HardyWeinberg: Statistical Tests and Graphics for Hardy-Weinberg Equilibrium

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 publication2016-03-29 20:04:32
MaintainerJan Graffelman <jan.graffelman@upc.edu>
LicenseGPL (>= 2)
Version1.5.6
http://www.r-project.org
http://www-eio.upc.edu/~jan

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...

Functions

af Man page
AFtest Man page
agcounts Man page
Alzheimer Man page
fisherz Man page
GenerateSamples Man page
HapMapCHBChr1 Man page
HardyWeinberg Man page
HardyWeinberg-package Man page
HWAlltests Man page
HWAlr Man page
HWAlrPlot Man page
HWChisq Man page
HWChisqMat Man page
HWChisqStats Man page
HWClo Man page
HWClr Man page
HWClrPlot Man page
HWCondProbAB Man page
HWD Man page
HWData Man page
HWExact Man page
HWExactMat Man page
HWExactPrevious Man page
HWExactStats Man page
HWf Man page
HWGenotypePlot Man page
HWIlr Man page
HWIlrPlot Man page
HWLratio Man page
HWMissing Man page
HWPerm Man page
HWPower Man page
HWQqplot Man page
HWQqplot Man page
HWTernaryPlot Man page
ifisherz Man page
mac Man page
maf Man page
MakeCounts Man page
MakeFactor Man page
Markers Man page
Mourant Man page
recode Man page
UniqueGenotypeCounts Man page
vaf Man page

Files

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

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