createLIMFromBiGG: Create a LIM model object from a BiGG database file

In BiGGR: Constraint based modeling in R using metabolic reconstruction databases

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 <[e-mail]>, Hannes hettling <[e-mail]>

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)

BiGGR documentation built on Nov. 8, 2020, 5:38 p.m.