visualizeInteractions-methods: Display a Circos plot of ChIA-pet interactions

In sirusb/R3CPET: 3CPET: Finding Co-factor Complexes in Chia-PET experiment using a Hierarchical Dirichlet Process

Description

This method can be used to draw a circos plot of the chromatin interactions located in the given genomic range.

Usage

## S4 method for signature 'ChiapetExperimentData,GRanges'
visualizeInteractions(object, range)

Arguments

object	a ChiapetExperimentData in which the interactions are already loaded. Check loadPETs for more info.
range	a GRanges object containing the genomic region of interest.

Value

A ciros plot of the selected region is displayed and a list containing the following objects is returned.

circos :

a GRanges object that contains the involved chromatin interactions.

plot :

a ggplot object containing plot.

Author(s)

Mohamed Nadhir Djekidel ([e-mail])

See Also

ChiapetExperimentData, loadPETs, ggbio, GRanges

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: 
  x <- ChiapetExperimentData(pet = petFile, tfbs=  tfbsFile, IsBed = FALSE, ppiType="HPRD", filter= TRUE) 
  ## plot intractions in the region of interest
  gr <- GRanges("chr1", IRanges(1240000,10300000))
  p <- visualizeInteractions(x, gr)
  p
  
## End(Not run)

sirusb/R3CPET documentation built on Oct. 12, 2020, 6 p.m.