celdatosce {celda} | R Documentation

## Convert old celda model object to `SCE` object

### Description

Convert a old celda model object (`celda_C`, `celda_G`, or `celda_CG` object) to a SingleCellExperiment object containing celda model information in `metadata` slot. Counts matrix is stored in the `"counts"` assay slot in `assays`.

### Usage

    celdatosce(celdaModel, counts, ...)

    ## S4 method for signature 'celda_C'
    celdatosce(
      celdaModel,
      counts,
      useAssay = "counts",
      altExpName = "featureSubset"
    )

    ## S4 method for signature 'celda_G'
    celdatosce(
      celdaModel,
      counts,
      useAssay = "counts",
      altExpName = "featureSubset"
    )

    ## S4 method for signature 'celda_CG'
    celdatosce(
      celdaModel,
      counts,
      useAssay = "counts",
      altExpName = "featureSubset"
    )

    ## S4 method for signature 'celdaList'
    celdatosce(
      celdaModel,
      counts,
      useAssay = "counts",
      altExpName = "featureSubset"
    )

### Arguments

`celdaModel` | A `celdaModel` or `celdaList` object generated using older versions of `celda`.
`counts` | A numeric matrix of counts used to generate `celdaModel`. Dimensions and MD5 checksum will be checked by compareCountMatrix.
`...` | Ignored. Placeholder to prevent check warning.
`useAssay` | A string specifying the name of the assay slot to use. Default "counts".
`altExpName` | The name for the altExp slot to use. Default "featureSubset".

### Value

A SingleCellExperiment object. Function parameter settings are stored in the metadata `"celda_parameters"` slot. Columns `celda_sample_label` and `celda_cell_cluster` in colData contain sample labels and celda cell population clusters. Column `celda_feature_module` in rowData contain feature modules.

### Examples

    data(celdaCMod, celdaCSim)
    sce <- celdatosce(celdaCMod, celdaCSim$counts)
    data(celdaGMod, celdaGSim)
    sce <- celdatosce(celdaGMod, celdaGSim$counts)
    data(celdaCGMod, celdaCGSim)
    sce <- celdatosce(celdaCGMod, celdaCGSim$counts)
    data(celdaCGGridSearchRes, celdaCGSim)
    sce <- celdatosce(celdaCGGridSearchRes, celdaCGSim$counts)

[Package celda version 1.6.1 Index]