getRegionsInNetwork-methods {R3CPET} | R Documentation

## list of interactions per network

### Description

This method can be used to retrieve the genomic coordinated of the DNA-interactions enriched for each network given a certain threshold.

### Usage

    ## S4 method for signature 'ChromMaintainers,ChiapetExperimentData,numeric'
    getRegionsInNetwork(hdaRes,data, net=1, thr=0.5, ...)

### Arguments

`hdaRes` | a `ChromMaintainers` object which already contains the calculated results
`data` | a `ChiapetExperimentData` object that contains the genomic location of all the interactions.
`net` | The ID of the network for which we want to get the list of the involved regions.
`thr` | Specify the minimum enrichment value to consider an interaction to be controlled by the network. by default it is 0.5
`...` | additional parameters not used for the moment.

### Value

a `GRanges` object is returned

### Author(s)

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

### See Also

`InferNetworks`, `ChiapetExperimentData`, `ChromMaintainers`

### 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 and do the clustering
        hlda<- InferNetworks(nets)

        ## return the DNA-interactions in cluster 3
        getRegionsIncluster(hlda,x,net=3)

    ## End(Not run)

[Package R3CPET version 1.16.0 Index]