updateResults-methods {R3CPET} | R Documentation

## 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

    ## 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

        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)

[Package R3CPET version 1.12.0 Index]