extractPathways: Extract all pathways from given database

In BiGGR: Constraint based modeling in R using metabolic reconstruction databases

Description

Extracts all pathway information from an rsbml document containing a metabolic reconstruction database (e.g. Recon2). The pathway information is parsed from the "<notes>" tag of each reaction.

Usage

extractPathways(database)

Arguments

database

an object of class SBMLDocument

Value

a list with length being the number of reactions in the database passed as argument each entry containing a character with the pathway information and the reaction IDs as names. For reactions without pathway annotation, the list will contain NA.

Note

If the reactions in the database document provided in the argument database do not contain any "<notes>" with tags with pathway information indicated by the string "SUBSYSTEM", no pathway information can be extracted.

Author(s)

Anand Gavai, Hannes Hettling

References

Thiele, I. et al. Nat Biotech, 2013

See Also

buildSBMLFromPathways getPathwaysForSBML

Examples

data(Recon2)
pathways.recon2 <- extractPathways(Recon2)

BiGGR documentation built on Nov. 8, 2020, 5:38 p.m.