Fast, non-interactive estimate of fluorophore brightness (background-
subtracted MFI) for every single-stained control listed in
control.def.file. Unlike get.brightness(), no scatter gate is
drawn: brightness is measured directly from the whole acquired file using
the top n.cells events in each fluorophore's peak detector, with
background subtracted using the matched universal-negative control.
The peak detector for each fluorophore is taken from spectra
(the output of get.spectra.automated()) rather than the nominal
channel column in the control table, so brightness is always
measured on the same channel the extracted spectrum is actually built
from, including any legacy refinement.
Usage
get.brightness.automated(
control.dir,
control.def.file,
asp,
spectra,
n.cells = 500L,
verbose = TRUE
)Arguments
- control.dir
Character. Path to the single-stained control FCS files.
- control.def.file
Character. Path to the control definition CSV.
- asp
The AutoSpectral parameter list from
get.autospectral.param(). Currently unused directly but accepted for interface consistency withget.spectra.automated()/get.spectral.variants(), and to allow future use (e.g. saturation thresholds).- spectra
Numeric matrix as returned by
get.spectra.automated(); fluorophores in rows (may include"AF", which is ignored), detectors in columns.- n.cells
Integer, default
500L. Number of brightest events (in the fluorophore's peak channel) averaged to estimate the positive MFI.- verbose
Logical, default
TRUE.