Gene Set Analysis Exploiting Pathway Topology

Documentation for package ‘clipper’ version 1.30.0

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.