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


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Documentation for package ‘ddepn’ version 1.9

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ddepn-package Dynamic Deterministic Effects Propagation Networks: Infer signalling networks from high througput array data.
addstimuli Add dummy stimulus nodes to the data matrix.
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 get.labels get.arrowhead get.arrowtail
get.arrowtail plotdetailed get.labels get.arrowhead get.arrowtail
get.labels plotdetailed 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_theta_consensus Plot the data and inferred model parameters.
hcc1954 hcc1954
hcc1954fcf hcc1954
hcc1954fcfmedian hcc1954
hcc1954raw hcc1954
kegggraph.to.detailed.adjacency kegggraph.to.detailed.adjacency
kegggraphs kegggraphs
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 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.