buildSBMLFromPathways {BiGGR} | R Documentation

## Build an SBML model for specific pathway(s) in a given database

### Description

Creates an SBML model containing all species, reactions and compartments that are part of (a) given pathway(s) in the database document (e.g. Recon2) passed as an argument.

### Usage

    buildSBMLFromPathways(query, database, match.exact=TRUE)

### Arguments

`query` | a `character` or a `vector` or `list` of `character` containing the names of the query pathways
`database` | an object of class `SBMLDocument`
`match.exact` | `logical` whether only the exact pathway name should be matched or whether a pathway should match if one keyword is in the pathway description in the database.

### Value

a rsbml `Model` object containing all reactions, species and compartments that are present in the database for the query pathway(s) or NULL if none of the pathways 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 pathway information indicated by the string "SUBSYSTEM", no pathway information can be extracted and thus the SBML model returned will be empty.

### Author(s)

Anand Gavai, Hannes Hettling

### References

Thiele, I. et al. Nat Biotech, 2013

### See Also

`extractPathways`

### Examples

    data("Recon2")
    database <- Recon2

    ##Get Model for specific pathway
    m1 <- buildSBMLFromPathways("Arginine and Proline Metabolism", database)

    ##Get Model for specific pathway "Metabolism": does not exist!
    m2 <- buildSBMLFromPathways("Metabolism", database)

    ##Get model of all pathways which contain keyword "metabolism"
    m3 <- buildSBMLFromPathways("Metabolism", database, match.exact=FALSE)

    ##Multi-query:
    query <- c("Transport, endoplasmic reticular", "Arginine and Proline Metabolism")
    m4 = buildSBMLFromPathways(query, database)
    m5 = buildSBMLFromPathways(query[1], database)
    length(m4@species)
    length(m5@species)

    ##different database
    data(H.pylori_ilT341)
    database <- H.pylori_ilT341
    m7 <- buildSBMLFromPathways("Metabolism", database, match.exact=FALSE)

[Package BiGGR version 1.22.0 Index]