extractGeneAssociations: Extract informations on genes from a given database

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

Description

Extracts all information on genes associated to reactions from an rsbml document containing a metabolic reconstruction database (e.g. Recon2). The associated information is parsed from the "<notes>" tag of each reaction's SBML representation.

Usage

extractGeneAssociations(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 containing the assiciated gene identifiers and the reaction IDs as names. For reactions without gene 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 gene information indicated by the string "GENE*ASSOCIATION" (the star stands for any character), no gene association information can be extracted and thus the returned SBML mdel is empty..

Author(s)

Anand Gavai, Hannes Hettling

References

Thiele, I. et al. Nat Biotech, 2013

See Also

buildSBMLFromGenes

Examples

data("Recon2")
database <- Recon2
gene.info <- extractGeneAssociations(database)

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