GenerateNetworks-methods {R3CPET} | R Documentation

## 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

    ## 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 (nde12@mails.tsinghua.edu.cn)

### 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)

[Package R3CPET version 1.12.0 Index]