Functional Microbiome Representation based on TreeSummarizedExperiment

Creates a ConsortiumMetabolism object representing metabolic interactions in a microbial community. The object contains information about metabolite consumption and production by different species, along with various metrics like flux sums and effective fluxes.

Usage

ConsortiumMetabolism(
  data,
  name = NA_character_,
  species_col = "species",
  metabolite_col = "met",
  flux_col = "flux",
  ...
)

Arguments

data: a DataFrame-like object that includes columns specifying the species, metabolites and fluxes in the microbiome. The fluxes can either be weighted or unweighted (all of magnitude 1).
name: a character scalar specifying the name of the Microbiome
species_col: Character scalar specifying the name of the species column, defaults to 'species'.
metabolite_col: Character scalar specifying the name of the metabolite column, defaults to 'met'.
flux_col: Character scalar specifying the name of the flux column, defaults to 'flux'.
...: Additional arguments to be passed to the constructor.

Value

A ConsortiumMetabolism object containing:

Assays for binary interactions, edge counts, consumption/production metrics
Row and column data about metabolites
Graph representation of the metabolic network
Original input data and computed edge information