buildNetworks {R3CPET} | R Documentation

## Building interaction networks connecting interacting regions

### Description

This methods uses the background PPI to try to build an interaction network that connects each interacting regions. If a `regionA` interacts with a `regionB` and if TF_A is the list of TF in `regionA` and TF_B is the list of TF in `regionB`, than we use the loaded PPI as a background network to connect each TF from TF_A to each TF in TF_B.

We suppose that a minimum number of physical interactions (minimum energy) are needed to connection each TF to the other. Thus, we take the shortest path in the PPI. at this stage, each network is a collection of edges.

### Usage

    ## S4 method for signature 'ChiapetExperimentData'
    buildNetworks(object, minFreq = 0.25, maxFreq = 0.75)

### Arguments

`object` | a `ChiapetExperimentData` object in which the interactions and TFBS and PPI are already loaded. Check `loadPETs`, `loadTFBS`, `loadPPI` for more info.
`minFreq` | After constructing the networks for all the interacting regions all edges that appear in less than `minFreq` of the networks are considered to be outliers.
`maxFreq` | After constructing the networks for all the interacting regions all edges that appear in more than `maxFreq` of the networks are considered to be interactions involving general TF and are removed.

### Value

A `NetworkCollection` object that contain the list of all the constructed networks and their sizes.

NOTE: interactions for which no TF was bound or no networks could be constructed or which was empty after filtering will not be considered.

### 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`, `createIndexes`

### 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)

      ## build networks connecting each interacting regions
      nets<- buildNetworks(x)
      nets

    ## End(Not run)

[Package R3CPET version 1.20.0 Index]