BiGGR (version 1.8.0)

getPathwaysForSBML: Extract all pathways from a database that are relevant for a given SBML model

Description

Extracts all pathway information from an rsbml document containing a metabolic reconstruction database (e.g. Recon2) and returns the subset of these pathways that is associated with the reactions in the given model. The pathway information is parsed from the "" tag of each reaction.

Usage

getPathwaysForSBML(model, database)

Arguments

database

an rsbml object of class SBMLDocument

model

an rsbml object of class Model

Value

A vector of type character that contains all the pathways relevant for the given model according to the specified database. Note that duplicate pathways do not appear twice in the return value.

References

Thiele, I. et al. Nat Biotech, 2013

See Also

buildSBMLFromPathways buildSBMLFromGenes extractPathways

Examples

##Build a model from query genes
data("Recon2")
database <- Recon2
query <- c("218.1", "223.1") ##query gene identifiers
m <- buildSBMLFromGenes(query, database)

##extract all pathways for that model
getPathwaysForSBML(m, database)