R3CPET (version 1.4.2)

GenerateNetworks-methods: Generate a list of igraph networks

Description

This methods converts the networks slot of a ChromMaintainers object, it reads the topEdge slot and convert it into a list of igraph objectts.

Usage

"GenerateNetworks"(object,...)

Arguments

object

a ChromMaintainers object

...

future options not considered for the moment.

Value

Returns ChromMaintainers object in which the networks slot is populated.

See Also

ChromMaintainers, InferNetworks

Examples

  ## get the different datasets path
  petFile <- file.path(system.file("example",package="R3CPET"),"HepG2_interactions.txt")  
  tfbsFile <- file.path(system.file("example",package="R3CPET"),"HepG2_TF.txt.gz")  
    
## Not run: 
#   data(RPKMS)
#   x <- ChiapetExperimentData(pet = petFile, tfbs=  tfbsFile, IsBed = FALSE, ppiType="HPRD", filter= TRUE) 
#   ## build the diffrent indexes
#   x <- createIndexes(x)
#   ## build networks connecting each interacting regions
#   nets<- buildNetworks(x)
# 
#   ## infer the networks
#   hlda<- InferNetworks(nets)
# 
#   hlda <- GenerateNetworks(hlda)
#   networks(hlda)
# ## End(Not run)