internal

moduleNetwork.aux

connectModules

fitBUM

dbum

rbum

qbum

pbum

getComponent

inv.logit

logit

bum.negLogLik

bum.mle

bum.EM

qqbum

bum.histogram

bum.dalt

bum.palt

bum.qalt

bum.ralt

nem.featureselection

createBN

which.is.max

fit.BN

exhaustive_BN

optimizemarginal

ingreed_BN

optimizecoregraph

graychange

is.dag

optimizemarginal.nuInf

parameters_continuous_Bayesian

parameters_continuous_ML

parameters_discrete_Bayesian

parameters_discrete_ML

score_continuous_Bayesian

score_continuous_ML

score_discrete_Bayesian

score_discrete_ML

FULLmLL

score

moduleNetwork

enumerate.models2

nem.greedy

nem.greedyMAP

pairwise.posterior

triples.posterior

nem.BN

data.likelihood

effect.likelihood

encode.interventions

erase.cycles

learn

learn.conditionals

PhiDistr

sample.effect.likelihood

sample.likelihood

score_BN

score.network

sim.interventions


  internal functions: do not call these functions directly. 


models

The package 'nem' allows to reconstruct features of pathways from the nested structure of perturbation effects. It takes as input (1.) a set of pathway components, which were perturbed, and (2.) phenotypic readout of these perturbations (e.g. gene expression, protein expression). The output is a directed graph representing the phenotypic hierarchy.

Holger Froehlich

(Dynamic) Nested Effects Models and Deterministic Effects Propagation Networks to reconstruct phenotypic hierarchies

internal function

internal functions: do not call these functions directly.

internal functions

internal: internal functions

Description

Usage

Arguments

Value