Find the neighborhood of a set of nodes.

# 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
)

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`.

Value

The neighborhood of the targeted genes.

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)

#> [[1]]
#> [[1]][[1]]
#> + 1/102 vertex, from 95e976f:
#> [1] 25
#> 
#> [[1]][[2]]
#> + 1/102 vertex, from 95e976f:
#> [1] 26
#> 
#> 
#> [[2]]
#> [[2]][[1]]
#> + 1/102 vertex, from 95e976f:
#> [1] 25
#> 
#> [[2]][[2]]
#> + 1/102 vertex, from 95e976f:
#> [1] 26
#> 
#> 
#> [[3]]
#> [[3]][[1]]
#> + 1/102 vertex, from 95e976f:
#> [1] 25
#> 
#> [[3]][[2]]
#> + 1/102 vertex, from 95e976f:
#> [1] 26
#> 
#>