\name{prunePaths}

 \alias{prunePaths}
 \title{Summarize the paths obtained by clipper according to their similarity.}
 \description{This function allows the user to chose only one
   representant of those paths that have more than 1-thr similarity. The
   best scoring path is choosen.}
 \usage{prunePaths(pathSummary, thr=NULL, clust=NULL, sep=";")}
 \arguments{
   \item{pathSummary}{a matrix resulting from clipper function.}
   \item{thr}{a dissimilarity threshold. NULL means no pruning.}
   \item{clust}{filename where path-cluster is saved. NULL means no
     cluster saved.}
   \item{sep}{the separator to split genes for similarity
     computation. Default = ;}
 }
 
 \value{a matrix}
 
 \seealso{\code{\link{clipper}}}
 
 \examples{

 toyEx <- matrix(c(1,1,5,3,5,2,5,3,8.2,3,2,1,0.3,0.1,2,1,"1;2;3;4;5","1;2;3",
 "1;2;3;4;5","1;2;3","1;2;3;4;5","1;2;3","1;2;3;4;5","1;2;3"),2,12)
 

 row.names(toyEx) <- c("1;5","1;3")
 toyEx
 prunePaths(toyEx, thr=0.1)
 }