Factory function to open a SOMA data frame for reading (lifecycle: maturing).
Usage
SOMADataFrameOpen(
uri,
mode = "READ",
platform_config = NULL,
tiledbsoma_ctx = NULL,
tiledb_timestamp = NULL,
soma_context = 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.
- soma_context
A SOMA context as created by
soma_context().
Value
A SOMA data frame stored at
uri opened in mode mode.
Examples
uri <- withr::local_tempfile(pattern = "soma-data-frame")
df <- data.frame(
soma_joinid = bit64::seq.integer64(0L, 99L),
group = sample(factor(c("g1", "g2")), size = 100L, replace = TRUE),
nCount = stats::rbinom(100L, 10L, 0.3)
)
(sch <- arrow::infer_schema(df))
#> Schema
#> soma_joinid: int64
#> group: dictionary<values=string, indices=int8>
#> nCount: int32
(sdf <- SOMADataFrameCreate(uri, sch, domain = list(soma_joinid = c(0, 100))))
#> <SOMADataFrame>
#> uri: /tmp/RtmpjD0Pq2/soma-data-frame2709598d69b0
#> dimensions: soma_joinid
#> attributes: group, nCount
sdf$write(arrow::as_arrow_table(df, schema = sch))
sdf$close()
(sdf <- SOMADataFrameOpen(uri))
#> <SOMADataFrame>
#> uri: /tmp/RtmpjD0Pq2/soma-data-frame2709598d69b0
#> dimensions: soma_joinid
#> attributes: group, nCount
head(as.data.frame(sdf$read()$concat()))
#> soma_joinid group nCount
#> 1 0 g2 0
#> 2 1 g1 4
#> 3 2 g2 6
#> 4 3 g2 3
#> 5 4 g1 2
#> 6 5 g2 1