createLIMFromSBML {BiGGR} | R Documentation |
creates a model file to be run for simulations of metabolic fluxes
createLIMFromSBML(model, maximize, equations=NULL, inequalities=NULL, constraints=NULL, externals=NULL, file.name="model.lim")
model |
an SBML object of reactions/metabolites participating in a metabolic pathway. |
maximize |
a character vector consisting the tag of the reaction(s) to be maximized or minimized |
equations |
a |
inequalities |
a |
constraints |
a |
externals |
a character vector of metabolites as provided by the user for speficific pathways for which FBA (flux balance analysis needs to be performed) |
file.name |
a character string specifying the name of the LIM file created by the function. |
A model file with with extension ".lim"
is created
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
##Create a LIM model file from a reactions file in the examples path <- system.file("extdata", "Glycolysis_TCA_recon1_reactionIDs.txt", package="BiGGR") reaction.ids <- scan(path, what=" ") data("H.sapiens_Recon_1") sbml.model <- buildSBMLFromReactionIDs(reaction.ids, H.sapiens_Recon_1) maximize <- c("R_ATPS4m - R_NDPK1m - R_HEX1 - R_PFK - R_PGK + R_PYK") externals <- c("M_glc_DASH_D_e", "M_lac_DASH_L_e", "M_ala_DASH_L_e", "M_gln_DASH_L_c", "M_h2o_e", "M_co2_e", "M_o2_e", "M_h_e", "M_pi_c", "M_o2s_m", "M_nh4_m", "M_adp_c", "M_atp_c", "M_nadp_c", "M_nadph_c", "M_h_c") equation.vars <- c("R_GLCt1r", "R_O2t", "R_L_LACt2r", "R_GLNtm") equation.values <- c(0.4, 2.4, 0.0, 0.0) eqns <- list(equation.vars, equation.values) constraints <- list(c("R_GLCt1r", "R_CYOOm3"), c(-1000, -1000), c(1000, 1000)) limfile.name <- tempfile() createLIMFromSBML(sbml.model, maximize, equations=eqns, inequalities=list("R_O2t", 2.4, "<="), constraints=constraints, externals=externals, file.name=limfile.name)