outputGenesPerNetworkToDir {R3CPET} | R Documentation

## List of genes controlled by each network

### Description

This helper methods get the set of genes located in the DNA-regions controlled by each network. A folder that contains a bunch of `.txt` files (one for each network) is generated. We consider (-2500bp, +2500bp) around the `TSS` of gene located in a region showing 0.5 or more enrichment for the network.

### Usage

    ## S4 method for signature 'ChromMaintainers,ChiapetExperimentData'
    outputGenesPerNetworkToDir(hdaRes,data,path="NetworksGenes", ...)

### Arguments

`hdaRes` | a `ChromMaintainers` object containing the enrichment values.
`data` | a `ChiapetExperimentData` object containing information about the interactions.
`path` | path of the folder to create. by default a folder named `NetworksGenes` is created in the current working directory.
`...` | additional parameters, not used for the moment.

### Value

The specified folder is created with a list `.txt` files each for each network that contain the list of genes.

### Author(s)

Mohamed Nadhir Djekidel (nde12@mails.tsinghua.edu.cn)

### See Also

`ChromMaintainers`, `InferNetworks`, `ChiapetExperimentData`

### 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 different indexes
        x <- createIndexes(x)

        ## build networks connecting each interacting regions
        nets<- buildNetworks(x)

        ## infer the networks
        hlda<- InferNetworks(nets)

        ## get the list of genes per network.
        outputGenesPerNetworkToDir(hlda,x)

    ## End(Not run)

[Package R3CPET version 1.22.0 Index]