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

Description Usage Arguments Note Author(s) References See Also Examples

View source: R/createLIMFromBiGG.R

Description

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

Usage

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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

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##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.