paxtoolsr (version 1.6.3)

getNeighbors: Get the neighbors of a set of IDs in a BioPAX file

Description

This function retrieves a set of neighbors for a set of IDs in a BioPAX file.

Usage

getNeighbors(inputFile, outputFile = NULL, idList)

Arguments

inputFile

a string with the name of the input BioPAX OWL file

outputFile

a string with the name of the output BioPAX OWL file

idList

a vector of IDs from the BioPAX OWL file

Value

• an XMLInternalDocument representing a BioPAX OWL file

concept

paxtoolsr

Details

Only entities in the input BioPAX file will be searched for neighbors. IDs used must be URIs for the entities of interest.

Examples

outFile <- tempfile()
results <- getNeighbors(system.file("extdata", 
  "raf_map_kinase_cascade_reactome.owl", package="paxtoolsr"), 
  outFile, 
  c("HTTP://WWW.REACTOME.ORG/BIOPAX/48887#PROTEIN2360_1_9606", 
    "HTTP://WWW.REACTOME.ORG/BIOPAX/48887#PROTEIN1631_1_9606"))