annotateExpression-methods {R3CPET} | R Documentation

## 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

    ## 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 (nde12@mails.tsinghua.edu.cn)

### 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)

[Package R3CPET version 1.20.0 Index]