scfetch (version 0.5.0)

ImportSeurat: 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,
  ...
)

Value

A Seurat object.

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.

Examples

if (FALSE) {
# 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")
}