/make.outcomes.R
R/HWQqplot.R
R/UniqueGenotypeCounts.R
R/alowcurve.R
R/HWClo.R
R/CompProbUpPower.R
R/HWChisqStats.R
R/HWABO.R
R/homozyg.R
R/mac.R
R/HWChisqUpperl.R
R/HWIlrPlot.R
R/af.R
R/FtoTheta.R
R/agcounts.R
R/generate.outcomes.R
R/DnegLow.R
R/HWLowercl.R
R/DposLow.R
R/HWTernaryPlot.R
R/HWD.R
R/fisherz.R
R/HWExactPrevious.R
R/HW.chi.mat.R
R/H0.R
R/CheckRoots.R
R/HWAlrPlot.R
R/heterozyg.R
R/allele.name.R
R/HWChisq.R
R/HWData.R
R/HWMissing.R
R/CritSam.R
R/missingentirerow.R
R/HWExactPower.R
R/Chisquarex.R
R/sample.prob.R
R/is.wholenumber.R
R/recode.R
R/ThetatoF.R
R/GenerateSamples.R
R/n.outcomes.R
R/HWExactStats.R
R/genlabels.R
R/H1.R
R/CompProbDown.R
R/HWCondProbAB.R
R/CompProbDownPower.R
R/HWIlr.R
R/AFtest.R
R/CombineChisquare.R
R/RcppExports.R
R/HWLratio.R
R/Chisquare.x.R
R/ifisherz.R
R/HWChisqccCurve.R
R/H2.R
R/sample.prob.last.R
R/HWExactMat.R
R/HWClr.R
R/CompProbUp.R
R/HWChisqLowerl.R
R/HWAlltests.R
R/ddir.R
R/HWChisqMat.R
R/HWUppercl.R
R/HWf.R
R/CombineExact.R
R/HWAlr.R
R/mipvalue.R
R/HWPosterior.R
R/DposUp.R
R/MakeFactor.R
R/vaf.R
R/maf.R
R/gmeanrow.R
R/DnegUp.R
R/odd.R
R/subsamples.prob.R
R/H3.R
R/combineC.R
R/HWPower.R
R/HWGenotypePlot.R
R/MakeCounts.R
R/getpvals.R
vignettes
vignettes/HWGeno1.pdf
vignettes/HWHapMapQQplot.pdf
vignettes/HapMapCHBChr1Exact.pdf
vignettes/HWGeno2.pdf
vignettes/HardyWeinberg.bib
vignettes/HapMapCHBChr1.pdf
vignettes/HardyWeinberg.Rnw
vignettes/HWHapMapIlr1.pdf
vignettes/HWHapMapQQplotInbred.pdf
vignettes/TernaryPlot.pdf
vignettes/HWHomHet2.pdf
vignettes/HWHapMapGeno1.pdf
vignettes/MourantQQPlot.pdf
vignettes/Simulated2.pdf
vignettes/HWHapMapQQplotSimulated.pdf
vignettes/HapMapCHBChr1Chisq.pdf
vignettes/MourantTP.pdf
vignettes/HWHapMapIlr2.pdf
vignettes/HWHapMapGeno2.pdf
MD5
build
build/vignette.rds
DESCRIPTION
man
man/HWIlr.Rd
man/MakeCounts.Rd
man/HWClr.Rd
man/HWChisq.Rd
man/genlabels.Rd
man/ifisherz.Rd
man/af.Rd
man/HWChisqMat.Rd
man/HWExactMat.Rd
man/HWD.Rd
man/HWExactPrevious.Rd
man/Alzheimer.Rd
man/HWAlr.Rd
man/HapMapCHBChr1.Rd
man/UniqueGenotypeCounts.Rd
man/Mourant.Rd
man/maf.Rd
man/HWExact.Rd
man/fisherz.Rd
man/agcounts.Rd
man/GenerateSamples.Rd
man/HWClo.Rd
man/HWPerm.Rd
man/HWChisqStats.Rd
man/HWPosterior.Rd
man/HWf.Rd
man/AFtest.Rd
man/HWMissing.Rd
man/HWCondProbAB.Rd
man/HWGenotypePlot.Rd
man/HWAlrPlot.Rd
man/vaf.Rd
man/HWData.Rd
man/HardyWeinberg-package.Rd
man/HWExactStats.Rd
man/HWQqplot.Rd
man/HWABO.Rd
man/ThetatoF.Rd
man/mac.Rd
man/MakeFactor.Rd
man/HWClrPlot.Rd
man/HWTernaryPlot.Rd
man/HWLratio.Rd
man/Markers.Rd
man/HWIlrPlot.Rd
man/HWPower.Rd
man/recode.Rd
man/HWAlltests.Rd
HardyWeinberg documentation built on May 19, 2017, 2:10 p.m.