BiGGR (version 1.8.0)

buildSBMLFromReactionIDs: Build an SBML model for specific reactions in a given database

Description

Creates an SBML model containing all species, reactions and compartments that are associated with a number of reaction identifiers in the database document (e.g. Recon2) passed as an argument.

Usage

buildSBMLFromReactionIDs(reaction.ids, database)

Arguments

reaction.ids

a character or a vector or list of character containing the names of the query reaction IDs

database

an object of class SBMLDocument

Value

a rsbml Model object containing all reactions, species and compartments that are present in the database for the query reaction(s) or NULL if none of the query reaction IDs is found in the database.

References

Thiele, I. et al. Nat Biotech, 2013

See Also

buildSBMLFromGenes

Examples

##get list of reactions with Recon 2 identifiers from examples
path <- system.file("extdata", "Glycolysis_TCA_recon2_reactionIDs.txt", package="BiGGR")
reaction.ids <- scan(path, what=" ")

data("Recon2")
model <- buildSBMLFromReactionIDs(reaction.ids, Recon2)