buildSBMLFromPathways: Build an SBML model for specific pathway(s) in a given...

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

Description

Creates an SBML model containing all species, reactions and compartments that are part of (a) given pathway(s) in the database document (e.g. Recon2) passed as an argument.

Usage

buildSBMLFromPathways(query, database, match.exact=TRUE)

Arguments

query	a character or a vector or list of character containing the names of the query pathways
database	an object of class SBMLDocument
match.exact	logical whether only the exact pathway name should be matched or whether a pathway should match if one keyword is in the pathway description in the database.

Value

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

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 and thus the SBML model returned will be empty.

Author(s)

Anand Gavai, Hannes Hettling

References

Thiele, I. et al. Nat Biotech, 2013

See Also

extractPathways

Examples

data("Recon2")
database <- Recon2

##Get Model for specific pathway
m1 <- buildSBMLFromPathways("Arginine and Proline Metabolism", database)

##Get Model for specific pathway "Metabolism": does not exist!
m2 <- buildSBMLFromPathways("Metabolism", database)

##Get model of all pathways which contain keyword "metabolism"
m3 <- buildSBMLFromPathways("Metabolism", database, match.exact=FALSE)

##Multi-query:
query <- c("Transport, endoplasmic reticular", "Arginine and Proline Metabolism")
m4 = buildSBMLFromPathways(query, database)
m5 = buildSBMLFromPathways(query[1], database)
length(m4@species)
length(m5@species)

##different database
data(H.pylori_ilT341)
database <- H.pylori_ilT341
m7 <- buildSBMLFromPathways("Metabolism", database, match.exact=FALSE)

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