Graphical Tests for Hardy-Weinberg Equilibrium


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Documentation for package ‘HardyWeinberg’ version 1.5.5

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HardyWeinberg-package Graphical tests for Hardy-Weinberg equilibrium
af Function to compute allele frequencies
Alzheimer Genotype frequencies for 70 SNPs related to Alzheimer's disease
fisherz Fisher's z transformation
GenerateSamples Generate genotypic compositions
HapMapCHBChr1 Genotype frequencies for 225 SNPs on chromosome 1 of the CHB population.
HardyWeinberg 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
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
HWExact Exact test for Hardy-Weinberg equilibrium
HWExactMat Matrix version of HWExact
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
HWLratio Likelihood ratio test for Hardy Weinberg equilibrium
HWMissing Test a bi-allelic marker for Hardy-Weinberg equilibrium in the presence of missing genotype information.
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 minor allele frequencies