Gate cells by intensity

Removes cells whose intensity on a given channel is outside the interval [min_intensity, max_intensity].

Usage

cr_qc_intensity(experiment, channel, min_intensity = NA, max_intensity = NA)

Arguments

experiment

A cr_experiment.

channel

Name of the channel column in cells.

min_intensity, max_intensity

Lower and upper bounds. Leave NA to skip either.

Value

A modified cr_experiment.

See also

cr_qc_gate() for a gate against each unit's own in-batch control rather than an absolute bound.

Other quality control: cr_apply_gate(), cr_balance_cells(), cr_exclude_small(), cr_qc_doublets(), cr_qc_filter(), cr_qc_gate(), cr_qc_gate_impact(), 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_intensity(exp, channel = "DAPI", min_intensity = 50)
#> ── cr_experiment ───────────────────────────────────────────────────────────────
#> • Cells: 2838 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