Man pages for nem
(Dynamic) Nested Effects Models and Deterministic Effects Propagation Networks to reconstruct phenotypic hierarchies
| BFSlevel | Build (generalized) hierarchy by Breath-First Search |
| BoutrosRNAi2002 | RNAi data on Drosophila innate immune response |
| closest.transitive.greedy | Find transitively closed graph most similar to the given one |
| enumerate.models | Exhaustive enumeration of models |
| generateNetwork | Random networks and data sampling |
| getDensityMatrix | Calculate density matrix from raw p-value matrix |
| infer.edge.type | Infer regulation direction for each edge |
| internal | internal functions |
| Ivanova2006RNAiTimeSeries | Perturbation Time Series |
| local.model.prior | Computes a prior to be used for edge-wise model inference |
| nem | Nested Effects Models - main function |
| nem.bootstrap | Bootstrapping for nested effect models |
| nem.calcSignificance | Statistical significance of network hypotheses |
| nem.consensus | Statistically stabile nested effects models |
| nem.cont.preprocess | Calculate classification probabilities of perturbation data... |
| nem.discretize | Discretize perturbation data according to control experiments |
| nem.jackknife | Jackknife for nested effect models |
| nemModelSelection | Model selection for nested effect models |
| network.AIC | AIC/BIC criterion for network graph |
| NiederbergerMediator2012 | Expression measurements upon perturbation of Mediator... |
| plotEffects | Plots data according to a phenotypic hierarchy |
| plot.nem | plot nested effect model |
| prior.EgeneAttach.EB | Initialize E-gene attachment prior for empirical Bayes |
| prune.graph | Prunes spurious edges in a phenotypic hierarchy |
| quicknem | Quick run of Nested Effects Models inference |
| SahinRNAi2008 | Combinatorial Protein Knockdowns in the ERBB Signaling... |
| SCCgraph | Combines Strongly Connected Components into single nodes |
| selectEGenes | Automatic selection of most relevant effect reporters |
| set.default.parameters | Get/set hyperparameters |
| sim.intervention | Simulate interventions in a Nested Effects Model |
| subsets | Subsets |
| transitive.closure | Computes the transitive closure of a directed graph |
| transitive.projections | Computes the transitive approximation of a directed graph |
| transitive.reduction | Computes the transitive reduction of a graph |
