Return Species in a Consortium — species • ramen

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 'ConsortiumMetabolismSet'
species(
  object,
  type = c("all", "generalists", "specialists"),
  quantileCutoff = 0.15
)

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

Arguments

object: A ConsortiumMetabolismAlignment object.
...: Additional arguments passed to methods.
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 pathways is returned. For "specialists", the bottom quantileCutoff fraction with the fewest pathways is returned. Defaults to 0.15 (i.e., 15 percent). Ignored when type = "all".

Value

A character vector of species names, or a tibble with species and pathway counts (for ConsortiumMetabolismSet).

A character vector representing the microorganisms.

A character vector of species names.

Methods (by class)

species(ConsortiumMetabolism): Return Species in a Microbiome
species(ConsortiumMetabolismSet): Return Species in a Microbiome
species(ConsortiumMetabolismAlignment): Return species from a ConsortiumMetabolismAlignment

Examples

cm <- synCM("test", n_species = 3, max_met = 5)
species(cm)
#> [1] "KAP4325W" "QAQ6136W" "HHC6277F"