API for AnaCoDa
Analysis of Codon Data under Stationarity using a Bayesian Framework
| Global functions | |
|---|---|
| AAToCodon | Man page |
| acfCSP | Man page Source code |
| acfMCMC | Man page Source code |
| addObservedSynthesisRateSet | Man page Source code |
| aminoAcids | Man page |
| calcCAI | Source code |
| calculateMarginalLogLikelihood | Man page Source code |
| calculateProbabilityVector | Source code |
| calculateSCUO | Man page Source code |
| checkModel | Source code |
| codonToAA | Man page |
| codons | Man page |
| combineThreeDimensionalTrace | Source code |
| combineTwoDimensionalTrace | Source code |
| confidenceInterval.plot | Source code |
| convergence.test | Man page Source code |
| convergence.test.Rcpp_MCMCAlgorithm | Source code |
| convergence.test.Rcpp_Trace | Source code |
| extractBaseInfo | Source code |
| findOptimalCodon | Man page Source code |
| fixDEta | Man page |
| fixDM | Man page |
| fixSphi | Man page |
| geomMean | Man page Source code |
| getAdaptiveWidth | Man page |
| getCAI | Man page Source code |
| getCAIweights | Man page Source code |
| getCSPEstimates | Man page Source code |
| getCSPbyLogit | Source code |
| getCodonCounts | Man page Source code |
| getCodonCountsForAA | Man page Source code |
| getCodonSpecificPosteriorMeanForCodon | Man page |
| getCodonSpecificPosteriorVarianceForCodon | Man page |
| getCodonSpecificQuantilesForCodon | Man page |
| getEstimatedMixtureAssignmentForGene | Man page |
| getEstimatedMixtureAssignmentProbabilitiesForGene | Man page |
| getExpressionEstimates | Man page Source code |
| getGroupList | Man page |
| getLogLikelihoodTrace | Man page |
| getLogPosteriorMean | Man page |
| getLogPosteriorTrace | Man page |
| getMixtureAssignmentEstimate | Man page Source code |
| getNSEProbabilityTrace | Source code |
| getNames | Man page Source code |
| getNc | Man page Source code |
| getNcAA | Man page Source code |
| getNoiseOffsetPosteriorMean | Man page |
| getNoiseOffsetVariance | Man page |
| getObservedSynthesisRateSet | Man page Source code |
| getSamples | Man page |
| getSelectionCoefficients | Man page Source code |
| getStdDevSynthesisRatePosteriorMean | Man page |
| getStdDevSynthesisRateVariance | Man page |
| getStepsToAdapt | Man page |
| getSynthesisRate | Man page |
| getSynthesisRatePosteriorMeanForGene | Man page |
| getSynthesisRatePosteriorVarianceForGene | Man page |
| getThinning | Man page |
| getTrace | Man page Source code |
| getTraceObject | Man page |
| initMutationCategories | Man page |
| initSelectionCategories | Man page |
| initializeCovarianceMatrices | Man page Source code |
| initializeFONSEParameterObject | Source code |
| initializeGenomeObject | Man page Source code |
| initializeMCMCObject | Man page Source code |
| initializeModelObject | Man page Source code |
| initializePANSEParameterObject | Source code |
| initializePAParameterObject | Source code |
| initializeParameterObject | Man page Source code |
| initializeROCParameterObject | Source code |
| initializeSynthesisRateByGenome | Man page |
| initializeSynthesisRateByList | Man page |
| initializeSynthesisRateByRandom | Man page |
| length.Rcpp_Genome | Man page Source code |
| loadFONSEParameterObject | Source code |
| loadMCMCObject | Man page Source code |
| loadPANSEParameterObject | Source code |
| loadPAParameterObject | Source code |
| loadParameterObject | Man page Source code |
| loadROCParameterObject | Source code |
| lower.panel.plot | Source code |
| optimalAsReference | Source code |
| plot.Rcpp_FONSEModel | Man page Source code |
| plot.Rcpp_FONSEParameter | Man page Source code |
| plot.Rcpp_MCMCAlgorithm | Man page Source code |
| plot.Rcpp_PAParameter | Source code |
| plot.Rcpp_ROCModel | Man page Source code |
| plot.Rcpp_ROCParameter | Man page Source code |
| plot.Rcpp_Trace | Man page Source code |
| plotAcceptanceRatios | Man page Source code |
| plotCSPdf | Source code |
| plotCodonSpecificParameters | Man page Source code |
| plotExpectedPhiTrace | Source code |
| plotExpressionTrace | Source code |
| plotFONSEHyperParameterTrace | Source code |
| plotHyperParameterTrace | Source code |
| plotMixtureProbability | Source code |
| plotPA | Source code |
| plotPANSEHyperParameterTrace | Source code |
| plotParameterObject | Source code |
| plotSinglePanel | Source code |
| readPhiValue | Man page |
| runMCMC | Man page Source code |
| setAdaptiveWidth | Man page |
| setBaseInfo | Source code |
| setGroupList | Man page |
| setRestartFileSettings | Man page |
| setRestartSettings | Man page Source code |
| setSamples | Man page |
| setStepsToAdapt | Man page |
| setThinning | Man page |
| simulateGenome | Man page |
| splitMatrix | Source code |
| subMatrices | Source code |
| summary.Rcpp_Genome | Man page Source code |
| upper.panel.plot | Source code |
| writeMCMCObject | Man page Source code |
| writeParameterObject | Man page Source code |
| writeParameterObject.Rcpp_FONSEParameter | Source code |
| writeParameterObject.Rcpp_PANSEParameter | Source code |
| writeParameterObject.Rcpp_PAParameter | Source code |
| writeParameterObject.Rcpp_ROCParameter | Source code |
