Score biofluid-residualized ALR

Usage

score_biofluid_residualized_alr(
  expr,
  meta,
  panel,
  biofluid_col = "biofluid",
  fit = NULL,
  feature_weights = NULL,
  train_expr = NULL,
  train_meta = NULL,
  outcome_col = "disease",
  cohort_col = "cohort",
  pseudocount = NULL,
  ...
)

Arguments

expr: Numeric matrix, samples x features.
meta: Data frame aligned to `expr`.
panel: Character vector of panel features.
biofluid_col: Column in `meta` with canonical or raw biofluid.
fit: Optional fit. If NULL, the fit is built on `expr` and `meta`.
feature_weights: Optional named numeric panel weights.
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`.
pseudocount: Optional additive pseudocount before log transform.
...: Additional arguments passed to `fit_biofluid_stratified_rclr()`.