Read Spectra

Reads in CSV files created by AutoSpectral or in the same format (fluorophores in rows, detectors in columns, first row is detector names, first column contains fluorophore names).

read.spectra(
  spectra.file,
  spectra.dir = "./table_spectra",
  remove.af = FALSE,
  af.param = "AF"
)

Arguments

spectra.file

File name for the spectra CSV file to be read.

spectra.dir

File path to the folder containing spectra.file. Default is table_spectra, where AutoSpectral saves the spectra files.

remove.af

Logical, default is FALSE. If TRUE, returns the spectral matrix without the default autofluorescence spectrum.

af.param

Name of the autofluorescence parameter. Default is AF. Note that any fluorophores can be removed from the matrix by supplying a character vector, e.g., c("BUV395", "PE"), if desired.

Value

A matrix containing the fluorophore spectra (fluorophore x detectors).