Run the whole uncertainty analysis over a scored cohort — run_gate

Driver called by run_cyraven() after populations are scored. It touches nothing the pipeline has already computed.

Usage

run_gate_uncertainty(
  pops,
  gates,
  verdicts,
  panel_of,
  spec,
  B = 100L,
  seed = 42L,
  max_events = 20000L,
  lod_events = 20L,
  loq_events = 50L
)

Arguments

pops: the per-sample scoring results
gates: the per-sample gate objects
verdicts: the per-sample staining verdicts
panel_of: named character vector mapping sample to panel
spec: population specification
B: bootstrap replicates
seed: base seed
max_events: cap on events per replicate
lod_events: events below which a population is not called detected
loq_events: events below which a population is detected but not quantified

Value

list(thresholds, frequencies, budget), each a data.frame or NULL