logLikelihood: Calculate the Log-likelihood of a celda model

In celda: CEllular Latent Dirichlet Allocation

Description

Calculate the log-likelihood for cell population and feature module cluster assignments on the count matrix, per celda model.

Usage

logLikelihood(x, celdaMod, ...)

## S4 method for signature 'SingleCellExperiment,ANY'
logLikelihood(x, useAssay = "counts", altExpName = "featureSubset")

## S4 method for signature 'matrix,celda_C'
logLikelihood(x, celdaMod)

## S4 method for signature 'matrix,celda_G'
logLikelihood(x, celdaMod)

## S4 method for signature 'matrix,celda_CG'
logLikelihood(x, celdaMod)

Arguments

x	A SingleCellExperiment object returned by celda_C, celda_G, or celda_CG, with the matrix located in the useAssay assay slot. Rows represent features and columns represent cells.
celdaMod	celda model object. Ignored if x is a SingleCellExperiment object.
...	Ignored. Placeholder to prevent check warning.
useAssay	A string specifying which assay slot to use. Default "counts".
altExpName	The name for the altExp slot to use. Default "featureSubset".

Value

The log-likelihood of the cluster assignment for the provided SingleCellExperiment.

See Also

'celda_C()' for clustering cells

Examples

data(sceCeldaC, sceCeldaCG)
loglikC <- logLikelihood(sceCeldaC)
loglikCG <- logLikelihood(sceCeldaCG)

celda documentation built on Nov. 8, 2020, 8:24 p.m.