HardyWeinberg: Statistical Tests and Graphics for Hardy-Weinberg Equilibrium

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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.

Author
Jan Graffelman <jan.graffelman@upc.edu>
Date of publication
2016-03-29 20:04:32
Maintainer
Jan Graffelman <jan.graffelman@upc.edu>
License
GPL (>= 2)
Version
1.5.6
URLs

View on CRAN

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
HapMapCHBChr1
Genotype frequencies for 225 SNPs on chromosome 1 of the CHB...
HardyWeinberg-package
Graphical tests for Hardy-Weinberg equilibrium
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
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
UniqueGenotypeCounts
Extract unique genotypic compositions from a matrix
vaf
Computes the sample variance of the allele frequency for a...

Files in this package

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