Man pages for cbg-ethz/pathTiMEx
Joint Inference of Mutually Exclusive Driver Pathways and their Progression Dynamics
| addAllGenesNotInTiMEx | Appends the genes as single clusters |
| addNoise | Add noise to a binary matrix |
| addPathBinary | Summarizes the inferred groups |
| cleanGroupys | Removes empty groups |
| clustMetrIterTiMEx | Assesses the performance of the inferred groups after running... |
| compareStructs | Compares two posets |
| computeScore | Computes clustering score |
| count.duplicates | Counts duplicates in a data frame |
| countPerfSims | Assesses how well each group was reconstructed |
| doPatForCBN | Produces 'pat' files for H-CBN |
| drawSamples | Draws samples from a pathTiMEx model |
| generateFixedModel | Generates a pathTiMEx model for given structure and... |
| generateRandomModel | Randomly generates a pathTiMEx model |
| generateStructureModel | Generates a pathTiMEx model for given parameters |
| genRandomPoset | Generates a poset |
| iterTiMExBinaryMats | Interative TiMEx on any binary dataset |
| iterTiMExSims | Performs TiMEx iteratively on a simulated dataset |
| make_linear_poset | Simulates a linear poset |
| optGroups | Locally optimizes pathway assignment |
| pathTiMEx-package | Joint Inference of Mutually Exclusive Driver Pathways and... |
| plotPoset | Plots a poset |
| plotPosetPaths | Plots a poset on pathways |
| returnAssignment | Returns assignment to groups as vector |
| returnMetricsClust | Evaluates performance of inference of groups |
| runCBN | Runs H-CBN |
| sampleMEPathways | Draws samples from a mutually exclusive pathway |
| summarizeSims | Assesses how well each group was reconstructed |
| topologicalSort | Computes the topological sort of a poset |
| transformAndWritePoset | Transforms poset |
| trans_reduction | Transforms a poset into its transitive reduction |
| writePosetForCBN | Writes a poset to a file |
