AdjacencyMatrix2pathway
                        Function to coerce an adjacency matrix to a
                        pathway
Clipper                 Function to use clipper method on microarray or
                        RNA-Seq data
DEGraph                 Function to use DEGraph method on microarray or
                        RNA-Seq data
KEGG2pathway            Function to parse KEGG KGML file into a pathway
PRS                     Function to use PRS method on microarray or
                        RNA-Seq data
PWEA                    Function to use PWEA method on microarray or
                        RNA-Seq data
SPIA                    Function to use SPIA method on microarray or
                        RNA-Seq data
TAPPA                   Function to use TAPPA method on microarray or
                        RNA-Seq data
ToPASeq-package         Package for topology-based pathway analysis of
                        microarray and RNASeq data
TopologyGSA             Function to use TopologyGSA method on
                        microarray or RNA-Seq data
collectWeightsPRS       Function to calculate gene-level weights for
                        topology-based pathway analysis
convertIdentifiersByVector
                        Function to convert identifiers in pathways by
                        user specified vector
estimateCF              Function to estimate multi-subunit protein
                        complexes and gene families in a pathway
graphNEL2pathway        Function to coerce a graphNEL to a pathway
makeDefaultEdgeData     Creates auxiliary data needed for SPIA method
pathway-class           Class '"pathway"'
preparePathways         Function to prepare pathways for topology-based
                        pathway analysis
reduceGraph             Function to reduce the pathway graph
res                     Function to extract parts of object
