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ARTIVA (version 1.2.3)

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

Description

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).

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Version

Install

install.packages('ARTIVA')

Monthly Downloads

25

Version

1.2.3

License

GPL (>= 2)

Maintainer

original version 10 by Sophie Lebre

Last Published

May 19th, 2015

Functions in ARTIVA (1.2.3)

CP.postDist

Function to compute the CPs posterior distribution for the ARTIVA network model from the the ouput samples of function ARTIVAsubnet.
priors

Set of possible priors for the number of changepoints (CPs) or incoming edges.
simulatedProfiles

Simulated gene expression profiles dataset.
ARTIVA-package

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

Drosphila life cycyle time series by Arbeitman et al 2002.
plotCP.postDist

Function to plot the estimated posterior distribution for the changepoints (CPs) number and position
ARTIVAnet

Function to run the ARTIVA procedure for Auto Regressive TIme-VArying network inference on several target genes
traceNetworks

Function to plot the network estimated with functions ARTIVAnet or ARTIVAsubnet
choosePriors

Function to plot an overview of possible priors for the number of changepoints and/or edges.
traceGeneProfiles

Function to plot the gene expression profiles
yeast

Yeast stress response data
ARTIVA-internal

Internal ARTIVA Functions
ARTIVAsubnetAnalysis

Function to estimate a regulatory time-varying network from the output of function ARTIVAsubnet.
geneNetworkSummary

Function to
ARTIVAsubnet

Function to recover Auto Regressive TIme-VArying interactions between a gene of interest (referred to as "target gene") and a set of genes which may explain the expression of the target gene.