# Nested Effects Models to reconstruct phenotypic hierarchies

## Documentation for package `nem' version 1.6.0

## User Guides and Package Vignettes

Read overview or browse directory.

## Help Pages

BFSlevel | Build (generalized) hierarchy by Breath-First Search
BoutrosRNAi2002 | RNAi data on Drosophila innate immune response
BoutrosRNAiDiscrete | RNAi data on Drosophila innate immune response
BoutrosRNAiExpression | RNAi data on Drosophila innate immune response
connectModules | Infers a phenotypic hierarchy using the module network
enumerate.models | Exhaustive enumeration of models
FULLmLL | Full marginal likelihood of a phenotypic hierarchy
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
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.ModuleNetwork | plot nested effect model
plot.nem | plot nested effect model
plot.pairwise | plot nested effect model
plot.score | plot nested effect model
plot.triples | plot nested effect model
print.ModuleNetwork | Infers a phenotypic hierarchy using the module network
print.pairwise | Infers a phenotypic hierarchy edge by edge
print.score | Computes the marginal likelihood of phenotypic hierarchies
print.triples | Infers a phenotypic hierarchy from triples
SCCgraph | Combines Strongly Connected Components into single nodes
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