getRegionsIncluster-methods {R3CPET} | R Documentation |
This method can be used to retrieve the genomic coordinated of the DNA-interactions in each cluster.
## S4 method for signature 'ChromMaintainers,ChiapetExperimentData,numeric' getRegionsIncluster(hdaRes,data, cluster=1, ...)
hdaRes |
a |
data |
a |
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. |
a GRanges
object is returned
Mohamed Nadhir Djekidel (nde12@mails.tsinghua.edu.cn)
clusterInteractions
, InferNetworks
,
ChiapetExperimentData
, ChromMaintainers
## 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)