A disk-based object for single-cell analysis

A disk-based object for single-cell analysis

Format

An R6Class object

See also

Super classes

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

Methods

Public methods

Inherited methods

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