Patterns (version 1.4)

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

Description

Find the neighborhood of a set of nodes.

Usage

# S4 method for omics_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 = F
)

Value

The neighborhood of the targeted genes.

Arguments

net

a omics_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

Bertrand Frederic, Myriam Maumy-Bertrand.

Examples

data(Selection)
data(infos)
#Find probesets for EGR1
pbst_EGR1 = infos[infos$hgnc_symbol=="EGR1", "affy_hg_u133_plus_2"]

gene_IDs = infos[match(Selection@name, infos$affy_hg_u133_plus_), "hgnc_symbol"]

data(network)
#A nv value can chosen using the cutoff function
nv=.11 
EGR1<-which(is.element(Selection@name,pbst_EGR1))
P<-position(network,nv=nv)

geneNeighborhood(network,targets=EGR1,nv=nv,ini=P,
label_v=gene_IDs)