outputGenesPerNetworkToDir-methods: List of genes controlled by each network

In R3CPET: 3CPET: Finding Co-factor Complexes in Chia-PET experiment using a Hierarchical Dirichlet Process

Description

This helper methods get the set of genes located in the DNA-regions controlled by each network. A folder that contains a bunch of .txt files (one for each network) is generated. We consider (-2500bp, +2500bp) around the TSS of gene located in a region showing 0.5 or more enrichment for the network.

Usage

## S4 method for signature 'ChromMaintainers,ChiapetExperimentData'
outputGenesPerNetworkToDir(hdaRes,data,path="NetworksGenes", ...)

Arguments

hdaRes	a ChromMaintainers object containing the enrichment values.
data	a ChiapetExperimentData object containing information about the interactions.
path	path of the folder to create. by default a folder named NetworksGenes is created in the current working directory.
...	additional parameters, not used for the moment.

Value

The specified folder is created with a list .txt files each for each network that contain the list of genes.

Author(s)

Mohamed Nadhir Djekidel ([e-mail])

See Also

ChromMaintainers, InferNetworks, ChiapetExperimentData

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: 
    data(RPKMS)
    x <- ChiapetExperimentData(pet = petFile, tfbs=  tfbsFile, IsBed = FALSE, ppiType="HPRD", filter= TRUE) 
    ## build the different indexes
    x <- createIndexes(x)

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

    ## infer the networks
    hlda<- InferNetworks(nets)

    ## get the list of genes per network.
    outputGenesPerNetworkToDir(hlda,x)


## End(Not run)

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