setGroupList

<p>of strings epresenting groups for parameters to be estimated. Should be one letter amino acid (ROC, FONSE) or list of sense codons (PA, PANSE).</p>

List

<p>Method of Parameter class (access via parameter$&lt;function name&gt;, where parameter is an object initialized by initializeParameterObject). Set amino acids (ROC, FONSE) or codons (PA, PANSE) for which parameters will be estimated. Note that non-default groupLists are still in beta testing and should be used with caution.</p>

Is a collection of models to analyze genome scale codon
data using a Bayesian framework. Provides visualization
routines and checkpointing for model fittings. Currently
published models to analyze gene data for selection on codon
usage based on Ribosome Overhead Cost (ROC) are: ROC (Gilchrist
et al. (2015) <doi:10.1093/gbe/evv087>), and ROC with phi
(Wallace & Drummond (2013) <doi:10.1093/molbev/mst051>). In
addition 'AnaCoDa' contains three currently unpublished models.
The FONSE (First order approximation On NonSense Error) model
analyzes gene data for selection on codon usage against of
nonsense error rates. The PA (PAusing time) and PANSE (PAusing
time + NonSense Error) models use ribosome footprinting data to
analyze estimate ribosome pausing times with and without
nonsense error rate from ribosome footprinting data.

setGroupList: setGroupList

Description

Arguments