HWPosterior {HardyWeinberg} | R Documentation |
Calculation of posterior probabilities and Bayes factors for Hardy-Weinberg tests at X-chromosomal variants.
Description
Function HWPosterior
calculates posterior probabilities and Bayes
factors for tests for Hardy-Weinberg equilibrium of autosomal and X-chromosomal
variants.
Usage
HWPosterior(males, females, verbose = TRUE, prior.af = c(0.5,0.5), prior.gf =
c(0.333,0.333,0.333), x.linked = FALSE, precision = 0.05)
Arguments
males |
A vector of male genotype counts. For autosomal variants, this should be a three-element named vector like (AA,AB,BB); for X-chromosomal variants it should be a two-element vector giving the counts of the hemizygous genotypes like (A,B). |
females |
A vector of female genotype counts. This should be a three-element named vector like (AA,AB,BB) |
verbose |
prints results if |
prior.af |
Beta prior parameters for male and female allele frequencies |
prior.gf |
Dirichlet prior parameters for female genotype frequencies |
x.linked |
logical indicating whether the variant is autosomal or X-chromosomal |
precision |
precision parameter for marginal likelihoods that require numeric integration |
Details
For X-chromosomal variants, four possible models are considered, and the posterior probabilities and Bayes factors for each model are calculated.
For autosomal variants, ten possible scenarios are considered, and the posterior probabilities for all models are calculated.
In general, default Dirichlet priors are used for genotype frequencies, and beta prior are used for allele frequencies.
Value
For X-chromosomal variants, a matrix with posterior probabilities and Bayes factors will be produced. For autosomal variants, a vector of posterior probabilities is produced.
Author(s)
Xavi Puig xavier.puig@upc.edu and Jan Graffelman jan.graffelman@upc.edu
References
Puig, X., Ginebra, J. and Graffelman, J. (2017) A Bayesian test for Hardy-Weinberg equilibrium of bi-allelic X-chromosomal markers. Heredity 119(4):226–236. doi:10.1038/hdy.2017.30.
Puig, X., Ginebra, J. and Graffelman, J. (2019) Bayesian model selection for the study of Hardy-Weinberg proportions and homogeneity of gender allele frequencies. Heredity 123(5), pp. 549-564. doi:10.1038/s41437-019-0232-0
See Also
HWChisq
, HWExact
, HWExactStats
Examples
#
# An X-chromosomal example
#
males <- c(A=43,B=13)
females <- c(AA=26,AB=19,BB=3)
out <- HWPosterior(males,females,verbose=TRUE,x.linked=TRUE)
#
# An autosomal example
#
data(JPTsnps)
males <- JPTsnps[1,1:3]
females <- JPTsnps[1,4:6]
post.prob <- HWPosterior(males,females,x.linked=FALSE)