Export a SingleCellExperiment R object as Python annData object

Writes all assays, colData, rowData, reducedDims, and altExps objects in a SingleCellExperiment to a Python annData object in the .h5ad format All parameters of Anndata.write_h5ad function (https://icb-anndata.readthedocs-hosted.com/en/stable/anndata.AnnData.write_h5ad.html) are available as parameters to this export function and set to defaults. Defaults can be overridden at function call.

exportSCEtoAnnData(
  sce,
  useAssay = "counts",
  outputDir = "./",
  prefix = "sample",
  overwrite = TRUE,
  compression = c("gzip", "lzf", "None"),
  compressionOpts = NULL,
  forceDense = FALSE
)

Arguments

sce: SingleCellExperiment R object to be exported.
useAssay: Character. The name of assay of interests that will be set as the primary matrix of the output AnnData. Default "counts".
outputDir: Path to the directory where .h5ad outputs will be written. Default is the current working directory.
prefix: Prefix to use for the name of the output file. Default "sample".
overwrite: Boolean. Default TRUE.
compression: If output file compression is required, this variable accepts 'gzip', 'lzf' or "None" as inputs. Default "gzip".
compressionOpts: Integer. Sets the compression level
forceDense: Default False Write sparse data as a dense matrix. Refer anndata.write_h5ad documentation for details. Default NULL.

Value

Generates a Python anndata object containing data from inSCE.

Examples

data(sce_chcl, package = "scds")
if (FALSE) {
exportSCEtoAnnData(sce=sce_chcl, compression="gzip")
}