Introduction | Install and load the package | The h5mread() function | Basic example | An example involving sparse data | A note about COO_SparseArray objects | Other functionality provided by the h5mread package | h5dim() and h5chunkdim() | Utility functions to manipulate the dimnames of an HDF5 dataset | H5File objects | Session information
Package: h5mread 1.5.0
Hervé Pagès
h5mread: A fast HDF5 reader
The main function in the h5mread package is h5mread(), which allows reading arbitrary data from an HDF5 dataset into R, similarly to what the h5read() function from the rhdf5 package does. In the case of h5mread(), the implementation has been optimized to make it as fast and memory-efficient as possible.
Authors:
h5mread_1.5.0.tar.gz
h5mread_1.5.0.zip(r-4.7)h5mread_1.5.0.zip(r-4.6)h5mread_1.5.0.zip(r-4.5)
h5mread_1.5.0.tgz(r-4.6-arm64)h5mread_1.5.0.tgz(r-4.6-x86_64)h5mread_1.5.0.tgz(r-4.5-x86_64)h5mread_1.5.0.tgz(r-4.5-arm64)
h5mread_1.5.0.tar.gz(r-4.7-arm64)h5mread_1.5.0.tar.gz(r-4.7-x86_64)h5mread_1.5.0.tar.gz(r-4.6-arm64)h5mread_1.5.0.tar.gz(r-4.6-x86_64)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
h5mread/json (API)
| # Install 'h5mread' in R: |
| install.packages('h5mread', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/bioconductor/h5mread/issues
On BioConductor:h5mread-1.5.0(bioc 3.24)h5mread-1.4.0(bioc 3.23)
infrastructuredatarepresentationdataimportu24ca289073curlopenssl
Last updated from:2a42d3c56c. Checks:4 NOTE, 5 FAIL, 1 OK, 4 WARNING. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | NOTE | 212 | ||
| linux-devel-arm64 | FAIL | 3783 | ||
| linux-devel-x86_64 | NOTE | 3363 | ||
| source / vignettes | OK | 367 | ||
| linux-release-arm64 | NOTE | 397 | ||
| linux-release-x86_64 | NOTE | 429 | ||
| macos-release-arm64 | WARNING | 366 | ||
| macos-release-x86_64 | FAIL | 3927 | ||
| macos-oldrel-arm64 | FAIL | 3701 | ||
| macos-oldrel-x86_64 | FAIL | 3824 | ||
| windows-devel | WARNING | 577 | ||
| windows-release | WARNING | 651 | ||
| windows-oldrel | WARNING | 575 | ||
| wasm-release | FAIL | 162 |
Exports:close.H5Fileclose.H5FileIDdestroy_H5DSetDescriptordim_as_integerfind_dims_to_collapseget_h5dimnamesget_h5mread_returned_typeh5chunkdimh5dimH5DSetDescriptorh5existsH5FileH5FileIDh5isdataseth5isgrouph5lsh5mreadh5mread_from_reshapedh5readDimnamesh5writeDimnamesopen.H5Fileopen.H5FileIDpathset_h5dimnamesshowvalidate_lengths_of_h5dimnames
Dependencies:abindBiocGenericsbiocmakedir.expiryfilelockgenericsIRangeslatticeMatrixMatrixGenericsmatrixStatsrhdf5rhdf5filtersRhdf5libS4ArraysS4VectorsSparseArrayXVector
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Get the dimensions of an HDF5 dataset | dim_as_integer h5chunkdim h5dim h5exists h5isdataset h5isgroup |
| H5File objects | character_OR_H5File character_OR_H5File-class class:character_OR_H5File class:H5DSetDescriptor class:H5File class:H5FileID close.H5File close.H5FileID coerce,H5File,H5IdComponent-method destroy_H5DSetDescriptor H5DSetDescriptor H5DSetDescriptor-class H5File H5File-class H5FileID H5FileID-class open.H5File open.H5FileID path,H5File-method show,H5DSetDescriptor-method show,H5File-method show,H5FileID-method |
| A wrapper to rhdf5::h5ls() that works on H5File objects | h5ls |
| An alternative to 'rhdf5::h5read' | get_h5mread_returned_type h5mread |
| Read data from a virtually reshaped HDF5 dataset | find_dims_to_collapse h5mread_from_reshaped |
| Write/read the dimnames of an HDF5 dataset | get_h5dimnames h5readDimnames h5writeDimnames set_h5dimnames validate_lengths_of_h5dimnames |
