Cascade (version 1.7)

geneNeighborhood: Find the neighborhood of a set of nodes.

Description

Find the neighborhood of a set of nodes.

Usage

geneNeighborhood(net,targets,...)

Arguments

net

a network object

targets

a vector containing the set of nodes

...

Optional arguments. See plot options.

Value

The neighborhood of the targeted genes.

References

Jung, N., Bertrand, F., Bahram, S., Vallat, L., and Maumy-Bertrand, M. (2014). Cascade: a R-package to study, predict and simulate the diffusion of a signal through a temporal gene network. Bioinformatics, btt705.

Vallat, L., Kemper, C. A., Jung, N., Maumy-Bertrand, M., Bertrand, F., Meyer, N., ... & Bahram, S. (2013). Reverse-engineering the genetic circuitry of a cancer cell with predicted intervention in chronic lymphocytic leukemia. Proceedings of the National Academy of Sciences, 110(2), 459-464.

Examples

# NOT RUN {
data(Selection)
data(network)
#A nv value can chosen using the cutoff function
nv=.11 
EGR1<-which(match(Selection@name,"EGR1")==1)
P<-position(network,nv=nv)

geneNeighborhood(network,targets=EGR1,nv=nv,ini=P,
label_v=network@name)
# }