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SOMA Example Datasets

Source: R/datasets.R
example-datasets.Rd

Access example SOMA objects bundled with the tiledbsoma package.

Use list_datasets() to list the available datasets and load_dataset() to load a dataset into memory using the appropriate SOMA class. The extract_dataset() method returns the path to the extracted dataset without loading it into memory.

Usage

list_datasets()

extract_dataset(name, dir = tempdir())

load_dataset(name, dir = tempdir(), tiledbsoma_ctx = NULL)

Arguments

name

The name of the dataset.

dir

The directory where the dataset will be extracted to (default: tempdir()).

tiledbsoma_ctx

Optional TileDB ‘Context’ object, defaults to NULL

Value

  • list_datasets() returns a character vector of the available datasets.

  • extract_dataset() returns the path to the extracted dataset.

  • load_dataset() returns a SOMA object.

Details

The SOMA objects are stored as tar.gz files in the package's extdata directory. Calling load_dataset() extracts the tar.gz file to the specified dir, inspects its metadata to determine the appropriate SOMA class to instantiate, and returns the SOMA object.

Examples

soma_pbmc_small <- load_dataset("soma-exp-pbmc-small")