getPathwaysForSBML {BiGGR} | R Documentation |
Extracts all pathway information from an rsbml document containing a metabolic reconstruction database (e.g. Recon2) and returns the subset of these pathways that is associated with the reactions in the given model. The pathway information is parsed from the "<notes>" tag of each reaction.
getPathwaysForSBML(model, database)
database |
an rsbml object of class |
model |
an rsbml object of class |
A vector of type character
that contains all the pathways
relevant for the given model according to the specified database. Note
that duplicate pathways do not appear twice in the return value.
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.
Anand Gavai, Hannes Hettling
Thiele, I. et al. Nat Biotech, 2013
buildSBMLFromPathways
buildSBMLFromGenes
extractPathways
##Build a model from query genes data("Recon2") database <- Recon2 query <- c("218.1", "223.1") ##query gene identifiers m <- buildSBMLFromGenes(query, database) ##extract all pathways for that model getPathwaysForSBML(m, database)