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Return Species in a Consortium

getSpecies.Rd

Usage

getSpecies(object, ...)

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

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

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

Arguments

object

a ConsortiumMetabolismAlignment Object

...

Object-specific arguments. See methods for details.

type

Character scalar giving the type of species to output.

quantileCutoff

Numeric scalar between 0 and 1 specifying the fraction of species to return when type is "generalists" or "specialists". For "generalists", the top quantileCutoff fraction of species with the most edges is returned. For "specialists", the bottom quantileCutoff fraction with the fewest edges is returned. Defaults to 0.15 (i.e., 15\

For ConsortiumMetabolism objects, a character vector of species names. For ConsortiumMetabolismSet objects, a tibble with columns species and n_edges.A character vector representing the microorganisms.A tibble with columns species and n_edges.A character vector representing the microorganisms. Retrieves species information from consortium metabolism objects. For ConsortiumMetabolismSet objects, species can be filtered by their metabolic versatility. For ConsortiumMetabolismSet objects, the type parameter allows filtering species by their metabolic characteristics:

  • all - Returns all species with their edge counts

  • generalists - Returns species with the most metabolic edges (top quantileCutoff fraction)

  • specialists - Returns species with the fewest metabolic edges (bottom quantileCutoff fraction)

Methods (by class)

  • getSpecies(ConsortiumMetabolism): Return Species in a Microbiome

  • getSpecies(ConsortiumMetabolismSet): Return Species in a Microbiome

  • getSpecies(ConsortiumMetabolismAlignment): Return Species in a Microbiome