hmmMargLlik

readPriorFromFile

Implements several methods for testing the variance component parameter in regression models that contain kernel-based random effects, including a maximum of adjusted scores test. Several kernels are supported, including a profile hidden Markov model mutual information kernel for protein sequence. This package is described in Fong et al. (2015) <DOI:10.1093/biostatistics/kxu056>.

Youyi Fong

Kernel Based Regression Models

Saheli Datta

Krisztian Sebestyen

Steve Park

Dave Geyer

hmmMargLlik function

<dl> <dt>dat</dt>
<dd>a matrix representation of a multiple sequence alignment, each row is a sequence, each column is a position</dd> <dt>aaPrior</dt>
<dd>a list of two elements, "alpha" "mix.coef", representing mixture Dirichlet prior</dd> <dt>tau</dt>
<dd>numeric</dd> <dt>priorFileName</dt>
<dd>string</dd>
</dl>

Arguments

Functions related to profile HMM — hmmMargLlik

<dl>

 <dt>dat</dt>
<dd>a matrix representation of a multiple sequence alignment, each row is a sequence, each column is a position</dd>

 <dt>aaPrior</dt>
<dd>a list of two elements, "alpha" "mix.coef", representing mixture Dirichlet prior</dd>

 <dt>tau</dt>
<dd>numeric</dd>

 <dt>priorFileName</dt>
<dd>string</dd>


</dl>

Functions related to profile HMM

hmmMargLlik: Functions related to profile HMM

Description

Usage

Arguments