HWLRtest {HardyWeinberg}

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 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")