Calculate Weights — calculate.weights • AutoSpectral

This function calculates weights for generating a weighted least-squares (WLS) unmixing matrix. It does so using mean expression levels in the provided FCS file. The provided FCS file should thus be representative of the data to which the unmixing matrix will be applied. One option would be to concatenate samples of all FCS files to be unmixed and use that as input to fcs.file.

Usage

calculate.weights(
  fcs.file,
  spectral.channels,
  save = FALSE,
  output.dir = "./table_spectra",
  filename = "weights.csv"
)

Arguments

fcs.file: A character string specifying the path to the FCS file.
spectral.channels: Character string specifying the names of the spectral detectors in the FCS file. Can be obtained from flow.control$spectral.channel or colnames(spectra).
save: Logical, if TRUE, save the weights to a CSV file in output.dir.
output.dir: Character string specifying the directory to save the CSV file, if generated.
filename: Character string specifying the filename for the CSV file. Default is weights.csv.

Value

A named numeric vector with weighting for each detector.