library("SpaNorm")
data(HumanDLPFC)
spe <- SpaNorm(HumanDLPFC, sample.p = 0.05, df.tps = 2, tol = 1e-2)(1/2) Retrieve precomputed SpaNorm model(2/2) Normalising dataisPolished(S4Vectors::metadata(spe)$SpaNorm)[1] FALSEDoes a SpaNormFit carry a converged per-gene polish?
Description
Does a SpaNormFit carry a converged per-gene polish?
Usage
isPolished(fit)
Arguments
fit
|
an object of class SpaNormFit. |
Value
TRUE iff fit has a non-empty polish slot, i.e. it was returned by polishSpaNorm() (or otherwise had its polish slot set). FALSE for a fresh fitSpaNorm()/SpaNorm() result, and for an object saved before this slot existed (checked via methods::.hasSlot(), since fit$polish/fit@polish would error on such an object).
Examples
Note
The code below runs when the site is built, on a small pre-fitted subset of HumanDLPFC (301 genes x 4015 spots; SpaNorm(sample.p = 0.05, df.tps = 2), SpaNormSVG() and SpaNormPCA() already applied) that is fitted once per build. The outputs are those of the code shown.