extractPathways {BiGGR} | R Documentation

## Extract all pathways from given database

### Description

Extracts all pathway information from an rsbml document containing a metabolic reconstruction database (e.g. Recon2). The pathway information is parsed from the "<notes>" tag of each reaction.

### Usage

    extractPathways(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` with the pathway information and the reaction IDs as names. For reactions without pathway 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 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` `getPathwaysForSBML`

### Examples

    data(Recon2)
    pathways.recon2 <- extractPathways(Recon2)

[Package BiGGR version 1.18.0 Index]