HDF5 datasets as array-like objects in R

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Documentation for package ‘HDF5Array’ version 1.35.5

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

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A C D E G H I L M N 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	H5File objects
coerce-method	HDF5 datasets as DelayedArray objects
coerce-method	Virtually reshaped HDF5 datasets as DelayedArray 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
extract_sparse_array-method	H5SparseMatrixSeed objects
extract_sparse_array-method	HDF5ArraySeed 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

-- N --

nzcount-method	h5ad central matrices (or matrices in the /layers group) as DelayedMatrix objects
nzcount-method	HDF5 sparse matrices as DelayedMatrix objects
nzcount-method	H5SparseMatrixSeed objects
nzcount-method	10x Genomics datasets as DelayedMatrix objects

-- O --

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 --

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

-- 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