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

## Documentation for package ‘paxtoolsr’ version 1.2.1

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

## Help Pages

downloadPc | Download Pathway Commons data
fetch | Fetch a set of IDs from a BioPAX OWL file
fromPsimi | Read PSIMI file
getNeighbors | Get the neighbors of a set of IDs in a BioPAX file
getPc | Get Pathway Commons BioPAX elements
getPcUrl | Get base Pathway Commons URL
graphPc | Get Pathway Commons BioPAX elements
idMapping | Map IDs to Primary Uniprot or ChEBI IDs
integrateBiopax | Integrate two BioPAX OWL files (DEPRECATED)
mergeBiopax | Merges two BioPAX OWL files
pcDirections | Acceptable Pathway Commons Directions
pcFormats | Acceptable Pathway Commons Formats
pcGraphQueries | Acceptable Pathway Commons Graph Queries
readGmt | Read in gene sets from GMT files
searchPc | Search Pathway Commons
splitSifnx | Split Extended SIF File
summarize | Summarize a BioPAX file
toGSEA | Converts a BioPAX OWL file to a GSEA GMT gene set
toLevel3 | Convert a 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