createIndexes-methods {R3CPET} | R Documentation

## 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

    ## 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

      ## 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)

[Package R3CPET version 1.24.0 Index]