extractGeneAssociations {BiGGR} | R Documentation

## Extract informations on genes from a given database

### 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)

[Package BiGGR version 1.22.0 Index]