outputGenesPerClusterToDir-methods {R3CPET} | R Documentation |
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.
## S4 method for signature 'ChromMaintainers,ChiapetExperimentData' outputGenesPerClusterToDir(hdaRes,data,path="ClustersGenes", ...)
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 that contain the list of genes.
Mohamed Nadhir Djekidel (nde12@mails.tsinghua.edu.cn)
ChromMaintainers
, InferNetworks
, ChiapetExperimentData
,
clusterInteractions
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)