Nested Effects Models to reconstruct phenotypic hierarchies


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Documentation for package ‘nem’ version 2.34.0

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B C D E F G I L M N O P Q R S T V W

-- B --

BFSlevel Build (generalized) hierarchy by Breath-First Search
BoutrosRNAi2002 RNAi data on Drosophila innate immune response
BoutrosRNAiDens RNAi data on Drosophila innate immune response
BoutrosRNAiDiscrete RNAi data on Drosophila innate immune response
BoutrosRNAiExpression RNAi data on Drosophila innate immune response
BoutrosRNAiLods RNAi data on Drosophila innate immune response
BoutrosRNAiLogFC 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

-- C --

CheckEdge Computes the transitive approximation of a directed graph
closest.transitive.greedy Find transitively closed graph most similar to the given one
connectModules internal functions
createBN internal functions

-- D --

dat Perturbation Time Series
dat.normalized Combinatorial Protein Knockdowns in the ERBB Signaling Pathway
dat.unnormalized Combinatorial Protein Knockdowns in the ERBB Signaling Pathway
data.likelihood internal functions
dbum internal functions
distdecrease Computes the transitive approximation of a directed graph
distincrease Computes the transitive approximation of a directed graph
distincrease1 Computes the transitive approximation of a directed graph
distsame Computes the transitive approximation of a directed graph

-- E --

EdgeEk Computes the transitive approximation of a directed graph
effect.likelihood internal functions
encode.interventions internal functions
enumerate.models Exhaustive enumeration of models
enumerate.models2 internal functions
erase.cycles internal functions
exhaustive_BN internal functions

-- F --

filterEGenes Automatic selection of most relevant effect reporters
fit.BN internal functions
fitBUM internal functions
FourNeighborhood Computes the transitive approximation of a directed graph
FULLmLL internal functions

-- G --

getComponent internal functions
getDensityMatrix Calculate density matrix from raw p-value matrix
getRelevantEGenes Automatic selection of most relevant effect reporters
graychange internal functions

-- I --

infer.edge.type Infer regulation direction for each edge
ingreed_BN internal functions
internal internal functions
inv.logit internal functions
is.dag internal functions
is.transitive Computes the transitive approximation of a directed graph
Ivanova2006RNAiTimeSeries Perturbation Time Series

-- L --

learn internal functions
learn.conditionals internal functions
local.model.prior Computes a prior to be used for edge-wise model inference
logit internal functions

-- M --

map.int2node Combinatorial Protein Knockdowns in the ERBB Signaling Pathway
mLL internal functions
moduleNetwork internal functions
moduleNetwork.aux internal functions

-- N --

nem Nested Effects Models - main function
nem.BN internal functions
nem.bootstrap Bootstrapping for nested effect models
nem.calcSignificance Statistical significance of network hypotheses
nem.consensus Statistically stabile nested effects models
nem.cont.preprocess Calculate classification probabilities of perturbation data according to control experiments
nem.discretize Discretize perturbation data according to control experiments
nem.featureselection internal functions
nem.greedy internal functions
nem.greedyMAP internal functions
nem.jackknife Jackknife for nested effect models
nemModelSelection Model selection for nested effect models
network.AIC AIC/BIC criterion for network graph
NiederbergerMediator2012 Expression measurements upon perturbation of Mediator subunits
NiederbergerMediatorLods Expression measurements upon perturbation of Mediator subunits
NiederbergerMediatorLogFC Expression measurements upon perturbation of Mediator subunits
NiederbergerMediatorPVals Expression measurements upon perturbation of Mediator subunits

-- O --

OneNeighborhood Computes the transitive approximation of a directed graph
optimizecoregraph internal functions
optimizemarginal internal functions
optimizemarginal.nuInf internal functions

-- P --

pairwise.posterior internal functions
parameters_continuous_Bayesian internal functions
parameters_continuous_ML internal functions
parameters_discrete_Bayesian internal functions
parameters_discrete_ML internal functions
pbum internal functions
PhiDistr internal functions
plot.dynoNEM plot nested effect model
plot.mc.eminem plot nested effect model
plot.ModuleNetwork plot nested effect model
plot.nem plot nested effect model
plot.nem.BN plot nested effect model
plot.nem.bootstrap plot nested effect model
plot.nem.consensus plot nested effect model
plot.nem.greedy plot nested effect model
plot.nem.greedyMAP plot nested effect model
plot.nem.jackknife plot nested effect model
plot.pairwise plot nested effect model
plot.score plot nested effect model
plot.triples plot nested effect model
plotEffects Plots data according to a phenotypic hierarchy
plotnem plot nested effect model
print.dynoNEM Nested Effects Models - main function
print.mc.eminem Nested Effects Models - main function
print.ModuleNetwork Nested Effects Models - main function
print.nem Nested Effects Models - main function
print.nem.BN Nested Effects Models - main function
print.nem.bootstrap Bootstrapping for nested effect models
print.nem.consensus Statistically stabile nested effects models
print.nem.greedy Nested Effects Models - main function
print.nem.greedyMAP Nested Effects Models - main function
print.nem.jackknife Jackknife for nested effect models
print.pairwise Nested Effects Models - main function
print.score Nested Effects Models - main function
print.triples Nested Effects Models - main function
prior.EgeneAttach.EB Initialize E-gene attachment prior for empirical Bayes
prune.graph Prunes spurious edges in a phenotypic hierarchy

-- Q --

qbum internal functions
qqbum internal functions
quicknem Quick run of Nested Effects Models inference

-- R --

rbum internal functions
remTwoEdges Computes the transitive approximation of a directed graph

-- S --

SahinRNAi2008 Combinatorial Protein Knockdowns in the ERBB Signaling Pathway
sample.effect.likelihood internal functions
sample.likelihood internal functions
sampleData Random networks and data sampling
sampleData.BN Random networks and data sampling
sampleRndNetwork Random networks and data sampling
SCCgraph Combines Strongly Connected Components into single nodes
score internal functions
score.network internal functions
score_BN internal functions
score_continuous_Bayesian internal functions
score_continuous_ML internal functions
score_discrete_Bayesian internal functions
score_discrete_ML internal functions
selectEGenes Automatic selection of most relevant effect reporters
set.default.parameters Get/set hyperparameters
sim.intervention Simulate interventions in a Nested Effects Model
sim.interventions internal functions
subsets Subsets

-- T --

ThreeNeighborhood Computes the transitive approximation of a directed graph
transitive.closure Computes the transitive closure of a directed graph
transitive.projections Computes the transitive approximation of a directed graph
transitive.reduction Computes the transitive reduction of a graph
transSubGr Computes the transitive approximation of a directed graph
triples.posterior internal functions
TwoNeighborhood Computes the transitive approximation of a directed graph

-- V --

VecToMat Computes the transitive approximation of a directed graph

-- W --

which.is.max internal functions