Description Usage Arguments Value Author(s) References See Also Examples
View source: R/geneNetworkSummary.R
This function is used for printing a summary of the gene network
estimated with the ARTIVA procedure (ARTIVAnet
, ARTIVAsubnet
) for Auto Regressive TIme-VArying network inference.
1 | geneNetworkSummary(ARTIVAnet, edgesThreshold)
|
ARTIVAnet |
Table containing the information to plot a time-varying regulatory
network. In particular, this table can be obtained with function
|
edgesThreshold |
Probability threshold for the selection of the edges to be plotted. |
NULL
Original version by S. Lebre and G. Lelandais, contribution of D. Servillo to the final version.
Statistical inference of the time-varying structure of gene-regulation networks S. Lebre, J. Becq, F. Devaux, M. P. H. Stumpf, G. Lelandais, BMC Systems Biology, 4:130, 2010.
ARTIVAnet
,ARTIVAsubnet
,
ARTIVAsubnetAnalysis
, CP.postDist
,
segmentModel.postDist
, plotCP.postDist
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 | # Load the ARTIVA R package
library(ARTIVA)
# Load the dataset with simulated gene expression profiles
data(simulatedProfiles)
# Name of the target gene to be analyzed with ARTIVA
targetGene = 1
# Names of the parent genes (typically transcription factors)
parentGenes = c("TF1", "TF2", "TF3", "TF4", "TF5")
# Run the ARTIVAsubnet function
# Note that the number of iterations in the RJ-MCMC sampling is reduced
# to 'niter=20000' in this example, but it should be increased (e.g. up to
# 50000) for a better estimation.
## Not run:
ARTIVAtest = ARTIVAsubnet(targetData = simulatedProfiles[targetGene,],
parentData = simulatedProfiles[parentGenes,],
targetName = targetGene,
parentNames = parentGenes,
segMinLength = 2,
edgesThreshold = 0.6,
niter= 2000,
savePictures=FALSE)
# Print a summary of the obtained network
geneNetworkSummary(ARTIVAtest$network, edgesThreshold = 0.3)
# List of target genes to be analyzed independantly with ARTIVA
targetGenes = c("TF3", 45, 50)
ARTIVAtest2 = ARTIVAnet(targetData = simulatedProfiles[targetGenes,],
parentData = simulatedProfiles[parentGenes,],
targetName = targetGenes,
parentNames = parentGenes,
segMinLength = 2,
edgesThreshold = 0.6,
niter= 2000,
savePictures=FALSE)
# Print a summary of the obtained network
geneNetworkSummary(ARTIVAtest2, edgesThreshold = 0.3)
# Re-compute a time-varying network from the output of function
# ARTIVAsubnet with new analysis parameters
analysis2 = ARTIVAsubnetAnalysis(ARTIVAsubnet=ARTIVAtest,
segMinLength = 3,
edgesThreshold = 0.5,
outputPath="ARTIVAsubnet2",
savePictures=FALSE)
# Print a summary of the network obtained with the 2nd analysis.
geneNetworkSummary(analysis2$network, edgesThreshold = 0.3)
## End(Not run)
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