outputGenesPerClusterToDir-methods {R3CPET} | R Documentation

## List of genes in each cluster

### Description

This helper methods get the set of genes located in the DNA-regions in each cluster. A folder that contain a bunch of `.txt` files (one for each cluster) is generated. We consider a gene to be part of a cluster if the (-1500bp, +500bp) around its `TSS` intersects with one of the DNA regions of the cluster.

### Usage

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

### Arguments

`hdaRes` | a `ChromMaintainers` object in which the DNA-interaction are already clustered.
`data` | a `ChiapetExperimentData` object containing information about the interactions.
`path` | path of the folder to create. by default a folder named `ClustersGenes` 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 that contain the list of genes.

### Author(s)

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

### See Also

`ChromMaintainers`, `InferNetworks`, `ChiapetExperimentData`, `clusterInteractions`

### Examples

        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:
        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)
        hlda<- clusterInteractions(hlda)

        ## get the list of genes per cluster.
        outputGenesPerClusterToDir(hlda,x)

    ## End(Not run)

[Package R3CPET version 1.12.0 Index]