Factory function to open a SOMA experiment for reading (lifecycle: maturing).
Usage
SOMAExperimentOpen(
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 experiment stored at
uri opened in mode mode.
Examples
uri <- withr::local_tempfile(pattern = "soma-experiment")
obs <- data.frame(
soma_joinid = bit64::seq.integer64(0L, 99L),
obs_id = paste0("cell_", seq_len(100L))
)
sch <- arrow::infer_schema(obs)
(exp <- SOMAExperimentCreate(uri))
#> <SOMAExperiment>
#> uri: /tmp/RtmpzG0UPS/soma-experiment29d27e80979d
sdf <- exp$add_new_dataframe(
"obs",
sch,
"soma_joinid",
list(soma_joinid = c(0, 100))
)
sdf$write(arrow::as_arrow_table(obs, schema = sch))
sdf$close()
exp$close()
(exp <- SOMAExperimentOpen(uri))
#> <SOMAExperiment>
#> uri: /tmp/RtmpzG0UPS/soma-experiment29d27e80979d
exp$obs
#> <SOMADataFrame>
#> uri: file:///tmp/RtmpzG0UPS/soma-experiment29d27e80979d/obs
#> dimensions: soma_joinid
#> attributes: obs_id