Score technology-residualized ALR

Usage

score_tech_residualized_alr(
  expr,
  meta,
  panel,
  technology_col = "technology",
  fit = NULL,
  train_expr = NULL,
  train_meta = NULL,
  outcome_col = "disease",
  cohort_col = "cohort",
  pivot_features = .ta_default_pivot_pool(),
  anchor_features = character(),
  min_pivot_present = 3L,
  pseudocount = NULL
)

Arguments

expr: Numeric matrix, samples x features.
meta: Data frame aligned to `expr`.
panel: Character vector of panel features.
technology_col: Column identifying technology class.
fit: Optional fit from `fit_tech_stratified_rclr()`.
train_expr: Optional training matrix when `fit` is NULL.
train_meta: Optional training metadata when `fit` is NULL.
outcome_col: Binary disease label column in `train_meta`.
cohort_col: Cohort column in `train_meta`.
pivot_features: Candidate ALR pivot features.
anchor_features: Optional train-selected fallback pivots.
min_pivot_present: Minimum pivots required for prediction.
pseudocount: Optional additive pseudocount before log transform.

Value

Numeric score vector.