simulateGenome

<p>a Genome object initialized by initializeGenomeObject</p>

genome

<p>Method of Model class (access via model$&lt;function name&gt;, where model is an object initialized by initializeModelObject). Will simulate a version of the given genome using the current set of parameters stored in the Parameter object. This can be written to a FASTA file using genome$writeFasta(&lt;filename&gt;,simulated = TRUE).</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addition 'AnaCoDa' contains three currently unpublished models.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.

simulateGenome: simulateGenome

Description

Arguments