B C D E F G I L M N O P Q R S T V W
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 |
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 |
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 |
EdgeEk | Computes the transitive approximation of a directed graph |
enumerate.models | Exhaustive enumeration of models |
exhaustive_BN | internal functions |
filterEGenes | Automatic selection of most relevant E-genes |
fit.BN | internal functions |
fitBUM | internal functions |
FourNeighborhood | Computes the transitive approximation of a directed graph |
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 E-genes |
graychange | internal functions |
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 |
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.BN | Bayesian Network Nested Effects Models |
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 | Infers a phenotypic hierarchy using a greedy search strategy |
nem.greedyMAP | Infers a phenotypic hierarchy using an alternating MAP optimization |
nem.jackknife | Jackknife for nested effect models |
nemModelSelection | model selection for nested effect models |
network.AIC | AIC criterion for network graph |
OneNeighborhood | Computes the transitive approximation of a directed graph |
optimizecoregraph | internal functions |
optimizemarginal | internal functions |
pairwise.posterior | Infers a phenotypic hierarchy edge by edge |
parameters_continuous_Bayesian | internal functions |
parameters_continuous_ML | internal functions |
parameters_discrete_Bayesian | internal functions |
parameters_discrete_ML | internal functions |
pbum | internal functions |
PhiDistr | Computes the marginal likelihood of phenotypic hierarchies |
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 |
plotEffects | Plots data according to a phenotypic hierarchy |
plotnem | plot nested effect model |
print.ModuleNetwork | Infers a phenotypic hierarchy using the module network |
print.nem | Nested Effects Models - main function |
print.nem.BN | Bayesian Network Nested Effects Models |
print.nem.bootstrap | Bootstrapping for nested effect models |
print.nem.consensus | Statistically stabile nested effects models |
print.nem.greedy | Infers a phenotypic hierarchy using a greedy search strategy |
print.nem.greedyMAP | Infers a phenotypic hierarchy using an alternating MAP optimization |
print.nem.jackknife | Jackknife for nested effect models |
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 |
remTwoEdges | Computes the transitive approximation of a directed graph |
sampleData | Random networks and data sampling |
sampleRndNetwork | Random networks and data sampling |
SCCgraph | Combines Strongly Connected Components into single nodes |
score | Computes the marginal likelihood of phenotypic hierarchies |
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 E-genes |
subsets | Subsets |
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 | Infers a phenotypic hierarchy from triples |
TwoNeighborhood | Computes the transitive approximation of a directed graph |
VecToMat | Computes the transitive approximation of a directed graph |
which.is.max | internal functions |