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

In R3CPET: 3CPET: Finding Co-factor Complexes in Chia-PET experiment using a Hierarchical Dirichlet Process

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

## S4 method for signature 'ChromMaintainers,data.frame'
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.

Author(s)

Mohamed Nadhir Djekidel ([e-mail])

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)

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