Find the neighborhood of a set of nodes.
Find the neighborhood of a set of nodes.
## 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 )
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'. |
The neighborhood of the targeted genes.
Nicolas Jung, Frédéric Bertrand , Myriam Maumy-Bertrand.
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.
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)
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