getPathwaysForSBML {BiGGR} | R Documentation

## Extract all pathways from a database that are relevant for a given SBML model

### Description

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.

### Usage

    getPathwaysForSBML(model, database)

### Arguments

`database` | an rsbml object of class `SBMLDocument`
`model` | an rsbml object of class `Model`

### Value

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.

### Note

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.

### Author(s)

Anand Gavai, Hannes Hettling

### References

Thiele, I. et al. Nat Biotech, 2013

### See Also

`buildSBMLFromPathways` `buildSBMLFromGenes` `extractPathways`

### Examples

    ##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)

[Package BiGGR version 1.20.0 Index]