importPEtabSBML: Import an SBML model and corresponding PEtab objects
In dlill/petab: PEtab support for R

importPEtabSBML

R Documentation

Import an SBML model and corresponding PEtab objects

Description

This function imports an SBML model and corresponding PEtab files, e.g. from the Benchmark collection.

Usage

importPEtabSBML(
  modelname = "Boehm_JProteomeRes2014",
  path2model = "BenchmarkModels/",
  testCases = FALSE,
  path2TestCases = "PEtabTests/",
  compile = TRUE,
  SBML_file = NULL,
  observable_file = NULL,
  condition_file = NULL,
  data_file = NULL,
  parameter_file = NULL
)

Arguments

`modelname`	name of folder containing all PEtab files of the model to be imported. NULL if file paths are defined separately (see below).
`path2model`	path to model folder
`path2TestCases`	path to feature test case folder
`compile`	if FALSE, g, ODEmodel and err are loaded from .RData (if present) and compilation time is saved
`SBML_file`	SBML model as .xml
`observable_file`	PEtab observable file as .tsv
`condition_file`	PEtab condition file as .tsv
`data_file`	PEtab data file as .tsv
`parameter_file`	PEtab parameter file as .tsv
`TestCases`	TRUE to load feature test cases

Details

Objects such as model equations, parameters or data are automatically assigned to the following standard variables and written to your current working directory (via <<-): reactions, observables, errors, g, x, p0, err, obj, mydata, ODEmodel, condition.grid, trafoL, pouter, times. Compiled objects (g, ODEmodel and err) are saved in .RData.