ddepn-package | Dynamic Deterministic Effects Propagation Networks: Infer signalling networks from high througput array 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 by time vector tp. |
calcpr | Calculate a structure prior. Usually called internally. |
center_ddepn | Perform centering of single replicate time courses. |
cls | DDEPN function tests. |
compare.graphs.tc | compare.graphs.tc |
create_signetwork | inhibMCMC Analysis: find significant edges from independent MCMC chains |
create_signetwork_cv | inhibMCMC Analysis: find significant edges from independent MCMC chains |
ddepn | ddepn |
draw_segments | inhibMCMC Analysis: find significant edges from independent MCMC chains |
esub | Fit an optimal smoothing spline to a data vector y, indexed by time vector tp. |
format_ddepn | Performs renaming of the colnames of dataset hcc1954 to make it suitable as input for the inference. |
gelman_diag | Convergence check by Gelman's potential scale reduction. |
get.arrowhead | plotdetailed_Rgraphviz get.labels get.arrowhead get.arrowtail |
get.arrowtail | plotdetailed_Rgraphviz get.labels get.arrowhead get.arrowtail |
get.labels | plotdetailed_Rgraphviz get.labels get.arrowhead get.arrowtail |
get.phi.final | Construct final network from GA or mcmc result. |
get.phi.final.mcmc | Construct final network from GA or mcmc result. |
get_gamma_consensus | Plot the data and inferred model parameters. |
get_theta_consensus | Plot the data and inferred model parameters. |
hcc1954 | hcc1954 |
hcc1954fcf | hcc1954 |
hcc1954fcfmedian | hcc1954 |
hcc1954raw | hcc1954 |
heatmapcolors | Plot the data and inferred model parameters. |
kegggraphs | kegggraphs |
layout.ellipsis | plotdetailed, layout.ellipsis |
makedata | Generate artificial dataset given a network and list of stimuli. |
make_edge_df | Boxplots of edge confidences obtained in inhibMCMC. |
mcmc_ddepn | mcmc_ddepn - Perform MCMC sampling for DDEPN. |
netga | netga - Perform network search using a genetic algorithm. |
perform_edge_test | inhibMCMC Analysis: find significant edges from independent MCMC chains |
perform_network_tests | inhibMCMC Analysis: find significant edges from independent MCMC chains |
plotdetailed | plotdetailed, layout.ellipsis |
plotdetailed_Rgraphviz | plotdetailed_Rgraphviz get.labels get.arrowhead get.arrowtail |
plotrepresult | Plot result of reconstruction. |
plot_edgeconfidences | Boxplots of edge confidences obtained in inhibMCMC. |
plot_mcmctraces | Trace plot for inhibMCMC posterior traces. |
plot_profiles | Plot the data and inferred model parameters. |
prior | Calculate a structure prior. Usually called internally. |
resume_ddepn | ddepn |
runmcmc | mcmc_ddepn - Perform MCMC sampling for DDEPN. |
run_checks | DDEPN function tests. |
signalnetwork | Sample a random signalling network. |
simulatedata | simulatedata |
wrapddepn | DDEPN function tests. |