R3CPET (version 1.4.2)

createIndexes-methods: Preparing TF indexes per region

Description

After loading the interactions and the TFBS, the createIndexes method can be used to build indexes for fast look-up for which which TF are located in which region. This method is an intermediate step needed for further analysis.

Usage

"createIndexes"(object, minOverlap = 50)

Arguments

object

a ChiapetExperimentData object in which the interactions and TFBS are already loaded. Check loadPETs and loadTFBS for more info.

minOverlap

The minimum overlap between a TF binding site and a region, to consider a TF as binding to that region. The default value is 50.

Value

A ChiapetExperimentData object in which the .dt slot is populated as a data.table object.

References

Mohamed Nadhir D, Yang C et al 3CPET: Finding Co-factor Complexes in Chia-PET experiment using a Hierarchical Dirichlet Process, ....

See Also

ChiapetExperimentData, loadTFBS , loadPETs, loadPPI

Examples

  ## 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
# ## End(Not run)