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

Documentation for package ‘paxtoolsr’ version 1.2.11

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