writeTSVmod: Write a model in TSV format for the 'sybil' R package

In dosorio/minval: MINimal VALidation for Stoichiometric Reactions

Write a model in TSV format for the 'sybil' R package

Description

This function converts a data.frame or a modelOrg model to TSV format for the 'sybil' R package. TSV format require three '.TSV' output files ('_react.tsv', '_met.tsv', '_desc.tsv').

Usage

writeTSVmod(modelData, modelID = "model", outputFile, boundary = "b")

Arguments

modelData	A modelOrg or a data.frame object. If a data.frame is given, it must contain following mandatory colnames: 'ID': A list of single character strings containing the reaction abbreviations, Entries in the field abbreviation are used as reaction ids, so they must be unique. 'REACTION': A set of stoichiometric reaction with the following characteristics: Arrows symbols must be given in the form '=>' or '<=>' Inverse arrow symbols '<=' or other types as: '-->', '<==>', '->' will not be parsed and will lead to errors. Arrow symbols and plus signs (+) must be surrounded by a space character Stoichiometric coefficients must be surrounded by a space character and not by parentheses. Each metabolite must have only one stoichiometric coefficient, substituents must be joined to metabolite name by a hyphen (-) symbol. Exchange reactions must have only one metabolite before arrow symbol Compartments must be given between square brackets ([compartment]) joined at the end of metabolite name Some examples of valid stoichiometric reactions are: H2O[c] + Urea-1-Carboxylate[c] <=> 2 CO2[c] + 2 NH3[c] ADP[c] + Phosphoenolpyruvate[c] => ATP[c] + Pyruvate[c] CO2[c] <=> 'GPR': A set of genes joined by boolean operators as AND or OR, rules may be nested by parenthesis. (optional: column can be empty), 'LOWER.BOUND': A list of numeric values containing the lower bounds of the reaction rates. If not set, zero is used for an irreversible reaction and -1000 for a reversible reaction. (optional: column can be empty), 'UPPER.BOUND': A list of numeric values containing the upper bounds of the reaction rates. If not set, 1000 is used by default. (optional: column can be empty), 'OBJECTIVE': A list of numeric values containing objective values (-1, 0 or 1) for each reaction (optional: column can be empty).
modelID	A single character string giving the modelID
outputFile	A writable path for the three '.TSV' output files.
boundary	A single character string specifying the compartment to be used as boundary

Value

A set of three '.TSV' files in a valid format to the 'sybil' R package.

Author(s)

Daniel Camilo Osorio <[e-mail]>

Examples

#' # Loading a metabolic model
glycolysis <- read.csv(system.file("extdata/glycolysisModel.csv",package = "minval"), sep='\t')

## Not run: 
# Writing a model in TSV format
writeTSVmod(modelData = glycolysis,modelID = "Glycolysis",outputFile = "glycolysis")


# Writing a modelOrg object in a SBML format
## Loading the sybil R package
library(sybil)

## Loading the data
data("Ec_core")

## Writing the modelOrg object in a SBML format
writeTSVmod(modelData = Ec_core,modelID = "E.coli",outputFile = "eColi")

## End(Not run)

dosorio/minval documentation built on May 24, 2022, 7:42 p.m.