createIndexes-methods: Preparing TF indexes per region

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

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

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## S4 method for signature 'ChiapetExperimentData'
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.

Author(s)

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

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

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  ## 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)

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