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

View on R-Forge

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.

Functions

addstimuli Man page
adjacencyMatrix_to_logicalRules Man page
bestgam Man page
bin2dec Man page
calcpr Man page
center_ddepn Man page
checkC Man page
cls Man page
compareGraphs Man page
coord Man page
create_signetwork Man page
create_signetwork_cv Man page
crossover Man page
ddepn Man page
ddepn-package Man page
detailed.to.simple.regulations Man page
draw_segments Man page
esub Man page
expand.gamma Man page
format_ddepn Man page
gelman_diag Man page
get.aic Man page
get.arrowhead Man page
get.arrowtail Man page
get.bic Man page
get.data Man page
getE Man page
getfirstphi Man page
get_gamma_consensus Man page
get.gammashifted Man page
get.labels Man page
get.partitions Man page
get.phi.final Man page
get.phi.final.mcmc Man page
get_reps_tps Man page
get_theta_consensus Man page
hcc1954 Man page
hcc1954fcf Man page
hcc1954fcfmedian Man page
hcc1954raw Man page
heatmapcolors Man page
initialphi Man page
internal.functions Man page
is_consistent Man page
kegggraphs Man page
layout.ellipsis Man page
likl Man page
makedata Man page
make_edge_df Man page
mcmc_accept Man page
mcmc_ddepn Man page
mcmc_move Man page
mcmc_performance Man page
netga Man page
order_experiments Man page
pad_data Man page
perform_edge_test Man page
perform.hmmsearch Man page
perform.hmmsearch_C Man page
perform.hmmsearch_C_globalest Man page
perform.hmmsearch_globalest Man page
perform.hmmsearch_R Man page
perform_network_tests Man page
pgs Man page
plotdetailed Man page
plotdetailed_Rgraphviz Man page
plot_edgeconfidences Man page
plotmatrix Man page
plot_mcmctraces Man page
plot_overlap Man page
plot_profiles Man page
plotrepresult Man page
posterior Man page
pri Man page
prior Man page
propagate.effect.set Man page
propagate.effect.simple Man page
random.gammaprime Man page
replicatecolumns Man page
resume_ddepn Man page
reverse.direction Man page
run_checks Man page
runmcmc Man page
samplephi Man page
signalnetwork Man page
simulatedata Man page
tp.median Man page
transitive.closure Man page
transitive.reduction Man page
trapezoid Man page
uniquegamma Man page
uniquegammaposs Man page
updateA Man page
viterbi Man page
wrapddepn Man page
zlambda Man page

Files

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

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