HWLratio: Likelihood ratio test for Hardy Weinberg equilibrium
In HardyWeinberg: Statistical Tests and Graphics for Hardy-Weinberg Equilibrium

HWLratio

R Documentation

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 jan.graffelman@upc.edu

References

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

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)
#
#

HardyWeinberg documentation built on May 29, 2024, 6:17 a.m.