clipper v1.12.0
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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Details
| Date | 2015-08-31 |
| License | AGPL-3 |
| suggests | ALL , BiocGenerics , BiocStyle , graphite , hgu95av2 , hgu95av2.db , MASS , RCytoscape (>= 1.6.3) , RUnit |
| depends | base (>= 2.15.0) , graph , Matrix , R (>= 2.15.0) |
| imports | Biobase , corpcor , gRbase (>= 1.6.6) , igraph , KEGGgraph , methods , qpgraph , RBGL , Rcpp |
| Contributors | Paolo Martini, Gabriele Sales, Chiara Romualdi |
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