Define Flow Control

Source: R/define_flow_control.r

A complex function designed to convert the single-stained control FCS files and the metadata control.def.file into a data structure for AutoSpectral. It reads the metadata file, locates the corresponding FCS files, determines the gates needed based on variables such as beads or cells, large.gate, and viability.gate, and then creates gates for each combination. It imports and gates the data in the FCS files and assigns various factors to track the data.

define.flow.control(
  control.dir,
  control.def.file,
  asp,
  gate = TRUE,
  parallel = FALSE,
  verbose = TRUE
)

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.

gate

Logical, default is TRUE, in which case, automated gating will be performed. If FALSE, the FCS files will be imported without automatically generated gates applied. That is, all data in the files will be used. This is intended to allow the user to pre-gate the files in commercial software.

parallel

Logical, default is FALSE, in which case parallel processing will not be used. Parallel processing will likely be faster when many small files are read in. If the data is larger, parallel processing may not accelerate the process much.

verbose

Logical, default is TRUE. Set to FALSE to suppress messages.

Value

A list (flow.control) with the following components:

  • filename: Names of the single-color control files.

  • fluorophore: Corresponding fluorophores used in the experiment.

  • antigen: Corresponding markers used in the experiment.

  • control.type: Type of control used (beads or cells).

  • universal.negative: Corresponding universal negative for each control.

  • viability: Logical factor; whether a control represents a viability marker.

  • large.gate: Logical factor; large gate setting.

  • autof.channel.idx: Index of the autofluorescence marker channel.

  • event.number.width: Width of the event number.

  • expr.data.max: Maximum expression data value.

  • expr.data.max.ceil: Ceiling of the maximum expression data value.

  • expr.data.min: Minimum expression data value.

  • channel: Preliminary peak channels for the fluorophores.

  • channel.n: Number of channels.

  • spectral.channel: Spectral channel information.

  • spectral.channel.n: Number of spectral channels.

  • sample: Sample names (fluorophores).

  • scatter.and.channel: FSC, SSC, and peak channel information.

  • scatter.and.channel.label: Labels for scatter and channel.

  • scatter.and.channel.spectral: FSC, SSC, and spectral channels.

  • scatter.parameter: Scatter parameters used for gating.

  • event: Event factor.

  • event.n: Number of events.

  • event.sample: Sample information for events. Links events to samples.

  • event.type: Type of events.

  • expr.data: Expression data used for extracting spectra.