buildSBMLFromGenes {BiGGR} | R Documentation

## Build an SBML model for specific genes in a given database

### Description

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.

### Usage

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

### Arguments

`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).

### 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.

### Value

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.

### 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

`buildSBMLFromPathways` `extractGeneAssociations`

### Examples

    ##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))

[Package BiGGR version 1.20.0 Index]