HWEmodelsMLE: 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
phatmatrix of $k \times k$ MLEs of genotype frequencies
qhatMLEs of $k$ allele frequencies under the HWE model
fqhatMLEs of $k$ allele frequencies under the single $f$ model
fsingleMLE of single $f$
fmaxloglikmaximized log-likelihood (without the normalizing constant), under the single $f$ model
fminestimated 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="" allele="" frequencies.<="" description="">
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.