Checks whether the control file used to define the single-stained control setup for AutoSpectral conforms to expectations and follows rules required for successful running of AutoSpectral.
Usage
validate.control.file(
control.dir,
control.def.file,
asp,
min.event.warning,
min.event.error,
legacy = FALSE,
allow.duplicate.controls = FALSE
)Arguments
- control.dir
File path to the single-stained control FCS files.
- control.def.file
CSV file defining the single-color control file names, fluorophores they represent, marker names, peak channels, and gating requirements.
- asp
The AutoSpectral parameter list.
- min.event.warning
The number of events in the entire FCS file that will trigger a warning if not met.
- min.event.error
The number of events in the entire FCS file that will trigger an error if not met.
- legacy
Logical. If
FALSE, gating-related columns will not be created and the control file will be suitable only for the new automated spectral extraction pipeline usingget.spectra.automated(). To use the version 1 "legacy" pipeline for the extraction of fluorophore spectra, using gating anddefine.flow.control(), setlegacy=TRUE.- allow.duplicate.controls
Logical, default
FALSE. IfFALSE, multiple controls for the same fluorophore are flagged as an error. Set toTRUEto permit them for diagnostic/QC use (e.g. comparing two preparations of the same conjugate); each will be assigned a uniquesampleidentifier. The resulting reference library still must be reduced to one row per fluorophore before it can be used for unmixing – seecheck.spectra.duplicates().