R3CPET (version 1.4.2)

updateResults-methods: update top maintain networks elements

Description

This helper method can be used to update the list of interactions constituting the chromatin maintainer networks by changing the threshold.

Usage

"updateResults"(object,nets,thr=0.5)

Arguments

object

a ChromMaintainers object in which the clusters are already calculated

nets

a NetworkCollection used to get the vocabulary list.

thr

The cut-off threshold. the top edges that have an enrichment value that sum up to a value >= thr are considered.

Value

a ChromMaintainers object in which the topNodes and topEdges tables are updated.

See Also

InferNetworks, NetworkCollection, ChromMaintainers

Examples

    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
#     hlda<- InferNetworks(nets)
#     topNodes(hlda)
# 
#     hlda <- updateResults(hlda, nets, 0.4)
#     topNodes(hlda)
#     ## End(Not run)