updateResults-methods: update top maintain networks elements

Description Usage Arguments Value Author(s) See Also Examples

Description

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

Usage

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## 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 (nde12@mails.tsinghua.edu.cn)

See Also

InferNetworks, NetworkCollection, ChromMaintainers

Examples

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    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.