BoutrosRNAi2002         RNAi data on Drosophila innate immune response
FULLmLL                 Full marginal likelihood of a phenotypic
                        hierarchy
SCCgraph                Combines Strongly Connected Components into
                        single nodes
enumerate.models        Exhaustive enumeration of models
local.model.prior       Computes a prior to be used for edge-wise model
                        inference
mLL                     Marginal likelihood of a phenotypic hierarchy
nem                     Nested Effects Models - main function
nem.discretize          Discretize perturbation data according to
                        control experiments
pairwise.posterior      Infers a phenotypic hierarchy edge by edge
plot.effects            Plots data according to a phenotypic hierarchy
prune.graph             Prunes spurious edges in a phenotypic hierarchy
score                   Computes the marginal likelihood of phenotypic
                        hierarchies
transitive.closure      Computes the transitive closure of a directed
                        graph
transitive.reduction    Computes the transitive reduction of a graph
