HWExact: Function to calculate Hardy-Weinburg exact p-values
In GWASExactHW: Exact Hardy-Weinburg testing for Genome Wide Association Studies
Description
Usage
Arguments
Value
Note
Author(s)
References
Examples
Description
This function calculates Hardy-Weinburg (Fisher's) exact p-values for GWAS SNP data.
Usage
1
HWExact(GenotypeCounts)
Arguments
GenotypeCounts
A dataframe of genotype counts, with columns called nAA, nAa and naa, one row for each SNP.
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
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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)
GWASExactHW documentation built on May 29, 2017, 6:08 p.m.
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Description Usage Arguments Value Note Author(s) References Examples
Description
This function calculates Hardy-Weinburg (Fisher's) exact p-values for GWAS SNP data.
Usage
1 | 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
1 2 3 4 5 6 7 8 | 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)
|
GWASExactHW documentation built on May 29, 2017, 6:08 p.m.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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