HardyWeinberg (version 1.7.8)

vaf: Computes the sample variance of the allele frequency for a biallelic marker.

Description

Function vaf computes the sample variance of the allele frequencies of a single sample or a matrix of samples.

Usage

vaf(X, hw = FALSE)

Value

a numeric vector of variances.

Arguments

X

vector or matrix with genotype counts (AA,AB,BB)

hw

assume Hardy-Weinberg proportions (hw=TRUE) or not (hw=FALSE)

Author

Jan Graffelman

Details

For biallelic markers the variance of the minor allele frequency equals the variance of the major allele frequency.

References

Weir, B.S. (1996) Genetic data analysis II. Sinauer Associates, Massachusetts. See Chapter 2.

See Also

af, maf

Examples

x <- c(MM=298,MN=489,NN=213)
pA <- af(x)
vA <- vaf(x)
cat("allele frequency:",pA,"\n")
cat("sample variance allele frequency:",vA,"\n")