Statistical Tests and Graphics for Hardy-Weinberg Equilibrium

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Documentation for package ‘HardyWeinberg’ version 1.7.8

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HardyWeinberg-package Statistical Tests and Graphics for Hardy-Weinberg Equilibrium
af Function to compute allele frequencies
AFtest Exact test of equality of allele frequencies for males and females
afx Function to compute X-chromosomal allele frequencies
agcounts Calculate allele and genotype counts for X-chromosomal markers
alleles Extract alleles
AllelesToTriangular Calculate triangular genotype matrix for vector(s) of alleles.
Alzheimer Genotype frequencies for 70 SNPs related to Alzheimer's disease
CEUchr22 Biallelic polymorphisms sampled from chromosome 22 of the CEU population of the 1000 Genomes project.
dgraffelmanweir.bi Calculate Graffelman-Weir exact density for bi-allelic X-chromosomal variant
dlevene Calculate Levene's exact density for k alleles
dlevene.bi Calculate Levene's density for a bi-allelic variant
EAFExact Exact test for equality of allele frequencies in males and females
fisherz Fisher's z transformation
fold Fold a square matrix
GenerateSamples Generate genotypic compositions
genlabels Label genotype counts of a vector or matrix
Glyoxalase Glyoxalase genotype data
HapMapCHBChr1 Genotype frequencies for 225 SNPs on chromosome 1 of the CHB population.
HardyWeinberg Statistical Tests and Graphics for Hardy-Weinberg Equilibrium
he Calculate expected heterozygosity (He)
HWABO Estimate allele frequencies and test for Hardy-Weinberg equilibrium with a tri-allelic ABO system.
HWAIC Compute Akaike's Information Criterion (AIC) for HWP and EAF models
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 equilibrium
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 Equilibrium
HWEM Estimation of contributions of two populations to a sample of genotype frequencies with the EM algorithm.
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 for sets of SNPs
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 coordinates
HWLindley Calculate a posteriori density for Lindley's alpha
HWLindley.cri Calculate a credible interval for Lindley's alpha for HWE,
HWLRAllTests Perform most relevant likelihood ratio test for Hardy-Weinberg equilibrium and equality of allele frequencies
HWLratio Likelihood ratio test for Hardy Weinberg equilibrium
HWLRtest Perform likelihood ratio test comparing two nested scenarios for a bi-allelic genetic variant, distinguishing the two sexes.
HWMissing Test a bi-allelic marker for Hardy-Weinberg equilibrium in the presence of missing genotype information.
HWNetwork Autosomal and X-chromosomal exact tests for HWE via a Network algorithm
HWPerm Permutation test for Hardy-Weinberg equilibrium
HWPerm.mult Permutation tests fo variants with multiple alleles
HWPosterior Calculation of posterior probabilities and Bayes factors for Hardy-Weinberg tests at X-chromosomal variants.
HWPower Compute the power of a test for Hardy-Weinberg equilibrium.
HWQQplot A Q-Q plot for Hardy-Weinberg equilibrium
HWQqplot A Q-Q plot for Hardy-Weinberg equilibrium
HWStr Testing a set of microsatellites (STRs) for Hardy-Weinberg equilibrium
HWStrata Asymptotic test for HWE across strata for a single biallelic marker
HWTernaryPlot Ternary plot with the Hardy-Weinberg acceptance region
HWTriExact Exact test for Hardy-Weinberg equilibrium and equality of allele frequencies for tri-allelic variants.
ifisherz Inverse Fisher z transformation
is.mono Detects autosomal and X-chromosomal monomorphic variants
JPTmultiallelicsChr7 Multi-allelic autosomal variants of the Japanese population of the 1000 genomes project
JPTmultiallelicsChrX Multi-allelic X-chromosomal variants of the Japanese population of the 1000 genomes project
JPTsnps Bi-allelic SNPs from a Japanese population stratified by gender
JPTtriallelicsChr7 Tri-allelic variants on chromosome 7 of the Japanese (JPT) sample of the 1000 genomes project
JPTtriallelicsChrX Tri-allelic variants on the X-chromosome of the Japanese (JPT) sample of the 1000 genomes project
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
n.alleles Number of alleles
NistSTRs NIST autosomal STR data
order.auto Reordering of autosomal genotype counts
order.x Reordering of X-chromosomal genotype counts
qqunif Q-Q plot for a uniform distribution.
recode Recode genotype information
shannon Shannon index
strsort Sort tokens of a set of strings
ThetatoF Convert theta to an inbreeding coefficient
toTriangular Convert a vector of genotype counts to triangular format
TSIXTriAllelics Tri-allelic polymorphisms on the X chromosome of the TSI population
UniqueGenotypeCounts Extract unique genotypic compositions from a matrix
vaf Computes the sample variance of the allele frequency for a biallelic marker.