#(3)	GREAT analysis 
#The following R code is a function to send requests to GREAT web server. The input bed file lists 4 variables: chromosome, bp of CpG start (CGstart in hg19), bp of CpG end (CGstart+1), and CpG name.  
#
#R code
#
library(rGREAT)
output.all={}
job = submitGreatJob(input, bg = background,
                     species               = "hg19",
                     includeCuratedRegDoms = TRUE,
                     rule                  = c("basalPlusExt"),
                     adv_upstream          = 5.0,
                     adv_downstream        = 1.0,
                     adv_span              = 50,
                     request_interval = 300,
                     version="3",
                     max_tries = 10)
#
ontology.all=availableOntologies(job)
print(ontology.all)

for(k in 1:length(ontology.all)){
  print(ontology.all[k])
  out0.list = tryCatch(getEnrichmentTables(job,ontology=ontology.all[k], download_by = "tsv"),error=function(e){NULL})
  if(!is.null(out0.list)){
    db0.list=as.list(names(out0.list))
    output<-Map(cbind,Database=db0.list,out0.list)
    output<-do.call('rbind',output)
    output.all=rbind(output.all,output)
  }
}