getSynthesisRatePosteriorVarianceForGene

number of samples over which to calculate variance

samples

corresponding index of gene in genome for which synthesis rate variance will be calculated. Should be a number between 1 and length(genome)

geneIndex

Should calculate variance using unbiased (N-1) or biased (N) correction

unbiased

log_scale

Method of Parameter class (access via parameter$&lt;function name&gt;, where parameter is an object initialized by initializeParameterObject). Get synthesis rate variance for a gene

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addition 'AnaCoDa' contains three currently unpublished models.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.

getSynthesisRatePosteriorVarianceForGene: getSynthesisRatePosteriorVarianceForGene

Description

Arguments

Value