HardyWeinberg: HWLRtest – R documentation

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HWLRtest

Perform likelihood ratio test comparing two nested scenarios for a bi-allelic genetic variant, distinguishing the two sexes.

Description

Program HWLRtest performs a likelihood ratio test comparing two scenarios for an autosomal bi-allelic genetic variant. The scenarios concern Hardy-Weinberg proportions (HWP) and equality of allele frequencies (EAF) in both sexes. The different scenarios are described by Graffelman & Weir (2017).

Usage

HWLRtest(x, y, scene.null = "S1", scene.alt = "S6", verbose = TRUE, tracing = 0)

Arguments

`x`	Male genotype counts
`y`	Female genotype counts
`scene.null`	Scenario under the null hypothesis (E.g. "S1")
`scene.alt`	Scenario under the alternative hypothesis (E.g. "S6")
`verbose`	print output or not
`tracing`	Show tracing of the numeric likelihood maximization (1) or not (0).

Details

The different scenarios are indicated with S1, S2, S3, S4, S6 and S6. S1 refers to Hardy-Weinber proportions and equality of allele frequencies. S2 refers to equality of allele frequencies and equality of inbreeding coefficients for the two sexes. S3 refers to equality of allele frequencies irrespective of HWP. S4 refers to HWP irrespective of allele frequencies. S5 refers to equality of inbreeding coefficients irrespective of allele frequencies. S6 is unrestricted.

Value

`G2`	Likelihood ratio statistic
`df`	Degrees of freedom of the likelihood ratio statistic
`pval`	p-value

Author(s)

Jan Graffelman jan.graffelman@upc.edu

References

Graffelman, J. and Weir, B.S. (2018) On the testing of Hardy-Weinberg proportions and equality of allele frequencies in males and females at bi-allelic genetic markers. Genetic Epidemiology 42(1) pp. 34–48 doi: 10.1002/gepi.22079

Examples

males <- c(AA=11,AB=32,BB=13) 
females <- c(AA=14,AB=23,BB=11)

#
# test EAF
#

lr1.out <- HWLRtest(males,females,scene.null="S3",scene.alt="S6")

#
# test EIC given EAF
#


lr2.out <- HWLRtest(males,females,scene.null="S2",scene.alt="S3")

#
# test HWP versus EIC, given EAF.
#

lr3.out <- HWLRtest(males,females,scene.null="S1",scene.alt="S2")

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