HWLRAllTests {HardyWeinberg}

Perform most relevant likelihood ratio test for Hardy-Weinberg equilibrium and equality of allele frequencies

Description

Function HWLRAllTests performs a set of likelihood ratio tests in relation with Hardy-Weinberg proportions (HWP) and equality of allele frequencies (EAF) for autosomal bi-allelic genetic variants.

Usage

HWLRAllTests(x, y)

Arguments

x

Male genotype counts (AA,AB,BB)

y

Female genotype counts (AA,AB,BB)

Details

Function HWLRAllTests calls HWLRtest and calculates the p-value of six different tests: 1) joint HWP and EAF (A-F); 2) EAF irrespective of HWP (C-F); 3) HWP irrespective of EAF (D-F); 4) HWP versus EIC (given EAF) (A-B); 5) EIC irrespective of EAF (E-F) and 6) HWP versus EIC. Letters refer to scenarios described by Graffelman & Weir (2018).

Value

A named vector with six p-values

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

HWLRtest

Examples

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