R3CPET (version 1.4.2)

outputGenesPerNetworkToDir: List of genes controlled by each network

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

"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.

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)