prunePaths: Summarize the paths obtained by clipper according to their...
In clipper: Gene Set Analysis Exploiting Pathway Topology

Description Usage Arguments Value See Also Examples

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.

1	prunePaths(pathSummary, thr=NULL, clust=NULL, sep=";")

`pathSummary`	a matrix resulting from clipper function.
`thr`	a dissimilarity threshold. NULL means no pruning.
`clust`	filename where path-cluster is saved. NULL means no cluster saved.
`sep`	the separator to split genes for similarity computation. Default = ;

a matrix

clipper

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)