# PaxtoolsR: Access Pathways from Multiple Databases through BioPAX and Pathway Commons

## Documentation for package ‘paxtoolsr’ version 1.16.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

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
downloadPc | Download Pathway Commons files (uses menu and cache)
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
topPathways | Retrieve top pathways
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
traverse | Access Pathway Commons using XPath-type expressions
validate | Validate BioPAX files