\name{hypergeoAn}
 \alias{hypergeoAn}
 \title{Runs an enrichment analysis per component using package \code{\link{GOstats}}.}
 \usage{
   hypergeoAn(icaSet, params,
     path = paste(resPath(params), "GOstatsEnrichAnalysis/", sep = "/"),
     SlistSel, hgCutoff = 0.01, db = "go", onto = "BP",
     cond = TRUE, universe, entrez2symbol)
 }
 \arguments{
   \item{icaSet}{An object of class \code{IcaSet}}
 
   \item{params}{An object of class
   \code{\link[MineICA:MineICAParams-class]{MineICAParams}}
   containing the parameters of the analysis}
 
   \item{path}{The path where results will be saved}
 
   \item{SlistSel}{A list of contributing gene projection
   values per component.  Each element of the list
   corresponds to a component and is restricted to the
   features or genes exceeding a given threshold. If
   missing, is computed by the function.}
 
   \item{hgCutoff}{The p-value threshold}
 
   \item{db}{The database to be used (\code{"GO"} or
   \code{"KEGG"})}
 
   \item{onto}{A character specifying the GO ontology to
   use. Must be one of \code{"BP"}, \code{"CC"}, or
   \code{"MF"}, see
   \code{\link[Category:GOHyperGParams-class]{GOHyperGParams}}.
   Only used when argument \code{db} is \code{"GO"}.}
 
   \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{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.}
 }
 \description{
   Runs an enrichment analysis of the contributing genes
   associated with each component, using the function
   \code{hyperGTest} of package
   \code{\link[GOstats]{GOstats}}. The easiest way to run
   enrichment analysis is to use function
   \code{\link{runEnrich}}.
 }
 \details{
   An annotation package must be available in
   \code{annotation(icaSet)} to provide the contents of the
   gene sets. If none corresponds to the technology you deal
   with, please choose the org.*.eg.db package according to
   the organism (for example org.Hs.eg.db for Homo sapiens).
   Save results of the enrichment tests in a '.rda' file
   located in
   \code{path}/\code{db}/\code{onto}/\code{zvalCutoff(params)}.
 }
 \examples{
 \dontrun{
 ## load an example of IcaSet
 data(icaSetCarbayo)
 
 ## define params
 # Use threshold 3 to select contributing genes.
 # Results of enrichment analysis will be written in path 'resPath(params)/GOstatsEnrichAnalysis'
 params <- buildMineICAParams(resPath="~/resMineICACarbayo/", selCutoff=3)
 
 ## Annotation package for IcaSetCarbayo is hgu133a.db.
 # check annotation package
 annotation(icaSetCarbayo)
 
 ## Define universe, i.e the set of EntrezGene IDs mapping to the feature IDs of the IcaSet object.
 universe <- as.character(na.omit(unique(unlist(AnnotationDbi::mget(featureNames(icaSetCarbayo),
                          hgu133aENTREZID, ifnotfound = NA)))))
 
 ## Apply enrichement analysis (of the contributing genes) to the first components using gene sets from KEGG.
 # Since an annotation package is available, we don't need to fill arg 'entrez2symbol'.
 # run the actual enrichment analysis
 hypergeoAn(icaSet=icaSetCarbayo[,,1], params=params, db="GO",onto="BP", universe=universe)
 }
 }
 \author{
   Anne Biton
 }
 \seealso{
   \code{\link{runEnrich}}, \code{\link[xtable]{xtable}},
   \code{\link[biomaRt]{useMart}},
   \code{\link[Category]{hyperGTest}},
   \code{\link[Category:GOHyperGParams-class]{GOHyperGParams}},
   \code{\link{mergeGostatsResults}}
 }