R/exportSCEtoAnndata.R
exportSCEtoAnnData.Rd
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 )
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 |
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 |
overwrite | Boolean. Default |
compression | If output file compression is required, this variable accepts
'gzip', 'lzf' or "None" as inputs. Default |
compressionOpts | Integer. Sets the compression level |
forceDense | Default |
Generates a Python anndata object containing data from inSCE
.
data(sce_chcl, package = "scds") if (FALSE) { exportSCEtoAnnData(sce=sce_chcl, compression="gzip") }