Get Universal Negative Control

This function identifies and processes the universal negative control for a given sample, including scatter matching and plotting.

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

Arguments

clean.expr.data

List containing cleaned expression data.

samp

Sample identifier.

universal.negatives

Named vector mapping samples to their universal negatives.

scatter.param

Vector of scatter parameters.

peak.channels

Named vector mapping samples to their peak channels.

downsample

Logical indicating whether to downsample the data.

negative.n

Number of negative events to select.

positive.n

Number of positive events to select.

spectral.channel

Vector of spectral channel names.

asp

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

control.type

Named vector mapping samples to their control types.

scatter.match

Logical indicating whether to perform scatter matching. Default is TRUE.

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 data frame containing the selected positive and scatter-matched negative events.