Access Pathways from Multiple Databases Through BioPAX and
Pathway Commons
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Documentation for package ‘paxtoolsr’ version 1.31.0
Help Pages
| addAttributeList | Add attributes using a list of vectors to an igraph object |
| convertDataFrameListsToVectors | Convert columns with list in data.frame to vector |
| 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 |