GenerateNetworks-methods: Generate a list of 'igraph' networks

In R3CPET: 3CPET: Finding Co-factor Complexes in Chia-PET experiment using a Hierarchical Dirichlet Process

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

## S4 method for signature 'ChromMaintainers'
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.

Author(s)

Mohamed Nadhir Djekidel ([e-mail])

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)

R3CPET documentation built on Nov. 8, 2020, 8:05 p.m.