addAttributeList        Add attributes using a list of vectors to an
                        igraph object
convertDataFrameListsToVectors
                        Convert columns with list in data.frame to
                        vector
convertIds              Covert IDs Using org.Hs.eg.db
convertSifToGmt         Convert SIF to GMT
downloadFile            Check Cache and Download File
downloadPc2             Download Pathway Commons files (uses menu and
                        cache)
downloadSignedPC        Download a SIF file containing only signed
                        interactions
fetch                   Fetch a set of IDs from a BioPAX OWL file
filterSif               Keep interactions in SIF network based on
                        certain criteria
getCacheFiles           List files in cache directory
getErrorMessage         Get Error Message for a Pathway Commons Error
getNeighbors            Get the neighbors of a set of IDs in a BioPAX
                        file
getPc                   Get Pathway Commons BioPAX elements
getPcDatabaseNames      Get a Pathway Commons Databases
getPcUrl                Get base Pathway Commons URL
getShortestPathSif      Get the shortest between two IDs (HGNC or
                        CHEBI)
getSifInteractionCategories
                        Get a list of categories of SIF interactions
graphPc                 Get Pathway Commons BioPAX elements
integrateBiopax         Integrate two BioPAX OWL files (DEPRECATED)
loadSifInIgraph         Load SIF as igraph Network
mapAttributes           Map Attributes from igraph to Cytoscape JSON
mapValues               Map values from One Vector to Another
mergeBiopax             Merges two BioPAX OWL files
pcDirections            Acceptable Pathway Commons Directions
pcFormats               Acceptable Pathway Commons Formats
pcGraphQueries          Acceptable Pathway Commons Graph Queries
processPcRequest        Process Pathway Commons request in various
                        formats
readBiopax              Read BioPAX files as XML documents
readGmt                 Read in gene sets from GMT files
readPcPathwaysInfo      Read in Pathway Commons Pathways Information
readSbgn                Read SBGN files as XML documents
readSif                 Read in a binary SIF file
readSifnx               Read in a Extended SIF file
searchListOfVectors     Search List of Vectors
searchPc                Search Pathway Commons
splitSifnxByPathway     Splits SIFNX entries into individual pathways
summarize               Summarize a BioPAX file
summarizeSif            Summarize a SIF Network
toCytoscape             Convert igraph to Cytoscape JSON
toGSEA                  Converts a BioPAX OWL file to a GSEA GMT gene
                        set
toLevel3                Convert a PSIMI or older BioPAX OWL file to
                        BioPAX Level 3
toSBGN                  Convert a BioPAX OWL file to SBGNML
toSif                   Convert a BioPAX OWL file to SIF
toSifnx                 Converts BioPAX OWL file to extended binary SIF
                        representation
topPathways             Retrieve top pathways
traverse                Access Pathway Commons using XPath-type
                        expressions
validate                Validate BioPAX files
