HardyWeinberg: HWLratio – R documentation

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HWLratio

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 an X-chromsomal SNP.
#
rs5968922 <-  c(A=392, B=212, AA=275, AB=296, BB=80)
HW.test <- HWLratio(rs5968922,x.linked=TRUE,verbose=TRUE)

HardyWeinberg

Statistical Tests and Graphics for Hardy-Weinberg Equilibrium

v1.7.2

GPL (>= 2)

Authors

Jan Graffelman [aut, cre], Christopher Chang [ctb], Xavi Puig [ctb], Jan Wigginton [ctb], Leonardo Ortoleva [ctb], William R. Engels [ctb]

Initial release

2021-04-28