Parallel backend for FlowCode-based spectral optimization in R.
Usage
optimize.flowcode(
raw_data,
unmixed,
unmix_fun,
combined_spectra,
weights,
pos_thresholds,
af_idx,
af_spectra,
flowcode_ids,
has_flowcode,
combo_fret,
fret_delta_list,
fret_delta_norms,
flowcode_combo_logical,
flowcode_fluors,
optimize_fluors,
variants,
delta_list,
delta_norms,
fluorophores,
af_idx_in_spectra,
asp,
k = 10L,
cell_weighting = FALSE,
cell_weight_regularize = FALSE,
nthreads = 1L,
parallel = TRUE
)Arguments
- raw_data
Numeric matrix (n_cells x n_detectors)
- unmixed
Numeric matrix (n_cells x n_fluors)
- unmix_fun
Unmixing function (WLS)
- combined_spectra
Numeric matrix (n_fluors x n_detectors)
- weights
Numeric vector (n_detectors)
- pos_thresholds
Numeric vector (n_fluors)
- af_idx
Integer vector (n_cells), 1-based AF indices
- af_spectra
Numeric matrix (n_af_variants x n_detectors)
- flowcode_ids
Integer vector (n_cells), 0 = no flowcode
- has_flowcode
Integer/logical vector (n_cells)
- combo_fret
List of FRET spectra matrices
- fret_delta_list
List of delta matrices
- fret_delta_norms
List of norm vectors
- flowcode_combo_logical
Integer matrix (n_combos x n_flowcode_fluors)
- flowcode_fluors
Character vector
- optimize_fluors
Character vector
- variants
List of variant matrices per fluorophore
- delta_list
List of delta matrices per fluorophore
- delta_norms
List of delta norms per fluorophore
- fluorophores
Character vector of fluorophore names
- af_idx_in_spectra
Integer, 0-based index of AF in spectra
- asp
The AutoSpectral parameter list.
- k
Integer, number of variants to test
- cell_weighting
Logical, use cell-specific weights
- cell_weight_regularize
Logical, regularize cell weights
- nthreads
Integer, number of threads
- parallel
Logical, whether to use parallel processing