Man pages for friend1ws/pmsignature
Extracting characteristic mutation signatures from a set of mutation data.
| alignmentSignature | From the list of Parameters from the getPMSignature function,... |
| bootPMSignature | Obtain the standard error estimates for parameters for... |
| 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 |
| convertSignatureMatrixToVector | the function for converting the mutation signature matrix to... |
| 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 |
| getBackgroudSignature | get mutation feature vector from context sequence data and... |
| getCosDistance | the function for calculating cosine distances between two... |
| getLogLikelihoodC | Calculate the value of the log-likelihood for given... |
| getMembershipValue | Get the values of estimated membership parameters |
| getMutationFeatureVector | Get mutation feature vector from context sequence data and... |
| getMutMembership | Obtain the standard error estimates for parameters for... |
| getMutNum | Obtain somatic mutation count for each sample |
| getPMSignature | Obtain the parameters for mutation signatures and memberships |
| getSignaturesForMultipleK | Generate the figure of mutation signature for multiple K... |
| getSignatureValue | Get the values of estimated signatures |
| makeSimData | Generate simulation data |
| 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... |
| PMSboundary | A functional for generating the function checking the... |
| readBGFile | Read and format the background vector data |
| readMFVFile | Read the raw mutation data with the mutation feature vector... |
| readMPFile | Read the raw mutation data of Mutation Position Format. |
| updateBackgroudSignatureFile | update the background signature file in the package... |
| 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... |
| visMembership | Visualize estimated membership parameters |
| visMembership2 | Visualize estimated membership parameters using ggvis |
| visPMS_full | visualize probabisitic mutaiton signature for the full model |
| visPMSignature | Visualize estimated probabilistic mutation signatures |
| visPMS_ind | visualize probabisitic mutaiton signature for the independent... |
