Package: alabaster.matrix 1.7.7

Aaron Lun

alabaster.matrix: Load and Save Artifacts from File

Save matrices, arrays and similar objects into file artifacts, and load them back into memory. This is a more portable alternative to serialization of such objects into RDS files. Each artifact is associated with metadata for further interpretation; downstream applications can enrich this metadata with context-specific properties.

Authors:Aaron Lun [aut, cre]

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alabaster.matrix.pdf |alabaster.matrix.html
alabaster.matrix/json (API)
NEWS

# Install 'alabaster.matrix' in R:
install.packages('alabaster.matrix', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))
Uses libs:
  • c++– GNU Standard C++ Library v3

On BioConductor:alabaster.matrix-1.7.6(bioc 3.21)alabaster.matrix-1.6.1(bioc 3.20)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

dataimportdatarepresentationcpp

7.08 score 8 packages 15 scripts 3.9k downloads 34 exports 28 dependencies

Last updated 4 days agofrom:e3f095f001. Checks:6 OK, 2 NOTE, 1 FAILURE. Indexed: yes.

TargetResultLatest binary
Doc / VignettesOKFeb 13 2025
R-4.5-win-x86_64NOTEFeb 13 2025
R-4.5-linux-x86_64NOTEFeb 13 2025
R-4.4-win-x86_64OKFeb 13 2025
R-4.4-mac-x86_64OKFeb 13 2025
R-4.4-mac-aarch64OKFeb 13 2025
R-4.3-win-x86_64OUTDATEDJan 25 2025
R-4.3-mac-x86_64OKFeb 13 2025
R-4.3-mac-aarch64OKFeb 13 2025

Exports:.createRawArraySeed.extractArrayDimnamesaltReloadDelayedObjectaltReloadDelayedObjectFunctionaltStoreDelayedObjectaltStoreDelayedObjectFunctionAmalgamatedArrayAmalgamatedArraySeedcomponentNamescreateExternalSeedDedupSessionDelayedArrayDelayedMaskextract_arrayextract_sparse_arrayextractComponentsis_sparseloadArrayloadWrapperArraymatrixClasspathpreserveDelayedOperationsreadArrayreadDelayedArrayreadSparseMatrixrecycleHdf5FilesregisterReloadDelayedObjectFunctionreloadDelayedObjectreloadDelayedObjectFunctionRegistryReloadedArrayReloadedArraySeedsaveObjectstageObjectstoreDelayedObjectwriteSparseMatrix

Dependencies:abindalabaster.basealabaster.schemasassortheadBiocGenericscrayoncurlDelayedArraygenericsh5mreadHDF5ArrayIRangesjsonlitejsonvalidatelatticeMatrixMatrixGenericsmatrixStatsR6Rcpprhdf5rhdf5filtersRhdf5libS4ArraysS4VectorsSparseArrayV8XVector

Saving arrays to artifacts and back again

Rendered fromuserguide.Rmdusingknitr::rmarkdownon Feb 13 2025.

Last update: 2024-11-20
Started: 2022-09-20

Readme and manuals

Help Manual

Help pageTopics
Amalgamated array classAmalgamatedArray AmalgamatedArray-class AmalgamatedArraySeed AmalgamatedArraySeed-class AmalgamatedMatrix-class coerce,AmalgamatedArray,AmalgamatedMatrix-method coerce,AmalgamatedMatrix,AmalgamatedArray-method componentNames DelayedArray,AmalgamatedArraySeed-method extractComponents matrixClass,AmalgamatedArray-method stageObject,AmalgamatedArray-method
Array loading utilities.createRawArraySeed .extractArrayDimnames createRawArraySeed
Delayed maskingchunkdim,DelayedMask-method DelayedMask DelayedMask-class dim,DelayedMask-method dimnames,DelayedMask-method extract_array,DelayedMask-method extract_sparse_array,DelayedMask-method is_sparse,DelayedMask-method path,DelayedMask-method
Preserve delayed operations during stagingpreserveDelayedOperations
Read a dense array from diskloadArray readArray
Read a delayed array from diskreadDelayedArray
Read a sparse matrix from diskreadSparseMatrix
Recycle existing HDF5 filesrecycleHdf5Files
Reloaded 'alabaster' arraycoerce,ReloadedArray,ReloadedMatrix-method coerce,ReloadedMatrix,ReloadedArray-method DelayedArray,ReloadedArraySeed-method matrixClass,ReloadedArray-method path,ReloadedArraySeed-method ReloadedArray ReloadedArray-class ReloadedArraySeed ReloadedArraySeed-class ReloadedMatrix-class saveObject,ReloadedArray-method
Save a multi-dimensional array to disksaveArray saveObject,array-method saveObject,denseMatrix-method stageObject,array-method stageObject,Matrix-method
Save DelayedArrays to disksaveDelayedArray saveObject,DelayedArray-method stageObject,DelayedArray-method stageObject,DelayedMatrix-method
Save a sparse matrix to disksaveObject,sparseMatrix-method saveObject,SVT_SparseMatrix-method saveSparseMatrix
Store/reload a DelayedArrayaltReloadDelayedObject altReloadDelayedObjectFunction altStoreDelayedObject altStoreDelayedObjectFunction createExternalSeedDedupSession registerReloadDelayedObjectFunction reloadDelayedObject reloadDelayedObjectFunctionRegistry storeDelayedObject storeDelayedObject,ANY-method storeDelayedObject,array-method storeDelayedObject,ConstantArraySeed-method storeDelayedObject,DelayedAbind-method storeDelayedObject,DelayedAperm-method storeDelayedObject,DelayedNaryIsoOp-method storeDelayedObject,DelayedSetDimnames-method storeDelayedObject,DelayedSubassign-method storeDelayedObject,DelayedSubset-method storeDelayedObject,DelayedUnaryIsoOpStack-method storeDelayedObject,DelayedUnaryIsoOpWithArgs-method storeDelayedObject,denseMatrix-method storeDelayedObject,sparseMatrix-method storeDelayedObject,SVT_SparseMatrix-method
DelayedArray wrapper seedloadWrapperArray WrapperArray WrapperArray-class WrapperArraySeed WrapperArraySeed-class
Write a sparse matrixwriteSparseMatrix