Man pages for paxtoolsr
PaxtoolsR: Access Pathways from Multiple Databases through BioPAX and Pathway Commons

addAttributeListAdd attributes using a list of vectors to an igraph object
convertDataFrameListsToVectorsConvert columns with list in data.frame to vector
convertSifToGmtConvert SIF to GMT
downloadFileCheck Cache and Download File
downloadPc2Download Pathway Commons files (uses menu and cache)
downloadSignedPCDownload a SIF file containing only signed interactions
fetchFetch a set of IDs from a BioPAX OWL file
filterSifKeep interactions in SIF network based on certain criteria
getCacheFilesList files in cache directory
getErrorMessageGet Error Message for a Pathway Commons Error
getNeighborsGet the neighbors of a set of IDs in a BioPAX file
getPcGet Pathway Commons BioPAX elements
getPcDatabaseNamesGet a Pathway Commons Databases
getPcUrlGet base Pathway Commons URL
getShortestPathSifGet the shortest between two IDs (HGNC or CHEBI)
getSifInteractionCategoriesGet a list of categories of SIF interactions
graphPcGet Pathway Commons BioPAX elements
integrateBiopaxIntegrate two BioPAX OWL files (DEPRECATED)
loadSifInIgraphLoad SIF as igraph Network
mapAttributesMap Attributes from igraph to Cytoscape JSON
mapValuesMap values from One Vector to Another
mergeBiopaxMerges two BioPAX OWL files
pcDirectionsAcceptable Pathway Commons Directions
pcFormatsAcceptable Pathway Commons Formats
pcGraphQueriesAcceptable Pathway Commons Graph Queries
processPcRequestProcess Pathway Commons request in various formats
readBiopaxRead BioPAX files as XML documents
readGmtRead in gene sets from GMT files
readPcPathwaysInfoRead in Pathway Commons Pathways Information
readSbgnRead SBGN files as XML documents
readSifRead in a binary SIF file
readSifnxRead in a Extended SIF file
searchListOfVectorsSearch List of Vectors
searchPcSearch Pathway Commons
splitSifnxByPathwaySplits SIFNX entries into individual pathways
summarizeSummarize a BioPAX file
summarizeSifSummarize a SIF Network
toCytoscapeConvert igraph to Cytoscape JSON
toGSEAConverts a BioPAX OWL file to a GSEA GMT gene set
toLevel3Convert a PSIMI or older BioPAX OWL file to BioPAX Level 3
topPathwaysRetrieve top pathways
toSBGNConvert a BioPAX OWL file to SBGNML
toSifConvert a BioPAX OWL file to SIF
toSifnxConverts BioPAX OWL file to extended binary SIF...
traverseAccess Pathway Commons using XPath-type expressions
validateValidate BioPAX files
paxtoolsr documentation built on Nov. 8, 2020, 8:29 p.m.