ImportSeurat: Convert Other Formats to SeuratObject.

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

Convert Other Formats to SeuratObject.

Description

Convert Other Formats to SeuratObject.

Usage

ImportSeurat(
  obj = NULL,
  assay = "RNA",
  from = c("SCE", "AnnData", "CellDataSet", "cell_data_set", "loom"),
  count.assay = "counts",
  data.assay = "logcounts",
  slot = "counts",
  anndata.file = NULL,
  loom.file = NULL,
  conda.path = NULL,
  ...
)

Arguments

obj	Other formats object (eg: SingleCellExperiment, CellDataSet). Default: NULL (used when from is "AnnData").
assay	Assay name to store expression matrices in SeuratObject. Default: RNA.
from	The source formats, chosen from "SCE" (SingleCellExperiment), "AnnData", "CellDataSet", "cell_data_set". Default: "SCE".
count.assay	The assay of source formats to save raw counts, used when from is "SCE" or cell_data_set. Default: counts.
data.assay	The assay of source formats to save log transformed counts, used when from is "SCE" or cell_data_set. Default: logcounts.
slot	Slot to store expression data as, used when from is "CellDataSet". Default: counts.
anndata.file	The file contains AnnData. Default: NULL.
loom.file	The file contains loom. Default: NULL.
conda.path	Conda environment path, used when from is "AnnData". Default: NULL.
...	Parameter for as.Seurat, sceasy::convertFormat, as.Seurat, as.Seurat, as.Seurat, corresponding to from.

Value

A Seurat object.

Examples

## Not run: 
# import data from SingleCellExperiment
seu.obj <- ImportSeurat(
  obj = sce.obj, from = "SCE", count.assay = "counts",
  data.assay = "logcounts", assay = "RNA"
)
# import data from CellDataSet
seu.obj <- ImportSeurat(obj = cds.obj, from = "CellDataSet", count.assay = "counts", assay = "RNA")
# import data from cell_data_set
seu.obj <- ImportSeurat(
  obj = sce.obj, from = "cell_data_set", count.assay = "counts",
  data.assay = "logcounts", assay = "RNA"
)
# import data from AnnData, need users to provide the file for conversion
seu.obj <- ImportSeurat(anndata.file = "path/to/h5ad", from = "AnnData", assay = "RNA")
# import data from loom, need users to provide the file for conversion
seu.obj <- ImportSeurat(loom.file = "path/to/loom", from = "loom")

## End(Not run)

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