sybil (version 1.0.2)

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 = "", 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 compartiment 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 beeing 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:
  ll{
      "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:
  ll{
      "abbreviation" 	met_id(model)   
"name"         	met_name(model) 
"compartment"  	met_comp(model) 
}
  
  The model description file has the following columns:
  ll{
      "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 """.
Returns TRUE on success.
The BiGG database http://bigg.ucsd.edu/.
[object Object]
read.table, modelorg2tsv, modelorg.
IO

encoding

utf8