Flag or remove doublets

Flags cells whose size or DNA content 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 = c("area", "channel"),
  k = 2.5
)

Arguments

experiment

A cr_experiment.

channel

Name of the channel column used when threshold_method = "channel" (for example a nuclear stain whose integrated intensity scales with DNA content). Ignored for threshold_method = "area".

threshold_method

"area" (default) thresholds the segmentation area; "channel" thresholds channel.

k

Multiplicative threshold: cells whose value exceeds k * median are removed. Default 2.5.

Value

A modified cr_experiment.

See also

Other quality control: cr_apply_gate(), cr_balance_cells(), cr_exclude_small(), cr_qc_filter(), cr_qc_gate(), cr_qc_gate_impact(), cr_qc_intensity(), cr_qc_manual(), cr_qc_report(), cr_qc_summary(), print.cr_qc_gate()

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
cr_qc_doublets(exp, channel = "DAPI", threshold_method = "channel")
#> ── cr_experiment ───────────────────────────────────────────────────────────────
#> • Cells: 2893 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