fetch: Fetch a set of IDs from a BioPAX OWL file

In BioPAX/paxtoolsr: Access Pathways from Multiple Databases Through BioPAX and Pathway Commons

Fetch a set of IDs from a BioPAX OWL file

Description

This function will create a subsetted object with specified URIs.

Usage

fetch(inputFile, outputFile = NULL, idList)

Arguments

inputFile	a string of 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 used in the fetch. IDs used must be URIs for the entities of interest. Additional properties such as cross-references for fetched entities will be included in the output.

Value

an XMLInternalDocument representing a BioPAX OWL file

Examples

outFile <- tempfile()
ids <- c("http://identifiers.org/uniprot/P36894", 
         "http://identifiers.org/uniprot/Q13873")
results <- fetch(system.file("extdata", "REACT_12034-3.owl", package="paxtoolsr"), 
                 outFile, ids)

BioPAX/paxtoolsr documentation built on Jan. 31, 2023, 4:22 a.m.