Run Universal Negative

This function processes universal negative samples to generate expression data based on specified parameters.

run.universal.negative(
  clean.expr,
  univ.sample,
  universal.negatives,
  scatter.param,
  peak.channels,
  downsample,
  negative.n,
  positive.n,
  spectral.channel,
  asp,
  control.type,
  scatter.match,
  intermediate.figures = FALSE,
  main.figures = TRUE,
  verbose = TRUE
)

Arguments

clean.expr

A matrix containing cleaned expression data.

univ.sample

A character vector specifying the names of universal negative samples.

universal.negatives

A list containing universal negative control parameters.

scatter.param

A character vector specifying the scatter parameters.

peak.channels

A character vector specifying the peak channels.

downsample

A numeric value indicating the downsampling factor.

negative.n

A numeric value indicating the number of negative events.

positive.n

A numeric value indicating the number of positive events.

spectral.channel

A character vector specifying the spectral channels.

asp

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

control.type

A character string specifying the type of control: beads or cells

scatter.match

A logical value indicating whether scatter matching is performed.

intermediate.figures

Logical, if TRUE returns additional figures to show the inner workings of the cleaning, including definition of low-AF cell gates on the PCA-unmixed unstained and spectral ribbon plots of the AF exclusion from the unstained. Default is FALSE to speed up processing.

main.figures

Logical, if TRUE creates the main figures to show the impact of intrusive autofluorescent event removal and scatter-matching for the negatives.

verbose

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

Value

A list containing the processed expression data for each universal negative sample.