"CBN2Path: an R/Bioconductor package for the analysis of cancer
progression pathways using Conjunctive Bayesian Networks
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Documentation for package ‘CBN2Path’ version 1.0.0
Help Pages
| base2Indexing | base2Indexing |
| base2IndVec | base2IndVec |
| bcbn | B-CBN |
| ctcbn | CT-CBN |
| ctcbnSingle | CT-CBN Single Batch |
| edgeMarginalized | edgeMarginalized |
| generateData | Generate Data |
| generateMatrixGenotypes | generateMatrixGenotypes |
| generateTCGAMatrix | Generate TCGA Genotype Matrix |
| genotypeFeasibility | genotypeFeasibility |
| genotypeMatrixMutator | genotypeMatrixMutator |
| getExamples | Get paths to examples |
| getRawTCGAData | Get Raw TCGA Data |
| hcbn | H-CBN |
| hcbnSingle | H-CBN Single Batch |
| jensenShannonDivergence | jensenShannonDivergence |
| pathEdgeMapper | pathEdgeMapper |
| pathNormalization | pathNormalization |
| pathProbCBN | pathProbCBN: quantifies pathway probabilities using the output of CT-CBN or H-CBN |
| pathProbQuartetBCBN | pathProbQuartetBCBN |
| pathProbQuartetCTCBN | pathProbQuartetCTCBN |
| pathProbQuartetHCBN | pathProbQuartetHCBN |
| pathProbQuartetRCBN | pathProbQuartetRCBN |
| pathProbSSWM | pathProbSSWM |
| pathwayCompatibilityQuartet | pathwayCompatibilityQuartet |
| pathwayFeasibility | pathwayFeasibility |
| pathwayGenotypeCompatibility | pathwayGenotypeCompatibility |
| pathwayWeightingRCBN | pathwayWeightingRCBN |
| permutations | permutations |
| posetWeightingRCBN | posetWeightingRCBN |
| predictability | predictability |
| readLambda | Read a .lambda file |
| readPattern | Read a .pat file |
| readPoset | Read a .poset file |
| readTime | Read a .time file |
| Spock | Poset and pattern/lambda data |
| transitiveClosure | Transitive Closure |
| visualizeCBNModel | Visualize CBN Model |
| visualizeFitnessLandscape | Visualize Fitness Landscape |
| visualizeProbabilities | Visualize Pathway Probabilities |