Run Autofluorescence Removal

Source: R/run_af_removal.R

This function runs the autofluorescence removal process on a list of samples, using the specified parameters and settings.

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

Arguments

clean.expr

List containing cleaned expression data.

af.removal.sample

Vector of sample names for which autofluorescence removal is to be performed.

spectral.channel

Vector of spectral channel names.

peak.channel

Vector of peak detection channels for fluorophores.

universal.negative

Name of the universal negative control.

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.

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.

main.figures

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

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 containing the expression data with autofluorescent events removed for each sample.