exportSCEtoAnnData: Export a SingleCellExperiment R object as Python annData...

In singleCellTK: Comprehensive and Interactive Analysis of Single Cell RNA-Seq Data

Description

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.

Usage

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

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' or 'lzf' as inputs. Default None.
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")
## Not run: 
exportSCEtoAnnData(sce=sce_chcl, compression="gzip")

## End(Not run)

singleCellTK documentation built on Nov. 8, 2020, 5:21 p.m.