createLIMFromBiGG {BiGGR} | R Documentation

## Create a LIM model object from a BiGG database file

### Description

Creates a LIM model object from a file containing reactions extreacted from BiGG to be run for simulations of metabolic fluxes

### Usage

    createLIMFromBiGG(reactions.filename, ...)

### Arguments

`reactions.filename` | file which contains the reactions extracted from the BiGG database
`...` | arguments passed to createLIMfromSBML

### Note

none

### Author(s)

Anand K. Gavai <anand.gavai@bioinformatics.nl>, Hannes hettling <j.hettling@vu.nl>

### References

Soetaert K, van Oevelen D (2009). LIM: Linear Inverse Model examples and solution methods. R package version 1.3

### See Also

`createLIMFromSBML`

### Examples

    ##maximize flux for reaction R_PYK
    maximize <- "R_PYK"

    ##setting equality constraint R_HEX = 1
    equation_var <- "R_HEX1"
    equation_value <- 1
    eq <- list(equation_var, equation_value)

    ##range  of  possible  fluxes for R_PYK
    constraint <- list("R_PYK", 0, 1000)
    externals  <-  c("glc_c",  "pyr_c",  "h_c","nad_c",
    			 "nadh_c",  "pi_c",  "fad_m",  "fadh2_m",
    			 "o2_c",  "adp_c",  "atp_c",  "nadp_c",
    			 "co2_c",  "o2_c",  "gdp_c",  "gtp_c")

    ##build LIM model from reactions file in package examples
    path <- system.file("extdata", "Reactions.txt", package="BiGGR")
    limfile.name <- tempfile()
    createLIMFromBiGG(path, maximize, equations=eq, constraints=constraint,
    			  externals=externals, file.name=limfile.name)

[Package BiGGR version 1.18.0 Index]