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

In Patterns: Deciphering Biological Networks with Patterned Heterogeneous Measurements

Find the neighborhood of a set of nodes.

Description

Find the neighborhood of a set of nodes.

Usage

## S4 method for signature '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(s)

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)
          

Patterns documentation built on Dec. 1, 2022, 5:09 p.m.