Package: alabaster.base 1.7.6
alabaster.base: Save Bioconductor Objects to File
Save Bioconductor data structures into file artifacts, and load them back into memory. This is a more robust and 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.
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alabaster.base.pdf |alabaster.base.html✨
alabaster.base/json (API)
NEWS
# Install 'alabaster.base' in R: |
install.packages('alabaster.base', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/artifactdb/alabaster.base/issues
On BioConductor:alabaster.base-1.7.4(bioc 3.21)alabaster.base-1.6.1(bioc 3.20)
datarepresentationdataimportzlibcpp
Last updated 16 days agofrom:0535541441. Checks:1 OK, 10 NOTE. Indexed: yes.
Target | Result | Latest binary |
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Doc / Vignettes | OK | Feb 04 2025 |
R-4.5-win-x86_64 | NOTE | Feb 04 2025 |
R-4.5-mac-x86_64 | NOTE | Feb 04 2025 |
R-4.5-mac-aarch64 | NOTE | Feb 04 2025 |
R-4.5-linux-x86_64 | NOTE | Feb 04 2025 |
R-4.4-win-x86_64 | NOTE | Feb 04 2025 |
R-4.4-mac-x86_64 | NOTE | Feb 04 2025 |
R-4.4-mac-aarch64 | NOTE | Feb 04 2025 |
R-4.3-win-x86_64 | NOTE | Feb 04 2025 |
R-4.3-mac-x86_64 | NOTE | Feb 04 2025 |
R-4.3-mac-aarch64 | NOTE | Feb 04 2025 |
Exports:.addMissingStringPlaceholderAttribute.altLoadObject.altStageObject.chooseMissingStringPlaceholder.createRedirection.loadObject.loadObjectInternal.processMcols.processMetadata.quickReadCsv.quickWriteCsv.restoreMetadata.saveBaseListFormat.saveDataFrameFormat.searchForMethods.stageObject.writeMetadataabsolutizePathacquireFileacquireMetadataaddMissingPlaceholderAttributeForHdf5addObjectToDedupSessionaltLoadObjectaltLoadObjectFunctionaltReadObjectaltReadObjectFunctionaltSaveObjectaltSaveObjectFunctionaltStageObjectaltStageObjectFunctionanyMissingas.Rfc3339checkObjectInDedupSessioncheckValidDirectorychooseMissingPlaceholderForHdf5cloneDirectorycreateDedupSessioncreateRedirectioncustomloadObjectHelperformatSaveEnvironmentgetSaveEnvironmenth5_casth5_create_vectorh5_guess_vector_chunksh5_object_existsh5_read_attributeh5_read_vectorh5_write_attributeh5_write_vectoris.missingis.Rfc3339listDirectorylistLocalObjectslistObjectsloadAtomicVectorloadBaseFactorloadBaseListloadDataFrameloadDataFrameFactorloadDirectoryloadObjectloadSaveEnvironmentmissingPlaceholderNamemoveObjectprocessMcolsprocessMetadataquickLoadObjectquickReadCsvquickStageObjectquickWriteCsvreadAtomicVectorreadBaseFactorreadBaseListreadDataFramereadDataFrameFactorreadLocalObjectreadMetadatareadObjectreadObjectFilereadObjectFunctionRegistryregisterReadObjectFunctionregisterSaveEnvironmentregisterValidateObjectDerivedFromregisterValidateObjectDimensionsFunctionregisterValidateObjectFunctionregisterValidateObjectHeightFunctionregisterValidateObjectSatisfiesInterfaceremoveObjectrestoreMetadatasaveBaseListFormatsaveDataFrameFormatsaveLocalObjectsaveMetadatasaveObjectsaveObjectFileschemaLocationssearchForMethodsstageObjecttransformVectorForHdf5useSaveEnvironmentvalidateDirectoryvalidateObjectwriteMetadata
Dependencies:alabaster.schemasassortheadBiocGenericscurlgenericsjsonlitejsonvalidateRcpprhdf5rhdf5filtersRhdf5libS4VectorsV8
Readme and manuals
Help Manual
Help page | Topics |
---|---|
Make an absolute file path | absolutizePath |
Acquire file or metadata | acquireFile acquireFile,character-method acquireMetadata acquireMetadata,character-method |
Alter the reading function | .altLoadObject .loadObject altLoadObject altLoadObjectFunction altReadObject altReadObjectFunction |
Alter the saving generic | .altStageObject .stageObject altSaveObject altSaveObjectFunction altStageObject altStageObjectFunction |
Find missing values | anyMissing is.missing |
Choose a missing value placeholder | .addMissingStringPlaceholderAttribute .chooseMissingStringPlaceholder addMissingPlaceholderAttributeForHdf5 chooseMissingPlaceholderForHdf5 missingPlaceholderName |
Clone an existing directory | cloneDirectory |
Deduplicate objects when saving | addObjectToDedupSession checkObjectInDedupSession createDedupSession |
Create a redirection file | .createRedirection createRedirection |
Track the environment used for saving objects | formatSaveEnvironment getSaveEnvironment loadSaveEnvironment registerSaveEnvironment useSaveEnvironment |
HDF5 utilities | h5_cast h5_create_vector h5_guess_vector_chunks h5_object_exists h5_read_attribute h5_read_vector h5_write_attribute h5_write_vector hdf5 |
List objects in a directory | listDirectory listLocalObjects listObjects |
Load all non-child objects in a directory | loadDirectory |
Move a non-child object in the staging directory | moveObject |
Convenience helpers for handling local directories | quickLoadObject quickStageObject readLocalObject saveLocalObject |
Quickly read and write a CSV file | .quickReadCsv .quickWriteCsv quickReadCsv quickWriteCsv |
Read an atomic vector from disk | loadAtomicVector readAtomicVector |
Read a factor from disk | loadBaseFactor readBaseFactor |
Read a base list from disk | loadBaseList readBaseList |
Read a DataFrame from disk | loadDataFrame readDataFrame |
Read a DataFrame factor from disk | loadDataFrameFactor readDataFrameFactor |
Read R-level metadata | .restoreMetadata readMetadata restoreMetadata |
Read an object from disk | .loadObjectInternal customloadObjectHelper loadObject readObject readObjectFunctionRegistry registerReadObjectFunction schemaLocations |
Utilities to read and save the object file | readObjectFile saveObjectFile |
Remove a non-child object from the staging directory | removeObject |
Representing Internet date/times | as.character.Rfc3339 as.POSIXct.Rfc3339 as.POSIXlt.Rfc3339 as.Rfc3339 as.Rfc3339.character as.Rfc3339.default as.Rfc3339.POSIXt c.Rfc3339 is.Rfc3339 Rfc3339 saveObject,Rfc3339-method [.Rfc3339 [<-.Rfc3339 [[.Rfc3339 [[<-.Rfc3339 |
Save atomic vectors to disk | saveAtomicVector saveObject,character-method saveObject,Date-method saveObject,double-method saveObject,integer-method saveObject,logical-method saveObject,numeric-method saveObject,numeric_version-method saveObject,POSIXct-method saveObject,POSIXlt-method stageObject,character-method stageObject,Date-method stageObject,double-method stageObject,integer-method stageObject,logical-method stageObject,numeric-method stageObject,POSIXct-method stageObject,POSIXlt-method |
Save a factor to disk | saveBaseFactor saveObject,factor-method stageObject,factor-method |
Save a base list to disk | .saveBaseListFormat saveBaseList saveBaseListFormat saveObject,List-method saveObject,list-method stageObject,List-method stageObject,list-method |
Choose the format for certain objects | .saveDataFrameFormat saveDataFrameFormat saveFormats |
Save R-level metadata to disk | .processMcols .processMetadata processMcols processMetadata saveMetadata |
Save objects to disk | .searchForMethods saveObject searchForMethods stageObject stageObject,ANY-method |
Save a DataFrame to disk | saveObject,data.frame-method saveObject,DataFrame-method stageObject,DataFrame-method |
Stage a DataFrameFactor object | saveObject,DataFrameFactor-method stageObject,DataFrameFactor-method |
Transform a vector to save in a HDF5 file | transformVectorForHdf5 |
Validate a directory of objects | checkValidDirectory validateDirectory |
Validate an object's on-disk representation | registerValidateObjectDerivedFrom registerValidateObjectDimensionsFunction registerValidateObjectFunction registerValidateObjectHeightFunction registerValidateObjectSatisfiesInterface validateObject |
Saving the metadata | .writeMetadata writeMetadata |