Perplexity is a statistical measure of how well a probability model can predict new data. Lower perplexity indicates a better model.
perplexity( x, celdaMod, useAssay = "counts", altExpName = "featureSubset", newCounts = NULL ) # S4 method for SingleCellExperiment,ANY perplexity( x, useAssay = "counts", altExpName = "featureSubset", newCounts = NULL ) # S4 method for ANY,celda_CG perplexity(x, celdaMod, newCounts = NULL) # S4 method for ANY,celda_C perplexity(x, celdaMod, newCounts = NULL) # S4 method for ANY,celda_G perplexity(x, celdaMod, newCounts = NULL)
x | Can be one of
|
---|---|
celdaMod | Celda model object. Only works if |
useAssay | A string specifying which assay
slot to use if |
altExpName | The name for the altExp slot to use. Default "featureSubset". |
newCounts | A new counts matrix used to calculate perplexity. If NULL,
perplexity will be calculated for the matrix in |
Numeric. The perplexity for the provided x
(and
celdaModel
).
data(sceCeldaCG) perplexity <- perplexity(sceCeldaCG) data(celdaCGSim, celdaCGMod) perplexity <- perplexity(celdaCGSim$counts, celdaCGMod) data(celdaCSim, celdaCMod) perplexity <- perplexity(celdaCSim$counts, celdaCMod) data(celdaGSim, celdaGMod) perplexity <- perplexity(celdaGSim$counts, celdaGMod)