loom-class: A class for connections to loom files

In mojaveazure/seurat-disk: Interfaces for HDF5-Based Single Cell File Formats

A class for connections to loom files

Description

A class for connections to loom files

A class for connections to loom files

Format

An R6Class object

Super classes

hdf5r::H5RefClass -> hdf5r::H5File -> SeuratDisk::scdisk -> loom

Methods

Public methods

• loom$add_attribute()

• loom$add_graph()

• loom$add_layer()

• loom$version()

• loom$timestamp()

• loom$last.modified()

Inherited methods

• hdf5r::H5RefClass$close()
• hdf5r::H5RefClass$dec_ref()
• hdf5r::H5RefClass$get_file_id()
• hdf5r::H5RefClass$get_obj_type()
• hdf5r::H5RefClass$get_ref()
• hdf5r::H5RefClass$inc_ref()
• hdf5r::H5RefClass$methods()
• hdf5r::H5File$attr_delete()
• hdf5r::H5File$attr_delete_by_idx()
• hdf5r::H5File$attr_delete_by_name()
• hdf5r::H5File$attr_exists()
• hdf5r::H5File$attr_exists_by_name()
• hdf5r::H5File$attr_get_number()
• hdf5r::H5File$attr_info_by_idx()
• hdf5r::H5File$attr_info_by_name()
• hdf5r::H5File$attr_name_by_idx()
• hdf5r::H5File$attr_open()
• hdf5r::H5File$attr_open_by_idx()
• hdf5r::H5File$attr_open_by_name()
• hdf5r::H5File$attr_rename()
• hdf5r::H5File$attr_rename_by_name()
• hdf5r::H5File$close_all()
• hdf5r::H5File$commit()
• hdf5r::H5File$create_attr()
• hdf5r::H5File$create_attr_by_name()
• hdf5r::H5File$create_dataset()
• hdf5r::H5File$create_group()
• hdf5r::H5File$create_reference()
• hdf5r::H5File$exists()
• hdf5r::H5File$file_info()
• hdf5r::H5File$flush()
• hdf5r::H5File$get_filename()
• hdf5r::H5File$get_filesize()
• hdf5r::H5File$get_intent()
• hdf5r::H5File$get_obj_count()
• hdf5r::H5File$get_obj_ids()
• hdf5r::H5File$get_obj_name()
• hdf5r::H5File$group_info()
• hdf5r::H5File$group_info_by_idx()
• hdf5r::H5File$group_info_by_name()
• hdf5r::H5File$link()
• hdf5r::H5File$link_copy_from()
• hdf5r::H5File$link_copy_to()
• hdf5r::H5File$link_create_external()
• hdf5r::H5File$link_create_hard()
• hdf5r::H5File$link_create_soft()
• hdf5r::H5File$link_delete()
• hdf5r::H5File$link_delete_by_idx()
• hdf5r::H5File$link_exists()
• hdf5r::H5File$link_info()
• hdf5r::H5File$link_info_by_idx()
• hdf5r::H5File$link_move_from()
• hdf5r::H5File$link_move_to()
• hdf5r::H5File$link_name_by_idx()
• hdf5r::H5File$link_value()
• hdf5r::H5File$link_value_by_idx()
• hdf5r::H5File$ls()
• hdf5r::H5File$mount()
• hdf5r::H5File$obj_copy_from()
• hdf5r::H5File$obj_copy_to()
• hdf5r::H5File$obj_info()
• hdf5r::H5File$obj_info_by_idx()
• hdf5r::H5File$obj_info_by_name()
• hdf5r::H5File$open()
• hdf5r::H5File$open_by_idx()
• hdf5r::H5File$path_valid()
• hdf5r::H5File$print()
• hdf5r::H5File$unmount()
• SeuratDisk::scdisk$chunk.points()
• SeuratDisk::scdisk$finalizer()
• SeuratDisk::scdisk$initialize()

---

Method add_attribute()

Add an attribute

Usage

loom$add_attribute(x, name, type = c("global", "row", "col"))

Arguments

x

Object to add as an attribute

name

Name to store attribute as

type

Type of attribute to add

---

Method add_graph()

Add a graph

Usage

loom$add_graph(x, name, type = c("col", "row"), verbose = TRUE)

Arguments

x

...

name

...

type

...

verbose

...

---

Method add_layer()

Add a layer to this loom file

Usage

loom$add_layer(x, name, transpose = TRUE, verbose = TRUE)

Arguments

x

An object to save as a layer

name

Name to store layer as

transpose

...

verbose

...

Returns

Invisibly returns NULL

---

Method version()

Get version information

Usage

loom$version()

Returns

A numeric_version object with the loom specification version information

---

Method timestamp()

Add a timestamp to a dataset or group as an HDF5 attribute

Usage

loom$timestamp(name = NULL)

Arguments

name

Name of dataset or group to add timestamp to; if NULL, timestamps the file as a whole

Returns

Invisibly returns the object

---

Method last.modified()

Retrieve a timestamp from a dataset or group

Usage

loom$last.modified(name = NULL, locale = FALSE)

Arguments

name

Name of dataset or group to retrieve timestamp from; if NULL, retrieves timestamp from at the file-level

locale

Change the timestamp of to the timezone of the locale

Returns

A character with the timestamp

See Also

H5File

mojaveazure/seurat-disk documentation built on Nov. 5, 2023, 9:40 a.m.