Calculate the Log-likelihood of a celda model

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

logLikelihood(x, celdaMod, useAssay = "counts", altExpName = "featureSubset")

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

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

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

# S4 method for 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.

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)