getCodonSpecificQuantilesForCodon

mixture to calculate CSP variance. Should be between 1 and n, where n is number of mixtures.

mixtureElement

number of samples to use for calculating variance

samples

codon

CSP to calculate variance for. 0: Mutation (ROC,FONSE) or Alpha (PA, PANSE). 1: Selection (ROC,FONSE), Lambda (PANSE), Lambda^prime (PA). 2: NSERate (PANSE)

paramType

vector of two doubles between 0 and 1 indicating range over which to calculate quantiles. &lt;0.0275, 0.975&gt; would give 95% quantiles.

probs

If model uses reference codon, then ignore this codon (fixed at 0). Should be TRUE for ROC and FONSE. Should be FALSE for PA and PANSE.

withoutReference

If true, calculate posterior mean on log scale. Should only be used for PA and PANSE.

log_scale

Method of Parameter class (access via parameter$&lt;function name&gt;, where parameter is an object initialized by initializeParameterObject). Calculate quantiles of CSP traces

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addition 'AnaCoDa' contains three currently unpublished models.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.

getCodonSpecificQuantilesForCodon: getCodonSpecificQuantilesForCodon

Description

Arguments

Value