clusterInteractions-methods: Grouping DNA interactions by enrichment profile

Description Usage Arguments Value Author(s) References See Also Examples

Description

This method aims at clustering the DNA interactions according to their partnership probability to the inferred chromatin maintainer networks.

Usage

1
2
## S4 method for signature 'ChromMaintainers'
clusterInteractions(object, method="sota", nbClus=20 )

Arguments

object

(Required) a non-empty ChromMaintainers object

method

(optional)used to specify the method to use. Only the method = "sota" is supported for the moment, the method='clues' is deprecated. The user needs to specify the number of clusters by setting the parameter nbClus, by default it is set to 20.

nbClus

(optional) The user-specified number of clusters. It is taken into consideration only if method = sota.

Value

A ChromMaintainers object in which the clusRes is populated as a sota.

Author(s)

Mohamed Nadhir Djekidel (nde12@mails.tsinghua.edu.cn)

References

Herrero, J., Valencia, A, and Dopazo, J. (2005). A hierarchical unsupervised growing neural network for clustering gene expression patterns. Bioinformatics, 17, 126-136.

See Also

ChromMaintainers, sota, InferNetworks

Examples

 1
 2
 3
 4
 5
 6
 7
 8
 9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
 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)

R3CPET documentation built on Nov. 8, 2020, 8:05 p.m.