Create Control File

A helper function to draft a description of your single stained control files such that AutoSpectral can understand and process them correctly. Given a set of single stained control fcs files, create.control.file will produce a csv file listing the matching peak detector channels for your fluorophores (if known). If your files contain bead or cell tags in the filename, it will assign your controls as cells or beads, and will automatically fill in the matching universal.negative filename when exactly one unstained/negative control shares that control.type. universal.negative is left blank when control.type could not be determined or when more than one unstained/negative control of that type exists (in which case you will need to set it manually). It will also assign the large.gate column based on the matched marker's entry in marker_database.csv. Bead controls are never assigned large.gate = TRUE, even if the matched marker is flagged as large.gate in the marker database. You will need to fill in any "No Match" results manually. You will need to add marker names manually.

Usage

create.control.file(
  control.dir,
  asp,
  control.files = NULL,
  fill.gate.name = TRUE,
  filename = "fcs_control_file",
  legacy = FALSE,
  output.dir = getwd()
)

Arguments

control.dir

file path to the single stained control fcs files

asp

The AutoSpectral parameter list. Generate using get.autospectral.param

control.files

Optional specification of the control files to use. This will override the default, which is to use all the FCS files in the control.dir to create the control file. Files and path(s) may be specified, allowing you to use files from different subdirectories. For instance, you may wish to exclude bead controls from a folder containing both bead and cell controls, saving you the work of deleting the lines from the created control file.

fill.gate.name

Logical, default is TRUE. Will attempt to automatically assign gate names for the gate.name column if TRUE.

filename

Character string defining the output filename. Default is "fcs_control_file", to which .csv will be appended.

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.

output.dir

location where the CSV file will be written. Default is the current working directory.

Value

No returns. Outputs a csv file called fcs_control_file.csv