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Look up a per-sample, per-marker threshold override

Source: R/thresholds.R
sample_override.Rd

Reads the sample_overrides: block of the config, which is keyed on sample identifier and then on marker:

Usage

sample_override(overrides, sample_id, marker)

Arguments

overrides

the sample_overrides list, or NULL

sample_id

sample identifier

marker

marker name

Value

a list carrying at least threshold, or NULL when none applies

Details

sample_overrides:
  D07:
    CCR7:
      threshold: 2.15
      reason: "valley found inside the negative mode, see gating_qc.png"
      set_by: "initials or name"

Sample and marker names are matched exactly, as they appear in thresholds_used.csv. A block naming a sample or marker that does not exist is inert rather than an error, because a config is routinely reused across cohorts that do not all contain the same tubes; unmatched entries are reported once by report_unused_overrides() rather than failing the run.