boundaryTurbo_F         Check whether the parameter F is within the
                        appropriate range
boundaryTurbo_Q         Check whether the parameter Q is within the
                        appropriate range
calcPMSLikelihood       A function for calculating the log-likelihood
                        from the data and parameters
convertFromTurbo_F      Restore the converted parameter F for turboEM
convertFromTurbo_Q      Restore the converted parameter Q for turboEM
convertToTurbo_F        Convert the parameter F so that turboEM can
                        treat
convertToTurbo_Q        Convert the parameter Q so that turboEM can
                        treat
EstimatedParameters-class
                        An S4 class representing the estimated
                        parameters
getLogLikelihoodC       Calculate the value of the log-likelihood for
                        given parameters
getMutationFeatureVector
                        Get mutation feature vector from context
                        sequence data and reference and alternate
                        allele information
hildaBarplot            Read the raw mutation data with the mutation
                        feature vector format, estimate and plot both
                        mutation signatures and their fractions
hildaDiffPlot           Read the raw mutation data with the mutation
                        feature vector format, estimate and plot both
                        mutation signatures and their fractions
hildaGlobalResult       Compute the Bayes factor
hildaLocalResult        Extract the posterior distributions of the mean
                        differences in muational exposures
hildaPlotSignature      Plot mutation signatures from HiLDA output
hildaReadMPFile         Read the raw mutation data of Mutation Position
                        Format.
hildaRhat               Output the maximum potential scale reduction
                        statistic of all parameters estimated
hildaTest               Apply HiLDA to statistically testing the global
                        difference in burdens of mutation signatures
                        between two groups
MetaInformation-class   An S4 class to represent a mutation meta
                        information common to many data types
MutationFeatureData-class
                        An S4 class representing the mutation data
mySquareEM              A function for estimating parameters using
                        Squared EM algorithm
pmBarplot               Plot both mutation signatures and their
                        mutational exposures from pmsignature output
pmgetSignature          Obtain the parameters for mutation signatures
                        and memberships
pmMultiBarplot          Plot both mutation signatures and their
                        mutational exposures from pmsignature output
                        for more than two groups
pmPlotSignature         Plot mutation signatures from pmsignature
                        output
PMSboundary             A functional for generating the function
                        checking the parameter (p) is within the
                        restricted conditions or not
updateMstepFQC          Update the parameter F and Q (M-step in the
                        EM-algorithm)
updatePMSParam          A function for updating parameters using
                        EM-algorithm
updateTheta_NormalizedC
                        Update the auxiliary parameters theta and
                        normalize them so that the summation of each
                        group sums to 1 (E-step), also calculate the
                        current log-likelihood value
visPMS                  visualize probabisitic mutaiton signature for
                        the independent model
