TENxMatrixSeed-class: TENxMatrixSeed objects

TENxMatrixSeed-classR Documentation

TENxMatrixSeed objects

Description

TENxMatrixSeed is a low-level helper class that is a direct extension of the H5SparseMatrixSeed class. It is used to represent a pointer to an HDF5 sparse matrix that is stored in the CSR/CSC/Yale format ("Compressed Sparse Row") and follows the 10x Genomics convention for storing the dimensions of the matrix.

Note that a TENxMatrixSeed object is not intended to be used directly. Most end users will typically create and manipulate a higher-level TENxMatrix object instead. See ?TENxMatrix for more information.

Usage

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

Arguments

filepath, group

See ?TENxMatrix for a description of these arguments.

Details

A TENxMatrixSeed object supports the same limited set of methods as an H5SparseMatrixSeed object. See ?H5SparseMatrixSeed for the details.

Value

TENxMatrixSeed() returns a TENxMatrixSeed object.

TENxMatrixSeed vs TENxMatrix objects

In order to have access to the full set of operations that are available for DelayedMatrix objects, a TENxMatrixSeed object first needs to be wrapped in a DelayedMatrix object, typically by calling the DelayedArray() constructor on it.

This is what the TENxMatrix() constructor function does.

Note that the result of this wrapping is a TENxMatrix object, which is just a TENxMatrixSeed object wrapped in a DelayedMatrix object.

See Also

  • TENxMatrix objects.

  • H5SparseMatrixSeed objects.

  • The TENxBrainData dataset (in the TENxBrainData package).

  • h5ls to list the content of an HDF5 file.

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"]]

## 'fname' is an HDF5 file. Use h5ls() to list its content:
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, group="mm10")
seed
path(seed)
dim(seed)
is_sparse(seed)
sparsity(seed)

DelayedArray(seed)
stopifnot(class(DelayedArray(seed)) == "TENxMatrix")

Bioconductor/HDF5Array documentation built on Feb. 9, 2024, 2:09 a.m.