A function to perform DAVID GO term analysis using R directly.

DAVID.R

### "transcript" parameter is the original matrix of normalized counts 
### "signifcant" parameter is the filtered matrix of significant genes (using desired cutoff)
### "email" is an email address needed to run the web service

go.david<-function(transcript,significant,email){
  require("RDAVIDWebService")
  if(dim(significant)[1] !=0){
  david<-DAVIDWebService$new(email=email)
  background<-addList(david, rownames(transcript), idType="ENSEMBL_GENE_ID",listName="full_transcript", listType="Background")
  sig.genes<-addList(david, rownames(significant), idType="ENSEMBL_GENE_ID",listName="significant", listType="Gene")
  termCluster<-getClusterReport(david, type="Term")

 
  if(length(members(termCluster)) !=0){
  go.data<-data.frame()
  for (cluster in 1:length(members(termCluster))){
    
    go.data<-rbind(go.data,cbind(cluster,members(termCluster)[[cluster]][,1:6]))
    
  }
  go.genes<-list()
  for(l in 1:dim(go.data)[1]){
    go.genes<- append(go.genes,paste(paste(unlist(getBM(attributes = c("external_gene_id"), filters = "ensembl_gene_id",values = trim.leading(unlist(strsplit(go.data[l,7],split=","))),mart=mart)),sep=","),collapse=","))
  }
  
  go.term.data<-cbind(go.data[,-7],as.data.frame(unlist(go.genes)))
 
  }
  }
  return(go.term.data)
}