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Get Edges From a ConsortiumMetabolism Object

getEdges.Rd

Usage

getEdges(object, ...)

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

# S4 method for class 'ConsortiumMetabolismSet'
getEdges(
  object,
  type = c("all", "pan-cons", "niche", "core", "aux"),
  quantileCutoff = 0.1
)

Arguments

object

A ConsortiumMetabolism or ConsortiumMetabolismSet object

...

Object-specific arguments. See methods for details.

type

Character scalar giving the type of edges to output.

quantileCutoff

Numeric scalar between 0 and 1 giving the quantile threshold to use for filtering edges. For "pan-cons" and "core" types, edges above 1 - quantileCutoff are returned. For "niche" and "aux" types, edges below quantileCutoff are returned. Defaults to 0.1 (i.e., top/bottom 10\

A tibble containing edge information including:

  • consumed/produced metabolites

  • number of species involved

  • consumption/production sums

  • effective consumption/production metrics

Retrieves the edges representing metabolic interactions between species. The argument type can be used to return only specific types of edges from a ConsortiumMetabolismSet object. For ConsortiumMetabolismSet objects, the type parameter determines which edges are returned:

  • all - Returns all edges

  • pan-cons - Returns edges present in most consortia (top 1 - quantileCutoff fraction)

  • niche - Returns rare edges (bottom quantileCutoff fraction of consortia)

  • core - Returns edges involving many species (top 1 - quantileCutoff fraction)

  • aux - Returns edges involving few species (bottom quantileCutoff fraction)

Methods (by class)

  • getEdges(ConsortiumMetabolism): Get Edges From a ConsortiumMetabolism Object

  • getEdges(ConsortiumMetabolismSet): Get Edges From a ConsortiumMetabolismSet Object