outputGenesPerNetworkToDir {R3CPET} | R Documentation |
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.
## S4 method for signature 'ChromMaintainers,ChiapetExperimentData' outputGenesPerNetworkToDir(hdaRes,data,path="NetworksGenes", ...)
hdaRes |
a |
data |
a |
path |
path of the folder to create. by default a folder named |
... |
additional parameters, not used for the moment. |
The specified folder is created with a list .txt
files each for each network that contain the list of genes.
Mohamed Nadhir Djekidel (nde12@mails.tsinghua.edu.cn)
ChromMaintainers
, InferNetworks
, ChiapetExperimentData
## 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)