Entry: BFSlevel
Aliases: BFSlevel
Keywords: graphs
Description: Build (generalized) hierarchy by Breath-First Search
URL: ../../../library/nem/html/BFSlevel.html

Entry: BoutrosRNAi2002
Aliases: BoutrosRNAiExpression BoutrosRNAiDiscrete BoutrosRNAiDens BoutrosRNAiLods BoutrosRNAiLogFC BoutrosRNAi2002
Keywords: datasets
Description: RNAi data on Drosophila innate immune response
URL: ../../../library/nem/html/BoutrosRNAi2002.html

Entry: SCCgraph
Aliases: SCCgraph
Keywords: graphs
Description: Combines Strongly Connected Components into single nodes
URL: ../../../library/nem/html/SCCgraph.html

Entry: SahinRNAi2008
Aliases: SahinRNAi2008 dat.normalized dat.unnormalized
Keywords: datasets
Description: Combinatorial Protein Knockdowns in the ERBB Signaling Pathway
URL: ../../../library/nem/html/SahinRNAi2008.html

Entry: closest.transitive.greedy
Aliases: closest.transitive.greedy
Keywords: models
Description: Find transitively closed graph most similar to the given one
URL: ../../../library/nem/html/closest.transitive.greedy.html

Entry: enumerate.models
Aliases: enumerate.models
Keywords: graphs
Description: Exhaustive enumeration of models
URL: ../../../library/nem/html/enumerate.models.html

Entry: generateNetwork
Aliases: sampleRndNetwork sampleData sampleData.BN
Keywords: graphs models
Description: Random networks and data sampling
URL: ../../../library/nem/html/generateNetwork.html

Entry: getDensityMatrix
Aliases: getDensityMatrix
Keywords: models
Description: Calculate density matrix from raw p-value matrix
URL: ../../../library/nem/html/getDensityMatrix.html

Entry: infer.edge.type
Aliases: infer.edge.type
Keywords: models
Description: Infer regulation direction for each edge
URL: ../../../library/nem/html/infer.edge.type.html

Entry: internal
Aliases: internal moduleNetwork.aux connectModules fitBUM dbum rbum qbum pbum getComponent inv.logit logit bum.negLogLik bum.mle bum.EM qqbum bum.histogram bum.dalt bum.palt bum.qalt bum.ralt nem.featureselection createBN which.is.max fit.BN exhaustive_BN optimizemarginal ingreed_BN optimizecoregraph graychange is.dag optimizemarginal.nuInf parameters_continuous_Bayesian parameters_continuous_ML parameters_discrete_Bayesian parameters_discrete_ML score_continuous_Bayesian score_continuous_ML score_discrete_Bayesian score_discrete_ML FULLmLL mLL score moduleNetwork enumerate.models2 nem.greedy nem.greedyMAP pairwise.posterior triples.posterior nem.BN data.likelihood effect.likelihood encode.interventions erase.cycles learn learn.conditionals PhiDistr sample.effect.likelihood sample.likelihood score_BN score.network sim.interventions
Keywords: models
Description: internal functions
URL: ../../../library/nem/html/internal.html

Entry: local.model.prior
Aliases: local.model.prior
Keywords: models
Description: Computes a prior to be used for edge-wise model inference
URL: ../../../library/nem/html/local.model.prior.html

Entry: nem
Aliases: nem print.nem print.nem.greedy print.nem.greedyMAP print.pairwise print.triples print.ModuleNetwork print.score print.nem.BN
Keywords: graphs models
Description: Nested Effects Models - main function
URL: ../../../library/nem/html/nem.html

Entry: nem.bootstrap
Aliases: nem.bootstrap print.nem.bootstrap
Keywords: graphs models
Description: Bootstrapping for nested effect models
URL: ../../../library/nem/html/nem.bootstrap.html

Entry: nem.calcSignificance
Aliases: nem.calcSignificance
Keywords: models
Description: Statistical significance of network hypotheses
URL: ../../../library/nem/html/nem.calcSignificance.html

Entry: nem.consensus
Aliases: nem.consensus print.nem.consensus
Keywords: graphs models
Description: Statistically stabile nested effects models
URL: ../../../library/nem/html/nem.consensus.html

Entry: nem.cont.preprocess
Aliases: nem.cont.preprocess
Keywords: graphs models
Description: Calculate classification probabilities of perturbation data according to control experiments
URL: ../../../library/nem/html/nem.cont.preprocess.html

Entry: nem.discretize
Aliases: nem.discretize
Keywords: graphs models
Description: Discretize perturbation data according to control experiments
URL: ../../../library/nem/html/nem.discretize.html

Entry: nem.jackknife
Aliases: nem.jackknife print.nem.jackknife
Keywords: models
Description: Jackknife for nested effect models
URL: ../../../library/nem/html/nem.jackknife.html

Entry: nemModelSelection
Aliases: nemModelSelection
Keywords: graphs models
Description: Model selection for nested effect models
URL: ../../../library/nem/html/nemModelSelection.html

Entry: network.AIC
Aliases: network.AIC
Keywords: graphs
Description: AIC/BIC criterion for network graph
URL: ../../../library/nem/html/network.AIC.html

Entry: plot.nem
Aliases: plot.nem plot.triples plot.pairwise plot.score plot.ModuleNetwork plot.nem.greedy plot.nem.greedyMAP plot.nem.bootstrap plot.nem.jackknife plot.nem.consensus plot.nem.BN plotnem
Keywords: models
Description: plot nested effect model
URL: ../../../library/nem/html/plot.nem.html

Entry: plotEffects
Aliases: plotEffects
Keywords: graphs
Description: Plots data according to a phenotypic hierarchy
URL: ../../../library/nem/html/plotEffects.html

Entry: prune.graph
Aliases: prune.graph
Keywords: graphs
Description: Prunes spurious edges in a phenotypic hierarchy
URL: ../../../library/nem/html/prune.graph.html

Entry: getRelevantEGenes
Aliases: getRelevantEGenes selectEGenes filterEGenes
Keywords: models
Description: Automatic selection of most relevant effect reporters
URL: ../../../library/nem/html/selectEGenes.html

Entry: set.default.parameters
Aliases: set.default.parameters
Keywords: graphs models
Description: Get/set hyperparameters
URL: ../../../library/nem/html/set.default.parameters.html

Entry: sim.intervention
Aliases: sim.intervention sim.intervention
Keywords: models
Description: Simulate interventions in a Nested Effects Model
URL: ../../../library/nem/html/sim.intervention.html

Entry: subsets
Aliases: subsets
Keywords: graphs
Description: Subsets
URL: ../../../library/nem/html/subsets.html

Entry: transitive.closure
Aliases: transitive.closure
Keywords: graphs
Description: Computes the transitive closure of a directed graph
URL: ../../../library/nem/html/transitive.closure.html

Entry: transitive.projections
Aliases: transitive.projections CheckEdge remTwoEdges transSubGr EdgeEk distdecrease distsame distincrease distincrease1 OneNeighborhood TwoNeighborhood ThreeNeighborhood FourNeighborhood VecToMat is.transitive
Keywords: graphs
Description: Computes the transitive approximation of a directed graph
URL: ../../../library/nem/html/transitive.projections.html

Entry: transitive.reduction
Aliases: transitive.reduction
Keywords: graphs
Description: Computes the transitive reduction of a graph
URL: ../../../library/nem/html/transitive.reduction.html
