Analysis of Codon Data under Stationarity using a Bayesian Framework


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Documentation for package ‘AnaCoDa’ version 0.1.4.4

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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