Flag or remove doublets

Flags cells whose area is far above the population median, which in microscopy typically indicates segmented doublets. The cells are removed and recorded in the QC log.

Usage

cr_qc_doublets(experiment, channel = NULL, threshold_method = "area", k = 2.5)

Arguments

experiment

A cr_experiment.

channel

Unused in the default method but kept for API symmetry; future implementations may use DNA content.

threshold_method

Currently only "area" is supported.

k

Multiplicative threshold: cells with area > k * median are removed. Default 2.5.

Value

A modified cr_experiment.

Examples

exp <- cr_example_experiment(seed = 1, n_cells_per_well = 30)
cr_qc_doublets(exp, threshold_method = "area")
#> ── cr_experiment ───────────────────────────────────────────────────────────────
#> • Cells: 2910 across 96 wells
#> • Channels: "DAPI", "marker_1", "marker_2", and "marker_3"
#> • Design: 6 treatment groups
#> • QC steps applied: 1
#> ℹ Metadata fields: project and sop