exportSCEtoAnnData {singleCellTK} | R Documentation |
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") ## Not run: exportSCEtoAnnData(sce=sce_chcl, compression="gzip") ## End(Not run)