Open a SOMA Object — SOMAOpen • tiledbsoma

Utility function to open the corresponding SOMA object given a URI (lifecycle: maturing).

Usage

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

Arguments

uri: URI for the TileDB object.
mode: One of “READ” or “WRITE”
platform_config: Optional platform configuration.
tiledbsoma_ctx: Optional 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.

Value

A SOMA object

Examples

dir <- withr::local_tempfile(pattern = "soma-open")
dir.create(dir, recursive = TRUE)

uri <- extract_dataset("soma-exp-pbmc-small", dir)
(exp <- SOMAOpen(uri))
#> <SOMAExperiment>
#>   uri: /tmp/RtmpzG0UPS/soma-open29d26f64b1a7/soma-exp-pbmc-small


uri <- extract_dataset("soma-dataframe-pbmc3k-processed-obs", dir)
(obs <- SOMAOpen(uri))
#> <SOMADataFrame>
#>   uri: /tmp/RtmpzG0UPS/soma-open29d26f64b1a7/soma-dataframe-pbmc3k-processed-obs
#>   dimensions: soma_joinid 
#>   attributes: orig.ident, nCount_RNA, nFeature_RNA, seurat_annotations, percent.mt, RNA_snn...