R3CPET (version 1.4.2)

getRegionsInNetwork-methods: 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

"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

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)