Man pages for AnaCoDa
Analysis of Codon Data under Stationarity using a Bayesian Framework

AAToCodonAmino Acid to codon set
acfCSPPlots ACF for codon specific parameter traces
acfMCMCAutocorrelation function for the likelihood or posterior...
addObservedSynthesisRateSetAdd gene observed synthesis rates
aminoAcidsAmino acids
calculateSCUOcalculates the synonymous codon usage order (SCUO)
codonsCodons
codonToAAtranslates codon to amino acid
convergence.testConvergence Test
findOptimalCodonFind and return list of optimal codons
geomMeanTake the geometric mean of a vector
getCAICalculate the Codon Adaptation Index
getCAIweightsCalculate the CAI codon weigths for a reference genome
getCodonCountsGet Codon Counts For all Amino Acids
getCodonCountsForAAGet Codon Counts For a specific Amino Acid
getCSPEstimatesReturn Codon Specific Paramters (or write to csv) estimates...
getExpressionEstimatesReturns the estimated phi posterior for a gene
getMixtureAssignmentEstimateReturns mixture assignment estimates for each gene
getNamesGene Names of Genome
getNcCalculate the Effective Number of Codons
getNcAACalculate the Effective Number of Codons for each Amino Acid
getObservedSynthesisRateSetGet gene observed synthesis rates
getSelectionCoefficientsCalculate Selection coefficients
getTraceextracts an object of traces from a parameter object.
initializeCovarianceMatricesInitialize Covariance Matrices
initializeGenomeObjectGenome Initialization
initializeMCMCObjectInitialize MCMC
initializeModelObjectModel Initialization
initializeParameterObjectInitialize Parameter
length.Rcpp_GenomeLength of Genome
loadMCMCObjectLoad MCMC Object
loadParameterObjectLoad Parameter Object
plotCodonSpecificHyperParametersPlot Codon Specific Hyper Parameter
plotCodonSpecificParametersPlot Codon Specific Parameter
plot.Rcpp_FONSEModelPlot Model Object
plot.Rcpp_FONSEParameterPlot Parameter
plot.Rcpp_MCMCAlgorithmPlot MCMC algorithm
plot.Rcpp_ROCModelPlot Model Object
plot.Rcpp_ROCParameterPlot Parameter
plot.Rcpp_TracePlot Trace Object
runMCMCRun MCMC
setRestartSettingsSet Restart Settings
summary.Rcpp_GenomeSummary of Genome
writeMCMCObjectWrite MCMC Object
writeParameterObjectWrite Parameter Object to a File
AnaCoDa documentation built on Sept. 21, 2018, 6:25 p.m.