Check Control File — check.control.file • AutoSpectral

Attempts to find potential failure points and input errors in the control file control.def.file used to define the single-stained control setup for AutoSpectral.

Usage

check.control.file(
  control.dir,
  control.def.file,
  asp,
  strict = FALSE,
  min.event.warning = 5000,
  min.event.error = 1000,
  legacy = 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 defined using get.autospectral.param.
strict: Logical. Controls whether the function triggers a break or continues and outputs a list of errors. Default is FALSE.
min.event.warning: The number of events in the entire FCS file that will trigger a warning if not met. Default is 5000.
min.event.error: The number of events in the entire FCS file that will trigger an error if not met. Default is 1000.
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 using get.spectra.automated(). To use the version 1 "legacy" pipeline for the extraction of fluorophore spectra, using gating and define.flow.control(), set legacy=TRUE.

Value

A dataframe of errors and warnings intended to help the user fix problems with the control.def.file.