TileDB Array Base Class

Base class for representing an individual TileDB array. (lifecycle: maturing)

Super class

tiledbsoma::TileDBObject -> TileDBArray

Active bindings

object

Access the underlying TileB object directly (either a tiledb::tiledb_array or tiledb::tiledb_group).

Methods

Public methods

• TileDBArray$open()

• TileDBArray$close()

• TileDBArray$print()

• TileDBArray$tiledb_array()

• TileDBArray$get_metadata()

• TileDBArray$set_metadata()

• TileDBArray$schema()

• TileDBArray$tiledb_schema()

• TileDBArray$dimensions()

• TileDBArray$shape()

• TileDBArray$maxshape()

• TileDBArray$used_shape()

• TileDBArray$non_empty_domain()

• TileDBArray$ndim()

• TileDBArray$attributes()

• TileDBArray$dimnames()

• TileDBArray$attrnames()

• TileDBArray$colnames()

• TileDBArray$index_column_names()

• TileDBArray$clone()

Inherited methods

• tiledbsoma::TileDBObject$class()
• tiledbsoma::TileDBObject$exists()
• tiledbsoma::TileDBObject$initialize()
• tiledbsoma::TileDBObject$is_open()
• tiledbsoma::TileDBObject$mode()
• tiledbsoma::TileDBObject$reopen()

---

Method open()

Open the SOMA object for read or write.

Usage

TileDBArray$open(mode = c("READ", "WRITE"), internal_use_only = NULL)

Arguments

mode

Mode to open in; defaults to READ.

internal_use_only

Character value to signal this is a 'permitted' call, as open() is considered internal and should not be called directly.

Returns

The object, invisibly

---

Method close()

Close the SOMA object.

Usage

TileDBArray$close()

Returns

The object, invisibly

---

Method print()

Print summary of the array. (lifecycle: maturing)

Usage

TileDBArray$print()

---

Method tiledb_array()

Return a TileDBArray object (lifecycle: maturing)

Usage

TileDBArray$tiledb_array(...)

Arguments

...

Optional arguments to pass to tiledb::tiledb_array()

Returns

A tiledb::tiledb_array object.

---

Method get_metadata()

Retrieve metadata from the TileDB array. (lifecycle: maturing)

Usage

TileDBArray$get_metadata(key = NULL)

Arguments

key

The name of the metadata attribute to retrieve.

Returns

A list of metadata values.

---

Method set_metadata()

Add list of metadata to the specified TileDB array. (lifecycle: maturing)

Usage

TileDBArray$set_metadata(metadata)

Arguments

metadata

Named list of metadata to add.

Returns

NULL

---

Method schema()

Retrieve the array schema as an Arrow schema (lifecycle: maturing)

Usage

TileDBArray$schema()

Returns

A arrow::schema object

---

Method tiledb_schema()

Retrieve the array schema as TileDB schema (lifecycle: maturing)

Usage

TileDBArray$tiledb_schema()

Returns

A tiledb::tiledb_array_schema object

---

Method dimensions()

Retrieve the array dimensions (lifecycle: maturing)

Usage

TileDBArray$dimensions()

Returns

A named list of tiledb::tiledb_dim objects

---

Method shape()

Retrieve the shape, i.e. the capacity of each dimension. Attempted reads and writes outside the shape will result in a runtime error: this is the purpose of shape. This will not necessarily match the bounds of occupied cells within the array. Using resize, this may be increased up to the hard limit which maxshape reports. (lifecycle: maturing)

Usage

TileDBArray$shape()

Returns

A named vector of dimension length (and the same type as the dimension)

---

Method maxshape()

Retrieve the hard limit up to which the array may be resized using the resize method. (lifecycle: maturing)

Usage

TileDBArray$maxshape()

Returns

A named vector of dimension length (and the same type as the dimension)

---

Method used_shape()

Retrieve the range of indexes for a dimension that were explicitly written. This method is deprecated as of TileDB-SOMA 1.13, and will be removed in TileDB-SOMA 1.16.

Usage

TileDBArray$used_shape(simplify = FALSE, index1 = FALSE)

Arguments

simplify

Return a vector of bit64::integer64s containing only the upper bounds.

index1

Return the used shape with 1-based indices (0-based indices are returned by default)

Returns

A list containing the lower and upper bounds for the used shape. If simplify = TRUE, returns a vector of only the upper bounds.

---

Method non_empty_domain()

Returns a named list of minimum/maximum pairs, one per index column, which are the smallest and largest values written on that index column.

Usage

TileDBArray$non_empty_domain(index1 = FALSE, max_only = FALSE)

Arguments

index1

Return the non-empty domain with 1-based indices.

max_only

Return only the max value per dimension, and return this as a vector. Names are dropped. (lifecycle: maturing)

Returns

Named list of minimum/maximum values, or integer vector of maximum values.

---

Method ndim()

Retrieve number of dimensions (lifecycle: maturing)

Usage

TileDBArray$ndim()

Returns

A scalar with the number of dimensions

---

Method attributes()

Retrieve the array attributes (lifecycle: maturing)

Usage

TileDBArray$attributes()

Returns

A list of tiledb::tiledb_attr objects

---

Method dimnames()

Retrieve dimension names (lifecycle: maturing)

Usage

TileDBArray$dimnames()

Returns

A character vector with the array's dimension names

---

Method attrnames()

Retrieve attribute names (lifecycle: maturing)

Usage

TileDBArray$attrnames()

Returns

A character vector with the array's attribute names

---

Method colnames()

Retrieve the names of all columns, including dimensions and attributes (lifecycle: maturing)

Usage

TileDBArray$colnames()

Returns

A character vector with the array's column names

---

Method index_column_names()

Retrieve names of index (dimension) columns (lifecycle: maturing)

Usage

TileDBArray$index_column_names()

Returns

A character vector with the array index (dimension) names

---

Method clone()

The objects of this class are cloneable with this method.

Usage

TileDBArray$clone(deep = FALSE)

Arguments

deep

Whether to make a deep clone.