HWLRtest: Perform likelihood ratio test comparing two nested scenarios...

In HardyWeinberg: Statistical Tests and Graphics for Hardy-Weinberg Equilibrium

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 [e-mail]

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 \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1002/gepi.22079")}

See Also

HWAIC

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