R3CPET (version 1.4.2)

getRegionsIncluster-methods: list of interactions per cluster

Description

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

Usage

"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

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)