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

Description Usage Arguments Details Value Examples

View source: R/getNeighbors.R

Description

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

Usage

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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

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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.