| Type: | Package |
| Title: | Exact Hardy-Weinburg Testing for Genome Wide Association Studies |
| Version: | 1.2 |
| Date: | 2024-03-11 |
| Author: | Ian Painter, University of Washington |
| Maintainer: | Stephanie Gogarten <sdmorris@uw.edu> |
| Description: | Exact Hardy-Weinburg testing (using Fisher's test) for SNP genotypes as typically obtained in a Genome Wide Association Study (GWAS). |
| License: | GPL-3 |
| LazyLoad: | yes |
| Repository: | CRAN |
| NeedsCompilation: | yes |
| Packaged: | 2024-03-12 03:48:51 UTC; stephanie |
| Date/Publication: | 2024-03-12 07:00:02 UTC |
Exact Hardy-Weinburg testing for Genome Wide Association Studies
Description
This package contains a function to do exact Hardy-Weinburg testing (using Fisher's test) over all or a selection of SNP genotypes as typically obtained in a Genome Wide Association Study (GWAS).
Details
| Package: | GWASExactHW |
| Type: | Package |
| Version: | 1.01 |
| Date: | 2013-01-04 |
| License: | GNU |
| LazyLoad: | yes |
The function HWExact runs fast Hardy-Weinburg testing for a set of bi-alleleic genotypes.
Author(s)
Ian Painter, University of Washington
Maintainer: Ian Painter <ipainter@u.washington.edu>
References
Wigginton, JE, Cutler, DJ, and Abecasis, GR (2005) A Note on Exact Tests of Hardy-Weinberg Equilibrium. American Journal of Human Genetics. 76
Function to calculate Hardy-Weinburg exact p-values
Description
This function calculates Hardy-Weinburg (Fisher's) exact p-values for GWAS SNP data.
Usage
HWExact(GenotypeCounts)
Arguments
GenotypeCounts |
A dataframe of genotype counts, with columns called |
Value
A vector of exact p-values.
Note
This function uses a C function SNPHWE.c written by Jan Wigginton as described in the above reference.
Author(s)
Ian Painter
References
Wigginton, JE, Cutler, DJ, and Abecasis, GR (2005) A Note on Exact Tests of Hardy-Weinberg Equilibrium. American Journal of Human Genetics. 76
Examples
pA<- runif(1)
pAA<- pA^2
pAa<- 2*pA*(1-pA)
paa<- (1-pA)^2
counts<- rmultinom(1000, 3000, c(pAA, pAa, paa) )
genotypes<- data.frame(nAA = counts[1,], nAa = counts[2,], naa = counts[3,])
hwPvalues<- HWExact(genotypes)