API for cbg-ethz/pcNEM
Probabilistic combinatorial nested effects model

Global functions
AdaSimulatedAnnealing Man page
BFSlevel Man page Source code
BoutrosRNAi2002 Man page
BoutrosRNAiDens Man page
BoutrosRNAiDiscrete Man page
BoutrosRNAiExpression Man page
BoutrosRNAiLods Man page
BoutrosRNAiLogFC Man page
CheckEdge Man page
D Man page
DAG.rescore Source code
DAGscore Source code
EMforMCMC Source code
EdgeEk Man page Source code
FULLmLL Man page Source code
FourNeighborhood Man page Source code
Ivanova2006RNAiTimeSeries Man page
KOmap Man page
NiederbergerMediator2012 Man page
NiederbergerMediatorLods Man page
NiederbergerMediatorLogFC Man page
NiederbergerMediatorPVals Man page
OneNeighborhood Man page Source code
PathNumber Source code
PhiDistr Man page Source code
SCCgraph Man page Source code
SahinRNAi2008 Man page
SearchNearestDAG Source code
ThreeNeighborhood Man page Source code
TwoNeighborhood Man page Source code
VecToMat Man page Source code
ancestor Source code
bum.EM Man page Source code
bum.dalt Man page Source code
bum.histogram Man page Source code
bum.mle Man page Source code
bum.negLogLik Man page Source code
bum.palt Man page Source code
bum.qalt Man page Source code
bum.ralt Man page Source code
calcLikelihood Source code
calculateHiddenPrior Source code
closest.transitive.greedy Man page Source code
connectModules Man page
connectModules.aux Source code
connectModules.orig Source code
connectModules2 Source code
createBN Man page Source code
dat Man page
dat.normalized Man page
dat.unnormalized Man page
data.likelihood Man page Source code
dbum Man page Source code
des_top_order Source code
distdecrease Man page Source code
distincrease Man page Source code
distincrease1 Man page Source code
distsame Man page Source code
dynoNEM.perturb Source code
dynoNEM.posteriorEGenePos Source code
dynoNEM_MCMC Source code
effect.likelihood Man page Source code
encode.interventions Man page Source code
enumerate.models Man page Source code
enumerate.models2 Man page Source code
erase.cycles Man page Source code
exhaustive_BN Man page Source code
filterEGenes Man page Source code
final_attachement Source code
fit.BN Man page Source code
fitBUM Man page Source code
get.deletions Source code
get.insertions Source code
get.reversions Source code
getComponent Man page Source code
getDensityMatrix Man page Source code
getFinalTheta Source code
getRelevantEGenes Man page Source code
getperturb.matrices Source code
graychange Man page
infer.edge.type Man page Source code
ingreed_BN Man page Source code
internal Man page
inv.logit Man page Source code
is.dag Man page Source code
is.transitive Man page Source code
learn Man page Source code
learn.conditionals Man page Source code
local.model.prior Man page Source code
logit Man page Source code
mLL Man page Source code
map.int2node Man page
mcmc Source code
moduleNetwork Man page Source code
moduleNetwork.aux Man page Source code
moduleNetwork.orig Source code
nem Man page Source code
nem.AdaSA Source code
nem.BN Man page Source code
nem.bootstrap Man page Source code
nem.bootstrap.list Source code
nem.calcSignificance Man page Source code
nem.consensus Man page Source code
nem.cont.preprocess Man page Source code
nem.discretize Man page Source code
nem.featureselection Man page Source code
nem.greedy Man page Source code
nem.greedyMAP Man page Source code
nem.jackknife Man page Source code
nemModelSelection Man page Source code
network.AIC Man page Source code
onLoad Source code
onestep_EMiNEM Source code
onestep_mcmc Source code
optimizecoregraph Man page Source code
optimizemarginal Man page Source code
optimizemarginal.nuInf Man page Source code
pairwise.posterior Man page Source code
parameters_continuous_Bayesian Man page
parameters_continuous_ML Man page
parameters_discrete_Bayesian Man page
parameters_discrete_ML Man page
pbum Man page Source code
plot.ModuleNetwork Man page Source code
plot.dynoNEM Man page Source code
plot.mc.eminem Man page Source code
plot.nem Man page Source code
plot.nem.BN Man page Source code
plot.nem.bootstrap Man page Source code
plot.nem.consensus Man page Source code
plot.nem.greedy Man page Source code
plot.nem.greedyMAP Man page Source code
plot.nem.jackknife Man page Source code
plot.pairwise Man page Source code
plot.score Man page Source code
plot.score.list Source code
plot.triples Man page Source code
plotEffects Man page Source code
plotnem Man page Source code
print.ModuleNetwork Man page Source code
print.dynoNEM Man page Source code
print.mc.eminem Man page Source code
print.nem Man page Source code
print.nem.BN Man page Source code
print.nem.bootstrap Man page Source code
print.nem.consensus Man page Source code
print.nem.greedy Man page Source code
print.nem.greedyMAP Man page Source code
print.nem.jackknife Man page Source code
print.pairwise Man page Source code
print.score Man page Source code
print.score.list Source code
print.triples Man page Source code
prior.EgeneAttach.EB Man page Source code
probmatrix.rescorenodes Source code
propersample Source code
prune.graph Man page Source code
qbum Man page Source code
qqbum Man page Source code
quicknem Man page Source code
rbum Man page Source code
rec.sample Source code
remTwoEdges Man page Source code
runMCMC Source code
sample.effect.likelihood Man page Source code
sample.likelihood Man page Source code
sampleData Man page Source code
sampleData.BN Man page
sampleData.pcnem Source code
sampleRndNetwork Man page Source code
score Man page Source code
score.aux Source code
score.network Man page Source code
score_BN Man page Source code
score_continuous_Bayesian Man page Source code
score_continuous_ML Man page Source code
score_discrete_Bayesian Man page Source code
score_discrete_ML Man page Source code
selectEGenes Man page
set.default.parameters Man page Source code
siRNA_gene_Expts Man page
sim.intervention Man page Man page Source code
sim.interventions Man page Source code
subsets Man page Source code
top_order Source code
transSubGr Man page Source code
transitive.closure Man page Source code
transitive.projections Man page Source code
transitive.reduction Man page Source code
triples.posterior Man page Source code
updateHidden Source code
which.is.max Man page
cbg-ethz/pcNEM documentation built on May 23, 2018, 3:30 p.m.