HDF5Array: TENxMatrixSeed-class – R documentation

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TENxMatrixSeed-class

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().

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:
seed <- TENxMatrixSeed(fname, "mm10")
seed
path(seed)
dim(seed)
sparsity(seed)

HDF5Array

HDF5 backend for DelayedArray objects

v1.18.1

Artistic-2.0

Authors

Hervé Pagès

Initial release