Package index

All functions

H5ADMatrix()

h5ad central matrices (or matrices in the /layers group) as DelayedMatrix objects

H5ADMatrixSeed()

H5ADMatrixSeed objects

H5SparseMatrix()

HDF5 sparse matrices as DelayedMatrix objects

H5SparseMatrixSeed() path(<H5SparseMatrixSeed>) dim(<H5SparseMatrixSeed>) dimnames(<H5SparseMatrixSeed>) chunkdim(<CSC_H5SparseMatrixSeed>) chunkdim(<CSR_H5SparseMatrixSeed>) extract_array(<H5SparseMatrixSeed>) extract_sparse_array(<CSC_H5SparseMatrixSeed>) extract_sparse_array(<CSR_H5SparseMatrixSeed>) extractNonzeroDataByCol(<CSC_H5SparseMatrixSeed>) extractNonzeroDataByRow(<CSR_H5SparseMatrixSeed>) is_sparse(<H5SparseMatrixSeed>) nzcount(<H5SparseMatrixSeed>)

H5SparseMatrixSeed objects

HDF5Array()

HDF5 datasets as DelayedArray objects

HDF5ArraySeed() path(<HDF5ArraySeed>) `path<-`(<HDF5ArraySeed>) dim(<HDF5ArraySeed>) dimnames(<HDF5ArraySeed>) type(<HDF5ArraySeed>) is_sparse(<HDF5ArraySeed>) `is_sparse<-`(<HDF5ArraySeed>) chunkdim(<HDF5ArraySeed>) extract_array(<HDF5ArraySeed>) extract_sparse_array(<HDF5ArraySeed>)

HDF5ArraySeed objects

ReshapedHDF5Array()

Virtually reshaped HDF5 datasets as DelayedArray objects

ReshapedHDF5ArraySeed()

ReshapedHDF5ArraySeed objects

TENxMatrix()

10x Genomics datasets as DelayedMatrix objects

TENxMatrixSeed()

TENxMatrixSeed objects

setHDF5DumpDir() setHDF5DumpFile() setHDF5DumpName() setHDF5DumpChunkLength() setHDF5DumpChunkShape() setHDF5DumpCompressionLevel() getHDF5DumpDir() getHDF5DumpFile() getHDF5DumpName() getHDF5DumpChunkLength() getHDF5DumpChunkShape() getHDF5DumpCompressionLevel() lsHDF5DumpFile() showHDF5DumpLog() getHDF5DumpChunkDim() appendDatasetCreationToHDF5DumpLog()

HDF5 dump management

saveHDF5SummarizedExperiment() loadHDF5SummarizedExperiment() quickResaveHDF5SummarizedExperiment()

Save/load an HDF5-based SummarizedExperiment object

writeHDF5Array()

Write an array-like object to an HDF5 file

writeTENxMatrix()

Write a matrix-like object as an HDF5-based sparse matrix