R3CPET (version 1.4.2)

visualizeInteractions: Display a Circos plot of ChIA-pet interactions

Description

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

Usage

"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.

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)