API for cbg-ethz/pcNEM
Probabilistic combinatorial nested effects model
| Global functions | |
|---|---|
| .onLoad | Source code |
| AdaSimulatedAnnealing | Man page |
| BFSlevel | Man page Source code |
| BoutrosRNAi2002 | Man page |
| BoutrosRNAiDens | Man page |
| BoutrosRNAiDiscrete | Man page |
| BoutrosRNAiExpression | Man page |
| BoutrosRNAiLods | Man page |
| BoutrosRNAiLogFC | Man page |
| CheckEdge | Man page |
| D | Man page |
| DAG.rescore | Source code |
| DAGscore | Source code |
| EMforMCMC | Source code |
| EdgeEk | Man page Source code |
| FULLmLL | Man page Source code |
| FourNeighborhood | Man page Source code |
| Ivanova2006RNAiTimeSeries | Man page |
| KOmap | Man page |
| NiederbergerMediator2012 | Man page |
| NiederbergerMediatorLods | Man page |
| NiederbergerMediatorLogFC | Man page |
| NiederbergerMediatorPVals | Man page |
| OneNeighborhood | Man page Source code |
| PathNumber | Source code |
| PhiDistr | Man page Source code |
| SCCgraph | Man page Source code |
| SahinRNAi2008 | Man page |
| SearchNearestDAG | Source code |
| ThreeNeighborhood | Man page Source code |
| TwoNeighborhood | Man page Source code |
| VecToMat | Man page Source code |
| ancestor | Source code |
| bum.EM | Man page Source code |
| bum.dalt | Man page Source code |
| bum.histogram | Man page Source code |
| bum.mle | Man page Source code |
| bum.negLogLik | Man page Source code |
| bum.palt | Man page Source code |
| bum.qalt | Man page Source code |
| bum.ralt | Man page Source code |
| calcLikelihood | Source code |
| calculateHiddenPrior | Source code |
| closest.transitive.greedy | Man page Source code |
| connectModules | Man page |
| connectModules.aux | Source code |
| connectModules.orig | Source code |
| connectModules2 | Source code |
| createBN | Man page Source code |
| dat | Man page |
| dat.normalized | Man page |
| dat.unnormalized | Man page |
| data.likelihood | Man page Source code |
| dbum | Man page Source code |
| des_top_order | Source code |
| distdecrease | Man page Source code |
| distincrease | Man page Source code |
| distincrease1 | Man page Source code |
| distsame | Man page Source code |
| dynoNEM.perturb | Source code |
| dynoNEM.posteriorEGenePos | Source code |
| dynoNEM_MCMC | Source code |
| effect.likelihood | Man page Source code |
| encode.interventions | Man page Source code |
| enumerate.models | Man page Source code |
| enumerate.models2 | Man page |
| erase.cycles | Man page Source code |
| exhaustive_BN | Man page |
| filterEGenes | Man page Source code |
| final_attachement | Source code |
| fit.BN | Man page Source code |
| fitBUM | Man page Source code |
| get.deletions | Source code |
| get.insertions | Source code |
| get.reversions | Source code |
| getComponent | Man page Source code |
| getDensityMatrix | Man page Source code |
| getFinalTheta | Source code |
| getRelevantEGenes | Man page Source code |
| getperturb.matrices | Source code |
| graychange | Man page |
| infer.edge.type | Man page Source code |
| ingreed_BN | Man page Source code |
| internal | Man page |
| inv.logit | Man page Source code |
| is.dag | Man page Source code |
| is.transitive | Man page Source code |
| learn | Man page Source code |
| learn.conditionals | Man page Source code |
| local.model.prior | Man page Source code |
| logit | Man page Source code |
| mLL | Man page Source code |
| map.int2node | Man page |
| mcmc | Source code |
| moduleNetwork | Man page Source code |
| moduleNetwork.aux | Man page Source code |
| moduleNetwork.orig | Source code |
| nem | Man page Source code |
| nem.AdaSA | Source code |
| nem.BN | Man page Source code |
| nem.bootstrap | Man page Source code |
| nem.bootstrap.list | Source code |
| nem.calcSignificance | Man page Source code |
| nem.consensus | Man page Source code |
| nem.cont.preprocess | Man page |
| nem.discretize | Man page Source code |
| nem.featureselection | Man page Source code |
| nem.greedy | Man page Source code |
| nem.greedyMAP | Man page Source code |
| nem.jackknife | Man page Source code |
| nemModelSelection | Man page Source code |
| network.AIC | Man page Source code |
| onestep_EMiNEM | Source code |
| onestep_mcmc | Source code |
| optimizecoregraph | Man page Source code |
| optimizemarginal | Man page Source code |
| optimizemarginal.nuInf | Man page Source code |
| pairwise.posterior | Man page |
| parameters_continuous_Bayesian | Man page |
| parameters_continuous_ML | Man page |
| parameters_discrete_Bayesian | Man page |
| parameters_discrete_ML | Man page |
| pbum | Man page Source code |
| plot.ModuleNetwork | Man page Source code |
| plot.dynoNEM | Man page Source code |
| plot.mc.eminem | Man page Source code |
| plot.nem | Man page Source code |
| plot.nem.BN | Man page Source code |
| plot.nem.bootstrap | Man page Source code |
| plot.nem.consensus | Man page Source code |
| plot.nem.greedy | Man page Source code |
| plot.nem.greedyMAP | Man page Source code |
| plot.nem.jackknife | Man page Source code |
| plot.pairwise | Man page Source code |
| plot.score | Man page Source code |
| plot.score.list | Source code |
| plot.triples | Man page Source code |
| plotEffects | Man page Source code |
| plotnem | Man page Source code |
| print.ModuleNetwork | Man page Source code |
| print.dynoNEM | Man page Source code |
| print.mc.eminem | Man page Source code |
| print.nem | Man page Source code |
| print.nem.BN | Man page Source code |
| print.nem.bootstrap | Man page Source code |
| print.nem.consensus | Man page Source code |
| print.nem.greedy | Man page Source code |
| print.nem.greedyMAP | Man page Source code |
| print.nem.jackknife | Man page Source code |
| print.pairwise | Man page Source code |
| print.score | Man page Source code |
| print.score.list | Source code |
| print.triples | Man page Source code |
| prior.EgeneAttach.EB | Man page Source code |
| probmatrix.rescorenodes | Source code |
| propersample | Source code |
| prune.graph | Man page Source code |
| qbum | Man page Source code |
| qqbum | Man page Source code |
| quicknem | Man page Source code |
| rbum | Man page Source code |
| rec.sample | Source code |
| remTwoEdges | Man page Source code |
| runMCMC | Source code |
| sample.effect.likelihood | Man page Source code |
| sample.likelihood | Man page Source code |
| sampleData | Man page Source code |
| sampleData.BN | Man page |
| sampleData.pcnem | Source code |
| sampleRndNetwork | Man page Source code |
| score | Man page Source code |
| score.aux | Source code |
| score.network | Man page Source code |
| score_BN | Man page Source code |
| score_continuous_Bayesian | Man page Source code |
| score_continuous_ML | Man page Source code |
| score_discrete_Bayesian | Man page Source code |
| score_discrete_ML | Man page Source code |
| selectEGenes | Man page |
| set.default.parameters | Man page Source code |
| siRNA_gene_Expts | Man page |
| sim.intervention | Man page Man page Source code |
| sim.interventions | Man page Source code |
| subsets | Man page Source code |
| top_order | Source code |
| transSubGr | Man page Source code |
| transitive.closure | Man page Source code |
| transitive.projections | Man page Source code |
| transitive.reduction | Man page Source code |
| triples.posterior | Man page Source code |
| updateHidden | Source code |
| which.is.max | Man page |
