Remove Autofluorescence Contamination — remove.af • AutoSpectral

This function removes autofluorescence contamination from a sample, using the specified parameters and settings.

remove.af(
  clean.expr,
  samp,
  spectral.channel,
  peak.channel,
  universal.negative,
  asp,
  scatter.param,
  negative.n = 500,
  positive.n = 1000,
  scatter.match = TRUE,
  main.figures = TRUE,
  intermediate.figures = FALSE,
  verbose = TRUE
)

Arguments

clean.expr: List containing cleaned expression data.
samp: Sample identifier.
spectral.channel: Vector of spectral channel names.
peak.channel: Vector of peak detection channels for fluorophores.
universal.negative: Named vector mapping samples to their matching negatives.
asp: The AutoSpectral parameter list. Prepare using get.autospectral.param
scatter.param: Vector of scatter parameters.
negative.n: Integer. Number of events to include in the downsampled negative population. Default is 500.
positive.n: Integer. Number of events to include in the downsampled positive population. Default is 1000.
scatter.match: Logical, default is TRUE. Whether to select negative events based on scatter profiles matching the positive events. Defines a region of FSC and SSC based on the distribution of selected positive events.
main.figures: Logical, if TRUE creates the main figures to show the impact of intrusive autofluorescent event removal and scatter-matching for the negatives.
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.
verbose: Logical, default is TRUE. Set to FALSE to suppress messages.

Value

A matrix containing the expression data with autofluorescent events removed for the sample.