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

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

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

Details

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

Value

an XMLInternalDocument representing a BioPAX OWL file

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")) 

paxtoolsr documentation built on Nov. 8, 2020, 8:29 p.m.