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 <email@example.com>|
|Date of publication||2016-03-29 20:04:32|
|Maintainer||Jan Graffelman <firstname.lastname@example.org>|
|License||GPL (>= 2)|
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...