# HDF5 backend for DelayedArray objects

## Documentation for package ‘HDF5Array’ version 1.29.3

- DESCRIPTION file.
- Package NEWS.

## Help Pages

A C D E G H I L M O P Q R S T U W

## -- A --

appendDatasetCreationToHDF5DumpLog | HDF5 dump management

## -- C --

character_OR_H5File | H5File objects
character_OR_H5File-class | H5File objects
chunkdim-method | H5SparseMatrixSeed objects
chunkdim-method | HDF5ArraySeed objects
chunkdim-method | ReshapedHDF5ArraySeed objects
chunkdim-method | Write an array-like object to an HDF5 file
chunkdim-method | Write a matrix-like object as an HDF5-based sparse matrix
class:character_OR_H5File | H5File objects
class:CSC_H5ADMatrixSeed | H5ADMatrixSeed objects
class:CSC_H5SparseMatrixSeed | H5SparseMatrixSeed objects
class:CSR_H5ADMatrixSeed | H5ADMatrixSeed objects
class:CSR_H5SparseMatrixSeed | H5SparseMatrixSeed objects
class:Dense_H5ADMatrixSeed | H5ADMatrixSeed objects
class:H5ADMatrix | h5ad central matrices (or matrices in the /layers group) as DelayedMatrix objects
class:H5ADMatrixSeed | H5ADMatrixSeed objects
class:H5DSetDescriptor | H5File objects
class:H5File | H5File objects
class:H5FileID | H5File objects
class:H5SparseMatrix | HDF5 sparse matrices as DelayedMatrix objects
class:H5SparseMatrixSeed | H5SparseMatrixSeed objects
class:HDF5Array | HDF5 datasets as DelayedArray objects
class:HDF5ArraySeed | HDF5ArraySeed objects
class:HDF5Matrix | HDF5 datasets as DelayedArray objects
class:HDF5RealizationSink | Write an array-like object to an HDF5 file
class:ReshapedHDF5Array | Virtually reshaped HDF5 datasets as DelayedArray objects
class:ReshapedHDF5ArraySeed | ReshapedHDF5ArraySeed objects
class:ReshapedHDF5Matrix | Virtually reshaped HDF5 datasets as DelayedArray objects
class:TENxMatrix | 10x Genomics datasets as DelayedMatrix objects
class:TENxMatrixSeed | TENxMatrixSeed objects
class:TENxRealizationSink | Write a matrix-like object as an HDF5-based sparse matrix
close-method | Write a matrix-like object as an HDF5-based sparse matrix
close.H5File | H5File objects
close.H5FileID | H5File objects
coerce-method | h5ad central matrices (or matrices in the /layers group) as DelayedMatrix objects
coerce-method | H5File objects
coerce-method | HDF5 sparse matrices as DelayedMatrix objects
coerce-method | H5SparseMatrixSeed objects
coerce-method | HDF5 datasets as DelayedArray objects
coerce-method | Virtually reshaped HDF5 datasets as DelayedArray objects
coerce-method | 10x Genomics datasets as DelayedMatrix objects
coerce-method | Write an array-like object to an HDF5 file
coerce-method | Write a matrix-like object as an HDF5-based sparse matrix
CSC_H5ADMatrixSeed | H5ADMatrixSeed objects
CSC_H5ADMatrixSeed-class | H5ADMatrixSeed objects
CSC_H5SparseMatrixSeed | H5SparseMatrixSeed objects
CSC_H5SparseMatrixSeed-class | H5SparseMatrixSeed objects
CSR_H5ADMatrixSeed | H5ADMatrixSeed objects
CSR_H5ADMatrixSeed-class | H5ADMatrixSeed objects
CSR_H5SparseMatrixSeed | H5SparseMatrixSeed objects
CSR_H5SparseMatrixSeed-class | H5SparseMatrixSeed objects

## -- D --

DelayedArray-method | h5ad central matrices (or matrices in the /layers group) as DelayedMatrix objects
DelayedArray-method | HDF5 sparse matrices as DelayedMatrix objects
DelayedArray-method | HDF5 datasets as DelayedArray objects
DelayedArray-method | Virtually reshaped HDF5 datasets as DelayedArray objects
DelayedArray-method | 10x Genomics datasets as DelayedMatrix objects
Dense_H5ADMatrixSeed | H5ADMatrixSeed objects
Dense_H5ADMatrixSeed-class | H5ADMatrixSeed objects
destroy_H5DSetDescriptor | H5File objects
dim-method | H5SparseMatrixSeed objects
dim-method | HDF5ArraySeed objects
dim-method | ReshapedHDF5ArraySeed objects
dimnames-method | H5ADMatrixSeed objects
dimnames-method | H5SparseMatrixSeed objects
dimnames-method | HDF5ArraySeed objects
dimnames-method | Write an array-like object to an HDF5 file
dimnames-method | Write a matrix-like object as an HDF5-based sparse matrix
dump-management | HDF5 dump management

## -- E --

extractNonzeroDataByCol | H5SparseMatrixSeed objects
extractNonzeroDataByCol-method | h5ad central matrices (or matrices in the /layers group) as DelayedMatrix objects
extractNonzeroDataByCol-method | HDF5 sparse matrices as DelayedMatrix objects
extractNonzeroDataByCol-method | H5SparseMatrixSeed objects
extractNonzeroDataByCol-method | 10x Genomics datasets as DelayedMatrix objects
extractNonzeroDataByRow | H5SparseMatrixSeed objects
extractNonzeroDataByRow-method | h5ad central matrices (or matrices in the /layers group) as DelayedMatrix objects
extractNonzeroDataByRow-method | HDF5 sparse matrices as DelayedMatrix objects
extractNonzeroDataByRow-method | H5SparseMatrixSeed objects
extract_array-method | H5SparseMatrixSeed objects
extract_array-method | HDF5ArraySeed objects
extract_array-method | ReshapedHDF5ArraySeed objects

## -- G --

getHDF5DumpChunkDim | HDF5 dump management
getHDF5DumpChunkLength | HDF5 dump management
getHDF5DumpChunkShape | HDF5 dump management
getHDF5DumpCompressionLevel | HDF5 dump management
getHDF5DumpDir | HDF5 dump management
getHDF5DumpFile | HDF5 dump management
getHDF5DumpName | HDF5 dump management
get_h5dimnames | Write/read the dimnames of an HDF5 dataset
get_h5mread_returned_type | An alternative to 'rhdf5::h5read'

## -- H --

H5ADMatrix | h5ad central matrices (or matrices in the /layers group) as DelayedMatrix objects
H5ADMatrix-class | h5ad central matrices (or matrices in the /layers group) as DelayedMatrix objects
H5ADMatrixSeed | H5ADMatrixSeed objects
H5ADMatrixSeed-class | H5ADMatrixSeed objects
H5DSetDescriptor | H5File objects
H5DSetDescriptor-class | H5File objects
H5File | H5File objects
H5File-class | H5File objects
H5FileID | H5File objects
H5FileID-class | H5File objects
h5ls | A wrapper to rhdf5::h5ls() that works on H5File objects
h5mread | An alternative to 'rhdf5::h5read'
h5mread_from_reshaped | Read data from a virtually reshaped HDF5 dataset
h5readDimnames | Write/read the dimnames of an HDF5 dataset
H5SparseMatrix | HDF5 sparse matrices as DelayedMatrix objects
H5SparseMatrix-class | HDF5 sparse matrices as DelayedMatrix objects
H5SparseMatrixSeed | H5SparseMatrixSeed objects
H5SparseMatrixSeed-class | H5SparseMatrixSeed objects
h5writeDimnames | Write/read the dimnames of an HDF5 dataset
HDF5-dump-management | HDF5 dump management
HDF5Array | HDF5 datasets as DelayedArray objects
HDF5Array-class | HDF5 datasets as DelayedArray objects
HDF5ArraySeed | HDF5ArraySeed objects
HDF5ArraySeed-class | HDF5ArraySeed objects
HDF5Matrix | HDF5 datasets as DelayedArray objects
HDF5Matrix-class | HDF5 datasets as DelayedArray objects
HDF5RealizationSink | Write an array-like object to an HDF5 file
HDF5RealizationSink-class | Write an array-like object to an HDF5 file

## -- I --

is_sparse-method | H5SparseMatrixSeed objects
is_sparse-method | HDF5ArraySeed objects
is_sparse-method | Write an array-like object to an HDF5 file
is_sparse<--method | HDF5 datasets as DelayedArray objects
is_sparse<--method | HDF5ArraySeed objects

## -- L --

loadHDF5SummarizedExperiment | Save/load an HDF5-based SummarizedExperiment object
lsHDF5DumpFile | HDF5 dump management

## -- M --

matrixClass-method | HDF5 datasets as DelayedArray objects
matrixClass-method | Virtually reshaped HDF5 datasets as DelayedArray objects

## -- O --

OLD_extract_sparse_array-method | H5SparseMatrixSeed objects
OLD_extract_sparse_array-method | HDF5ArraySeed objects
open.H5File | H5File objects
open.H5FileID | H5File objects

## -- P --

path-method | H5File objects
path-method | H5SparseMatrixSeed objects
path-method | HDF5ArraySeed objects
path<--method | H5SparseMatrixSeed objects
path<--method | HDF5ArraySeed objects

## -- Q --

quickResaveHDF5SummarizedExperiment | Save/load an HDF5-based SummarizedExperiment object

## -- R --

read_sparse_block-method | h5ad central matrices (or matrices in the /layers group) as DelayedMatrix objects
read_sparse_block-method | HDF5 sparse matrices as DelayedMatrix objects
read_sparse_block-method | H5SparseMatrixSeed objects
read_sparse_block-method | 10x Genomics datasets as DelayedMatrix objects
ReshapedHDF5Array | Virtually reshaped HDF5 datasets as DelayedArray objects
ReshapedHDF5Array-class | Virtually reshaped HDF5 datasets as DelayedArray objects
ReshapedHDF5ArraySeed | ReshapedHDF5ArraySeed objects
ReshapedHDF5ArraySeed-class | ReshapedHDF5ArraySeed objects
ReshapedHDF5Matrix | Virtually reshaped HDF5 datasets as DelayedArray objects
ReshapedHDF5Matrix-class | Virtually reshaped HDF5 datasets as DelayedArray objects

## -- S --

saveHDF5SummarizedExperiment | Save/load an HDF5-based SummarizedExperiment object
setHDF5DumpChunkLength | HDF5 dump management
setHDF5DumpChunkShape | HDF5 dump management
setHDF5DumpCompressionLevel | HDF5 dump management
setHDF5DumpDir | HDF5 dump management
setHDF5DumpFile | HDF5 dump management
setHDF5DumpName | HDF5 dump management
set_h5dimnames | Write/read the dimnames of an HDF5 dataset
show-method | H5File objects
show-method | H5SparseMatrixSeed objects
showHDF5DumpLog | HDF5 dump management
sparsity | H5SparseMatrixSeed objects
sparsity-method | h5ad central matrices (or matrices in the /layers group) as DelayedMatrix objects
sparsity-method | HDF5 sparse matrices as DelayedMatrix objects
sparsity-method | H5SparseMatrixSeed objects
sparsity-method | 10x Genomics datasets as DelayedMatrix objects

## -- T --

t-method | H5ADMatrixSeed objects
t-method | H5SparseMatrixSeed objects
t.CSC_H5ADMatrixSeed | H5ADMatrixSeed objects
t.CSC_H5SparseMatrixSeed | H5SparseMatrixSeed objects
t.CSR_H5ADMatrixSeed | H5ADMatrixSeed objects
t.CSR_H5SparseMatrixSeed | H5SparseMatrixSeed objects
TENxMatrix | 10x Genomics datasets as DelayedMatrix objects
TENxMatrix-class | 10x Genomics datasets as DelayedMatrix objects
TENxMatrixSeed | TENxMatrixSeed objects
TENxMatrixSeed-class | TENxMatrixSeed objects
TENxRealizationSink | Write a matrix-like object as an HDF5-based sparse matrix
TENxRealizationSink-class | Write a matrix-like object as an HDF5-based sparse matrix
type-method | HDF5ArraySeed objects
type-method | Write an array-like object to an HDF5 file
type-method | Write a matrix-like object as an HDF5-based sparse matrix

## -- U --

updateObject-method | HDF5ArraySeed objects

## -- W --

writeHDF5Array | Write an array-like object to an HDF5 file
writeTENxMatrix | Write a matrix-like object as an HDF5-based sparse matrix
write_block-method | Write an array-like object to an HDF5 file
write_block-method | Write a matrix-like object as an HDF5-based sparse matrix