celdatosce: Convert old celda model object to 'SCE' object

In campbio/celda: CEllular Latent Dirichlet Allocation

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,
  useAssay = "counts",
  altExpName = "featureSubset"
)

## 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.
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)

campbio/celda documentation built on April 5, 2024, 11:47 a.m.