updateResults-methods {R3CPET} | R Documentation |
This helper method can be used to update the list of interactions constituting the chromatin maintainer networks by changing the threshold.
## S4 method for signature 'ChromMaintainers,NetworkCollection,numeric' updateResults(object,nets,thr=0.5)
object |
a |
nets |
a |
thr |
The cut-off threshold. the top edges that have an enrichment value that sum up to a value >= |
a ChromMaintainers
object in which the topNodes
and topEdges
tables are updated.
Mohamed Nadhir Djekidel (nde12@mails.tsinghua.edu.cn)
InferNetworks
, NetworkCollection
, ChromMaintainers
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)