TileDBGroup: TileDB Group Base Class

In TileDB-Inc/tiledbsc: TileDB Single Cell SOMA API

TileDB Group Base Class

Description

Base class for interacting with TileDB groups

Details

Initialization

Upon initialization a new group is created if one does not already exist at the specified uri.

Value

A named list of group members.

The array object.

Super class

tiledbsc::TileDBObject -> TileDBGroup

Public fields

members

Named list of members in the group

Methods

Public methods

• TileDBGroup$new()

• TileDBGroup$print()

• TileDBGroup$group_exists()

• TileDBGroup$tiledb_group()

• TileDBGroup$list_objects()

• TileDBGroup$list_object_uris()

• TileDBGroup$add_member()

• TileDBGroup$remove_member()

• TileDBGroup$count_members()

• TileDBGroup$list_members()

• TileDBGroup$list_member_uris()

• TileDBGroup$get_members()

• TileDBGroup$get_member()

• TileDBGroup$get_metadata()

• TileDBGroup$add_metadata()

• TileDBGroup$clone()

Inherited methods

• tiledbsc::TileDBObject$class()
• tiledbsc::TileDBObject$exists()

---

Method new()

Create a new TileDBGroup object.

Usage

TileDBGroup$new(uri, verbose = TRUE, config = NULL, ctx = NULL)

Arguments

uri

TileDB array URI

verbose

Print status messages

config

optional configuration

ctx

optional tiledb context

---

Method print()

Print summary of the group.

Usage

TileDBGroup$print()

---

Method group_exists()

Check if the group exists.

Usage

TileDBGroup$group_exists()

Returns

TRUE if the group exists, FALSE otherwise.

---

Method tiledb_group()

Return a tiledb_group object

Usage

TileDBGroup$tiledb_group(...)

Arguments

...

Optional arguments to pass to tiledb::tiledb_array()

Returns

A tiledb::tiledb_group object.

---

Method list_objects()

List the TileDB objects within the group.

Usage

TileDBGroup$list_objects(type = NULL)

Arguments

type

The type of object to list, either "ARRAY", or "GROUP". By default all object types are listed.

Returns

A data.frame with columns URI and TYPE.

---

Method list_object_uris()

List URIs for TileDB objects within the group.

Usage

TileDBGroup$list_object_uris(type = NULL, prefix = NULL)

Arguments

type

The type of object to list, either "ARRAY", or "GROUP". By default all object types are listed.

prefix

Filter URIs whose basename contain an optional prefix.

Returns

A character vector of object URIs with names corresponding to the basename of the object.

---

Method add_member()

Add new member to the group.

Usage

TileDBGroup$add_member(object, name = NULL, relative = NULL)

Arguments

object

The TileDBArray or TileDBGroup object to add.

name

The name to use for the member. By default the base name of the object's URI is used.

relative

A logical value indicating whether the new member's URI is relative to the group's URI.

---

Method remove_member()

Remove member from the group.

Usage

TileDBGroup$remove_member(name)

Arguments

name

The name of the member to remove.

---

Method count_members()

Count the number of members in the group.

Usage

TileDBGroup$count_members()

Returns

Integer count of members in the group.

---

Method list_members()

List the members of the group.

Usage

TileDBGroup$list_members(type = NULL)

Arguments

type

The type of member to list, either "ARRAY", or "GROUP". By default all member types are listed.

Returns

A data.frame with columns URI, TYPE, and NAME.

---

Method list_member_uris()

List URIs for group members

Usage

TileDBGroup$list_member_uris(type = NULL, prefix = NULL)

Arguments

type

The type of member to list, either "ARRAY", or "GROUP". By default all member types are listed.

prefix

Filter for members whose name contains an optional prefix.

Returns

A character vector of member URIs, named for the group member

---

Method get_members()

Retrieve arrays within the group that meet the specified criteria.

Usage

TileDBGroup$get_members(type = NULL, prefix = NULL)

Arguments

type

The type of group members to list, either "ARRAY", or "GROUP".

prefix

String prefix to filter the member names.

---

Method get_member()

Retrieve a group member.

Usage

TileDBGroup$get_member(name)

Arguments

name

The name of the array to retrieve.

---

Method get_metadata()

Retrieve metadata from the TileDB group.

Usage

TileDBGroup$get_metadata(key = NULL, prefix = NULL)

Arguments

key

The name of the metadata attribute to retrieve.

prefix

Filter metadata using an optional prefix. Ignored if key is not NULL.

Returns

A list of metadata values.

---

Method add_metadata()

Add list of metadata to the TileDB group.

Usage

TileDBGroup$add_metadata(metadata, prefix = "")

Arguments

metadata

Named list of metadata to add.

prefix

Optional prefix to add to the metadata attribute names.

Returns

NULL

---

Method clone()

The objects of this class are cloneable with this method.

Usage

TileDBGroup$clone(deep = FALSE)

Arguments

deep

Whether to make a deep clone.

TileDB-Inc/tiledbsc documentation built on Aug. 26, 2023, 2:32 p.m.