readPhiValue

filename

<p>Method of Parameter class (access via parameter$&lt;function name&gt;, where parameter is an object initialized by initializeParameterObject). Read synthesis rate values from file. File should be two column file &lt;gene_id,phi&gt; and is expected to have a header row</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addition 'AnaCoDa' contains three currently unpublished models.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.

readPhiValue: readPhiValue

Description

Arguments