clipper |
Dissect the pathway to find the path with the greatest association with phenotype. |
cliqueMeanTest |
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. |