Apply a QC gate to an experiment

Removes the cells of every unit the gate excluded, records the step in the QC log and stores the gate on the experiment so the decision remains auditable after the data have been trimmed.

Usage

cr_apply_gate(experiment, gate, units = NULL, drop_disputed = FALSE)

Arguments

experiment

A cr_experiment.

gate

A cr_qc_gate from cr_qc_gate().

units

Optional character vector of unit identifiers to remove instead of gate$excluded, for a reviewed exclusion list.

drop_disputed

Also drop the units whose verdict depends on which control centre is used. Default FALSE.

Value

A modified cr_experiment. The gate is stored in metadata$qc_gate.

See also

cr_qc_gate(), cr_qc_gate_impact(), cr_qc_report().

Other quality control: cr_balance_cells(), cr_exclude_small(), cr_qc_doublets(), 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 = 40)
gate <- cr_qc_gate(exp, "marker_1", "Untreated", batch_vars = "replicate")
exp2 <- cr_apply_gate(exp, gate)
cr_qc_summary(exp2)
#> # A tibble: 1 × 7
#>   step         parameters cells_before cells_after cells_removed percent_removed
#>   <chr>        <chr>             <int>       <int>         <int>           <dbl>
#> 1 cr_apply_ga… unit=well…         3852        3781            71            1.84
#> # ℹ 1 more variable: timestamp <dttm>