Read a single-cell file (or 10x triplet) into a SingleCellExperiment

Low-level reader: given already-downloaded local file(s), dispatch on format to the appropriate Bioconductor importer and return a SingleCellExperiment (or a Seurat object with as = "Seurat"). Use this for full control; see getGEOSingleCell for the high-level convenience wrapper.

Usage

readGEOSingleCell(x, format = NULL, as = c("SingleCellExperiment", "Seurat"))

Arguments

x

A path to a single file (.h5/.h5ad/.rds), a directory containing a 10x triplet, or a character vector of the triplet files.

format

One of "10x_mtx", "10x_h5", "h5ad", "rds". If NULL (default), guessed from x.

as

Output class, one of "SingleCellExperiment" (default) or "Seurat" (coerced via the Seurat package, an optional dependency).

Value

A SingleCellExperiment, or a Seurat object if as = "Seurat".

Details

Supported formats: "10x_mtx" (a directory, or the matrix/barcodes/ features files, read via TENxIO), "10x_h5" (CellRanger HDF5, TENxIO), "h5ad" (AnnData, anndataR), and "rds" (a saved SingleCellExperiment or Seurat object; detected by class). loom is not supported – read it with LoomExperiment directly.

See also

getGEOSingleCell, geoSingleCellManifest