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

DDEPN (Dynamic Deterministic Effects Propagation Networks): Infer signalling networks for timecourse data. Given a matrix of high-throughput genomic or proteomic timecourse data, generated after external perturbation of the biological system, DDEPN models the time-dependent propagation of active and passive states depending on a network structure. Optimal network structures given the experimental data are reconstructed. Two network inference algorithms can be used: inhibMCMC, a Markov Chain Monte Carlo sampling approach and GA, a Genetic Algorithm network optimisation. Inclusion of prior biological knowledge can be done using different network prior models.

AuthorChristian Bender
Date of publication2015-01-11 17:18:18
MaintainerChristian Bender <benderpkg@gmail.com>
LicenseGPL (>=2)
Version2.2.3

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Man pages

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.

Files in this package

ddepn/DESCRIPTION
ddepn/NAMESPACE
ddepn/R
ddepn/R/addstimuli.R ddepn/R/adjacencyMatrix_to_logicalRules.R ddepn/R/bestgam.R ddepn/R/center_ddepn.R ddepn/R/compareGraphs.R ddepn/R/coord.R ddepn/R/create_signetwork.R ddepn/R/crossover.R ddepn/R/ddepn.R ddepn/R/expand.gamma.R ddepn/R/format_ddepn.R ddepn/R/gelman_diag.R ddepn/R/get.phi.final.R ddepn/R/getfirstphi.R ddepn/R/internal.functions.R ddepn/R/likl.R ddepn/R/makedata.R ddepn/R/mcmc_accept.R ddepn/R/mcmc_ddepn.R ddepn/R/mcmc_move.R ddepn/R/mcmc_performance.R ddepn/R/modelcomparison.R ddepn/R/netga.R ddepn/R/perform.hmmsearch.R ddepn/R/plot_edgeconfidences.R ddepn/R/plot_mcmctraces.R ddepn/R/plot_overlap.R ddepn/R/plot_profiles.R ddepn/R/plotdetailed.R ddepn/R/plotdetailed_Rgraphviz.R ddepn/R/plotrepresult.R ddepn/R/posterior.R ddepn/R/prior.R ddepn/R/propagate.effect.R ddepn/R/random.gammaprime.R ddepn/R/run_checks.R ddepn/R/samplephi.R ddepn/R/signalnetwork.R ddepn/R/simulatedata.R ddepn/R/uniquegamma.R ddepn/R/zlambda.R
ddepn/build
ddepn/build/vignette.rds
ddepn/data
ddepn/data/hcc1954.RData
ddepn/data/hcc1954raw.RData
ddepn/data/kegggraphs.RData
ddepn/inst
ddepn/inst/doc
ddepn/inst/doc/ddepn.R
ddepn/inst/doc/ddepn.Rnw
ddepn/inst/doc/ddepn.pdf
ddepn/man
ddepn/man/addstimuli.Rd ddepn/man/adjacencyMatrix_to_logicalRules.Rd ddepn/man/bestgam.Rd ddepn/man/center_ddepn.Rd ddepn/man/compareGraphs.Rd ddepn/man/coord.Rd ddepn/man/create_signetwork.Rd ddepn/man/crossover.Rd ddepn/man/ddepn-package.Rd ddepn/man/ddepn.Rd ddepn/man/expand.gamma.Rd ddepn/man/format_ddepn.Rd ddepn/man/gelman_diag.Rd ddepn/man/get.phi.final.Rd ddepn/man/getfirstphi.Rd ddepn/man/hcc1954.Rd ddepn/man/internal.functions.Rd ddepn/man/kegggraphs.Rd ddepn/man/likl.Rd ddepn/man/makedata.Rd ddepn/man/mcmc_accept.Rd ddepn/man/mcmc_ddepn.Rd ddepn/man/mcmc_move.Rd ddepn/man/mcmc_performance.Rd ddepn/man/modelcomparison.Rd ddepn/man/netga.Rd ddepn/man/perform.hmmsearch.Rd ddepn/man/plot_edgeconfidences.Rd ddepn/man/plot_mcmctraces.Rd ddepn/man/plot_overlap.Rd ddepn/man/plot_profiles.Rd ddepn/man/plotdetailed.Rd ddepn/man/plotdetailed_Rgraphviz.Rd ddepn/man/plotrepresult.Rd ddepn/man/posterior.Rd ddepn/man/prior.Rd ddepn/man/propagate.effect.Rd ddepn/man/random.gammaprime.Rd ddepn/man/run_checks.Rd ddepn/man/samplephi.Rd ddepn/man/signalnetwork.Rd ddepn/man/simulatedata.Rd ddepn/man/uniquegamma.Rd ddepn/man/zlambda.Rd
ddepn/src
ddepn/src/perform_hmmsearch.c
ddepn/src/perform_hmmsearch.h
ddepn/src/perform_hmmsearch_globalest.c
ddepn/src/perform_hmmsearch_globalest.h
ddepn/src/utility_functions.c
ddepn/src/utility_functions.h
ddepn/vignettes
ddepn/vignettes/OLDmcmcoutput.pdf
ddepn/vignettes/ddepn.Rnw
ddepn/vignettes/examplenet.pdf
ddepn/vignettes/mcmcedgeconf.pdf
ddepn/vignettes/mcmcoutput.pdf
ddepn/vignettes/mcmcoutput1.pdf
ddepn/vignettes/mcmcoutput2.pdf
ddepn/vignettes/mcmcprofiles.pdf
ddepn/vignettes/mcmctest3_2_stats.pdf
ddepn/vignettes/netgaresult.pdf
ddepn/vignettes/netmcmcresult.pdf
ddepn/vignettes/references.bib
ddepn/vignettes/scorenetgatest.pdf

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