read_sbml: Main driver to parse an SBML model.

In cdiener/dycone: dycone - analyze the dynamic landscape of metabolome data

Description

This function wraps around sbml_* functions but also performs some basic sanity checks and adjustments which are:

• Gives information about the used level and version and whether the FBC package is used.

• Checks whether there are species that do not appear in reactions (warning).

• Checks whether all species references in reactions are defined in the species list (error).

• Maps lower and upper flux bounds to its respective global parameters.

Usage

read_sbml(sbml_file)

Arguments

sbml_file

A SBML file. This can be a file on the disk or the location to an online resource.

Value

A list containing three elements:

species

The species (metabolites or molecules) in the model in a data frame. Boundary metabolites are removed automatically.

params

The global parameters defined for the model.

reactions

The reactions in the model as an "reactions" object.

See Also

sbml_species, sbml_params and sbml_reactions to read only parts of an SBML model.

Examples

# requires internet connection
m_url <- "http://www.ebi.ac.uk/biomodels-main/download?mid=BIOMD0000000042"
read_sbml(m_url)

cdiener/dycone documentation built on May 13, 2019, 2:41 p.m.