R3CPET (version 1.4.2)

outputGenesPerClusterToDir-methods: List of genes in each cluster

Description

This helper methods get the set of genes located in the DNA-regions in each cluster. A folder that contain a bunch of .txt files (one for each cluster) is generated. We consider a gene to be part of a cluster if the (-1500bp, +500bp) around its TSS intersects with one of the DNA regions of the cluster.

Usage

"outputGenesPerClusterToDir"(hdaRes,data,path="ClustersGenes", ...)

Arguments

hdaRes

a ChromMaintainers object in which the DNA-interaction are already clustered.

data

a ChiapetExperimentData object containing information about the interactions.

path

path of the folder to create. by default a folder named ClustersGenes 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 that contain the list of genes.

See Also

ChromMaintainers, InferNetworks, ChiapetExperimentData, clusterInteractions

Examples

    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 different indexes
#     x <- createIndexes(x)
# 
#     ## build networks connecting each interacting regions
#     nets<- buildNetworks(x)
# 
#     ## infer the networks
#     hlda<- InferNetworks(nets)
#     hlda<- clusterInteractions(hlda)
# 
#     ## get the list of genes per cluster.
#     outputGenesPerClusterToDir(hlda,x)
# 
# ## End(Not run)