perplexity: Calculate the perplexity from a single celda model

In compbiomed/celda: CEllular Latent Dirichlet Allocation

Description

Perplexity can be seen as a measure of how well a provided set of cluster assignments fit the data being clustered.

Usage

perplexity(counts, celda.mod, new.counts = NULL)

Arguments

counts	Integer matrix. Rows represent features and columns represent cells. This matrix should be the same as the one used to generate 'celda.mod'.
celda.mod	Celda object of class "celda_C", "celda_G" or "celda_CG".
new.counts	A new counts matrix used to calculate perplexity. If NULL, perplexity will be calculated for the 'counts' matrix. Default NULL.

Value

Numeric. The perplexity for the provided count data and model.

Examples

perplexity = perplexity(celda.CG.sim$counts, celda.CG.mod)

compbiomed/celda documentation built on May 25, 2019, 3:58 a.m.