This function runs the autofluorescence removal process on a list of samples, using the specified parameters and settings.
Usage
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,
threads = 1,
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
TRUEreturns 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
TRUEcreates 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. Set toTRUEto run in parallel.- threads
Number of cores to use for parallel processing, default is
1.- verbose
Logical, default is
TRUE. Set toFALSEto suppress messages.