TENxMatrixSeed objects

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.

Examples

## The 1.3 Million Brain Cell Dataset from 10x Genomics is available
## via ExperimentHub:
library(ExperimentHub)
hub <- ExperimentHub()
query(hub, "TENxBrainData")
#> ExperimentHub with 8 records
#> # snapshotDate(): 2025-04-12
#> # $dataprovider: 10X Genomics
#> # $species: Mus musculus
#> # $rdataclass: character
#> # additional mcols(): taxonomyid, genome, description,
#> #   coordinate_1_based, maintainer, rdatadateadded, preparerclass, tags,
#> #   rdatapath, sourceurl, sourcetype 
#> # retrieve records with, e.g., 'object[["EH1039"]]' 
#> 
#>            title                                                            
#>   EH1039 | Brain scRNA-seq data, 'HDF5-based 10X Genomics' format           
#>   EH1040 | Brain scRNA-seq data, 'dense matrix' format                      
#>   EH1041 | Brain scRNA-seq data, sample (column) annotation                 
#>   EH1042 | Brain scRNA-seq data, gene (row) annotation                      
#>   EH1689 | Brain scRNA-seq data 20k subset, 'HDF5-based 10x Genomics' format
#>   EH1690 | Brain scRNA-seq data 20k subset, 'dense matrix' format           
#>   EH1691 | Brain scRNA-seq data 20k subset, sample (column) annotation      
#>   EH1692 | Brain scRNA-seq data 20k subset, gene (row) annotation           
fname <- hub[["EH1039"]]
#> see ?TENxBrainData and browseVignettes('TENxBrainData') for documentation
#> loading from cache

## 'fname' is an HDF5 file. Use h5ls() to list its content:
h5ls(fname)
#>   group       name       otype  dclass        dim
#> 0     /       mm10   H5I_GROUP                   
#> 1 /mm10   barcodes H5I_DATASET  STRING    1306127
#> 2 /mm10       data H5I_DATASET INTEGER 2624828308
#> 3 /mm10 gene_names H5I_DATASET  STRING      27998
#> 4 /mm10      genes H5I_DATASET  STRING      27998
#> 5 /mm10    indices H5I_DATASET INTEGER 2624828308
#> 6 /mm10     indptr H5I_DATASET INTEGER    1306128
#> 7 /mm10      shape H5I_DATASET INTEGER          2

## 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
#> <27998 x 1306127> sparse TENxMatrixSeed object of type "integer":
#> # dirname: /github/home/.cache/R/ExperimentHub
#> # basename: 7b946c52a4b_1039
#> # group: /mm10
path(seed)
#> [1] "/github/home/.cache/R/ExperimentHub/7b946c52a4b_1039"
dim(seed)
#> [1]   27998 1306127
is_sparse(seed)
#> [1] TRUE
sparsity(seed)
#> [1] 0.9282225

DelayedArray(seed)
#> <27998 x 1306127> sparse TENxMatrix object of type "integer":
#>                      AAACCTGAGATAGGAG-1 ... TTTGTCATCTGAAAGA-133
#> ENSMUSG00000051951                    0   .                    0
#> ENSMUSG00000089699                    0   .                    0
#> ENSMUSG00000102343                    0   .                    0
#> ENSMUSG00000025900                    0   .                    0
#> ENSMUSG00000109048                    0   .                    0
#>                ...                    .   .                    .
#> ENSMUSG00000079808                    0   .                    0
#> ENSMUSG00000095041                    1   .                    0
#> ENSMUSG00000063897                    0   .                    0
#> ENSMUSG00000096730                    0   .                    0
#> ENSMUSG00000095742                    0   .                    0
stopifnot(class(DelayedArray(seed)) == "TENxMatrix")