Introduction | Creating a Parquet dataset | Accessing data | Filtering | Working with peaks | Controlling the dataset layout | Querying collections of mzPeak archives | How the dataset interfaces with mzPeak's model | Searching for peaks across runs | Sample metadata | The in-memory metadata cache | Streaming large mzML files | Performance | Saving and reloading the backend | Session information
Package: MsBackendParquet 0.99.7
Ossama Edbali
MsBackendParquet: Apache Parquet-based Mass Spectrometry Data Backend
Mass spectrometry (MS) data backend for the Spectra Bioconductor package that stores and retrieves spectra and peak data from on-disk Apache Parquet datasets. Spectra metadata together with m/z and intensity values are stored in a columnar Parquet format that supports compression, dictionary encoding and Hive-style partitioning. Datasets are written with the Apache Arrow R bindings and queried with DuckDB. Spectra variables are held in a bounded in-memory index so that filtering and metadata access are fast while peak data remains on disk.
Authors:
MsBackendParquet_0.99.7.tar.gz
MsBackendParquet_0.99.7.zip(r-4.7-x86_64)MsBackendParquet_0.99.7.zip(r-4.7-arm64)MsBackendParquet_0.99.7.zip(r-4.6-x86_64)MsBackendParquet_0.99.7.zip(r-4.6-arm64)MsBackendParquet_0.99.7.zip(r-4.5-x86_64)
MsBackendParquet_0.99.7.tgz(r-4.6-x86_64)MsBackendParquet_0.99.7.tgz(r-4.6-arm64)MsBackendParquet_0.99.7.tgz(r-4.5-x86_64)MsBackendParquet_0.99.7.tgz(r-4.5-arm64)
MsBackendParquet_0.99.7.tar.gz(r-4.7-arm64)MsBackendParquet_0.99.7.tar.gz(r-4.7-x86_64)MsBackendParquet_0.99.7.tar.gz(r-4.6-arm64)MsBackendParquet_0.99.7.tar.gz(r-4.6-x86_64)
MsBackendParquet_0.99.7.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
MsBackendParquet/json (API)
| # Install 'MsBackendParquet' in R: |
| install.packages('MsBackendParquet', repos = c('https://biocstaging.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/ossedb/msbackendparquet/issues
infrastructuremassspectrometrymetabolomicsproteomicsdataimport
Last updated from:cd1cc1c59d. Checks:1 NOTE, 15 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
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| bioc-checks | NOTE | 166 | ||
| linux-devel-arm64 | OK | 309 | ||
| linux-devel-x86_64 | OK | 350 | ||
| source / vignettes | OK | 293 | ||
| linux-release-arm64 | OK | 282 | ||
| linux-release-x86_64 | OK | 346 | ||
| macos-release-arm64 | OK | 369 | ||
| macos-release-x86_64 | OK | 529 | ||
| macos-oldrel-arm64 | OK | 258 | ||
| macos-oldrel-x86_64 | OK | 531 | ||
| windows-devel-arm64 | OK | 454 | ||
| windows-devel-x86_64 | OK | 403 | ||
| windows-release-arm64 | OK | 458 | ||
| windows-release-x86_64 | OK | 293 | ||
| windows-oldrel-x86_64 | OK | 244 | ||
| wasm-release | OK | 147 |
Exports:addMzPeakArchivesbackendInitializebackendMergebuildProjectioncentroidedcreateMsBackendParquetDatasetcreateMzPeakDatasetdataStoragedropProjectionextractByIndexfilterContainsMzfilterDataOriginfilterMsLevelfilterPrecursorMzRangefilterPrecursorMzValuesfilterRtfilterSampleDataintensityintensity<-invalidateDatasetCachemanifestRunsMsBackendParquetmzmz<-mzMLToParquetmzstackConditionmzstackErrornewManifestpeaksDatapeaksVariablesprecScanNumreadManifestresetrunDatarunData<-runVariablesshowsmoothedspectraDataspectraNamesspectraNames<-supportsSetBackendticuniqueMsLevelswriteManifest
Dependencies:arrowassertthatBHBiobaseBiocGenericsbiocmakeBiocParallelbitbit64cliclueclustercodetoolscpp11data.tableDBIdir.expiryduckdbfilelockformatRfsfutile.loggerfutile.optionsgenericsglueIRangesjsonlitelambda.rlifecyclemagrittrMASSMetaboCoreUtilsMsCoreUtilsmzRncdf4ProtGenericspurrrR6RcppRhdf5librlangS4VectorssnowSpectratidyselectvctrswithr
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Build or drop signal projections | buildProjection dropProjection |
| Create a Parquet dataset from raw MS data or a 'Spectra' object | createMsBackendParquetDataset |
| Build a queryable dataset from mzPeak archives | addMzPeakArchives createMzPeakDataset |
| Select spectra containing a peak at a given m/z | filterContainsMz |
| Select spectra by their run's sample metadata | filterSampleData |
| Apache Parquet-based MS data backend | $<-,MsBackendParquet-method backendBpparam,MsBackendParquet-method backendInitialize,MsBackendParquet-method backendMerge,MsBackendParquet-method centroided,MsBackendParquet-method dataStorage,MsBackendParquet-method extractByIndex,MsBackendParquet,ANY-method filterDataOrigin,MsBackendParquet-method filterMsLevel,MsBackendParquet-method filterPrecursorMzRange,MsBackendParquet-method filterPrecursorMzValues,MsBackendParquet-method filterRt,MsBackendParquet-method intensity,MsBackendParquet-method intensity<-,MsBackendParquet-method MsBackendParquet MsBackendParquet-class mz,MsBackendParquet-method mz<-,MsBackendParquet-method peaksData,MsBackendParquet-method peaksVariables,MsBackendParquet-method precScanNum,MsBackendParquet-method reset,MsBackendParquet-method show,MsBackendParquet-method smoothed,MsBackendParquet-method spectraData,MsBackendParquet-method spectraNames,MsBackendParquet-method spectraNames<-,MsBackendParquet-method supportsSetBackend,MsBackendParquet-method tic,MsBackendParquet-method uniqueMsLevels,MsBackendParquet-method [,MsBackendParquet-method |
| Convert mzML (or related) files into a Parquet dataset | mzMLToParquet |
| Typed mzStack error conditions | mzstack-conditions mzstackCondition mzstackError |
| Read and write an mzStack manifest | invalidateDatasetCache manifestRuns mzstack-manifest newManifest readManifest writeManifest |
| Per-run sample metadata | runData runData<- runVariables |
