Get Metabolites — metabolites • ramen

Retrieves the metabolites involved in the metabolic network. For ConsortiumMetabolism objects, the result can optionally be restricted to a specific species and/or direction ("consumed" or "produced").

Usage

metabolites(object, ...)

# S4 method for class 'ConsortiumMetabolism'
metabolites(
  object,
  species = NULL,
  direction = c("all", "consumed", "produced")
)

# S4 method for class 'ConsortiumMetabolismAlignment'
metabolites(object)

# S4 method for class 'ConsortiumMetabolismSet'
metabolites(object)

Arguments

object: A ConsortiumMetabolism, ConsortiumMetabolismSet, or ConsortiumMetabolismAlignment object.
...: Additional arguments. For ConsortiumMetabolism: species (character scalar; restrict to metabolites involved with this species) and direction (one of "all", "consumed", or "produced"; defaults to "all").
species: Optional length-1 character scalar. If supplied, restrict the result to metabolites involved in pathways that include this species. Defaults to NULL (all species).
direction: One of "all" (default), "consumed", or "produced". Restricts the result to metabolites in the given role across the (possibly species-filtered) pathways.

Value

A character vector containing the names of metabolites in the network.

Examples

cm <- synCM("test", n_species = 3, max_met = 5)
metabolites(cm)
#> [1] "met5" "met3" "met1" "met2" "met4"
## Metabolites consumed by a specific species:
sp <- species(cm)[1]
metabolites(cm, species = sp, direction = "consumed")
#> [1] "met3" "met5"