\name{addGenesToGoReport}
 \alias{addGenesToGoReport}
 \title{Add Symbol IDs to hyperGTest results}
 \usage{
   addGenesToGoReport(hgOver, universe,
     db = c("GO", "KEGG"), onto = c("CC", "MF", "BP"),
     annotation = NULL, entrez2symbol = NULL)
 }
 \arguments{
   \item{hgOver}{Output of function
   \code{\link[Category]{hyperGTest}}}
 
   \item{universe}{A vector including all IDs on which
   enrichment analysis was applied}
 
   \item{db}{The database to use, default is c("GO","KEGG")}
 
   \item{onto}{A string specifying the GO ontology to use.
   Must be one of "BP", "CC", or "MF", see
   \code{\link[Category:GOHyperGParams-class]{GOHyperGParams}}.
   Only used when argument \code{db} is "GO".}
 
   \item{annotation}{An annotation package}
 
   \item{entrez2symbol}{A vector indexed by Entrez Gene ID
   and filled with the corresponding Gene Symbols}
 }
 \value{
   A data.frame containing the summary of the output of
   function hyperGTest (\code{summary(hgOver)}) with an
   additional column providing the gene Symbols included in
   the significant gene sets.
 }
 \description{
   Add gene Symbols contained in gene sets selected as
   significant by \code{\link[Category]{hyperGTest}}
   function
 }
 \details{
   This function takes as inputs the outputs of
   \code{\link[Category]{hyperGTest}} which takes Entrez
   Gene IDs as inputs to perform the enrichment analysis.
   The goal of this function is to select the Entrez Gene
   IDs responsible for the significant enrichment of a given
   gene set and annotate them in to gene Symbol IDs. When
   the annotation package \code{annotation} was used to map
   feature IDs to Entrez Gene ID, it can also be used here
   to map Entrez and Symbol IDs. If the annotation package
   was not used, but the Entrez Gene IDs were directly
   provided to the hyperGtest function, \code{annotation} is
   expected to be NULL and \code{entrez2symbol} must be
   specified.
 
   This function returns the outputs of function
   \code{\link[Category]{hyperGTest}} which contain:
   \describe{ \item{DB, ID, Term}{The database, the gene set
   ID, and the gene Set name,} \item{P-value}{probability of
   observing the number of genes annotated for the gene set
   among the selected gene list, knowing the total number of
   annotated genes among the universe}, \item{Expected
   counts}{expected number of genes in the selected gene
   list to be found at each tested category term/gene set,}
   \item{Odds ratio}{odds ratio for each category term
   tested which is an indicator of the level of enrichment
   of genes within the list as against the universe,}
   \item{Counts}{number of genes in the selected gene list
   which are annotated for the gene set,} \item{Size}{number
   of genes from the universe annotated for the gene set.}}
 }
 \author{
   Anne Biton
 }
 \seealso{
   \code{\link[Category]{hyperGTest}},
   \code{\link[Category:GOHyperGParams-class]{GOHyperGParams}}
 }
 \keyword{internal}