Correct batch effects

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, or a character vector of several column names that jointly define a batch (they are collapsed with cr_batch_key()). Columns are looked up in design first and then in cells.

channel

Channel to correct.

method

"median_center" or "combat".

Value

A modified cr_experiment.

Details

Batch correction removes a batch offset from the measured signal. It is not a substitute for cr_standardize_batch(), which expresses every cell relative to the control cells of its own batch and leaves the measured signal untouched.

See also

cr_batch_key(), cr_standardize_batch()

Other batch standardization functions: cr_batch_key(), cr_batch_reference(), cr_standardize_batch()

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

# A batch defined by more than one column
exp$design$plate <- rep(c("P1", "P2"), length.out = nrow(exp$design))
cr_correct_batch(exp, batch_var = c("batch", "plate"),
                 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