clusterInteractions-methods {R3CPET} | R Documentation |
This method aims at clustering the DNA interactions according to their partnership probability to the inferred chromatin maintainer networks.
## S4 method for signature 'ChromMaintainers' clusterInteractions(object, method="sota", nbClus=20 )
object |
(Required) a non-empty |
method |
(optional)used to specify the method to use. Only the |
nbClus |
(optional) The user-specified number of clusters. It is taken into consideration only if |
A ChromMaintainers
object in which the clusRes
is populated as a sota
.
Mohamed Nadhir Djekidel (nde12@mails.tsinghua.edu.cn)
Herrero, J., Valencia, A, and Dopazo, J. (2005). A hierarchical unsupervised growing neural network for clustering gene expression patterns. Bioinformatics, 17, 126-136.
ChromMaintainers
, sota
, InferNetworks
data(RPKMS) ## 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: x <- ChiapetExperimentData(pet = petFile, tfbs= tfbsFile, IsBed = FALSE, ppiType="HPRD", filter= TRUE) ## build the diffrent indexes x <- createIndexes(x) x ## build networks connecting each interacting regions nets<- buildNetworks(x) ## infer the networks hlda<- InferNetworks(nets) #cluster hlda<- clusterInteractions(hlda) #Display heatmap plot3CPETRes(hlda,type="heatmap") hlda ## End(Not run)