SOMA Array Base Class

SOMA Array Base Class

SOMA Array Base Class

Details

Virtual base class to add array-specific functionality to the SOMAObject class (lifecycle: maturing).

See also

Derived classes: SOMADataFrame, SOMANDArrayBase

Super class

tiledbsoma::SOMAObject -> SOMAArrayBase

Methods

Public methods

• SOMAArrayBase$open()

• SOMAArrayBase$close()

• SOMAArrayBase$allows_duplicates()

• SOMAArrayBase$is_sparse()

• SOMAArrayBase$schema()

• SOMAArrayBase$attributes()

• SOMAArrayBase$attrnames()

• SOMAArrayBase$dimensions()

• SOMAArrayBase$dimnames()

• SOMAArrayBase$colnames()

• SOMAArrayBase$index_column_names()

• SOMAArrayBase$shape()

• SOMAArrayBase$maxshape()

• SOMAArrayBase$non_empty_domain()

• SOMAArrayBase$ndim()

• SOMAArrayBase$print()

• SOMAArrayBase$clone()

Inherited methods

• tiledbsoma::SOMAObject$class()
• tiledbsoma::SOMAObject$exists()
• tiledbsoma::SOMAObject$get_metadata()
• tiledbsoma::SOMAObject$initialize()
• tiledbsoma::SOMAObject$is_open()
• tiledbsoma::SOMAObject$mode()
• tiledbsoma::SOMAObject$reopen()
• tiledbsoma::SOMAObject$set_metadata()

---

Method open()

Open the SOMA object for read or write.

Note: open() is considered internal and should not be called directly; use factory functions (eg. SOMASparseNDArrayOpen()) instead.

Usage

SOMAArrayBase$open(mode = c("READ", "WRITE", "DELETE"))

Arguments

mode

Mode to open the object in.

Returns

Return sself.

---

Method close()

Close the SOMA array.

Usage

SOMAArrayBase$close()

Returns

Invisibly returns self.

---

Method allows_duplicates()

Does an array allow duplicates?

Usage

SOMAArrayBase$allows_duplicates()

Returns

TRUE if the underlying TileDB array allows duplicates; otherwise FALSE.

---

Method is_sparse()

Is an array sparse?

Usage

SOMAArrayBase$is_sparse()

Returns

TRUE if the underlying TileDB array is sparse; otherwise FALSE.

---

Method schema()

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

Usage

SOMAArrayBase$schema()

Returns

An Arrow Schema object.

---

Method attributes()

Retrieve the array attributes.

Usage

SOMAArrayBase$attributes()

Returns

A named list of array attributes; each entry contains the following named entries:

• “name”: name of the attribute.

• “type”: datatype of the attribute.

• “ncells”: number of values per dimension cell.

• “nullable”: is the attribute nullable.

• “filter_list”: a list with filter information; this list contains the following entries:

  • “filter_type”

  • “compression_level”

  • “bit_width”

  • “positive_delta”

  • “float_bytewidth”

  • “float_factor”

  • “float_offset”

---

Method attrnames()

Retrieve attribute names (lifecycle: maturing).

Usage

SOMAArrayBase$attrnames()

Returns

A character vector with the array's attribute names.

---

Method dimensions()

Retrieve the array dimensions (lifecycle: maturing)

Usage

SOMAArrayBase$dimensions()

Returns

A named list of array dimensions; each entry contains the following named entries:

• “name”: name of the dimension.

• “type”: datatype of the dimension.

• “ncells”: number of values per dimension cell.

• “domain”: domain of the dimension.

• “tile”: tile of the dimension.

• “filter_list”: a list with filter information; this list contains the following entries:

  • “filter_type”

  • “compression_level”

  • “bit_width”

  • “positive_delta”

  • “float_bytewidth”

  • “float_factor”

  • “float_offset”

---

Method dimnames()

Retrieve dimension names (lifecycle: maturing).

Usage

SOMAArrayBase$dimnames()

Returns

A character vector with the array's dimension names.

---

Method colnames()

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

Usage

SOMAArrayBase$colnames()

Returns

A character vector with the array's column names.

---

Method index_column_names()

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

Usage

SOMAArrayBase$index_column_names()

Returns

A character vector with the array index (dimension) names

---

Method shape()

Retrieve the shape, i.e. the capacity of each dimension Attempted reads and writes outside the shape will result in a run-time 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

SOMAArrayBase$shape()

Returns

A named vector of dimension length and of 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

SOMAArrayBase$maxshape()

Returns

A named vector of dimension length and of the same type as the dimension.

---

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

SOMAArrayBase$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

SOMAArrayBase$ndim()

Returns

A scalar with the number of dimensions.

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Method print()

Print-friendly representation of the object.

Usage

SOMAArrayBase$print()

Returns

Invisibly returns self.

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Method clone()

The objects of this class are cloneable with this method.

Usage

SOMAArrayBase$clone(deep = FALSE)

Arguments

deep

Whether to make a deep clone.