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

1

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. (2010). Bayesian methods for examining Hardy-Weinberg equilibrium. Biometrics; Vol 66:257-65

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

Examples

1
2