Functional Microbiome Representation

Creates a ConsortiumMetabolism object representing metabolic interactions in a microbial community. The object stores metabolite consumption and production by different species, along with flux sums and effective fluxes.

Usage

ConsortiumMetabolism(
  data,
  name = NA_character_,
  growth = NULL,
  species_col = "species",
  metabolite_col = "metabolite",
  flux_col = "flux",
  verbose = FALSE
)

Arguments

data

a data.frame with columns for species, metabolites and fluxes. Fluxes can be weighted or unweighted (magnitude 1).

name

Character scalar giving the consortium name.

growth

Optional named numeric vector of per-species growth rates (e.g. FBA objective values). Names must match species in data. Stored in metadata(cm)$growth and retrievable via the growth accessor.

species_col

Character scalar for the species column name, defaults to "species".

metabolite_col

Character scalar for the metabolite column name, defaults to "metabolite".

flux_col

Character scalar for the flux column name, defaults to "flux".

verbose

Logical scalar. If TRUE, prints progress messages during construction. Defaults to FALSE.

Value

A ConsortiumMetabolism object.

Slots

Name

character. Display name for the consortium.

Description

character. Optional short description.

Pathways

data.frame. Pathway list of metabolic interactions with per-pathway metrics (species count, flux sums, flux-corrected effective fluxes, and Hill-1 effective number of contributing species).

Weighted

logical. Whether flux magnitudes are used.

InputData

data.frame. Original input data (species, metabolite, flux columns).

Metabolites

character. Unique metabolite identifiers.

Graphs

list. List containing an igraph object of the metabolic network.

See also

TreeSummarizedExperiment-class

Examples

cm <- synCM("example", n_species = 3, max_met = 5)
cm
#> 
#> ── ConsortiumMetabolism 
#> Name: "example"
#> Weighted metabolic network: 3 species, 3 metabolites, 4 pathways.
#> Pathways per species: min 1, mean 1.3, max 2.