R3CPET (version 1.4.2)

annotateExpression-methods: Add the gene expression attribute to the graph nodes

Description

This method is a kinda of helper method, it helps the user to add for each node in the inferred chromatin maintainer network the RPKM attributes. It is useful if the user want to save the networks as ".gml" files and visualize them using software such as Gephi or Cytoscape. Or maybe if he wants to know which networks are highly expressed then others.

Usage

"annotateExpression"(object, RPKMS)

Arguments

object

a ChromMaintainers object in which the networks are already present

RPKMS

a two columns data.frame, where the first column contains the name of the gene and the second contains the expression values

Value

A ChromMaintainers object in which the networks are annotated.

See Also

ChromMaintainers, InferNetworks

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: 
#   x <- ChiapetExperimentData(pet = petFile, tfbs=  tfbsFile, IsBed = FALSE, ppiType="HPRD", filter= TRUE) 
#   ## build the diffrent indexes
#   x <- createIndexes(x)
#   x
#   
# ## build the different indexes
# x <- createIndexes(x)
# 
# ## build networks connecting each interacting regions
# nets<- buildNetworks(x)
# 
# ## infer the networks
# hlda<- InferNetworks(nets)
# 
# networks(hlda)
# 
# ## Annotate networks
# hlda<- annotateExpression(hlda,as.data.frame(RPKMS))
# 
# ## Notice the addition of the RPKM attribute to each network
# networks(hlda)
# ## End(Not run)