perplexity {celda} | R Documentation

## Calculate the perplexity of a celda model

### Description

Perplexity is a statistical measure of how well a probability model can predict new data. Lower perplexity indicates a better model.

### Usage

    perplexity(
      x,
      celdaMod,
      useAssay = "counts",
      altExpName = "featureSubset",
      newCounts = NULL
    )

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

    ## S4 method for signature 'ANY,celda_CG'
    perplexity(x, celdaMod, newCounts = NULL)

    ## S4 method for signature 'ANY,celda_C'
    perplexity(x, celdaMod, newCounts = NULL)

    ## S4 method for signature 'ANY,celda_G'
    perplexity(x, celdaMod, newCounts = NULL)

### Arguments

`x` | Can be one of 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. Integer counts matrix. Rows represent features and columns represent cells. This matrix should be the same as the one used to generate `celdaMod`.
`celdaMod` | Celda model object. Only works if `x` is an integer counts matrix.
`useAssay` | A string specifying which assay slot to use if `x` is a SingleCellExperiment object. Default "counts".
`altExpName` | The name for the altExp slot to use. Default "featureSubset".
`newCounts` | A new counts matrix used to calculate perplexity. If NULL, perplexity will be calculated for the matrix in `useAssay` slot in `x`. Default NULL.

### Value

Numeric. The perplexity for the provided `x` (and `celdaModel`).

### Examples

    data(sceCeldaCG)
    perplexity <- perplexity(sceCeldaCG)
    data(celdaCGSim, celdaCGMod)
    perplexity <- perplexity(celdaCGSim$counts, celdaCGMod)
    data(celdaCSim, celdaCMod)
    perplexity <- perplexity(celdaCSim$counts, celdaCMod)
    data(celdaGSim, celdaGMod)
    perplexity <- perplexity(celdaGSim$counts, celdaGMod)

[Package celda version 1.8.1 Index]