R/OutputGOBasedDEfromFeatures2.R

In aiminy/PathwaySJ: A R package for GO term enrichment analysis with the flexible bias factor adjustment

#' OutputGOBasedDEfromFeatures2
#'
#' Reformat genewised results from JunctionSeq, and use this one to get enriched GO terms
#'
#' @param re.PJ.gene.based
#' @param gene.model
#' @param Output_file
#'
#' @return
#' @export
#'
#' @examples
#'
#' RE.exon.sj.all.gene<-OutputGOBasedDEfromFeatures2(re.PJ.gene.based,gene.model,"GO_exon_sj_use_all_gene.xls")
#'
#'
#'
OutputGOBasedDEfromFeatures2<-function(re.PJ.gene.based,gene.model,Output_file){

  re2<-ReformatData(re.PJ.gene.based)

  Re.Go.adjusted.by.exon.SJ<-GotermAnalysisUseReformatedData(re2,ad="exon_SJ",sub_feature=NULL,0.05,"hg19","ensGene",gene_model=gene.model)

  Re<-Re.Go.adjusted.by.exon.SJ

  head(Re.Go.adjusted.by.exon.SJ[[1]])

  #select GO term(10<=numInCat<=300 and BP only)

  index.select<-which(Re.Go.adjusted.by.exon.SJ[[1]]$numInCat>=10&Re.Go.adjusted.by.exon.SJ[[1]]$numInCat<=300&Re.Go.adjusted.by.exon.SJ[[1]]$ontology=="BP")

  Re.Go.adjusted.by.exon.SJ.select<-Re.Go.adjusted.by.exon.SJ[[1]][index.select,]

  over_represented_pvalue_adjusted<-p.adjust(Re.Go.adjusted.by.exon.SJ.select$over_represented_pvalue,method="BH")

  Re.Go.adjusted.by.exon.SJ.select.with.adjP<-cbind(Re.Go.adjusted.by.exon.SJ.select[,c(1,2)],over_represented_pvalue_adjusted,Re.Go.adjusted.by.exon.SJ.select[,-c(1,2,3)])


  dataset2<- Re.Go.adjusted.by.exon.SJ.select.with.adjP

  dataset2[sapply(dataset2, is.list)] <-
    sapply(dataset2[sapply(dataset2, is.list)],
           function(x)sapply(x, function(y) paste(unlist(y),collapse=", ") ) )

  Re2<-list(EnrichedGO=Re[[1]],Pwf=Re[[2]],SelectedEnrichedGO=dataset2)

  write.table(dataset2,file=Output_file,row.names = FALSE,quote=FALSE,sep="\t")

  return(Re2)

}