getRegionsInNetwork-methods {R3CPET} | R Documentation |
This method can be used to retrieve the genomic coordinated of the DNA-interactions enriched for each network given a certain threshold.
## S4 method for signature 'ChromMaintainers,ChiapetExperimentData,numeric' getRegionsInNetwork(hdaRes,data, net=1, thr=0.5, ...)
hdaRes |
a |
data |
a |
net |
The ID of the network for which we want to get the list of the involved regions. |
thr |
Specify the minimum enrichment value to consider an interaction to be controlled by the network. by default it is 0.5 |
... |
additional parameters not used for the moment. |
a GRanges
object is returned
Mohamed Nadhir Djekidel (nde12@mails.tsinghua.edu.cn)
InferNetworks
, ChiapetExperimentData
, ChromMaintainers
## get the different datasets path 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 and do the clustering hlda<- InferNetworks(nets) ## return the DNA-interactions in cluster 3 getRegionsIncluster(hlda,x,net=3) ## End(Not run)