clipper v1.12.0

by Paolo Martini

Gene Set Analysis Exploiting Pathway Topology

Implements topological gene set analysis using a two-step empirical approach. It exploits graph decomposition theory to create a junction tree and reconstruct the most relevant signal path. In the first step clipper selects significant pathways according to statistical tests on the means and the concentration matrices of the graphs derived from pathway topologies. Then, it "clips" the whole pathway identifying the signal paths having the greatest association with a specific phenotype.

Functions in clipper

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