outputGenesPerClusterToDir-methods: List of genes in each cluster

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 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

## S4 method for signature 'ChromMaintainers,ChiapetExperimentData'
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.

Author(s)

Mohamed Nadhir Djekidel ([e-mail])

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)

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