# Gene set analysis exploiting pathway topology

## Documentation for package ‘clipper’ version 1.4.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

clipper | Dissect the pathway to find the path with the greatest association with phenotype.
clipperAllRoots | Dissect the pathway to find the path with the greatest association with phenotype.
cliqueMeanTest | Mean test for cliques.
cliqueMixedTest | Mean test for cliques.
cliquePairedTest | Paired mean test for cliques.
cliqueVarianceTest | Variance test for cliques.
deleteEdge | Remove an edge from 'graphNel' object.
easyClip | Easy clip analysis.
easyLook | Summarize clipper output.
getGraphEntryGenes | Extract all the possible entry point (genes with no entering edges) from graph.
getJunctionTreePaths | Extract the shortest paths along the junction tree of the graph.
nameCliques | Generate clique names from their own elements.
pathQ | Whole pathway test using qpipf.
plotInCytoscape | Plot a pathway graph in Cytoscape highlighting the relevant path.
prunePaths | Summarize the paths obtained by clipper according to their similarity.