Parse a reaction table to an intermediate, long format

Source: R/parsing_and_conversion.R

The long format can also be suitable for manipulating equations.

reactiontbl_to_expanded(reaction_table, regex_arrow = "<?[-=]+>")

Arguments

reaction_table

A data frame describing the metabolic model.
regex_arrow

Regular expression for the arrow splitting sides of the reaction equation.

Value

A list of data frames:

  • rxns, which has one row per reaction,

  • mets, which has one row for each metabolite, and

  • stoich, which has one row for each time a metabolite appears in a reaction.

Details

The reaction_table must have columns:

  • abbreviation,

  • equation,

  • uppbnd,

  • lowbnd, and

  • obj_coef.

See also

Other parsing_and_conversion: expanded_to_ROI(), expanded_to_glpk(), expanded_to_gurobi(), reactiontbl_to_gurobi()

Examples


if (FALSE) {
data(ecoli_core)
library(dplyr)
try(library(ROI.plugin.ecos)) # make a solver available to ROI

roi_model <- ecoli_core %>%
  reactiontbl_to_expanded %>%
  expanded_to_ROI

if(length(ROI::ROI_applicable_solvers(roi_model))>=1){
  roi_result <- ROI::ROI_solve(roi_model)

  ecoli_core_with_flux <- ecoli_core %>%
    mutate(flux = roi_result[['solution']])
}
}