Projects query data onto reference gene expression programs (spectra) using non-negative least squares (NNLS). For each cell, solves the optimization:
$$\min_{w_i \geq 0} ||x_i - H^T w_i||_2^2$$
where \(x_i\) is the expression vector for cell i, \(H\) is the reference spectra matrix (programs x genes), and \(w_i\) is the usage vector.
Usage
fit_usage(
X,
H,
method = c("cd", "active_set"),
max_iter = 1000L,
tol = 1e-08,
n_workers = 1L,
verbose = TRUE
)Arguments
- X
Query matrix (cells x genes), should be pre-processed
- H
Reference spectra matrix (programs x genes)
- method
Solver method: "cd" for coordinate descent (default), "active_set" for Lawson-Hanson active set algorithm
- max_iter
Maximum iterations per cell (default: 1000)
- tol
Convergence tolerance (default: 1e-8)
- n_workers
Number of parallel workers for batch processing (default: 1)
- verbose
Print progress messages (default: TRUE)