modelorg2tsv: Write an Instance of Class modelorg to File
In sybil: Efficient Constrained Based Modelling

Description Usage Arguments Details Value Author(s) References See Also

The function modelorg2tsv writes the content of an instance of class modelorg to text files in a character-separated value format adopted from the BiGG database output.

  modelorg2tsv(model, prefix, suffix, extMetFlag = "b",
               fielddelim = "\t", entrydelim = ", ",
               makeClosedNetwork = FALSE,
               onlyReactionList = FALSE,
               minimalSet = FALSE,
               fpath = SYBIL_SETTINGS("PATH_TO_MODEL"), ...)

`model`	An object of class `modelorg`.
`prefix`	A single character string giving the prefix for three possible output files (see Details below).
`suffix`	A single character string giving the file name extension. If missing, the value of `suffix` depends on the argument `fielddelim`, see Details below. Default: `"tsv"`.
`extMetFlag`	A single character string giving the identificator for metabolites which are outside the system boundary. Only necessary, if the model is a closed one. Default: `"b"`.
`fielddelim`	A single character string giving the value separator. Default: `"\t"`.
`entrydelim`	A single character string giving the a separator for values containing more than one entry. Default: `", "`.
`makeClosedNetwork`	Boolean. If set to `TRUE`, external metabolites (which are outside the system boundary) will be added to the model. These metabolites participate in reactions, transporting metabolites across the system boundary. The metabolite id will be the same as for the metabolite inside the system, but the compartment type is set to the value of argument `extMetFlag`. For example, most models contain a transport reaction for glucose: `glc[c] <==>` If `makeClosedNetwork` is set to `TRUE`, this reaction will be written as `glc[c] <==> glc[b]` with the letter `b` being the default value for `extMetFlag`. Default: `FALSE`.
`onlyReactionList`	Boolean. If set to `TRUE`, only one file containing all reaction equations will be produced (output file has one column). Default: `FALSE`.
`minimalSet`	Boolean. If set to `TRUE`, only one file containing the fields `"abbreviation"`, `"equation"`, `"lowbnd"`, `"uppbnd"` and `"obj_coef"` will be produced (output file has five columns). Default: `FALSE`.
`fpath`	A single character string giving the path to a certain directory in which the output files will be stored. Default: `SYBIL_SETTINGS("PATH_TO_MODEL")`.
`...`	Further arguments passed to `write.table`, e.g. the Boolean argument `quote` can be used here.

The function modelorg2tsv produces three output files: a reactions list, a metabolites list and a model description file.

The reactions list has the following columns:

`"abbreviation"`	`react_id(model)`
`"name"`	`react_name(model)`
`"equation"`	the reaction equations
`"reversible"`	`react_rev(model)`
`"compartment"`	reaction compartment(s)
`"lowbnd"`	`lowbnd(model)`
`"uppbnd"`	`uppbnd(model)`
`"obj_coef"`	`obj_coef(model)`
`"rule"`	`gpr(model)`
`"subsystem"`	`subSys(model)`

The metabolites list has the following columns:

`"abbreviation"`	`met_id(model)`
`"name"`	`met_name(model)`
`"compartment"`	`met_comp(model)`

The model description file has the following columns:

`"name"`	`mod_name(model)`
`"id"`	`mod_id(model)`
`"description"`	`mod_desc(model)`
`"compartment"`	`mod_compart(model)`
`"abbreviation"`	unique compartment abbreviations
`"Nmetabolites"`	number of metabolites
`"Nreactions"`	number of reactions
`"Ngenes"`	number of independend genes
`"Nnnz"`	number of non-zero elements in the stoichiometric matrix