Man pages for ddepn
Dynamic Deterministic Effects Propagation Networks: Infer signalling networks for timecourse RPPA data.
| addstimuli | Add dummy stimulus nodes to the data matrix. |
| adjacencyMatrix_to_logicalRules | Convert adjacency matrix to logical rules. |
| bestgam | Fit an optimal smoothing spline to a data vector y, indexed... |
| center_ddepn | Perform centering of single replicate time courses. |
| compareGraphs | compareGraphs |
| coord | coord - compute coordinates for a given index. |
| create_signetwork | inhibMCMC Analysis: find significant edges from independent... |
| crossover | crossover - perform crossing over of two networks |
| ddepn | ddepn |
| ddepn-package | Dynamic Deterministic Effects Propagation Networks: Infer... |
| expand.gamma | expand.gamma |
| format_ddepn | Performs renaming of the colnames of dataset hcc1954 to make... |
| gelman_diag | Convergence check by Gelman's potential scale reduction. |
| getfirstphi | Helper function for netga. |
| get.phi.final | Construct final network from GA or mcmc result. |
| hcc1954 | hcc1954 |
| internal.functions | internal.functions get.data plotmatrix get.gammashifted... |
| kegggraphs | kegggraphs |
| likl | likl - Likelihood computation for given network,... |
| makedata | Generate artificial dataset given a network and list of... |
| mcmc_accept | mcmc_accept - accept move or not |
| mcmc_ddepn | mcmc_ddepn - Perform MCMC sampling for DDEPN. |
| mcmc_move | mcmc_move - Perform MCMC step |
| mcmc_performance | mcmc_performance - Performance plot for MCMC |
| modelcomparison | get.aic, get.bic |
| netga | netga - Perform network search using a genetic algorithm. |
| perform.hmmsearch | perform.hmmsearch - Do system state optimisation using a... |
| plotdetailed | plotdetailed, layout.ellipsis |
| plotdetailed_Rgraphviz | plotdetailed_Rgraphviz get.labels get.arrowhead get.arrowtail |
| plot_edgeconfidences | Boxplots of edge confidences obtained in inhibMCMC. |
| plot_mcmctraces | Trace plot for inhibMCMC posterior traces. |
| plot_overlap | Plot a reconstructed network in comparison with a prior... |
| plot_profiles | Plot the data and inferred model parameters. |
| plotrepresult | Plot result of reconstruction. |
| posterior | Posterior probability calculation. |
| prior | Calculate a structure prior. Usually called internally. |
| propagate.effect | propagate.effect.set propagate.effect.simple |
| random.gammaprime | random.gammaprime |
| run_checks | DDEPN function tests. |
| samplephi | sample random initial networks |
| signalnetwork | Sample a random signalling network. |
| simulatedata | simulatedata |
| uniquegamma | uniquegamma |
| zlambda | Compute normalisation factor for prior information. |
