updateResults-methods: update top maintain networks elements

In sirusb/R3CPET: 3CPET: Finding Co-factor Complexes in Chia-PET experiment using a Hierarchical Dirichlet Process

Description

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

Usage

## S4 method for signature 'ChromMaintainers,NetworkCollection,numeric'
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.

Author(s)

Mohamed Nadhir Djekidel ([e-mail])

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)

sirusb/R3CPET documentation built on Oct. 12, 2020, 6 p.m.