Man pages for HiLDA
Conducting statistical inference on comparing the mutational exposures of mutational signatures by using hierarchical latent Dirichlet allocation
| 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... |
| 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... |
| getMutationFeatureVector | Get mutation feature vector from context sequence data and... |
| hildaBarplot | Read the raw mutation data with the mutation feature vector... |
| hildaDiffPlot | Read the raw mutation data with the mutation feature vector... |
| hildaGlobalResult | Compute the Bayes factor |
| hildaLocalResult | Extract the posterior distributions of the mean differences... |
| 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... |
| hildaTest | Apply HiLDA to statistically testing the global difference in... |
| MetaInformation-class | An S4 class to represent a mutation meta information common... |
| MutationFeatureData-class | An S4 class representing the mutation data |
| mySquareEM | A function for estimating parameters using Squared EM... |
| pmBarplot | Plot both mutation signatures and their mutational exposures... |
| pmgetSignature | Obtain the parameters for mutation signatures and memberships |
| pmMultiBarplot | Plot both mutation signatures and their mutational exposures... |
| pmPlotSignature | Plot mutation signatures from pmsignature output |
| PMSboundary | A functional for generating the function checking the... |
| 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... |
| visPMS | visualize probabisitic mutaiton signature for the independent... |
