createServer-methods: Explore results in a web browser

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

Description

To facilitate the interaction of the user with the package, we added an additional web interface using the shiny package. The user can check some basic statistics about the row data and he can explore the results and generate some graphs.

Usage

## S4 method for signature 
## 'ChiapetExperimentData,NetworkCollection,ChromMaintainers'
createServer(x,nets,hlda)

Arguments

x	a ChiapetExperimentData object in which the interactions, TFBS and the index tables are already created.
nets	a NetworkCollection object containing the list of the used TF and the initial interaction networks.
hlda	a ChromMaintainers object in which the results are already calculated.

Value

A webpage is opened.

Author(s)

Mohamed Nadhir Djekidel ([e-mail])

See Also

NetworkCollection, ChiapetExperimentData, ChromMaintainers

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: 
  data(RPKMS)
  x <- ChiapetExperimentData(pet = petFile, tfbs=  tfbsFile, IsBed = FALSE, ppiType="HPRD", filter= TRUE) 
  ## build the diffrent indexes
  x <- createIndexes(x)

  ## build networks connecting each interacting regions
  nets<- buildNetworks(x)

  ## infer the networks and do the clustering 
  hlda<- InferNetworks(nets)
  hlda<- clusterInteractions(hlda)

  ## Run the server
  createServer(x, nets, hlda)


## End(Not run)

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