createLIMFromBiGG {BiGGR} | R Documentation |
Creates a LIM model object from a file containing reactions extreacted from BiGG to be run for simulations of metabolic fluxes
createLIMFromBiGG(reactions.filename, ...)
reactions.filename |
file which contains the reactions extracted from the BiGG database |
... |
arguments passed to createLIMfromSBML |
none
Anand K. Gavai <anand.gavai@bioinformatics.nl>, Hannes hettling <j.hettling@vu.nl>
Soetaert K, van Oevelen D (2009). LIM: Linear Inverse Model examples and solution methods. R package version 1.3
##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)