geneNeighborhood,omics_network-method {Patterns} | R Documentation |
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)
[Package Patterns version 1.5 Index]