modelorg2tsv: Write an Instance of Class modelorg to File

Description

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.

Usage

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

Arguments

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.

Value

Returns TRUE on success.

Details

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

If onlyReactionList is set to TRUE, only the reactions list containing the column "equation" is produced.

Please read the package vignette for detailed information about file formats and examples.

All fields in the output files are in double quotes. In order to read them in with readTSVmod, set argument quoteChar to "\"".

References

The BiGG database http://bigg.ucsd.edu/.