Searches a metabolic network for metabolites that can be produced but not consumed, and vice versa.
Arguments
- object
Model of class ModelOrg
Value
A list with two elements: "dem" is a character vector with the IDs of identified dead end metabolites. "der" is a character vector with IDs of reactions, that involve at least one of the dead end metabolites.
Note
The algorithm is adapted from the original 'sybil' package, which in turn is adapted from the implementation in 'cobratoolbox'. Important detail: The algorithm function in the 'sybil' package may return different results than this cobrar implementation. This is because the 'sybil' function does not take into account the possibility that an irreversible reaction is defined in the direction RHS to LHS (lower bound > 0 and upper bound = 0).
Examples
fpath <- system.file("extdata", "e_coli_core.xml", package="cobrar")
mod <- readSBMLmod(fpath)
deadEndMetabolites(mod)
#> $dem
#> [1] "gln__L_e" "mal__L_e" "fru_e" "fum_e"
#>
#> $der
#> [1] "EX_fru_e" "EX_fum_e" "EX_gln__L_e" "EX_mal__L_e" "FRUpts2"
#> [6] "FUMt2_2" "GLNabc" "MALt2_2"
#>