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 |
calculateSCUO | calculates the synonymous codon usage order (SCUO) |
calculate_marginal_log_likelihood | Calculates the marginal log-likelihood for a set of parameters |
codons | Codons |
codonToAA | translates codon to amino acid |
convergence.test | Convergence Test |
findOptimalCodon | Find and return list of optimal codons |
geomMean | Take the geometric mean of a vector |
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 |
getCSPEstimates | Return Codon Specific Paramters (or write to csv) estimates as data.frame |
getExpressionEstimates | Returns the estimated phi posterior for a gene |
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 |
getObservedSynthesisRateSet | Get gene observed synthesis rates |
getSelectionCoefficients | Calculate Selection coefficients |
getTrace | extracts an object of traces from a parameter object. |
initializeCovarianceMatrices | Initialize Covariance Matrices |
initializeGenomeObject | Genome Initialization |
initializeMCMCObject | Initialize MCMC |
initializeModelObject | Model Initialization |
initializeParameterObject | Initialize Parameter |
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 |
plotCodonSpecificParameters | Plot Codon Specific Parameter |
runMCMC | Run MCMC |
setRestartSettings | Set Restart Settings |
summary.Rcpp_Genome | Summary of Genome |
writeMCMCObject | Write MCMC Object |
writeParameterObject | Write Parameter Object to a File |