SCELoom: Data Format Conversion between SingleCellExperiment and loom.

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

Data Format Conversion between SingleCellExperiment and loom.

Description

Data Format Conversion between SingleCellExperiment and loom.

Usage

SCELoom(
  from = c("SingleCellExperiment", "loom"),
  to = c("loom", "SingleCellExperiment"),
  sce = NULL,
  loom.file = NULL,
  ...
)

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: loom.
sce	The SingleCellExperiment object to convert. Default: NULL.
loom.file	File used to save or contains loom results. Default: NULL.
...	Parameters for sceasy::convertFormat and sceasy::convertFormat.

Value

NULL or SingleCellExperiment.

Examples

## Not run: 
# convert from loom to SingleCellExperiment, need users to provide the loom file
sce.obj <- SCELoom(
  from = "loom", to = "SingleCellExperiment",
  loom.file = "path/to/loom"
)
# convert from SingleCellExperiment to loom, need users to provide the loom file
SCELoom(
  from = "SingleCellExperiment", to = "loom", sce = sce.obj,
  loom.file = "path/to/loom"
)

## End(Not run)

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