Constructs a tiledb_array object backed by a persisted tiledb array uri

tiledb_array returns a new object. This class is experimental.

Usage

tiledb_array(
  uri,
  query_type = c("READ", "WRITE"),
  is.sparse = NA,
  attrs = character(),
  extended = TRUE,
  selected_ranges = list(),
  selected_points = list(),
  query_layout = character(),
  datetimes_as_int64 = FALSE,
  encryption_key = character(),
  query_condition = new("tiledb_query_condition"),
  timestamp_start = as.POSIXct(double(), origin = "1970-01-01"),
  timestamp_end = as.POSIXct(double(), origin = "1970-01-01"),
  return_as = get_return_as_preference(),
  query_statistics = FALSE,
  strings_as_factors = getOption("stringsAsFactors", FALSE),
  keep_open = FALSE,
  sil = list(),
  dumpbuffers = character(),
  buffers = list(),
  ctx = tiledb_get_context(),
  as.data.frame = FALSE
)

tiledb_dense(...)

tiledb_sparse(...)

Arguments

uri: uri path to the tiledb dense array
query_type: optionally loads the array in "READ" or "WRITE" only modes.
is.sparse: optional logical switch, defaults to "NA" letting array determine it
attrs: optional character vector to select attributes, default is empty implying all are selected, the special value NA_character_ has the opposite effect and implies no attributes are returned.
extended: optional logical switch selecting wide ‘data.frame’ format, defaults to TRUE
selected_ranges: optional A list with matrices where each matrix i describes the (min,max) pair of ranges selected for dimension i
selected_points: optional A list with vectors where each vector i describes the points selected in dimension i
query_layout: optional A value for the TileDB query layout, defaults to an empty character variable indicating no special layout is set
datetimes_as_int64: optional A logical value selecting date and datetime value representation as ‘raw’ integer64 and not as Date, POSIXct or nanotime objects.
encryption_key: optional A character value with an AES-256 encryption key in case the array was written with encryption.
query_condition: optional tiledb_query_condition object, by default uninitialized without a condition; this functionality requires TileDB 2.3.0 or later
timestamp_start: optional A POSIXct Datetime value determining the inclusive time point at which the array is to be openened. No fragments written earlier will be considered.
timestamp_end: optional A POSIXct Datetime value determining the inclusive time point until which the array is to be openened. No fragments written earlier later be considered.
return_as: optional A character value with the desired tiledb_array conversion, permitted values are ‘asis’ (default, returning a list of columns), ‘array’, ‘matrix’,‘data.frame’, ‘data.table’, ‘tibble’, ‘arrow_table’, or ‘arrow’ (as an alias for ‘arrow_table’; here ‘data.table’, ‘tibble’ and ‘arrow’ require the respective packages to be installed. The existing as.* arguments take precedent over this.
query_statistics: optional A logical value, defaults to ‘FALSE’; if ‘TRUE’ the query statistics are returned (as a JSON string) via the attribute ‘query_statistics’ of the return object.
strings_as_factors: An optional logical to convert character columns to factor type; defaults to the value of getOption("stringsAsFactors", FALSE).
keep_open: An optional logical to not close after read or write
sil: optional A list, by default empty to store schema information when query objects are parsed.
dumpbuffers: An optional character variable with a directory name (relative to /dev/shm) for writing out results buffers (for internal use / testing)
buffers: An optional list with full pathnames of shared memory buffers to read data from
ctx: optional tiledb_ctx
as.data.frame: An optional deprecated alternative to return_as="data.frame" which has been deprecated and removed, but is still used in one BioConductor package; this argument will be removed once the updated package has been released.
...: Used as a pass-through for tiledb_dense and tiledb_sparse aliasing

Value

tiledb_array object