Analysis of Codon Data under Stationarity using a Bayesian
Framework
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Documentation for package ‘AnaCoDa’ version 0.1.4.4
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 |