getNoiseOffsetVariance

mixture index to use. Should be number between 0 and n-1, where n is number of mixtures

index

number of samples over which to calculate variance

samples

If TRUE, should calculate variance using unbiased (N-1). Otherwise, used biased (N) correction

unbiased

Method of Parameter class (access via parameter$&lt;function name&gt;, where parameter is an object initialized by initializeParameterObject). Calculate variance of noise offset parameter used when fitting model with empirical estimates of synthesis rates (ie. withPhi fits)

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addition 'AnaCoDa' contains three currently unpublished models.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.

getNoiseOffsetVariance: getNoiseOffsetVariance

Description

Arguments

Value