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.

Author
Christian Bender
Date of publication
2015-01-11 17:18:18
Maintainer
Christian Bender <benderpkg@gmail.com>
License
GPL (>=2)
Version
2.2.3

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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