ragt2ridges (version 0.3.4)

pruneMotifStats: Network motif list subsetting.

Description

Limit a list of network motifs as returned by the motifStatsVAR1-function to those involving a particular node.

Usage

pruneMotifStats(motifList, id)

Arguments

motifList

A list with motifs as returned by the motifStatsVAR1-function.

id

A integer representing the node of interest.

Value

An object of class list with slots:

selfregulators

A list of motifs specified as matrices with each row one of the motif's paths and in the last column the sign of the path's contribution.

feedbackpairs

A list of motifs specified as matrices with each row one of the motif's paths and in the last column the sign of the path's contribution.

feedforwardloops

A list of motifs specified as matrices with each row one of the motif's paths and in the last column the sign of the path's contribution.

feedbackloops

A list of motifs specified as matrices with each row one of the motif's paths and in the last column the sign of the path's contribution.

bifans

A list of motifs specified as matrices with each row one of the motif's paths and in the last column the sign of the path's contribution.

diamonds

A list of motifs specified as matrices with each row one of the motif's paths and in the last column the sign of the path's contribution.

Future versions of this function may include additional slots reporting more motif types.

References

Alon, U. (2007), ``Network motifs: theory and experimental approaches'', Nature Reviews Genetics, 8, 450-461.

See Also

graphVAR1, motifStatsVAR1

Examples

# NOT RUN {
# specify lag one autoregression model
sparseA <- matrix(runif(2500), ncol=50)
sparseA[sparseA < 0.9] <- 0

# find motifs 
motifList <- motifStatsVAR1(sparseA)

# prune motif list
pruneMotifStats(motifList, 1)
# }