perplexity {celda}R Documentation

Calculate the perplexity from a single celdaModel

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, celdaMod, newCounts = NULL)

Arguments

counts

Integer matrix. Rows represent features and columns represent cells. This matrix should be the same as the one used to generate 'celdaMod'.

celdaMod

celdaModel. Options available in 'celda::availableModels'.

newCounts

A newCounts 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

data(celdaCGSim, celdaCGMod)
perplexity <- perplexity(celdaCGSim$counts, celdaCGMod)

[Package celda version 1.0.4 Index]