SOMA Example Datasets — example-datasets • tiledbsoma

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() function 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, which 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

list_datasets()
#> [1] "soma-dataframe-pbmc3k-processed-obs" "soma-exp-pbmc-small-pre-1.15"       
#> [3] "soma-exp-pbmc-small"                

dir <- withr::local_tempfile(pattern = "pbmc-small")
dir.create(dir, recursive = TRUE)
dest <- extract_dataset("soma-exp-pbmc-small", dir)
list.files(dest)
#> [1] "__group"            "__meta"             "__tiledb_group.tdb"
#> [4] "ms"                 "obs"                "uns"               
dir <- withr::local_tempfile(pattern = "pbmc_small")
dir.create(dir, recursive = TRUE)
(exp <- load_dataset("soma-exp-pbmc-small", dir))
#> <SOMAExperiment>
#>   uri: /tmp/RtmpzG0UPS/pbmc_small29d25fbd91ef/soma-exp-pbmc-small