R/resultsByOntology.R

In spell098/rnaseq_app:

#' Results by ontology
#' Return the rows from the results topTable
#' @param selectedOntology The ontology term selected
#' @param results The results of one comparison
#' @param ontology An object
#' @examples
#' expr.matrix <- readRDS("data/expr_matrix_LGVD.rds")
#' results <- readRDS("data/results_LGVD.rds")
#' annotation1 = annotate_ensembl(rownames(expr.matrix))
#' go=annotation1[[2]]
#' typeID=annotation1[[4]]
#' result <- results[[1]]
#' ontology <- geneOntology(results,go,typeID,nrow(expr.matrix))
#' selectedOntology <- names(ontology[[1]][[3]])[1]
#' resultsByOntology <- resultsByOntology(selectedOntology,result,ontology[[1]])
#' @seealso
#' \code{\link{}}
#' @export
resultsByOntology = function(selectedOntology,result,ontology){
  resultsOntologies = vector("list",length(selectedOntology))
  names(resultsOntologies) = selectedOntology

  for(i in 1:length(selectedOntology)){
    selected <- selectedOntology[i]
    genes <- ontology[[3]][selected]
    resultsOntologies[[i]] <- result[match(genes[[1]],as.character(result$ensembl_gene_id)),]
    resultsOntologies[[i]] <- cbind(resultsOntologies[[i]],rep(selected,nrow(resultsOntologies[[i]])))
    colnames(resultsOntologies[[i]])[ncol(resultsOntologies[[i]])] <- "Ontology"
  }
  resultsOntology = do.call(rbind, resultsOntologies)
  resultsOntology$Ontology = as.character(resultsOntology$Ontology)
  resultsOntology2 = resultsOntology
  for(j in 1:nrow(resultsOntology)){
    duplicates=grep(as.character(resultsOntology[j,]$ensembl_gene_id),as.character(resultsOntology$ensembl_gene_id))
    resultsOntology2[j,]$Ontology = paste(resultsOntology[duplicates,"Ontology"],collapse=",")
  }
  resultsOntology3 = unique(resultsOntology2)
  return(resultsOntology3)
}