Package: Spectra 1.17.1

RforMassSpectrometry Package Maintainer

Spectra: Spectra Infrastructure for Mass Spectrometry Data

The Spectra package defines an efficient infrastructure for storing and handling mass spectrometry spectra and functionality to subset, process, visualize and compare spectra data. It provides different implementations (backends) to store mass spectrometry data. These comprise backends tuned for fast data access and processing and backends for very large data sets ensuring a small memory footprint.

Authors:RforMassSpectrometry Package Maintainer [cre], Laurent Gatto [aut], Johannes Rainer [aut], Sebastian Gibb [aut], Philippine Louail [aut], Jan Stanstrup [ctb], Nir Shahaf [ctb], Mar Garcia-Aloy [ctb]

Spectra_1.17.1.tar.gz
Spectra_1.17.1.zip(r-4.5)Spectra_1.17.1.zip(r-4.4)Spectra_1.17.1.zip(r-4.3)
Spectra_1.17.1.tgz(r-4.4-any)Spectra_1.17.1.tgz(r-4.3-any)
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Spectra.pdf |Spectra.html✨
Spectra/json (API)
NEWS

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

Peer review:

Bug tracker:https://github.com/rformassspectrometry/spectra/issues

Datasets:

On BioConductor:Spectra-1.17.0(bioc 3.21)Spectra-1.16.0(bioc 3.20)

infrastructureproteomicsmassspectrometrymetabolomicsbioconductorhacktoberfestmass-spectrometry

12.85 score 38 stars 33 packages 215 scripts 3.3k downloads 54 mentions 133 exports 21 dependencies

Last updated 2 days agofrom:0deee7b7c4. Checks:OK: 1 NOTE: 5 ERROR: 1. Indexed: no.

TargetResultDate
Doc / VignettesOKNov 22 2024
R-4.5-winNOTENov 22 2024
R-4.5-linuxNOTENov 22 2024
R-4.4-winNOTENov 22 2024
R-4.4-macNOTENov 22 2024
R-4.3-winNOTENov 22 2024
R-4.3-macERRORNov 22 2024

Exports:acquisitionNumaddProcessingapplyProcessingasDataFramebackendBpparambackendInitializebackendMergebackendParallelFactorbackendRequiredSpectraVariablesbincentroidedcentroided<-chunkapplycollisionEnergycollisionEnergy<-combinePeakscombinePeaksDatacombineSpectracompareSpectracomputeMzDeltasconcatenateSpectracontainsMzcontainsNeutralLosscoreSpectraVariablescountIdentificationsdataOrigindataOrigin<-dataStoragedataStorage<-dataStorageBasePathdataStorageBasePath<-deisotopeSpectradropNaSpectraVariablesentropyestimatePrecursorIntensityestimatePrecursorMzexportextractByIndexfilterAcquisitionNumfilterDataOriginfilterDataStoragefilterEmptySpectrafilterFourierTransformArtefactsfilterIntensityfilterIsolationWindowfilterMsLevelfilterMzRangefilterMzValuesfilterPeaksRangesfilterPolarityfilterPrecursorChargefilterPrecursorIsotopesfilterPrecursorMaxIntensityfilterPrecursorMzfilterPrecursorMzRangefilterPrecursorMzValuesfilterPrecursorPeaksfilterPrecursorScanfilterRangesfilterRtfilterValuesintensityintensity<-ionCountisCentroidedisEmptyisolationWindowLowerMzisolationWindowLowerMz<-isolationWindowTargetMzisolationWindowTargetMz<-isolationWindowUpperMzisolationWindowUpperMz<-isReadOnlyjoinPeaksjoinPeaksGnpsjoinPeaksNonejoinSpectraDataMsBackendCachedMsBackendDataFrameMsBackendHdf5PeaksMsBackendMemoryMsBackendMzRmsLevelmsLevel<-mzmz<-neutralLosspeaksDatapeaksData<-peaksVariablespickPeaksplotMzDeltaplotSpectraplotSpectraMirrorplotSpectraOverlaypolaritypolarity<-ppmprecScanNumprecursorChargeprecursorIntensityprecursorMzprecursorMz<-PrecursorMzParamprocessingChunkFactorprocessingChunkSizeprocessingChunkSize<-processingLogreduceSpectrareplaceIntensitiesBelowresetrtimertime<-scalePeaksscanIndexselectSpectraVariablessetBackendshowsmoothsmoothedsmoothed<-SpectraspectraDataspectraData<-spectraNamesspectraNames<-spectrapplyspectraVariableMappingspectraVariablessplitsupportsSetBackendticuniqueMsLevels

Dependencies:BHBiocGenericsBiocParallelclueclustercodetoolscpp11formatRfsfutile.loggerfutile.optionsgenericsIRangeslambda.rMASSMetaboCoreUtilsMsCoreUtilsProtGenericsRcppS4Vectorssnow

Creating new MsBackend classes

Rendered fromMsBackend.Rmdusingknitr::rmarkdownon Nov 22 2024.

Last update: 2024-10-25
Started: 2023-01-12

Description and usage of Spectra objects

Rendered fromSpectra.Rmdusingknitr::rmarkdownon Nov 22 2024.

Last update: 2024-10-03
Started: 2019-06-13

Large-scale data handling and processing with Spectra

Rendered fromSpectra-large-scale.Rmdusingknitr::rmarkdownon Nov 22 2024.

Last update: 2024-03-12
Started: 2023-11-30

Readme and manuals

Help Manual

Help pageTopics
Data manipulation and analysis methodsaddProcessing addProcessing,Spectra-method applyProcessing bin bin,Spectra-method containsMz containsMz,Spectra-method containsNeutralLoss containsNeutralLoss,Spectra-method entropy entropy,ANY-method entropy,Spectra-method pickPeaks pickPeaks,Spectra-method processingLog replaceIntensitiesBelow replaceIntensitiesBelow,Spectra-method reset reset,Spectra-method scalePeaks smooth smooth,Spectra-method spectrapply spectrapply,Spectra-method
Apply a function stepwise to chunks of datachunkapply
Aggregating and combining mass peaks datacombinePeaks combinePeaks,Spectra-method
Combine peaks with similar m/z across spectracombinePeaksData
Spectra similarity calculationscompareSpectra compareSpectra,Spectra,missing-method compareSpectra,Spectra,Spectra-method
Merging, aggregating and splitting Spectrac,Spectra-method combineSpectra concatenateSpectra joinSpectraData split split,Spectra,ANY-method
Count the number of identifications per scancountIdentifications
Filter and subset Spectra objectsdeisotopeSpectra dropNaSpectraVariables dropNaSpectraVariables,Spectra-method filterAcquisitionNum filterAcquisitionNum,Spectra-method filterDataOrigin filterDataOrigin,Spectra-method filterDataStorage filterDataStorage,Spectra-method filterEmptySpectra filterEmptySpectra,Spectra-method filterFourierTransformArtefacts,Spectra-method filterIntensity filterIntensity,Spectra-method filterIsolationWindow filterIsolationWindow,Spectra-method filterMsLevel filterMsLevel,Spectra-method filterMzRange filterMzRange,Spectra-method filterMzValues filterMzValues,Spectra-method filterPolarity filterPolarity,Spectra-method filterPrecursorCharge filterPrecursorCharge,Spectra-method filterPrecursorIsotopes filterPrecursorMaxIntensity filterPrecursorMz,Spectra-method filterPrecursorMzRange filterPrecursorMzRange,Spectra-method filterPrecursorMzValues filterPrecursorMzValues,Spectra-method filterPrecursorPeaks filterPrecursorScan filterPrecursorScan,Spectra-method filterRanges filterRanges,Spectra-method filterRt filterRt,Spectra-method filterValues filterValues,Spectra-method reduceSpectra selectSpectraVariables selectSpectraVariables,Spectra-method [,Spectra-method
Estimate Precursor IntensitiesestimatePrecursorIntensity estimatePrecursorIntensity,Spectra-method
Estimating precursor m/z valus for DDA dataestimatePrecursorMz
Fast fourier transform artefact filterfft_spectrum filterFourierTransformArtefacts
Filter peaks based on spectra and peaks variable rangesfilterPeaksRanges
Join (map) peaks of two spectrajoinPeaks joinPeaksGnps joinPeaksNone
Mass spectrometry data backends$,MsBackend-method $<-,MsBackend-method acquisitionNum,MsBackend-method backendBpparam backendBpparam,MsBackend-method backendInitialize backendInitialize,MsBackend-method backendInitialize,MsBackendDataFrame-method backendInitialize,MsBackendMemory-method backendMerge,list-method backendMerge,MsBackend-method backendParallelFactor,MsBackend-method backendParallelFactor,MsBackendHdf5Peaks-method backendParallelFactor,MsBackendMzR-method backendRequiredSpectraVariables backendRequiredSpectraVariables,MsBackend-method centroided,MsBackend-method centroided<-,MsBackend-method class:MsBackend collisionEnergy,MsBackend-method collisionEnergy<-,MsBackend-method dataOrigin,MsBackend-method dataOrigin<-,MsBackend-method dataStorage,MsBackend-method dataStorage<-,MsBackend-method dataStorageBasePath dataStorageBasePath,MsBackend-method dataStorageBasePath,MsBackendMzR-method dataStorageBasePath<- dataStorageBasePath<-,MsBackend-method dataStorageBasePath<-,MsBackendMzR-method dropNaSpectraVariables,MsBackend-method export,MsBackend-method extractByIndex extractByIndex,MsBackend,ANY-method extractByIndex,MsBackend,missing-method filterAcquisitionNum,MsBackend-method filterDataOrigin,MsBackend-method filterDataStorage,MsBackend-method filterEmptySpectra,MsBackend-method filterIsolationWindow,MsBackend-method filterMsLevel,MsBackend-method filterPolarity,MsBackend-method filterPrecursorCharge,MsBackend-method filterPrecursorMz,MsBackend-method filterPrecursorMzRange,MsBackend-method filterPrecursorMzValues,MsBackend-method filterPrecursorScan,MsBackend-method filterRanges,MsBackend-method filterRt,MsBackend-method filterValues,MsBackend-method intensity,MsBackend-method intensity<-,MsBackend-method ionCount,MsBackend-method isCentroided,MsBackend-method isEmpty,MsBackend-method isolationWindowLowerMz,MsBackend-method isolationWindowLowerMz<-,MsBackend-method isolationWindowTargetMz,MsBackend-method isolationWindowTargetMz<-,MsBackend-method isolationWindowUpperMz,MsBackend-method isolationWindowUpperMz<-,MsBackend-method isReadOnly,MsBackend-method length,MsBackend-method lengths,MsBackend-method MsBackend MsBackend-class MsBackendDataFrame MsBackendDataFrame-class MsBackendHdf5Peaks MsBackendMemory MsBackendMemory-class MsBackendMzR MsBackendMzR-class msLevel,MsBackend-method msLeveL<-,MsBackend-method msLevel<-,MsBackend-method mz,MsBackend-method mz<-,MsBackend-method peaksData,MsBackend-method peaksData<-,MsBackend-method peaksVariables,MsBackend-method polarity,MsBackend-method polarity<-,MsBackend-method precScanNum,MsBackend-method precursorCharge,MsBackend-method precursorIntensity,MsBackend-method precursorMz,MsBackend-method precursorMz<-,MsBackend-method reset,MsBackend-method rtime,MsBackend-method rtime<-,MsBackend-method scanIndex,MsBackend-method selectSpectraVariables,MsBackend-method smoothed,MsBackend-method smoothed<-,MsBackend-method spectraData,MsBackend-method spectraData<-,MsBackend-method spectraNames,MsBackend-method spectraNames<-,MsBackend-method spectraVariables,MsBackend-method split,MsBackend,ANY-method supportsSetBackend supportsSetBackend,MsBackend-method tic,MsBackend-method uniqueMsLevels,MsBackend-method [,MsBackend-method [[,MsBackend-method [[<-,MsBackend-method
Base MsBackend class providing data caching mechanism$,MsBackendCached-method $<-,MsBackendCached-method acquisitionNum,MsBackendCached-method backendInitialize,MsBackendCached-method centroided,MsBackendCached-method centroided<-,MsBackendCached-method collisionEnergy,MsBackendCached-method collisionEnergy<-,MsBackendCached-method dataOrigin,MsBackendCached-method dataOrigin<-,MsBackendCached-method dataStorage,MsBackendCached-method extractByIndex,MsBackendCached,ANY-method intensity,MsBackendCached-method ionCount,MsBackendCached-method isEmpty,MsBackendCached-method isolationWindowLowerMz,MsBackendCached-method isolationWindowLowerMz<-,MsBackendCached-method isolationWindowTargetMz,MsBackendCached-method isolationWindowTargetMz<-,MsBackendCached-method isolationWindowUpperMz,MsBackendCached-method isolationWindowUpperMz<-,MsBackendCached-method length,MsBackendCached-method lengths,MsBackendCached-method MsBackendCached MsBackendCached-class msLevel,MsBackendCached-method mz,MsBackendCached-method polarity,MsBackendCached-method polarity<-,MsBackendCached-method precursorCharge,MsBackendCached-method precursorIntensity,MsBackendCached-method precursorMz,MsBackendCached-method rtime,MsBackendCached-method rtime<-,MsBackendCached-method scanIndex,MsBackendCached-method selectSpectraVariables,MsBackendCached-method show,MsBackendCached-method smoothed,MsBackendCached-method smoothed<-,MsBackendCached-method spectraData,MsBackendCached-method spectraData<-,MsBackendCached-method spectraVariables,MsBackendCached-method [,MsBackendCached-method
Calculate Neutral Loss SpectraneutralLoss neutralLoss,Spectra,PrecursorMzParam-method PrecursorMzParam
MZ delta Quality ControlcomputeMzDeltas plotMzDelta
Parallel and chunk-wise processing of 'Spectra'backendBpparam,Spectra-method processingChunkFactor processingChunkSize processingChunkSize<-
The Spectra class to manage and access MS datadataStorageBasePath,Spectra-method dataStorageBasePath<-,Spectra-method export export,Spectra-method setBackend setBackend,Spectra,MsBackend-method Spectra Spectra,ANY-method Spectra,character-method Spectra,missing-method Spectra,MsBackend-method Spectra-class
Plotting SpectraplotSpectra plotSpectraMirror plotSpectraMirror,Spectra-method plotSpectraOverlay spectra-plotting
Accessing mass spectrometry data$,Spectra-method $<-,Spectra-method acquisitionNum acquisitionNum,Spectra-method asDataFrame centroided centroided,Spectra-method centroided<-,Spectra-method collisionEnergy collisionEnergy,Spectra-method collisionEnergy<-,Spectra-method coreSpectraVariables dataOrigin dataOrigin,Spectra-method dataOrigin<-,Spectra-method dataStorage dataStorage,Spectra-method intensity intensity,Spectra-method ionCount ionCount,Spectra-method isCentroided isCentroided,Spectra-method isEmpty isEmpty,Spectra-method isolationWindowLowerMz isolationWindowLowerMz,Spectra-method isolationWindowLowerMz<-,Spectra-method isolationWindowTargetMz isolationWindowTargetMz,Spectra-method isolationWindowTargetMz<-,Spectra-method isolationWindowUpperMz isolationWindowUpperMz,Spectra-method isolationWindowUpperMz<-,Spectra-method length,Spectra-method lengths lengths,Spectra-method msLevel msLevel,Spectra-method mz mz,Spectra-method peaksData peaksData,Spectra-method peaksVariables peaksVariables,Spectra-method polarity polarity,Spectra-method polarity<-,Spectra-method precScanNum,Spectra-method precursorCharge precursorCharge,Spectra-method precursorIntensity precursorIntensity,Spectra-method precursorMz precursorMz,Spectra-method precursorMz<-,Spectra-method rtime rtime,Spectra-method rtime<-,Spectra-method scanIndex scanIndex,Spectra-method smoothed smoothed,Spectra-method smoothed<-,Spectra-method spectraData spectraData,Spectra-method spectraData<-,Spectra-method spectraNames spectraNames,Spectra-method spectraNames<-,Spectra-method spectraVariables spectraVariables,Spectra-method tic tic,Spectra-method uniqueMsLevels uniqueMsLevels,Spectra-method [[,Spectra-method [[<-,Spectra-method
Mapping between spectra variables and data file fieldsspectraVariableMapping