\name{computeGeneSetsOverlap}
 \alias{computeGeneSetsOverlap}
 \alias{computeGeneSetsOverlap,list,character-method}
 \alias{computeGeneSetsOverlap,list,ExpressionSet-method}
 \alias{computeGeneSetsOverlap,GeneSetCollection,character-method}
 \alias{computeGeneSetsOverlap,GeneSetCollection,ExpressionSet-method}
 

 \encoding{latin1}
 

 \title{
 Compute gene-sets overlap
 }
 \description{
 Calculates the overlap among every pair of gene-sets given as input.
 }
 \usage{
 \S4method{computeGeneSetsOverlap}{list,character}(gSets, uniqGenes, min.sz=1, max.sz=Inf)
 \S4method{computeGeneSetsOverlap}{list,ExpressionSet}(gSets, uniqGenes, min.sz=1, max.sz=Inf)
 \S4method{computeGeneSetsOverlap}{GeneSetCollection,character}(gSets, uniqGenes, min.sz=1, max.sz=Inf)
 \S4method{computeGeneSetsOverlap}{GeneSetCollection,ExpressionSet}(gSets, uniqGenes, min.sz=1, max.sz=Inf)
 }
 \arguments{
   \item{gSets}{Gene sets given either as a \code{list} or a \code{GeneSetCollection} object.}
   \item{uniqGenes}{Vector of unique genes to be considered when calculating the overlaps.}
   \item{min.sz}{Minimum size.}
   \item{max.sz}{Maximum size.}
 }
 
 \details{
 This function calculates the overlap between every pair of gene sets
 of the input argument \code{gSets}. Before this calculation takes place,
 the gene sets in \code{gSets} are firstly filtered to discard genes that do not
 match to the identifiers in \code{uniqGenes}. Secondly, they are further
 filtered to meet the minimum and/or maximum size specified with the arguments
 \code{min.sz} and \code{max.sz}. The overlap between two gene sets is calculated
 as the number of common genes between the two gene sets divided by the smallest
 size of the two gene sets.
 }
 \value{
 A gene-set by gene-set matrix of the overlap among every pair of gene sets.
 }
 \references{

 \enc{H�nzelmann}{Hanzelmann}, S., Castelo, R. and Guinney, J.
 GSVA: Gene set variation analysis for microarray and RNA-Seq data.
 \emph{BMC Bioinformatics}, 14:7, 2013.

 }
 \author{J. Guinney}
 \seealso{
   \code{\link{filterGeneSets}}
 }
 \examples{
 
 geneSets <- list(set1=as.character(1:4), set2=as.character(4:10))
 
 computeGeneSetsOverlap(geneSets, unique(unlist(geneSets)))
 
 }
 \keyword{Gene set}