Return Species in a Consortium

Returns the species present in a consortium or set of consortia.

Usage

species(object, ...)

# S4 method for class 'ConsortiumMetabolism'
species(object)

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

# S4 method for class 'ConsortiumMetabolismSet'
species(
  object,
  type = c("all", "generalists", "specialists"),
  quantileCutoff = 0.15,
  ...
)

Arguments

object

A ConsortiumMetabolismSet object.

...

Additional arguments passed to methods.

type

Character scalar. One of "all" (default), "generalists" (top fraction by pathway count), or "specialists" (bottom fraction).

quantileCutoff

Numeric scalar in (0, 1) giving the fraction of species to label as generalists or specialists. Defaults to 0.15.

Value

A character vector of species names.

Methods (by class)

• species(ConsortiumMetabolism): Return Species in a ConsortiumMetabolism

• species(ConsortiumMetabolismAlignment): Return species from a ConsortiumMetabolismAlignment

• species(ConsortiumMetabolismSet): Return Species in a ConsortiumMetabolismSet, optionally filtered to metabolic generalists or specialists by pathway count.

Note

BiocGenerics::species (deprecated) sometimes resolves first when typing ?species interactively. Use ?ramen::species to land on this page.

Examples

cm <- synCM("test", n_species = 3, max_met = 5)
species(cm)
#> [1] "NRS6841X" "IFU334T"  "VUY8963S"