Man pages for ddepn
Dynamic Deterministic Effects Propagation Networks: Infer signalling networks for timecourse RPPA data.

addstimuliAdd dummy stimulus nodes to the data matrix.
adjacencyMatrix_to_logicalRulesConvert adjacency matrix to logical rules.
bestgamFit an optimal smoothing spline to a data vector y, indexed...
center_ddepnPerform centering of single replicate time courses.
coordcoord - compute coordinates for a given index.
create_signetworkinhibMCMC Analysis: find significant edges from independent...
crossovercrossover - perform crossing over of two networks
ddepn-packageDynamic Deterministic Effects Propagation Networks: Infer...
format_ddepnPerforms renaming of the colnames of dataset hcc1954 to make...
gelman_diagConvergence check by Gelman's potential scale reduction.
getfirstphiHelper function for netga.
get.phi.finalConstruct final network from GA or mcmc result.
internal.functionsinternal.functions plotmatrix get.gammashifted...
likllikl - Likelihood computation for given network,...
makedataGenerate artificial dataset given a network and list of...
mcmc_acceptmcmc_accept - accept move or not
mcmc_ddepnmcmc_ddepn - Perform MCMC sampling for DDEPN.
mcmc_movemcmc_move - Perform MCMC step
mcmc_performancemcmc_performance - Performance plot for MCMC
modelcomparisonget.aic, get.bic
netganetga - Perform network search using a genetic algorithm.
perform.hmmsearchperform.hmmsearch - Do system state optimisation using a...
plotdetailedplotdetailed, layout.ellipsis
plotdetailed_Rgraphvizplotdetailed_Rgraphviz get.labels get.arrowhead get.arrowtail
plot_edgeconfidencesBoxplots of edge confidences obtained in inhibMCMC.
plot_mcmctracesTrace plot for inhibMCMC posterior traces.
plot_overlapPlot a reconstructed network in comparison with a prior...
plot_profilesPlot the data and inferred model parameters.
plotrepresultPlot result of reconstruction.
posteriorPosterior probability calculation.
priorCalculate a structure prior. Usually called internally.
propagate.effectpropagate.effect.set propagate.effect.simple
run_checksDDEPN function tests.
samplephisample random initial networks
signalnetworkSample a random signalling network.
zlambdaCompute normalisation factor for prior information.
ddepn documentation built on May 2, 2019, 4:42 p.m.