Infer Metabolite Production Potential

Infer metabolite production potential for each cell type based on enzyme expression patterns. Production potential reflects a cell type's capacity to synthesize and secrete metabolites for intercellular communication.

inferProduction(
  object,
  method = "combined",
  mean_method = "arithmetic",
  min_expression = 0,
  min_pct = 0.1,
  consider_degradation = TRUE,
  consider_secretion = TRUE,
  normalize = TRUE,
  verbose = TRUE
)

Arguments

object

A scMetaLink object

method

Character. Scoring method: "mean", "proportion", or "combined"

mean_method

Character. Method for calculating mean expression: "arithmetic" (standard mean) or "trimean" (more robust to outliers and dropout). Trimean is recommended for single-cell data with high dropout rates.

min_expression

Numeric. Minimum expression threshold

min_pct

Numeric. Minimum percentage of expressing cells (0-1)

consider_degradation

Logical. Subtract degradation enzyme expression

consider_secretion

Logical. Weight by secretion potential

normalize

Logical. Normalize scores across cell types

verbose

Logical. Print progress messages

Value

Updated scMetaLink object with production_scores slot filled