annotateExpression-methods {R3CPET} | R Documentation |
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.
## S4 method for signature 'ChromMaintainers,data.frame' annotateExpression(object, RPKMS)
object |
a |
RPKMS |
a two columns |
A ChromMaintainers
object in which the networks are annotated.
Mohamed Nadhir Djekidel (nde12@mails.tsinghua.edu.cn)
ChromMaintainers
, InferNetworks
## 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)