Cascade (version 2.1)

geneNeighborhood,network-method: Find the neighborhood of a set of nodes.

Description

Find the neighborhood of a set of nodes.

Usage

# S4 method for 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
)

Value

The neighborhood of the targeted genes.

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`.

Author

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)