ExportSeurat: Export SeuratObject to Other Formats.

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

Export SeuratObject to Other Formats.

Description

Export SeuratObject to Other Formats.

Usage

ExportSeurat(
  seu.obj,
  assay = NULL,
  reduction = NULL,
  to = c("SCE", "AnnData", "CellDataSet", "cell_data_set", "loom"),
  anndata.file = NULL,
  loom.file = NULL,
  conda.path = NULL,
  ...
)

Arguments

seu.obj	A seurat object.
assay	Which assay to use. Default: NULL (get with DefaultAssay).
reduction	Name of DimReduc to set to main reducedDim in cds.
to	The target format, chosen from "SCE" (SingleCellExperiment), "AnnData", "CellDataSet", "cell_data_set", "loom". Default: "SCE".
anndata.file	File used to save AnnData results. Default: NULL.
loom.file	File used to save loom results. Default: NULL.
conda.path	Conda environment path, used when to is "AnnData". Default: NULL.
...	Parameter for as.SingleCellExperiment, sceasy::convertFormat, as.CellDataSet, as.cell_data_set, SaveLoom, corresponding to to.

Value

Object corresponding to to.

Examples

## Not run: 
library(Seurat)
# export to SingleCellExperiment
sce.obj <- ExportSeurat(seu.obj = pbmc_small, assay = "RNA", to = "SCE")
# export to CellDataSet
cds.obj <- ExportSeurat(seu.obj = pbmc_small, assay = "RNA", reduction = "tsne", to = "CellDataSet")
# export to cell_data_set
cds3.obj <- ExportSeurat(seu.obj = pbmc_small, assay = "RNA", to = "cell_data_set")
# export to AnnData, need users to provide the conda path and the output file
ExportSeurat(
  seu.obj = pbmc_small, assay = "RNA", to = "AnnData", conda.path = "/path/to/anaconda3",
  anndata.file = "/path/to/pbmc_small.h5ad"
)
# export to loom, need users to provide the output file
ExportSeurat(
  seu.obj = pbmc_small, assay = "RNA", to = "loom",
  loom.file = "/path/to/pbmc_small.loom"
)

## End(Not run)

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