SCEAnnData: Data Format Conversion between SingleCellExperiment and...

In scfetch: Access and Format Single-Cell RNA-Seq Datasets from Public Resources

Data Format Conversion between SingleCellExperiment and AnnData.

Description

Data Format Conversion between SingleCellExperiment and AnnData.

Usage

SCEAnnData(
  from = c("SingleCellExperiment", "AnnData"),
  to = c("AnnData", "SingleCellExperiment"),
  sce = NULL,
  anndata.file = NULL,
  slot.name = "counts",
  ...
)

Arguments

from	The source data format to convert, chosen from SingleCellExperiment and AnnData. Default: SingleCellExperiment.
to	The target data format to convert, chosen from AnnData and SingleCellExperiment. Default: AnnData.
sce	The SingleCellExperiment object to convert. Default: NULL.
anndata.file	File used to save or contains AnnData results. Default: NULL.
slot.name	Slot name used to save count matrix, used when converting from AnnData to SingleCellExperiment. Default: counts.
...	Parameters for writeH5AD and readH5AD.

Value

NULL or SingleCellExperiment.

Examples

## Not run: 
library(scRNAseq)
seger <- SegerstolpePancreasData()
SCEAnnData(from = "SingleCellExperiment", to = "AnnData", sce = seger, X_name = "counts")
# need users to provide the output file
sce <- SCEAnnData(
  from = "AnnData", to = "SingleCellExperiment",
  anndata.file = "path/to/seger.h5ad"
)

## End(Not run)

scfetch documentation built on Nov. 22, 2023, 1:09 a.m.