Nested Effects Models to reconstruct phenotypic hierarchies


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Documentation for package ‘nem’ version 2.2.1

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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
bum.dalt internal functions
bum.EM internal functions
bum.histogram internal functions
bum.mle internal functions
bum.negLogLik internal functions
bum.palt internal functions
bum.qalt internal functions
bum.ralt internal functions
connectModules internal functions
CONTmLL Marginal likelihood of a phenotypic hierarchy with continuous data
dbum internal functions
enumerate.models Exhaustive enumeration of models
filterEGenes Automatic selection of most relevant S-genes
fitBUM internal functions
FULLmLL Full marginal likelihood of a phenotypic hierarchy
getComponent internal functions
getDensityMatrix Calculate density matrix from raw p-value matrix
getRelevantEGenes Automatic selection of most relevant S-genes
internal internal functions
inv.logit internal functions
local.model.prior Computes a prior to be used for edge-wise model inference
logit internal functions
mLL Marginal likelihood of a phenotypic hierarchy
moduleNetwork Infers a phenotypic hierarchy using the module network
moduleNetwork.aux internal functions
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
pbum internal functions
PhiDistr Computes the marginal likelihood of phenotypic hierarchies
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.nem.greedy Infers a phenotypic hierarchy using a greedy search strategy
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
prune.graph Prunes spurious edges in a phenotypic hierarchy
qbum internal functions
qqbum internal functions
rbum internal functions
SCCgraph Combines Strongly Connected Components into single nodes
score Computes the marginal likelihood of phenotypic hierarchies
selectEGenes Automatic selection of most relevant S-genes
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