buildSBMLFromReactionIDs: Build an SBML model for specific reactions in a given...
In BiGGR: Constraint based modeling in R using metabolic reconstruction databases

Description Usage Arguments Value Author(s) References See Also Examples

View source: R/buildSBMLFromReactionIDs.R

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.

1	buildSBMLFromReactionIDs(reaction.ids, database)

`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`

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.

Anand Gavai, Hannes Hettling

Thiele, I. et al. Nat Biotech, 2013

buildSBMLFromGenes

##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)