Infer metabolite sensing capability for each cell type based on receptor and transporter expression. Sensing capability reflects a cell type's capacity to detect and respond to extracellular metabolites.
inferSensing(
object,
method = "combined",
mean_method = "arithmetic",
min_expression = 0,
min_pct = 0.1,
weight_by_affinity = TRUE,
include_transporters = TRUE,
use_hill = FALSE,
hill_n = 1,
hill_Kh = 0.5,
normalize = TRUE,
verbose = TRUE
)A scMetaLink object
Character. Scoring method: "mean", "proportion", or "combined"
Character. Method for calculating mean expression: "arithmetic" (standard mean) or "trimean" (more robust to outliers and dropout).
Numeric. Minimum expression threshold
Numeric. Minimum percentage of expressing cells (0-1)
Logical. Weight by receptor-metabolite affinity score
Logical. Include uptake transporters in sensing
Logical. Apply Hill function transformation to model receptor binding saturation kinetics. When TRUE, high expression levels show diminishing returns, reflecting biological receptor saturation.
Numeric. Hill coefficient (cooperativity). Default 1 (no cooperativity). Values > 1 indicate positive cooperativity.
Numeric. Half-maximal response threshold (0-1 scale after normalization). Default 0.5. Lower values mean saturation occurs at lower expression levels.
Logical. Normalize scores across cell types
Logical. Print progress messages
Updated scMetaLink object with sensing_scores slot filled
The Hill function transformation models receptor-ligand binding dynamics: $$P = \frac{E^n}{K_h^n + E^n}$$ where E is expression, n is the Hill coefficient, and Kh is the half-maximal threshold. This reflects the biological reality that receptor signaling saturates at high ligand/receptor concentrations.