# Analysis of Codon Data under Stationarity using a Bayesian Framework

## Documentation for package ‘AnaCoDa’ version 0.1.4.4

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

AAToCodon | Amino Acid to codon set
acfCSP | Plots ACF for codon specific parameter traces
acfMCMC | Autocorrelation function for the likelihood or posterior trace
addObservedSynthesisRateSet | Add gene observed synthesis rates
aminoAcids | Amino acids
calculateMarginalLogLikelihood | Calculates the marginal log-likelihood for a set of parameters
calculateSCUO | calculates the synonymous codon usage order (SCUO)
codons | Codons
codonToAA | translates codon to amino acid
convergence.test | Convergence Test
findOptimalCodon | Find and return list of optimal codons
fixDEta | fixDEta
fixDM | fixDM
fixSphi | fixSphi
geomMean | Take the geometric mean of a vector
getAdaptiveWidth | getAdaptiveWidth
getCAI | Calculate the Codon Adaptation Index
getCAIweights | Calculate the CAI codon weigths for a reference genome
getCodonCounts | Get Codon Counts For all Amino Acids
getCodonCountsForAA | Get Codon Counts For a specific Amino Acid
getCodonSpecificPosteriorMeanForCodon | getCodonSpecificPosteriorMeanForCodon
getCodonSpecificPosteriorVarianceForCodon | getCodonSpecificPosteriorVarianceForCodon
getCodonSpecificQuantilesForCodon | getCodonSpecificQuantilesForCodon
getCSPEstimates | Return Codon Specific Paramters (or write to csv) estimates as data.frame
getEstimatedMixtureAssignmentForGene | getEstimatedMixtureAssignmentForGene
getEstimatedMixtureAssignmentProbabilitiesForGene | getEstimatedMixtureAssignmentProbabilitiesForGene
getExpressionEstimates | Returns the estimated phi posterior for a gene
getGroupList | getGroupList
getLogLikelihoodTrace | getLogLikelihoodTrace
getLogPosteriorMean | getLogPosteriorMean
getLogPosteriorTrace | getLogPosteriorTrace
getMixtureAssignmentEstimate | Returns mixture assignment estimates for each gene
getNames | Gene Names of Genome
getNc | Calculate the Effective Number of Codons
getNcAA | Calculate the Effective Number of Codons for each Amino Acid
getNoiseOffsetPosteriorMean | getNoiseOffsetPosteriorMean
getNoiseOffsetVariance | getNoiseOffsetVariance
getObservedSynthesisRateSet | Get gene observed synthesis rates
getSamples | getSamples
getSelectionCoefficients | Calculate Selection coefficients
getStdDevSynthesisRatePosteriorMean | getStdDevSynthesisRatePosteriorMean
getStdDevSynthesisRateVariance | getStdDevSynthesisRateVariance
getStepsToAdapt | getStepsToAdapt
getSynthesisRate | getSynthesisRate
getSynthesisRatePosteriorMeanForGene | getSynthesisRatePosteriorMeanForGene
getSynthesisRatePosteriorVarianceForGene | getSynthesisRatePosteriorVarianceForGene
getThinning | getThinning
getTrace | extracts an object of traces from a parameter object.
getTraceObject | getTraceObject
initializeCovarianceMatrices | Initialize Covariance Matrices
initializeGenomeObject | Genome Initialization
initializeMCMCObject | Initialize MCMC
initializeModelObject | Model Initialization
initializeParameterObject | Initialize Parameter
initializeSynthesisRateByGenome | initializeSynthesisRateByGenome
initializeSynthesisRateByList | initializeSynthesisRateByList
initializeSynthesisRateByRandom | initializeSynthesisRateByRandom
initMutationCategories | initMutationCategories
initSelectionCategories | initSelectionCategories
length.Rcpp_Genome | Length of Genome
loadMCMCObject | Load MCMC Object
loadParameterObject | Load Parameter Object
plot.Rcpp_FONSEModel | Plot Model Object
plot.Rcpp_FONSEParameter | Plot Parameter
plot.Rcpp_MCMCAlgorithm | Plot MCMC algorithm
plot.Rcpp_ROCModel | Plot Model Object
plot.Rcpp_ROCParameter | Plot Parameter
plot.Rcpp_Trace | Plot Trace Object
plotAcceptanceRatios | Plot Acceptance ratios
plotCodonSpecificParameters | Plot Codon Specific Parameter
readPhiValue | readPhiValue
runMCMC | Run MCMC
setAdaptiveWidth | setAdaptiveWidth
setGroupList | setGroupList
setRestartFileSettings | setRestartFileSettings
setRestartSettings | Set Restart Settings
setSamples | setSamples
setStepsToAdapt | setStepsToAdapt
setThinning | setThinning
simulateGenome | simulateGenome
summary.Rcpp_Genome | Summary of Genome
writeMCMCObject | Write MCMC Object
writeParameterObject | Write Parameter Object to a File