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


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Documentation for package ‘paxtoolsr’ version 1.12.0

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addAttributeList Add attributes using a list of vectors to an igraph object
convertSifnxIds Convert IDs in a SIFNX
convertSifToSpia Convert SIF Interaction Types to SPIA types
convertToDF Convert Results from readSifnx to data.frame
convertToDT Convert Results from readSifnx to data.table
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
extractIds Extract IDs from an Extended SIF
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
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
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
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
skip_on_bioc Skip a test if on Bioconductor
splitSifnxByPathway Splits SIFNX entries into individual pathways
summarize Summarize a BioPAX file
summarizeSif Summarize a SIF Network
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