R: list of interactions per cluster

getRegionsIncluster-methods {R3CPET}

R Documentation

list of interactions per cluster

Description

This method can be used to retrieve the genomic coordinated of the DNA-interactions in each cluster.

Usage

## S4 method for signature 'ChromMaintainers,ChiapetExperimentData,numeric'
getRegionsIncluster(hdaRes,data, cluster=1, ...)

Arguments

`hdaRes`	a `ChromMaintainers` object in which the clusters are already calculated
`data`	a `ChiapetExperimentData` object that contains the genomic location of all the interactions.
`cluster`	The ID of the cluster for which we want to get the list of the involved regions.
`...`	additional parameters not used for the moment.

Value

a GRanges object is returned

Author(s)

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

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)
    hlda<- clusterInteractions(hlda)

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


## End(Not run)

[Package R3CPET version 1.20.0 Index]