gofhwex {EQUIVNONINF}

Critical constants of the exact UMPU test for approximate compatibility of a SNP genotype distribution with the Hardy-Weinberg model

Description

The function computes the critical constants defining the uniformly most powerful unbiased test for equivalence of the population distribution of the three genotypes distinguishable in terms of a single nucleotide polymorphism (SNP), to a distribution being in Hardy-Weinberg equilibrium (HWE).
The test is conditional on the total count S of alleles of the kind of interest, and the parameter \theta, in terms of which equivalence shall be established, is defined by \theta = \frac{\pi_2^2}{\pi_1(1-\pi_1-\pi_2)}, with \pi_1 and \pi_2 denoting the population frequence of homozygotes of the 1st kind and heterozygotes, respectively.

Usage

gofhwex(alpha,n,s,del1,del2) 

Arguments

alpha

significance level

n

number of genotyped individuals

s

observed count of alleles of the kind of interest

del1

absolute value of the lower equivalence limit to \theta/4 - 1

del2

upper equivalence limit to \theta/4 - 1

Value

alpha

significance level

n

number of genotyped individuals

s

observed count of alleles of the kind of interest

del1

absolute value of the lower equivalence limit to \theta/4 - 1

del2

upper equivalence limit to \theta/4 - 1

C1

left-hand limit of the critical interval for the observed number X_2 of heterozygotes

C2

right-hand limit of the critical interval for the observed number X_2

GAM1

probability of rejecting the null hypothesis when it turns out that X_2=C_1

GAM2

probability of rejecting the null hypothesis for X_2=C_2

Author(s)

Stefan Wellek <[e-mail]>
Peter Ziegler <[e-mail]>

References

Wellek S: Tests for establishing compatibility of an observed genotype distribution with Hardy-Weinberg equilibrium in the case of a biallelic locus. Biometrics 60 (2004), 694-703.

Goddard KAB, Ziegler A, Wellek S: Adapting the logical basis of tests for Hardy-Weinberg equilibrium to the real needs of association studies in human and medical genetics. Genetic Epidemiology 33 (2009), 569-580.

Wellek S: Testing statistical hypotheses of equivalence and noninferiority. Second edition. Boca Raton: Chapman & Hall/CRC Press, 2010, \S 9.4.2.

Examples

gofhwex(0.05,475,429,1-1/1.96,0.96)