Adjust a continuous assay with ComBat — adjust_combat • bulkMAE

Adjust a continuous assay with ComBat

Usage

adjust_combat(
  x,
  experiment,
  batch,
  assay,
  preserve = NULL,
  parametric = TRUE,
  mean_only = FALSE,
  reference_batch = NULL,
  ...
)

Arguments

x: A MultiAssayExperiment object.
experiment: Optional experiment name.
batch: Metadata column name or batch vector.
assay: Assay name or one-based assay index.
preserve: Optional formula for biological covariates to preserve.
parametric: Use parametric empirical Bayes priors.
mean_only: Adjust batch means but not scales.
reference_batch: Optional reference batch.
...: Additional arguments passed to sva::ComBat().

Value

A corrected feature-by-sample matrix.