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 BoutrosRNAi2002
Keywords: datasets
Description: RNAi data on Drosophila innate immune response
URL: ../../../library/nem/html/BoutrosRNAi2002.html

Entry: FULLmLL
Aliases: FULLmLL
Keywords: models
Description: Full marginal likelihood of a phenotypic hierarchy
URL: ../../../library/nem/html/FULLmLL.html

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

Entry: enumerate.models
Aliases: enumerate.models
Keywords: graphs
Description: Exhaustive enumeration of models
URL: ../../../library/nem/html/enumerate.models.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: mLL
Aliases: mLL
Keywords: models
Description: Marginal likelihood of a phenotypic hierarchy
URL: ../../../library/nem/html/mLL.html

Entry: moduleNetwork
Aliases: moduleNetwork moduleNetwork.aux connectModules print.ModuleNetwork
Keywords: graphs
Description: Infers a phenotypic hierarchy using the module network
URL: ../../../library/nem/html/moduleNetwork.html

Entry: nem
Aliases: nem
Keywords: graphs models
Description: Nested Effects Models - main function
URL: ../../../library/nem/html/nem.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: 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 criterion for network graph
URL: ../../../library/nem/html/network.AIC.html

Entry: pairwise.posterior
Aliases: pairwise.posterior print.pairwise
Keywords: graphs
Description: Infers a phenotypic hierarchy edge by edge
URL: ../../../library/nem/html/pairwise.posterior.html

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

Entry: plot.nem
Aliases: plot.nem plot.triples plot.pairwise plot.score plot.ModuleNetwork
Keywords: models
Description: plot nested effect model
URL: ../../../library/nem/html/plot.nem.html

Entry: score
Aliases: score print.score
Keywords: models
Description: Computes the marginal likelihood of phenotypic hierarchies
URL: ../../../library/nem/html/score.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.reduction
Aliases: transitive.reduction
Keywords: graphs
Description: Computes the transitive reduction of a graph
URL: ../../../library/nem/html/transitive.reduction.html

Entry: triples.posterior
Aliases: triples.posterior print.triples
Keywords: graphs
Description: Infers a phenotypic hierarchy from triples
URL: ../../../library/nem/html/triples.posterior.html
