Package: alabaster.base 1.5.3
Aaron Lun
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.
Authors:
alabaster.base_1.5.3.tar.gz
alabaster.base_1.5.3.zip(r-4.5)alabaster.base_1.5.3.zip(r-4.4)alabaster.base_1.5.3.zip(r-4.3)
alabaster.base_1.5.3.tgz(r-4.4-arm64)alabaster.base_1.5.3.tgz(r-4.4-x86_64)alabaster.base_1.5.3.tgz(r-4.3-arm64)alabaster.base_1.5.3.tgz(r-4.3-x86_64)
alabaster.base_1.5.3.tar.gz(r-4.5-noble)alabaster.base_1.5.3.tar.gz(r-4.4-noble)
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')) |
On BioConductor:alabaster.base-1.5.2(bioc 3.20)alabaster.base-1.4.1(bioc 3.19)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
Last updated 19 days agofrom:02c5473799
Exports:.addMissingStringPlaceholderAttribute.altLoadObject.altStageObject.chooseMissingStringPlaceholder.createRedirection.loadObject.loadObjectInternal.processMcols.processMetadata.quickReadCsv.quickWriteCsv.restoreMetadata.saveBaseListFormat.saveDataFrameFormat.searchForMethods.stageObject.writeMetadataacquireFileacquireMetadataaddMissingPlaceholderAttributeForHdf5altLoadObjectaltLoadObjectFunctionaltReadObjectaltReadObjectFunctionaltSaveObjectaltSaveObjectFunctionaltStageObjectaltStageObjectFunctionanyMissingas.Rfc3339checkValidDirectorychooseMissingPlaceholderForHdf5createRedirectioncustomloadObjectHelperh5_casth5_create_vectorh5_guess_vector_chunksh5_object_existsh5_read_attributeh5_read_vectorh5_write_attributeh5_write_vectoris.missingis.Rfc3339listDirectorylistLocalObjectslistObjectsloadAtomicVectorloadBaseFactorloadBaseListloadDataFrameloadDataFrameFactorloadDirectoryloadObjectmissingPlaceholderNamemoveObjectprocessMcolsprocessMetadataquickLoadObjectquickReadCsvquickStageObjectquickWriteCsvreadAtomicVectorreadBaseFactorreadBaseListreadDataFramereadDataFrameFactorreadLocalObjectreadMetadatareadObjectreadObjectFilereadObjectFunctionRegistryregisterReadObjectFunctionregisterValidateObjectDimensionsFunctionregisterValidateObjectFunctionregisterValidateObjectHeightFunctionremoveObjectrestoreMetadatasaveBaseListFormatsaveDataFrameFormatsaveLocalObjectsaveMetadatasaveObjectsaveObjectFileschemaLocationssearchForMethodsstageObjecttransformVectorForHdf5validateDirectoryvalidateObjectwriteMetadata
Dependencies:alabaster.schemasBiocGenericscurljsonlitejsonvalidateRcpprhdf5rhdf5filtersRhdf5libS4VectorsV8
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| 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 |
| Create a redirection file | .createRedirection createRedirection |
| 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,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,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 |
| Check if a staging directory is valid | checkValidDirectory validateDirectory |
| Validate an object's on-disk representation | registerValidateObjectDimensionsFunction registerValidateObjectFunction registerValidateObjectHeightFunction validateObject |
| Saving the metadata | .writeMetadata writeMetadata |
