clusterProbability {celda} | R Documentation

## Get the conditional probabilities of cell in subpopulations from celda model

### 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)

[Package celda version 1.6.1 Index]