Optional ComBat-seq followed by rCLR scoring.

Optional ComBat-seq followed by rCLR scoring.

Usage

score_combat_seq_then_rclr(
  expr,
  meta,
  panel,
  batch_col = NULL,
  disease_col = NULL,
  allow_transductive = FALSE,
  pseudocount = 0.5
)

Arguments

expr

Numeric count matrix, samples x features.

meta

Data frame aligned to `expr`.

panel

Character vector of panel features.

batch_col

Optional batch column. Defaults to inferred kit column.

disease_col

Optional disease-label column passed to ComBat-seq.

allow_transductive

Logical. Must be TRUE because this comparator is transductive and should not be treated as a frozen deployable scorer.

pseudocount

Additive pseudocount before rCLR scoring.