Package: MsBackendParquet 0.99.9

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:Ossama Edbali [aut, cre], Ralf Johannes Maria Weber [aut], Johannes Rainer [ctb], BioFAIR UK [fnd]

MsBackendParquet_0.99.9.tar.gz
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manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
MsBackendParquet/json (API)

# Install 'MsBackendParquet' in R:
install.packages('MsBackendParquet', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/computational-metabolomics/msbackendparquet/issues

On BioConductor:MsBackendParquet-0.99.9(bioc 3.24)

infrastructuremassspectrometrymetabolomicsproteomicsdataimport

3.85 score 1 stars 10 scripts 60 downloads 45 exports 40 dependencies

Last updated from:e24075795b. Checks:1 NOTE, 14 ERROR, 1 OK. Indexed: yes.

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bioc-checksNOTE185
linux-devel-arm64ERROR304
linux-devel-x86_64ERROR397
source / vignettesERROR272
linux-release-arm64ERROR305
linux-release-x86_64ERROR358
macos-release-arm64ERROR254
macos-release-x86_64ERROR3871
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windows-devel-arm64ERROR405
windows-devel-x86_64ERROR392
windows-release-arm64ERROR415
windows-release-x86_64ERROR310
windows-oldrel-x86_64ERROR290
wasm-releaseOK147

Exports:addMzPeakArchivesbackendInitializebackendMergebuildProjectioncentroidedcreateMsBackendParquetDatasetcreateMzPeakDatasetdataStoragedropProjectionextractByIndexfilterContainsMzfilterDataOriginfilterMsLevelfilterPrecursorMzRangefilterPrecursorMzValuesfilterRtfilterSampleDataintensityintensity<-invalidateDatasetCachemanifestRunsMsBackendParquetmzmz<-mzMLToParquetmzstackConditionmzstackErrornewManifestpeaksDatapeaksVariablesprecScanNumreadManifestresetrunDatarunData<-runVariablesshowsmoothedspectraDataspectraNamesspectraNames<-supportsSetBackendticuniqueMsLevelswriteManifest

Dependencies:arrowassertthatBHBiocGenericsBiocParallelbitbit64cliclueclustercodetoolscpp11data.tableDBIduckdbformatRfsfutile.loggerfutile.optionsgenericsglueIRangesjsonlitelambda.rlifecyclemagrittrMASSMetaboCoreUtilsMsCoreUtilsProtGenericspurrrR6RcpprlangS4VectorssnowSpectratidyselectvctrswithr

Readme and manuals

Help Manual

Help pageTopics
Build or drop signal projectionsbuildProjection dropProjection
Create a Parquet dataset from raw MS data or a 'Spectra' objectcreateMsBackendParquetDataset
Build a queryable dataset from mzPeak archivesaddMzPeakArchives createMzPeakDataset
Select spectra containing a peak at a given m/zfilterContainsMz
Select spectra by their run's sample metadatafilterSampleData
Apache Parquet-based MS data backendMsBackendParquet-package $<-,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 datasetmzMLToParquet
Typed mzStack error conditionsmzstack-conditions mzstackCondition mzstackError
Read and write an mzStack manifestinvalidateDatasetCache manifestRuns mzstack-manifest newManifest readManifest writeManifest
Per-run sample metadatarunData runData<- runVariables