HWLratio {HardyWeinberg}

Likelihood ratio test for Hardy Weinberg equilibrium

Description

HWLratio performs the Likelihood ratio test for Hardy Weinberg equilibrium, both for autosomal and X-chromosomal markers.

Usage

HWLratio(X, verbose = TRUE, x.linked = FALSE) 

Arguments

X

X a vector containing the genotypic counts (AA,AB,BB).

verbose

verbose = TRUE prints results, verbose = FALSE is silent.

x.linked

x.linked=FALSE indicates the marker is autosomal (default), and x.linked=TRUE indicates it resides on the X-chromosome.

Value

HWLratio returns a list with the components:

Lambda

the likelihood ratio

G2

-2*log(Lambda)

pval

the p-value

Author(s)

Jan Graffelman [e-mail]

References

Weir, B.S. (1996) Genetic data analysis II. Sinauer Associates, Massachusetts. See Chapter 3.

See Also

HWChisq

Examples

x <- c(298,489,213)
names(x) <- c("MM","MN","NN")
HW.test <- HWLratio(x,verbose=TRUE)
#
# Test for X-chromsomal SNPs.
#
rs5968922 <-  c(A=392, B=212, AA=275, AB=296, BB=80)
HW.test <- HWLratio(rs5968922,x.linked=TRUE,verbose=TRUE)
#
#
#
y <- c(GG=48, CG=209, CC=277, G=129, C=337) 
HWLratio(y,x.linked=TRUE)
#
#