HWEmodelsMLE {HWEBayes}R Documentation

Evaluates the maximum likelihood estimates of the parameters of various models in the k allele case

Description

Function to obtain the MLEs of parameters under the HWE, single f and saturated models. For the single f model numerical maximization is required if k>2, where k is the number of alleles.

Usage

HWEmodelsMLE(nvec)

Arguments

nvec vector of genotype frequencies in the order n_{11}, n_{21}, n_{22}, ..., n_{k1}, n_{k2}, ..., n_{kk}.

Value

phat matrix of k times k MLEs of genotype frequencies
qhat MLEs of k allele frequencies under the HWE model
fqhat MLEs of k allele frequencies under the single f model
fsingle MLE of single f
fmaxloglik maximized log-likelihood (without the normalizing constant), under the single f model
fmin estimated lower bound of f_{min} in the single f model. Under the single f model f_{min} < f <1 where f_{min}=-p_{min}/(1-p_{min}) and p_{min} is the minimum of the allele frequencies.

Author(s)

Jon Wakefield (jonno@u.washington.edu)

References

Wakefield, J. (2009). Bayesian methods for examining Hardy-Weinberg equilibrium. Biometrics.

Weir, B.S. (1996). Genetic Data Analysis II. Sunderland MA: Sinauer.

Examples

data(DiabRecess)
HWEmodelsMLE(nvec=DiabRecess)

[Package HWEBayes version 1.0 Index]