factor_intensities estimates a non-negative matrix D that optimizes the objective function \(F = ||X - C*D - offset||^2\),
where offset is either column-specific offset or a "1-rank nmf term": product of row vector and column vector
factor_intensities(
C,
X,
fit.nmf = TRUE,
fit.factor = FALSE,
qp.exact = FALSE,
n.iter = 200,
qp.iter = 10,
rel.error.cutoff = 1e-05,
extrapolate = TRUE,
extrapolate.const = TRUE,
extrapolate.convex = FALSE,
q.factor = 1,
verbose = TRUE,
n.cores = 1
)Numeric matrices.
Numeric matrices.
A boolean. Fit both intensities and spectrum of the offset residuals.
A boolean. Fit only spectrum of the offset residuals (keep intensities constant across samples).
A boolean. Estimate intensities using exact quadratic programming (qp.exact = TRUE) or inexact QP via gradient decent with extrapolation (qp.exact = FALSE).
An integer. Number of iterations.
= 1e+1 An integer. Number of iterations of inexact QP.
A numeric. Relative error cutoff between iterations to stop iterations.
A boolean. Use Nesterov-like extrapolation at each iteration.
A boolean. Use extrapolation scheme that adds a constant extrapolation q.factor (described below) at each iteration.
A boolean. Use Nesterov extrapolation scheme.
A numeric. Specification of a a constant extrapolation factor used in case of extrapolate.const = T.
A boolean. Print per-iteration information (by default TRUE).
An integer. Number of cores to use.
Fitted matrix D.