\name{doEnrichment}
 \alias{doEnrichment}
 \title{Runs enrichment analysis of contributing genes}
 \usage{
   doEnrichment(compSel, chip, onto, hgCutoff, cond,
     universe, path, db, pack.annot.EID, Slist, it, cutoff,
     entrez2symbol)
 }
 \arguments{
   \item{compSel}{A list containing three elements
   \describe{ \item{compSel}{the projection values of
   contributing genes that were selected based on their
   absolute projection} \item{compSel_neg}{the projection
   values of contributing genes that have negative
   projections} \item{compSel_pos}{the projection values of
   contributing genes that have positive projections}}}
 
   \item{chip}{The annotation package}
 
   \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{hgCutoff}{The p-value threshold}
 
   \item{cond}{A logical indicating whether the calculation
   should conditioned on the GO structure, see
   \code{\link[Category:GOHyperGParams-class]{GOHyperGParams}}.}
 
   \item{universe}{The universe for the hypergeometric
   tests, see
   \code{\link[Category:GOHyperGParams-class]{GOHyperGParams}}.}
 
   \item{path}{The path where results will be saved}
 
   \item{db}{The used database to use ('GO' or 'KEGG')}
 
   \item{pack.annot.EID}{The name of the environment of the
   annotation package containing the annotation for Entrez
   Gene.}
 
   \item{Slist}{The list of gene projections across all
   components}
 
   \item{it}{The index of the component}
 
   \item{cutoff}{The threshold applied on the gene
   projections, used to select the contributing genes}
 
   \item{entrez2symbol}{A vector of all gene Symbols
   involved in the analysis indexed by their Entrez Gene
   IDs. It is only used when \code{annotation(params)} is
   empty, and allows to associate gene sets to Symbols.}
 }
 \value{
   Object of class \code{GOHyperGResult-class}
 }
 \description{
   doEnrichment This internal function is called by
   \code{hypergeoAn} and runs hypergeometric tests through
   function \code{hyperGTest} to associate the contributing
   genes of a component to gene sets.
 }
 \author{
   Anne Biton
 }
 \keyword{internal}