Man pages for cbg-ethz/TiMEx
Finding Mutually Exclusive Groups of Alterations in Cancer Datasets
| analyzePairs | Finds all mutually exclusive pairs in a dataset |
| breast | Breast cancer dataset |
| breastGroups | Metagroups of genes in breast cancer |
| breastOutput | Mutually exclusive groups in breast cancer |
| breastSubsampling | Stability of mutually exclusive groups in breast cancer |
| breastSubtypes | Breast cancer subtypes |
| breastSubtypesOutput | Mutually exclusive groups in breast cancer subtypes |
| doMaxCliques | Identifies maximal cliques from pairwise testing information |
| doMetagene | Creates metagroups of genes |
| findSignifCliques | Tests all maximal cliques for mutual exclusivity |
| gbmDendrix | Glioblastoma dataset used by Dendrix |
| gbmDendrixOutput | Mutually exclusive groups in the glioblastoma dataset used by... |
| gbmDendrixSubsampling | Stability of mutually exclusive groups in the glioblastoma... |
| gbmMuex | Glioblastoma dataset used by muex |
| gbmMuexOutput | Mutually exclusive groups in the glioblastoma dataset used by... |
| gbmMuexSubsampling | Stability of mutually exclusive groups in the glioblastoma... |
| ovarian | Ovarian cancer dataset |
| ovarianGroups | Metagroups of genes in ovarian cancer |
| ovarianOutput | Mutually exclusive groups in ovarian cancer |
| ovarianSubsampling | Stability of mutually exclusive groups in ovarian cancer |
| plotGroupByName | Plots a Mutually Exclusive group |
| produceGenesGroup | (internal) main function to simulate genes corresponding to... |
| produceTablesSignifGroups | Produces tables with groups |
| recoverAllNamesGroups | Recovers members of the metagroups |
| removeLowFreqs | Removes alterations based on frequency |
| simulateGenes | Generates data from the TiMEx model |
| subsampleAnalysis | Assesses the stability of groups by subsampling |
| testCliqueAsGroup | Tests whether a given group is mutually exclusive |
| TiMEx | Finds mutually exclusive groups |
| TiMEx-package | The main usages of TiMEx |
