Summary,pDisRes-method
                        Summarize the results of a Pathway-Express
                        analysis
Summary,peRes-method    Summarize the results of a Pathway-Express
                        analysis
alpha1MR                Compute alpha weights
alphaMLG                Compute alpha weights
compute.fisher          Combine independent p-values using the Fisher
                        method
compute.normalInv       Combine independent p-values using the normal
                        inversion method
keggPathwayGraphs       Download and parse KEGG pathway data
keggPathwayNames        Obtain KEGG pathway titles
nodeWeights             Retrieve the node weights of a graph
pDis                    Primary dis-regulation: Pathway analysis
                        approach based on the unexplained
                        dis-regulation of genes
pDisPathway-class       Class that encodes the result of pDis analysis
                        for a single pathway
pDisRes-class           Primary dis-regulation (pDis) result class
pe                      Pathway-Express: Pathway analysis of signaling
                        pathways
peEdgeRenderInfo        Extract edge render information from a
                        'pePathway-class' object
peNodeRenderInfo        Extract node render information from a
                        'pePathway-class' object
pePathway-class         Class that encodes the result of
                        Pathway-Express for a single pathway
peRes-class             Pathway-Express result class
plot,pePathway,missing-method
                        Plot pathway level statistics
plot,peRes,missing-method
                        Plot Pathway-Express result
setEdgeWeights          Set gene weights based on edge type
setNodeWeights          Set node weights
summary.pDisRes         Summarize the results of a primary
                        dis-regulation (pDis) analysis
summary.peRes           Summarize the results of a Pathway-Express
                        analysis
