Perform Flux Variability Analysis with or without relaxed optimality constraint
Arguments
- model
Model of class ModelOrg
- react
Character vector of reaction IDs tested for flux variability. If NULL, all reactions are tested.
- opt.factor
Numeric value > 0 to define the required fraction of the objective function value. E.g. 0.8 sets the constraint, that in the flux variability analysis, the objective function value must at least be 80% of the original optimal value.
See also
Other Flux prediction algorithms:
fba(),
pfba(),
pfbaHeuristic()
Examples
fpath <- system.file("extdata", "e_coli_core.xml", package="cobrar")
mod <- readSBMLmod(fpath)
# Get flux variability for all exchange reactions
fvares <- fva(mod, react = mod@react_id[grepl("^EX_",mod@react_id)],
opt.factor = 0.9)
fvares
#> react growth.fraction min.flux max.flux
#> 1 EX_ac_e 0.9 0.000000 3.813556
#> 2 EX_acald_e 0.9 0.000000 2.542370
#> 3 EX_akg_e 0.9 0.000000 1.430083
#> 4 EX_co2_e 0.9 15.206526 26.528850
#> 5 EX_etoh_e 0.9 0.000000 2.214323
#> 6 EX_for_e 0.9 0.000000 11.322324
#> 7 EX_fru_e 0.9 0.000000 0.000000
#> 8 EX_fum_e 0.9 0.000000 0.000000
#> 9 EX_glc__D_e 0.9 -10.000000 -9.046611
#> 10 EX_gln__L_e 0.9 0.000000 0.000000
#> 11 EX_glu__L_e 0.9 0.000000 1.271185
#> 12 EX_h_e 0.9 15.777779 27.100103
#> 13 EX_h2o_e 0.9 20.935920 32.258244
#> 14 EX_lac__D_e 0.9 0.000000 2.145125
#> 15 EX_mal__L_e 0.9 0.000000 0.000000
#> 16 EX_nh4_e 0.9 -5.559972 -4.288787
#> 17 EX_o2_e 0.9 -25.619543 -17.992432
#> 18 EX_pi_e 0.9 -3.214895 -2.893406
#> 19 EX_pyr_e 0.9 0.000000 2.542370
#> 20 EX_succ_e 0.9 0.000000 1.674244