A disk-based object for single-cell analysis
A disk-based object for single-cell analysis
An R6Class
object
hdf5r::H5RefClass
-> hdf5r::H5File
-> scdisk
Inherited methods
new()
Create a new scdisk
object
scdisk$new( filename = NULL, mode = c("a", "r", "r+", "w", "w-", "x"), validate = TRUE, ... )
filename
Name of on-disk file to connect to
mode
How to open the file, choose from:
Create new or open existing file, allow read and write
Open existing file, allow read only
Open existing file, allow read and write
Create new file (deleting any existing one), allow read and write
Create new file (error if exists), allow read and write
validate
Validate the file upon connection
...
Extra arguments passed to validation routine
finalizer()
Handle the loss of reference to this scdisk
object
scdisk$finalizer()
chunk.points()
Generate chunk points for a dataset
scdisk$chunk.points( dataset, MARGIN = getOption(x = "SeuratDisk.chunking.MARGIN", default = "largest"), csize = NULL )
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
A matrix where each row is a chunk, column 1 is start points, column 2 is end points