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
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
geomMean Man page Source code
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
getExpressionEstimates Man page Source code
getMixtureAssignmentEstimate Man page Source code
getNames Man page Source code
getNc Man page Source code
getNcAA Man page Source code
getObservedSynthesisRateSet Man page Source code
getSelectionCoefficients Man page Source code
getTrace Man page Source code
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
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_ROCModel Man page Source code
plot.Rcpp_ROCParameter Man page Source code
plot.Rcpp_Trace Man page Source code
plotCSPdf Source code
plotCodonSpecificHyperParameters Man page Source code
plotCodonSpecificParameters Man page Source code
plotExpectedPhiTrace Source code
plotExpressionTrace Source code
plotHyperParameterTrace Source code
plotMixtureProbability Source code
plotParameterObject Source code
plotSinglePanel Source code
runMCMC Man page Source code
setBaseInfo Source code
setRestartSettings Man page Source code
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
AnaCoDa documentation built on Sept. 21, 2018, 6:25 p.m.