getRegionsInNetwork-methods: list of interactions per network

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 enriched for each network given a certain threshold.

Usage

## S4 method for signature 'ChromMaintainers,ChiapetExperimentData,numeric'
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

Author(s)

Mohamed Nadhir Djekidel ([e-mail])

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)

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