R/do_ORA.R

In nicohuttmann/pOmics: Framework for proteomics data analysis

#' Performs overexpression enrichment on logical protein vector with specified
#' Ontology
#'
#' @param proteins character vector
#' @param database database to use
#' @param pvalueCutoff p-value/confidence threshold to exclude terms
#' @param pAdjustMethod one of "none", "BH" (Benjamini-Hochberg correction),
#' "hochberg", "bonferroni", "holm", "hommel", "BY", "fdr"
#' @param qvalueCutoff q-value cutoff for annotations
#' @param minGSSize minimum number of annotated proteins to be included
#' @param maxGSSize maximum number of annotated proteins to be included
#' @param dataset dataset
#'
#' @return
#' @export
#'
#'
do_ORA <- function(proteins,
                   database,
                   pvalueCutoff = 0.05,
                   pAdjustMethod = "none",
                   qvalueCutoff = 0.2,
                   minGSSize = 10,
                   maxGSSize = 500,
                   algorithm = "classic",
                   dataset) {

  # Check if any significant proteins are present
  if (sum(proteins) == 0) return(NULL)

  # TERM2GENE data frame
  if (is.data.frame(database))
    results <- do_ORA_TERM2GENE(proteins = proteins,
                                pvalueCutoff = pvalueCutoff,
                                pAdjustMethod = pAdjustMethod,
                                qvalueCutoff = qvalueCutoff,
                                minGSSize = minGSSize,
                                maxGSSize = maxGSSize,
                                database = database)

  # Gene Ontology
  else if (database %in% c("CC", "BP", "MF"))
    results <- do_ORA_GO(proteins = proteins,
                         pvalueCutoff = pvalueCutoff,
                         pAdjustMethod = pAdjustMethod,
                         qvalueCutoff = qvalueCutoff,
                         minGSSize = minGSSize,
                         maxGSSize = maxGSSize,
                         database = database,
                         dataset = dataset)
  # KEGG

  else if (database %in% c("Kegg", "KEGG", "kegg"))
    results <- do_ORA_KEGG(proteins = proteins,
                           pvalueCutoff = pvalueCutoff,
                           pAdjustMethod = pAdjustMethod,
                           qvalueCutoff = qvalueCutoff,
                           minGSSize = minGSSize,
                           maxGSSize = maxGSSize,
                           dataset = dataset)

  # Reactome
  else if (database %in% c("Reactome", "reactome", "REACTOME"))
    results <- do_ORA_Reactome(proteins = proteins,
                               pvalueCutoff = pvalueCutoff,
                               pAdjustMethod = pAdjustMethod,
                               qvalueCutoff = qvalueCutoff,
                               minGSSize = minGSSize,
                               maxGSSize = maxGSSize,
                               dataset = dataset)


  # unknown database
  else return(NULL)

  # Return results
  return(results)

}