An S4 class for a TileDB Array

This class replaces the earlier (and now removed) tiledb_dense and tiledb_sparse and provides equivalent functionality based on a refactored implementation utilising newer TileDB features.

Slots

ctx

A TileDB context object

uri

A character despription with the array URI

is.sparse

A logical value whether the array is sparse or not

attrs

A character vector to select particular column ‘attributes’; default is an empty character vector implying ‘all’ columns, the special value NA_character_ has the opposite effect and selects ‘none’.

extended

A logical value, defaults to TRUE, indicating whether index columns are returned as well.

selected_ranges

An optional list with matrices where each matrix i describes the (min,max) pair of ranges for dimension i

selected_points

An optional list with vectors where each vector i describes the selected points for dimension i

query_layout

An optional character value

datetimes_as_int64

A logical value

encryption_key

A character value

query_condition

A Query Condition object

timestamp_start

A POSIXct datetime variable for the inclusive interval start

timestamp_end

A POSIXct datetime variable for the inclusive interval start

return_as

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’ (where the last two are synomyms); note that ‘data.table’, ‘tibble’ and ‘arrow’ require the respective packages to be installed.

query_statistics

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.

sil

An optional and internal list object with schema information, used for parsing queries.

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

strings_as_factors

An optional logical to convert character columns to factor type

keep_open

An optional logical to not close after read or write

ptr

External pointer to the underlying implementation