getRegionsIncluster-methods: list of interactions per cluster

In R3CPET: 3CPET: Finding Co-factor Complexes in Chia-PET experiment using a Hierarchical Dirichlet Process

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 ([e-mail])

See Also

clusterInteractions, 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)
    hlda<- clusterInteractions(hlda)

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


## End(Not run)

R3CPET documentation built on Nov. 8, 2020, 8:05 p.m.