Nested Effects Models to reconstruct phenotypic hierarchies


[Package List] [Top]

Documentation for package `nem' version 1.2.0

User Guides and Package Vignettes

Read overview or browse directory.

Help Pages

BoutrosRNAi2002 RNAi data on Drosophila innate immune response
BoutrosRNAiDiscrete RNAi data on Drosophila innate immune response
BoutrosRNAiExpression RNAi data on Drosophila innate immune response
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
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
plot.nem Nested Effects Models - main function
plot.pairwise Infers a phenotypic hierarchy edge by edge
plot.score Computes the marginal likelihood of phenotypic hierarchies
print.nem Nested Effects Models - main function
print.pairwise Infers a phenotypic hierarchy edge by edge
print.score Computes the marginal likelihood of phenotypic hierarchies
prune.graph Prunes spurious edges in a phenotypic hierarchy
SCCgraph Combines Strongly Connected Components into single nodes
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