API for Bioconductor/HDF5Array
HDF5 backend for DelayedArray objects

Global functions
.ID_is_closed Source code
.ID_to_H5IdComponent Source code
.Mindex_as_index_list Source code
.OLD_extract_sparse_array_from_H5SparseMatrixSeed Source code
.OLD_extract_sparse_array_from_HDF5ArraySeed Source code
.append_data Source code
.append_indptr Source code
.append_row_indices Source code
.as_HDF5Array Source code
.as_TENxMatrix Source code
.check_HDF5SummarizedExperiment_h5_file Source code
.check_data_and_subdata Source code
.check_dimnames Source code
.check_filepath_and_name Source code
.check_group Source code
.check_h5dimnames Source code
.check_viewport Source code
.close_H5FileID_xp Source code
.create_empty_data Source code
.create_empty_indptr Source code
.create_empty_row_indices Source code
.destroy_H5DSetDescriptor_xp Source code
.extract_array_from_H5SparseMatrixSeed Source code
.extract_array_from_HDF5ArraySeed Source code
.extract_array_from_ReshapedHDF5ArraySeed Source code
.extract_data_from_adjacent_cols Source code
.extract_nonzero_csc_sparse_data_by_col Source code
.find_rownames_dataset Source code
.from_CSC_H5SparseMatrixSeed_to_dgCMatrix Source code
.from_CSR_H5SparseMatrixSeed_to_dgCMatrix Source code
.from_H5ADMatrix_to_dgCMatrix Source code
.from_H5SparseMatrix_to_dgCMatrix Source code
.from_TENxMatrix_to_dgCMatrix Source code
.get_H5FileID_xp_ID Source code
.get_HDF5Array_global_option Source code
.get_current_col_index Source code
.get_data_indices_by_col Source code
.get_data_name Source code
.get_dataset_creation_global_counter Source code
.get_dataset_creation_global_counter_filepath Source code
.get_dump_autofile Source code
.get_dump_autoname Source code
.get_dump_names_global_counter Source code
.get_dump_names_global_counter_filepath Source code
.get_dump_specfile Source code
.get_dump_specname Source code
.get_h5dataset Source code
.get_sparse_matrix_dim Source code
.get_sparse_matrix_layout Source code
.get_unique_assay2h5_links Source code
.h5closefile Source code
.h5mread2 Source code
.h5mread_and_collapse_dims Source code
.h5openS3file Source code
.h5openfile Source code
.h5openlocalfile Source code
.linear_extract_nonzero_data_by_col Source code
.load_SummarizedExperiment_package Source code
.load_csc_sparse_data Source code
.load_h5ad_dimnames Source code
.load_h5ad_rownames Source code
.load_linear_csc_sparse_data Source code
.load_random_csc_sparse_data Source code
.load_tenx_barcodes Source code
.load_tenx_rownames Source code
.locked_path Source code
.map_h5_path_to_rds_path Source code
.new_H5FileID_xp Source code
.normarg_chunkdim Source code
.normarg_group Source code
.normarg_h5dimnames Source code
.normarg_method Source code
.onLoad Source code
.onUnload Source code
.open_H5FileID_xp Source code
.random_extract_nonzero_data_by_col Source code
.read_HDF5SummarizedExperiment Source code
.read_counter Source code
.read_h5dataset_first_val Source code
.read_h5sparse_data Source code
.read_h5sparse_dim Source code
.read_h5sparse_indices Source code
.read_h5sparse_indptr Source code
.read_h5sparse_layout Source code
.read_sparse_block_from_H5SparseMatrixSeed Source code
.safe_file_rename Source code
.sequence2 Source code
.serialize_HDF5SummarizedExperiment Source code
.set_H5FileID_xp_ID Source code
.set_HDF5Array_global_option Source code
.set_dump_autofiles_mode Source code
.set_dump_autonames_mode Source code
.set_dump_dir Source code
.set_dump_specfile Source code
.set_dump_specname Source code
.stop_if_cannot_quick_resave Source code
.test Source code
.validate_HDF5ArraySeed Source code
.validate_h5dimnames_lengths Source code
.write_HDF5SummarizedExperiment Source code
.write_TENx_component Source code
.write_barcodes Source code
.write_counter Source code
.write_genes Source code
.write_shape Source code
CSC_H5ADMatrixSeed Man page
CSC_H5ADMatrixSeed-class Man page
CSC_H5SparseMatrixSeed Man page
CSC_H5SparseMatrixSeed-class Man page
CSR_H5ADMatrixSeed Man page
CSR_H5ADMatrixSeed-class Man page
CSR_H5SparseMatrixSeed Man page
CSR_H5SparseMatrixSeed-class Man page
DelayedArray,H5ADMatrixSeed-method Man page
DelayedArray,H5SparseMatrixSeed-method Man page
DelayedArray,HDF5ArraySeed-method Man page
DelayedArray,ReshapedHDF5ArraySeed-method Man page
DelayedArray,TENxMatrixSeed-method Man page
Dense_H5ADMatrixSeed Man page
Dense_H5ADMatrixSeed-class Man page
H5ADMatrix Man page Source code
H5ADMatrix-class Man page
H5ADMatrixSeed Man page Source code
H5ADMatrixSeed-class Man page
H5DSetDescriptor Man page Source code
H5DSetDescriptor-class Man page
H5File Man page Source code
H5File-class Man page
H5FileID Man page Source code
H5FileID-class Man page
H5SparseMatrix Man page Source code
H5SparseMatrix-class Man page
H5SparseMatrixSeed Man page Source code
H5SparseMatrixSeed-class Man page
HDF5-dump-management Man page
HDF5Array Man page Source code
HDF5Array-class Man page
HDF5Array-internals Man page
HDF5ArraySeed Man page Source code
HDF5ArraySeed-class Man page
HDF5Array_global_option_is_set Source code
HDF5Matrix Man page
HDF5Matrix-class Man page
HDF5RealizationSink Man page Source code
HDF5RealizationSink-class Man page
OLD_extract_sparse_array,H5SparseMatrixSeed-method Man page
OLD_extract_sparse_array,HDF5ArraySeed-method Man page
ReshapedHDF5Array Man page Source code
ReshapedHDF5Array-class Man page
ReshapedHDF5ArraySeed Man page Source code
ReshapedHDF5ArraySeed-class Man page
ReshapedHDF5Matrix Man page
ReshapedHDF5Matrix-class Man page
TENxMatrix Man page Source code
TENxMatrix-class Man page
TENxMatrixSeed Man page Source code
TENxMatrixSeed-class Man page
TENxRealizationSink Man page Source code
TENxRealizationSink-class Man page
add_prefix_to_basename Source code
appendDatasetCreationToHDF5DumpLog Man page Source code
character_OR_H5File Man page
character_OR_H5File-class Man page
check_and_delete_files Man page Source code
check_ordered_uaselection Source code
check_uaselection Source code
chunkdim,CSC_H5SparseMatrixSeed-method Man page
chunkdim,CSR_H5SparseMatrixSeed-method Man page
chunkdim,HDF5ArraySeed-method Man page
chunkdim,HDF5RealizationSink-method Man page
chunkdim,ReshapedHDF5ArraySeed-method Man page
chunkdim,TENxRealizationSink-method Man page
class:CSC_H5ADMatrixSeed Man page
class:CSC_H5SparseMatrixSeed Man page
class:CSR_H5ADMatrixSeed Man page
class:CSR_H5SparseMatrixSeed Man page
class:Dense_H5ADMatrixSeed Man page
class:H5ADMatrix Man page
class:H5ADMatrixSeed Man page
class:H5DSetDescriptor Man page
class:H5File Man page
class:H5FileID Man page
class:H5SparseMatrix Man page
class:H5SparseMatrixSeed Man page
class:HDF5Array Man page
class:HDF5ArraySeed Man page
class:HDF5Matrix Man page
class:HDF5RealizationSink Man page
class:ReshapedHDF5Array Man page
class:ReshapedHDF5ArraySeed Man page
class:ReshapedHDF5Matrix Man page
class:TENxMatrix Man page
class:TENxMatrixSeed Man page
class:TENxRealizationSink Man page
class:character_OR_H5File Man page
close,TENxRealizationSink-method Man page
close.H5File Man page Source code
close.H5FileID Man page Source code
coerce,ANY,HDF5Array-method Man page
coerce,ANY,HDF5Matrix-method Man page
coerce,ANY,ReshapedHDF5Matrix-method Man page
coerce,ANY,TENxMatrix-method Man page
coerce,CSC_H5SparseMatrixSeed,dgCMatrix-method Man page
coerce,CSC_H5SparseMatrixSeed,sparseMatrix-method Man page
coerce,CSR_H5SparseMatrixSeed,dgCMatrix-method Man page
coerce,CSR_H5SparseMatrixSeed,sparseMatrix-method Man page
coerce,DelayedArray,HDF5Array-method Man page
coerce,DelayedArray,TENxMatrix-method Man page
coerce,DelayedMatrix,HDF5Matrix-method Man page
coerce,DelayedMatrix,TENxMatrix-method Man page
coerce,H5ADMatrix,dgCMatrix-method Man page
coerce,H5ADMatrix,sparseMatrix-method Man page
coerce,H5File,H5IdComponent-method Man page
coerce,H5SparseMatrix,dgCMatrix-method Man page
coerce,H5SparseMatrix,sparseMatrix-method Man page
coerce,HDF5Array,HDF5Matrix-method Man page
coerce,HDF5Matrix,HDF5Array-method Man page
coerce,HDF5RealizationSink,DelayedArray-method Man page
coerce,HDF5RealizationSink,HDF5Array-method Man page
coerce,HDF5RealizationSink,HDF5ArraySeed-method Man page
coerce,ReshapedHDF5Array,ReshapedHDF5Matrix-method Man page
coerce,ReshapedHDF5Matrix,ReshapedHDF5Array-method Man page
coerce,TENxMatrix,dgCMatrix-method Man page
coerce,TENxMatrix,sparseMatrix-method Man page
coerce,TENxRealizationSink,DelayedArray-method Man page
coerce,TENxRealizationSink,TENxMatrix-method Man page
coerce,TENxRealizationSink,TENxMatrixSeed-method Man page
collapse_dims Source code
compute_max_string_size Source code
create_and_log_HDF5_dataset Source code
create_dir Man page Source code
destroy_H5DSetDescriptor Man page Source code
dim,H5SparseMatrixSeed-method Man page
dim,HDF5ArraySeed-method Man page
dim,ReshapedHDF5ArraySeed-method Man page
dim_as_integer Source code
dimnames,Dense_H5ADMatrixSeed-method Man page
dimnames,H5SparseMatrixSeed-method Man page
dimnames,HDF5ArraySeed-method Man page
dimnames,HDF5RealizationSink-method Man page
dimnames,TENxRealizationSink-method Man page
dump-management Man page
extractNonzeroDataByCol Man page
extractNonzeroDataByCol,CSC_H5SparseMatrixSeed-method Man page
extractNonzeroDataByCol,H5ADMatrix-method Man page
extractNonzeroDataByCol,H5SparseMatrix-method Man page
extractNonzeroDataByCol,TENxMatrix-method Man page
extractNonzeroDataByRow Man page
extractNonzeroDataByRow,CSR_H5SparseMatrixSeed-method Man page
extractNonzeroDataByRow,H5ADMatrix-method Man page
extractNonzeroDataByRow,H5SparseMatrix-method Man page
extract_array,H5SparseMatrixSeed-method Man page
extract_array,HDF5ArraySeed-method Man page
extract_array,ReshapedHDF5ArraySeed-method Man page
find_dims_to_collapse Source code
getHDF5DumpChunkDim Man page Source code
getHDF5DumpChunkLength Man page Source code
getHDF5DumpChunkShape Man page Source code
getHDF5DumpCompressionLevel Man page Source code
getHDF5DumpDir Man page Source code
getHDF5DumpFile Man page Source code
getHDF5DumpName Man page Source code
get_HDF5_dump_logfile Source code
get_global_counter Source code
get_h5dimnames Man page Source code
get_h5mread_returned_type Man page Source code
h5append Source code
h5chunkdim Source code
h5createDataset2 Source code
h5dim Source code
h5exists Source code
h5getdimlabels Source code
h5getdimscales Source code
h5isdataset Source code
h5isdimscale Source code
h5isgroup Source code
h5length Source code
h5ls Man page Source code
h5mread Man page Source code
h5mread_from_reshaped Man page Source code
h5readDimnames Man page Source code
h5setdimlabels Source code
h5setdimscales Source code
h5summarize Source code
h5writeDimnames Man page Source code
has_trailing_slash Source code
init_HDF5_dataset_creation_global_counter Source code
init_HDF5_dump_names_global_counter Source code
init_global_counter Source code
is_sparse,H5SparseMatrixSeed-method Man page
is_sparse,HDF5ArraySeed-method Man page
is_sparse,HDF5RealizationSink-method Man page
is_sparse<-,HDF5Array-method Man page
is_sparse<-,HDF5ArraySeed-method Man page
loadHDF5SummarizedExperiment Man page Source code
lock_file Source code
lsHDF5DumpFile Man page Source code
map_starts_to_chunks Source code
matrixClass,HDF5Array-method Man page
matrixClass,ReshapedHDF5Array-method Man page
normalize_compression_level Source code
normalize_dump_filepath Source code
normalize_dump_name Source code
normarg_h5_filepath Source code
normarg_h5_name Source code
open.H5File Man page Source code
open.H5FileID Man page Source code
path,H5File-method Man page
path,H5SparseMatrixSeed-method Man page
path,HDF5ArraySeed-method Man page
path<-,H5SparseMatrixSeed-method Man page
path<-,HDF5ArraySeed-method Man page
quickResaveHDF5SummarizedExperiment Man page Source code
read_h5sparse_component Source code
read_sparse_block,H5ADMatrix-method Man page
read_sparse_block,H5SparseMatrix-method Man page
read_sparse_block,H5SparseMatrixSeed-method Man page
read_sparse_block,TENxMatrix-method Man page
reduce_uaselection Source code
replace_dir Man page Source code
restore_absolute_assay2h5_links Man page Source code
saveHDF5SummarizedExperiment Man page Source code
setHDF5DumpChunkLength Man page Source code
setHDF5DumpChunkShape Man page Source code
setHDF5DumpCompressionLevel Man page Source code
setHDF5DumpDir Man page Source code
setHDF5DumpFile Man page Source code
setHDF5DumpName Man page Source code
set_h5dimnames Man page Source code
shorten_assay2h5_links Man page Source code
show,H5DSetDescriptor-method Man page
show,H5File-method Man page
show,H5FileID-method Man page
show,H5SparseMatrixSeed-method Man page
showHDF5DumpLog Man page Source code
sparsity Man page
sparsity,H5ADMatrix-method Man page
sparsity,H5SparseMatrix-method Man page
sparsity,H5SparseMatrixSeed-method Man page
sparsity,TENxMatrix-method Man page
stop_if_bad_dir Man page Source code
t,CSC_H5ADMatrixSeed-method Man page
t,CSC_H5SparseMatrixSeed-method Man page
t,CSR_H5ADMatrixSeed-method Man page
t,CSR_H5SparseMatrixSeed-method Man page
t.CSC_H5ADMatrixSeed Man page Source code
t.CSC_H5SparseMatrixSeed Man page Source code
t.CSR_H5ADMatrixSeed Man page Source code
t.CSR_H5SparseMatrixSeed Man page Source code
trim_trailing_slashes Source code
type,HDF5ArraySeed-method Man page
type,HDF5RealizationSink-method Man page
type,TENxRealizationSink-method Man page
unlock_file Source code
updateObject,HDF5ArraySeed-method Man page
validate_HDF5ArraySeed_dataset_geometry Man page Source code
validate_h5_absolute_path Source code
validate_h5_dataset_name Source code
validate_lengths_of_h5dimnames Source code
writeHDF5Array Man page Source code
writeTENxMatrix Man page Source code
write_block,HDF5RealizationSink-method Man page
write_block,TENxRealizationSink-method Man page
write_h5_assays Man page Source code
Bioconductor/HDF5Array documentation built on Feb. 9, 2024, 2:09 a.m.