BFSlevel                Build (generalized) hierarchy by Breath-First
                        Search
BoutrosRNAi2002         RNAi data on Drosophila innate immune response
CONTmLL                 Marginal likelihood of a phenotypic hierarchy
                        with continuous data
FULLmLL                 Full marginal likelihood of a phenotypic
                        hierarchy
SCCgraph                Combines Strongly Connected Components into
                        single nodes
enumerate.models        Exhaustive enumeration of models
getDensityMatrix        Calculate density matrix from raw p-value
                        matrix
getRelevantEGenes       Automatic selection of most relevant S-genes
internal                internal functions
local.model.prior       Computes a prior to be used for edge-wise model
                        inference
mLL                     Marginal likelihood of a phenotypic hierarchy
moduleNetwork           Infers a phenotypic hierarchy using the module
                        network
nem                     Nested Effects Models - main function
nem.cont.preprocess     Calculate classification probabilities of
                        perturbation data according to control
                        experiments
nem.discretize          Discretize perturbation data according to
                        control experiments
nem.greedy              Infers a phenotypic hierarchy using a greedy
                        search strategy
nemModelSelection       model selection for nested effect models
network.AIC             AIC criterion for network graph
pairwise.posterior      Infers a phenotypic hierarchy edge by edge
plot.effects            Plots data according to a phenotypic hierarchy
plot.nem                plot nested effect model
prune.graph             Prunes spurious edges in a phenotypic hierarchy
score                   Computes the marginal likelihood of phenotypic
                        hierarchies
subsets                 Subsets
transitive.closure      Computes the transitive closure of a directed
                        graph
transitive.reduction    Computes the transitive reduction of a graph
triples.posterior       Infers a phenotypic hierarchy from triples
