Open a SOMA Collection — SOMACollectionOpen • tiledbsoma

Factory function to open a SOMA collection for reading (lifecycle: maturing).

Usage

SOMACollectionOpen(
  uri,
  mode = "READ",
  platform_config = NULL,
  tiledbsoma_ctx = NULL,
  tiledb_timestamp = NULL,
  context = NULL
)

Arguments

uri: URI for the TileDB object.
mode: One of “READ” or “WRITE”.
platform_config: Optional platform configuration.
tiledbsoma_ctx: Optional (DEPRECATED) SOMATileDBContext.
tiledb_timestamp: Optional Datetime (POSIXct) for TileDB timestamp; defaults to the current time. If not NULL, all members accessed through the collection inherit the timestamp.
context: Optional SOMAContext object used for TileDB operations. If a context is not provided, then the default context will be used. Call set_default_context once before other SOMA operations to configure the default context.

Value

A SOMA collection stored at uri opened in mode mode.

Examples

uri <- withr::local_tempfile(pattern = "soma-collection")

(col <- SOMACollectionCreate(uri))
#> <SOMACollection>
#>   uri: /tmp/Rtmpfr8mYm/soma-collection2a7e1ef348d5
col$add_new_sparse_ndarray("sparse", arrow::float64(), shape = c(100L, 100L))
#> <SOMASparseNDArray>
#>   uri: /tmp/Rtmpfr8mYm/soma-collection2a7e1ef348d5/sparse
#>   dimensions: soma_dim_0, soma_dim_1 
#>   attributes: soma_data 
col$close()

(col <- SOMACollectionOpen(uri))
#> <SOMACollection>
#>   uri: /tmp/Rtmpfr8mYm/soma-collection2a7e1ef348d5
col$names()
#> [1] "sparse"