initMutationCategories

list of files containing starting values. Number of files should equal the number of categories.

files

number of mutation categories (should be less than or equal to number of mixtures)

numCategories

Can use this parameter to fix mutation at current values (won't change over course of MCMC run)

Initialize values for mutation CSP. File should be of comma-separated with header. Three columns should be of order Amino_acid,Codon,Value

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addition 'AnaCoDa' contains three currently unpublished models.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.

initMutationCategories: initMutationCategories

Description

Arguments