Write a MIFlowCyt-structured report of the run — write

Emits the parts of the ISAC MIFlowCyt checklist a run can establish on its own, and marks the parts that require a human as outstanding rather than leaving them out.

Usage

write_miflowcyt(
  path,
  reads,
  opt = NULL,
  spec = NULL,
  transforms = NULL,
  fpr = NULL,
  thresholds = NULL,
  removal = NULL
)

Arguments

path: output file
reads: the per-sample list returned by the reading stage
opt: parsed options
spec: population specification, as scored
transforms: named list of per-panel transform objects
fpr: panel fingerprint result, for the panel-to-sample assignment
thresholds: the thresholds_used.csv table, or NULL
removal: what removed events before gating: "peacoqc", "drop_unstable_events", or NULL when nothing did

Value

the path, invisibly

Details

The instrument and data-file sections are read from the FCS keyword block. The data-analysis section is read from the run itself, so it cannot disagree with what was actually computed.