clusterProbability: Get the conditional probabilities of cell in subpopulations...

In celda: CEllular Latent Dirichlet Allocation

Description

Calculate the conditional probability of each cell belonging to each subpopulation given all other cell cluster assignments and/or each feature belonging to each module given all other feature cluster assignments in a celda model.

Usage

clusterProbability(sce, ...)

## S4 method for signature 'SingleCellExperiment'
clusterProbability(
  sce,
  useAssay = "counts",
  altExpName = "featureSubset",
  log = FALSE
)

Arguments

sce	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.
...	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".
log	Logical. If FALSE, then the normalized conditional probabilities will be returned. If TRUE, then the unnormalized log probabilities will be returned. Default FALSE.

Value

A list containging a matrix for the conditional cell subpopulation cluster and/or feature module probabilities.

See Also

'celda_C()' for clustering cells

Examples

data(sceCeldaCG)
clusterProb <- clusterProbability(sceCeldaCG, log = TRUE)
data(sceCeldaC)
clusterProb <- clusterProbability(sceCeldaC)

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