TENxMatrixSeed-class {HDF5Array}R Documentation

TENxMatrixSeed objects

Description

TENxMatrixSeed is a low-level helper class for representing a pointer to an HDF5-based sparse matrix like one used by 10x Genomics for the 1.3 Million Brain Cell Dataset. TENxMatrixSeed objects are not intended to be used directly. Most end-users should create and manipulate TENxMatrix objects instead. See ?TENxMatrix for more information.

Usage

## Constructor function:
TENxMatrixSeed(filepath, group="mm10")

Arguments

filepath, group

See ?TENxMatrix for a description of these arguments.

Details

No operation can be performed directly on a TENxMatrixSeed object. It first needs to be wrapped in a DelayedMatrix object. The result of this wrapping is a TENxMatrix object (a TENxMatrix object is just a TENxMatrixSeed object wrapped in a DelayedMatrix object).

Value

TENxMatrixSeed() returns a TENxMatrixSeed object.

See ?TENxMatrix for the value returned by sparsity() and extractNonzeroDataByCol().

See Also

Examples

## The 1.3 Million Brain Cell Dataset from 10x Genomics is available
## via ExperimentHub:
library(ExperimentHub)
hub <- ExperimentHub()
query(hub, "TENxBrainData")
fname <- hub[["EH1039"]]

## The structure of this HDF5 file can be seen using the h5ls() command
## from the rhdf5 package:
library(rhdf5)
h5ls(fname)

## The 1.3 Million Brain Cell Dataset is represented by the "mm10"
## group. We point the TENxMatrixSeed() constructor to this group
## to create a TENxMatrixSeed object representing the dataset:
x <- TENxMatrixSeed(fname, "mm10")
x
path(x)
dim(x)
sparsity(x)

[Package HDF5Array version 1.12.2 Index]