Does a SpaNormFit carry a converged per-gene polish?
Value
TRUE iff fit has a non-empty polish slot,
i.e. it was returned by polishSpaNorm() (or otherwise had its
polish slot set). FALSE for a fresh
fitSpaNorm()/SpaNorm() result, and for an object saved
before this slot existed (checked via methods::.hasSlot(), since
fit$polish/fit@polish would error on such an object).
Examples
data(HumanDLPFC)
# \donttest{
spe <- SpaNorm(HumanDLPFC, sample.p = 0.05, df.tps = 2, tol = 1e-2)
#> (1/2) Fitting SpaNorm model
#> 201 cells/spots sampled to fit model
#> iter: 1, estimating gene-wise dispersion
#> iter: 1, log-likelihood: -1185444.215197
#> iter: 1, fitting NB model
#> iter: 1, iter: 1, log-likelihood: -1185444.215197
#> iter: 1, iter: 2, log-likelihood: -839781.689791
#> iter: 1, iter: 3, log-likelihood: -746711.491368
#> iter: 1, iter: 4, log-likelihood: -730472.651002
#> iter: 1, iter: 5, log-likelihood: -728064.170265
#> iter: 1, iter: 6, log-likelihood: -727668.850714
#> iter: 1, iter: 7, log-likelihood: -727584.876497
#> iter: 1, iter: 8, log-likelihood: -727560.469215 (converged)
#> iter: 2, estimating gene-wise dispersion
#> iter: 2, log-likelihood: -727322.375691
#> iter: 2, fitting NB model
#> iter: 2, iter: 1, log-likelihood: -727322.375691
#> iter: 2, iter: 2, log-likelihood: -727197.061571
#> iter: 2, iter: 3, log-likelihood: -727192.389828 (converged)
#> iter: 3, log-likelihood: -727192.389828 (converged)
#> (2/2) Normalising data
isPolished(S4Vectors::metadata(spe)$SpaNorm)
#> [1] FALSE
# }