Import SMETANA Detailed Output

Imports raw SMETANA --detailed output (one TSV file per consortium) into a ConsortiumMetabolism (single file/data.frame) or ConsortiumMetabolismSet (directory of files). The raw format has columns community, medium, receiver, donor, compound, scs, mus, mps, smetana, where each row describes a cross-feeding interaction: donor produces compound, receiver consumes it. This function collapses those directed interactions into ramen's (species, metabolite, flux) edge-list representation.

Usage

importSmetana(
  data,
  name = NULL,
  use_scores = TRUE,
  normalize_ids = TRUE,
  verbose = TRUE
)

Arguments

data

Either a file path to a single SMETANA TSV, a directory path containing multiple SMETANA TSVs, or a pre-loaded data.frame with the required columns (receiver, donor, compound, and smetana if use_scores = TRUE).

name

Consortium (or set) name as a length-1 character scalar. If NULL (default), names are derived from the input filename(s) by stripping the .tsv_detailed.tsv suffix. Required when data is a data.frame. If data is a directory, name is passed through to ConsortiumMetabolismSet().

use_scores

If FALSE, flux is binary (+1 for production, -1 for consumption). If TRUE (default), flux magnitude is the SMETANA score, aggregated by max() when the same (species, compound) pair appears across multiple interaction partners.

normalize_ids

If TRUE (default), normalize compound IDs via .normalizeBiggIds() (strips M_ prefix and _e compartment suffix).

verbose

If TRUE (default), emit progress messages via cli progress messages.

Value

A ConsortiumMetabolism object if data is a single file or data.frame; a ConsortiumMetabolismSet if data is a directory.

See also

ConsortiumMetabolism(), ConsortiumMetabolismSet(), importMisosoup()

Examples

if (FALSE) {
# Single file -> ConsortiumMetabolism
cm <- importSmetana("path/to/bq_0.tsv_detailed.tsv")

# Directory of files -> ConsortiumMetabolismSet
cms <- importSmetana("path/to/bq_subsample/")

# Weighted fluxes
cm <- importSmetana("path/to/bq_0.tsv_detailed.tsv", use_scores = TRUE)
}