Correct batch effects — cr_correct

Applies a simple batch correction. "median_center" shifts each batch's median to the overall median. "combat" delegates to sva::ComBat when available.

Usage

cr_correct_batch(
  experiment,
  batch_var,
  channel,
  method = c("median_center", "combat")
)

Arguments

experiment: A cr_experiment.
batch_var: Name of the batch variable. Must exist in design.
channel: Channel to correct.
method: "median_center" or "combat".

Value

A modified cr_experiment.

Examples

exp <- cr_example_experiment(seed = 1, n_cells_per_well = 30)
exp$design$batch <- rep(c("b1", "b2"), length.out = nrow(exp$design))
cr_correct_batch(exp, batch_var = "batch", channel = "marker_1")
#> ── cr_experiment ───────────────────────────────────────────────────────────────
#> • Cells: 2911 across 96 wells
#> • Channels: "DAPI", "marker_1", "marker_2", and "marker_3"
#> • Design: 6 treatment groups
#> • QC steps applied: 0
#> ℹ Metadata fields: project and sop