Description Usage Arguments Details Value Author(s) References See Also Examples
View source: R/motifStatsVAR1.r
Function that detects standard network motifs from the lag-one autoregression relationships as implied by the VAR(1) model.
1 | motifStatsVAR1(sparseA, verbose=TRUE)
|
sparseA |
A |
verbose |
A |
Six types of motifs are detected: self-regulators, feedback pairs, feedforward loops, feedback loops, bi-fans, and diamonds (cf. Alon, 2007 for details). A detected motif is reported by the paths that
constitute them. In line with Alon (2007), who distinguishes subtypes of these motived based on the sign of the path's contribution, the latter is also reported. When verbose=TRUE
the summary output is also visualized. See this plot for the definition of the motifs in terms of the VAR(1) time series chain graph.
An object of class list
with slots:
selfregulators |
A |
feedbackpairs |
A |
feedforwardloops |
A |
feedbackloops |
A |
bifans |
A |
diamonds |
A |
Future versions of this function may include additional slots reporting more motif types.
Wessel N. van Wieringen <w.vanwieringen@vumc.nl>.
Alon, U. (2007), “Network motifs: theory and experimental approaches”, Nature Reviews Genetics, 8, 450-461.
ridgeVAR1
, sparsifyVAR1
, graphVAR1
, nodeStatsVAR1
1 2 3 4 5 6 | # specify lag one autoregression model
sparseA <- matrix(runif(2500), ncol=50)
sparseA[sparseA < 0.9] <- 0
# find motifs
motifList <- motifStatsVAR1(sparseA)
|
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.