ARTIVA: Time-Varying DBN Inference with the ARTIVA (Auto Regressive TIme VArying) Model

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Reversible Jump MCMC (RJ-MCMC)sampling for approximating the posterior distribution of a time varying regulatory network, under the Auto Regressive TIme VArying (ARTIVA) model (for a detailed description of the algorithm, see Lebre et al. BMC Systems Biology, 2010). Starting from time-course gene expression measurements for a gene of interest (referred to as "target gene") and a set of genes (referred to as "parent genes") which may explain the expression of the target gene, the ARTIVA procedure identifies temporal segments for which a set of interactions occur between the "parent genes" and the "target gene". The time points that delimit the different temporal segments are referred to as changepoints (CP).

Author
S. Lebre and G. Lelandais.
Date of publication
2015-05-20 01:09:27
Maintainer
S. Lebre <sophie.lebre@icube.unistra.fr>
License
GPL (>= 2)
Version
1.2.3

View on CRAN

Man pages

ARTIVA-internal
Internal ARTIVA Functions
ARTIVAnet
Function to run the ARTIVA procedure for Auto Regressive...
ARTIVA-package
Time-Varying DBN Inference with the ARTIVA (Auto Regressive...
ARTIVAsubnet
Function to recover Auto Regressive TIme-VArying interactions...
ARTIVAsubnetAnalysis
Function to estimate a regulatory time-varying network from...
choosePriors
Function to plot an overview of possible priors for the...
CP.postDist
Function to compute the CPs posterior distribution for the...
drosophila
Drosphila life cycyle time series by Arbeitman et al 2002.
geneNetworkSummary
Function to
plotCP.postDist
Function to plot the estimated posterior distribution for the...
priors
Set of possible priors for the number of changepoints (CPs)...
simulatedProfiles
Simulated gene expression profiles dataset.
traceGeneProfiles
Function to plot the gene expression profiles
traceNetworks
Function to plot the network estimated with functions...
yeast
Yeast stress response data

Files in this package

ARTIVA
ARTIVA/NAMESPACE
ARTIVA/data
ARTIVA/data/priors.rda
ARTIVA/data/yeast.rda
ARTIVA/data/datalist
ARTIVA/data/drosophila.rda
ARTIVA/data/simulatedProfiles.rda
ARTIVA/R
ARTIVA/R/ARTIVAsubnetAnalysis.R
ARTIVA/R/sampleK.R
ARTIVA/R/ARTIVAnet.R
ARTIVA/R/psmall.svd.R
ARTIVA/R/traceGeneProfiles.R
ARTIVA/R/ARTIVAsubnet.R
ARTIVA/R/cp.shift.R
ARTIVA/R/computeRho4.R
ARTIVA/R/updateSigMulti.R
ARTIVA/R/PlotFunction.R
ARTIVA/R/computeRho3.R
ARTIVA/R/plotSegmentModel.postDist.R
ARTIVA/R/sampleBxy.R
ARTIVA/R/PSRF.R
ARTIVA/R/sampleBinit.R
ARTIVA/R/rinvgamma.R
ARTIVA/R/cp.death.R
ARTIVA/R/segment.update.R
ARTIVA/R/nsmall.svd.R
ARTIVA/R/positive.svd.R
ARTIVA/R/bdu.R
ARTIVA/R/segPos.R
ARTIVA/R/init.R
ARTIVA/R/CPposition.R
ARTIVA/R/plotCP.postDist.R
ARTIVA/R/fast.svd.R
ARTIVA/R/CP.postDist.R
ARTIVA/R/cp.computeAlpha.R
ARTIVA/R/readInput.R
ARTIVA/R/pseudoinverse.R
ARTIVA/R/sampleDelta2.R
ARTIVA/R/sampleParms.R
ARTIVA/R/sampleSig2.R
ARTIVA/R/dinvgamma.R
ARTIVA/R/buildXY.R
ARTIVA/R/geneNetworkSummary.R
ARTIVA/R/computePx.R
ARTIVA/R/choosePriors.R
ARTIVA/R/hasSeg.R
ARTIVA/R/segmentModel.postDist.R
ARTIVA/R/traceNetworks.R
ARTIVA/R/main.R
ARTIVA/R/cp.birth.R
ARTIVA/MD5
ARTIVA/DESCRIPTION
ARTIVA/man
ARTIVA/man/simulatedProfiles.Rd
ARTIVA/man/traceGeneProfiles.Rd
ARTIVA/man/ARTIVA-package.Rd
ARTIVA/man/ARTIVAsubnet.Rd
ARTIVA/man/geneNetworkSummary.Rd
ARTIVA/man/CP.postDist.Rd
ARTIVA/man/yeast.Rd
ARTIVA/man/priors.Rd
ARTIVA/man/plotCP.postDist.Rd
ARTIVA/man/ARTIVA-internal.Rd
ARTIVA/man/ARTIVAsubnetAnalysis.Rd
ARTIVA/man/ARTIVAnet.Rd
ARTIVA/man/choosePriors.Rd
ARTIVA/man/drosophila.Rd
ARTIVA/man/traceNetworks.Rd