R/GotermAnalysis2GetAllGOTerms_AdjustedByNumOfJunctionWithinOneGene.R

In SCCC-BBC/GOSJ:

GotermAnalysis2GetAllGOTerms_AdjustedByNumOfJunctionWithinOneGene<-function(Data4Goterm,ad="GL",sub_feature=NULL,threshold,file_prefix){

  if(is.null(sub_feature)){Data4Goterm.sub_feature<-Data4Goterm}
  else{Data4Goterm.sub_feature<-Data4Goterm[grep(sub_feature,Data4Goterm[,8]),]}


  print(dim(Data4Goterm.sub_feature))

  Data4Goterm.sub_feature.geneID.NumOfJunctions<-Data4Goterm.sub_feature[,c(1,11)]

  print(dim(Data4Goterm.sub_feature.geneID.NumOfJunctions))

  Data4Goterm.sub_feature.Sig<-Data4Goterm.sub_feature[which(Data4Goterm.sub_feature[,7]<threshold),]

  #GO term analysis using GOSeq
  All.gene.id.based.on.sub_feature<-unique(unlist(strsplit(Data4Goterm.sub_feature[,1],"\\+")))
  #length(All.gene.id.based.on.sub_feature)
  All.gene.id.index<-rep(0,length(All.gene.id.based.on.sub_feature))
  names(All.gene.id.index)=All.gene.id.based.on.sub_feature

  All.genes.based.on.Sig.sub_feature<-unique(unlist(strsplit(Data4Goterm.sub_feature.Sig[,1],"\\+")))

  gene.DE_interest<-as.integer(which( All.gene.id.based.on.sub_feature %in% All.genes.based.on.Sig.sub_feature ))

  All.gene.id.index[gene.DE_interest]<-1

  gene.with.matched.junction<-which(Data4Goterm.sub_feature.geneID.NumOfJunctions[,1] %in% c(names(All.gene.id.index)))

  num.junction.4.matched.gene<-Data4Goterm.sub_feature.geneID.NumOfJunctions[gene.with.matched.junction,2]

  names.4.matched.gene<-Data4Goterm.sub_feature.geneID.NumOfJunctions[gene.with.matched.junction,1]

  All.gene.id.index.2<-All.gene.id.index[which(names(All.gene.id.index) %in% c(names.4.matched.gene))]

  print(length(All.gene.id.index.2))


if(ad=="GL"){
pwf.DE_interest=nullp(All.gene.id.index.2,"mm10","ensGene",plot.fit = FALSE)
}
else
{
pwf.DE_interest=nullp(All.gene.id.index.2,"mm10","ensGene",bias.data = num.junction.4.matched.gene,plot.fit = FALSE)
}


  GO.wall.DE_interest=goseq(pwf.DE_interest,"mm10","ensGene")
  enriched.GO.DE_interest=GO.wall.DE_interest[p.adjust(GO.wall.DE_interest$over_represented_pvalue,method="BH")<threshold,]
  re<-list()

  re[[1]]<-GO.wall.DE_interest
  re[[2]]<-pwf.DE_interest
  return(re)

  }