buildSBMLFromGenes: Build an SBML model for specific genes in a given database
In hettling/BiGGR: Constraint based modeling in R using metabolic reconstruction databases

Description Usage Arguments Details Value Note Author(s) References See Also Examples

Creates an SBML model containing all species, reactions and compartments that are associated with (a) specific gene(s) in the database document (e.g. Recon2) passed as an argument.

1	buildSBMLFromGenes(query, database, logical.fun="any")

`query`	a `character` or a `vector` or `list` of `character` containing the query genes with identifiers as specified in the database.
`database`	an object of class `SBMLDocument`
`logical.fun`	function which specifies the logical relation of the query genes within the reactions (e.g. `all` or `any`, see details).

The function all as argument logical.fun would mean that all genes in the query have to be associated with a certain reaction from the database in order to be included in the returned model. The default any means that a reaction is included if any of the query genes are associated with it. Custom functions are possible if they take a vector of type logical as an argument and return a logical. The argument of logical.fun is a vector of type logical having the same length as the query and for each gene the value is TRUE if it is associated with a specific reaction. See 'examples' section for an example of a custom function as logical.fun.

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

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

buildSBMLFromPathways extractGeneAssociations

##Query genes in Recon 2 database
data("Recon2")
database <- Recon2
m1 <- buildSBMLFromGenes("8884.1", database)
m2 <- buildSBMLFromGenes(c("8884.1", "6509.1"), database)

##different databases
data(H.pylori_ilT341)
database <- H.pylori_ilT341
m3 <- buildSBMLFromGenes("HP0069", database)

data(M.barkeri_iAF692)
database <- M.barkeri_iAF692
m4 <- buildSBMLFromGenes(c("MBd0456", "MBd4814", "MBd4098"), database)


data(S.aureus_iSB619)
database <- S.aureus_iSB619
m5 <- buildSBMLFromGenes(c("SA0594", "SA1599", "SA0950", "SA0259"), database)

database <- Recon2
query <- c("218.1", "223.1")
m6 <- buildSBMLFromGenes(query, database)
m7 <- buildSBMLFromGenes(query, database, logical.fun="all")
##m6 has more reactions than m7
## because m7 has only reactions which match both genes in the query
length(m6@reactions) > length(m7@reactions)

##Custom logical function: Get model with all reactions
## which are not associated with the query gene
m8 <- buildSBMLFromGenes(query, database, logical.fun=function(x)!any(x))