geneNeighborhood,network-method {Cascade}

Find the neighborhood of a set of nodes.

Description

Find the neighborhood of a set of nodes.

Usage

## S4 method for signature 'network'
geneNeighborhood(
  net,
  targets,
  nv = 0,
  order = length(net@time_pt) - 1,
  label_v = NULL,
  ini = NULL,
  frame.color = "white",
  label.hub = FALSE,
  graph = TRUE,
  names = FALSE
)

Arguments

net

a network object

targets

a vector containing the set of nodes

nv

the level of cutoff. Defaut to 0.

order

of the neighborhood. Defaut to 'length(net@time_pt)-1'.

label_v

vector defining the vertex labels.

ini

using the “position” function, you can fix the position of the nodes.

frame.color

color of the frames.

label.hub

logical ; if TRUE only the hubs are labeled.

graph

plot graph of the network. Defaults to 'TRUE'.

names

return names of the neighbors. Defaults to 'FALSE'.

Value

The neighborhood of the targeted genes.

Author(s)

Nicolas Jung, Frédéric Bertrand , Myriam Maumy-Bertrand.

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

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)