Subtract background from a channel — cr_background_subtract • cellreportR

Computes a per-well background estimate and subtracts it from every cell in that well. Negative values are clipped to zero.

Usage

cr_background_subtract(
  experiment,
  channel,
  method = c("percentile", "modal", "empty_wells"),
  q = 0.05,
  empty_wells = NULL
)

Arguments

experiment: A cr_experiment.
channel: Channel name.
method: Background estimator. "percentile" (default) uses a low percentile (default 5th), "modal" uses the mode of a kernel density estimate, and "empty_wells" uses the median intensity of wells listed in empty_wells.
q: Percentile for "percentile" method (0-1, default 0.05).
empty_wells: Character vector of well IDs for "empty_wells".

Value

A modified cr_experiment.

See also

cr_normalize(), cr_standardize_batch()

Other normalization functions: cr_normalize()

Examples

exp <- cr_example_experiment(seed = 1, n_cells_per_well = 30)
cr_background_subtract(exp, 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