vaf {HardyWeinberg}

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)

Arguments

X

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

hw

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

Details

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

Value

a numeric vector of variances.

Author(s)

Jan Graffelman [e-mail]

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")