scdisk-class: A disk-based object for single-cell analysis

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

A disk-based object for single-cell analysis

Description

A disk-based object for single-cell analysis

A disk-based object for single-cell analysis

Format

An R6Class object

Super classes

hdf5r::H5RefClass -> hdf5r::H5File -> scdisk

Methods

Public methods

• scdisk$new()

• scdisk$finalizer()

• scdisk$chunk.points()

• scdisk$timestamp()

• scdisk$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()

---

Method new()

Create a new scdisk object

Usage

scdisk$new(
  filename = NULL,
  mode = c("a", "r", "r+", "w", "w-", "x"),
  validate = TRUE,
  ...
)

Arguments

filename

Name of on-disk file to connect to

mode

How to open the file, choose from:

a

Create new or open existing file, allow read and write

r

Open existing file, allow read only

r+

Open existing file, allow read and write

w

Create new file (deleting any existing one), allow read and write

w-, x

Create new file (error if exists), allow read and write

validate

Validate the file upon connection

...

Extra arguments passed to validation routine

---

Method finalizer()

Handle the loss of reference to this scdisk object

Usage

scdisk$finalizer()

---

Method chunk.points()

Generate chunk points for a dataset

Usage

scdisk$chunk.points(
  dataset,
  MARGIN = getOption(x = "SeuratDisk.chunking.MARGIN", default = "largest"),
  csize = NULL
)

Arguments

dataset

Name of dataset

MARGIN

Direction to chunk in; defaults to largest dimension of dataset

csize

Size of chunk; defaults to hdf5r-suggested chunk size

Returns

A matrix where each row is a chunk, column 1 is start points, column 2 is end points

---

Method timestamp()

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

Usage

scdisk$timestamp(
  name = NULL,
  attr = "ts",
  tz = "UTC",
  format = TSFormats(type = "R")
)

Arguments

name

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

attr

Name of attribute to store timestamp ass

tz, format

See Timestamp

Returns

Invisilby returns the object

---

Method last.modified()

Retrieve a timestamp from a dataset or group

Usage

scdisk$last.modified(
  name = NULL,
  attr = "ts",
  locale = TRUE,
  tz = "UTC",
  format = TSFormats(type = "R")
)

Arguments

name

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

attr

Name of attribute to retrieve timestamp from

locale

Change the timestamp of to the timezone of the locale

tz, format

See Timestamp

Returns

A character with the timestamp

See Also

H5File

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