extractGeneAssociations {BiGGR} | R Documentation |
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.
extractGeneAssociations(database)
database |
an object of class |
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
.
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..
Anand Gavai, Hannes Hettling
Thiele, I. et al. Nat Biotech, 2013
data("Recon2") database <- Recon2 gene.info <- extractGeneAssociations(database)