Package: Spectra 1.15.3

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_1.15.3.tar.gz
Spectra_1.15.3.zip(r-4.5)Spectra_1.15.3.zip(r-4.4)Spectra_1.15.3.zip(r-4.3)
Spectra_1.15.3.tgz(r-4.4-any)Spectra_1.15.3.tgz(r-4.3-any)
Spectra_1.15.3.tar.gz(r-4.5-noble)Spectra_1.15.3.tar.gz(r-4.4-noble)
Spectra_1.15.3.tgz(r-4.4-emscripten)Spectra_1.15.3.tgz(r-4.3-emscripten)
Spectra.pdf |Spectra.html✨
Spectra/json (API)
NEWS

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

Peer review:

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

Datasets:

On BioConductor:Spectra-1.15.3(bioc 3.20)Spectra-1.14.1(bioc 3.19)

bioconductor-package

127 exports 5.94 score 20 dependencies 29 dependents 54 mentions

Last updated 1 months agofrom:4a7522e713

Exports:acquisitionNumaddProcessingapplyProcessingbackendBpparambackendInitializebackendMergebackendParallelFactorbincentroidedcentroided<-chunkapplycollisionEnergycollisionEnergy<-combinePeakscombinePeaksDatacombineSpectracompareSpectracomputeMzDeltasconcatenateSpectracontainsMzcontainsNeutralLosscoreSpectraVariablescountIdentificationsdataOrigindataOrigin<-dataStoragedataStorage<-dataStorageBasePathdataStorageBasePath<-deisotopeSpectradropNaSpectraVariablesentropyestimatePrecursorIntensityestimatePrecursorMzexportfilterAcquisitionNumfilterDataOriginfilterDataStoragefilterEmptySpectrafilterFourierTransformArtefactsfilterIntensityfilterIsolationWindowfilterMsLevelfilterMzRangefilterMzValuesfilterPolarityfilterPrecursorChargefilterPrecursorIsotopesfilterPrecursorMaxIntensityfilterPrecursorMzfilterPrecursorMzRangefilterPrecursorMzValuesfilterPrecursorPeaksfilterPrecursorScanfilterRangesfilterRtfilterValuesintensityintensity<-ionCountisCentroidedisEmptyisolationWindowLowerMzisolationWindowLowerMz<-isolationWindowTargetMzisolationWindowTargetMz<-isolationWindowUpperMzisolationWindowUpperMz<-isReadOnlyjoinPeaksjoinPeaksGnpsjoinPeaksNonejoinSpectraDataMsBackendCachedMsBackendDataFrameMsBackendHdf5PeaksMsBackendMemoryMsBackendMzRmsLevelmzmz<-neutralLosspeaksDatapeaksData<-peaksVariablespickPeaksplotMzDeltaplotSpectraplotSpectraMirrorplotSpectraOverlaypolaritypolarity<-ppmprecScanNumprecursorChargeprecursorIntensityprecursorMzPrecursorMzParamprocessingChunkFactorprocessingChunkSizeprocessingChunkSize<-processingLogreduceSpectrareplaceIntensitiesBelowresetrtimertime<-scalePeaksscanIndexselectSpectraVariablessetBackendshowsmoothsmoothedsmoothed<-SpectraspectraDataspectraData<-spectraNamesspectraNames<-spectrapplyspectraVariableMappingspectraVariablessplitsupportsSetBackendticuniqueMsLevels

Dependencies:BHBiocGenericsBiocParallelclueclustercodetoolscpp11formatRfsfutile.loggerfutile.optionsIRangeslambda.rMASSMetaboCoreUtilsMsCoreUtilsProtGenericsRcppS4Vectorssnow

Creating new MsBackend classes

Rendered fromMsBackend.Rmdusingknitr::rmarkdownon Jul 06 2024.

Last update: 2024-03-12
Started: 2023-01-12

Description and usage of Spectra objects

Rendered fromSpectra.Rmdusingknitr::rmarkdownon Jul 06 2024.

Last update: 2024-05-22
Started: 2019-06-13

Large-scale data handling and processing with Spectra

Rendered fromSpectra-large-scale.Rmdusingknitr::rmarkdownon Jul 06 2024.

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

Readme and manuals

Help Manual

Help pageTopics
The Spectra class to manage and access MS data$,Spectra-method $<-,Spectra-method acquisitionNum,Spectra-method addProcessing,Spectra-method applyProcessing backendBpparam,Spectra-method bin,Spectra-method c,Spectra-method centroided,Spectra-method centroided<-,Spectra-method collisionEnergy,Spectra-method collisionEnergy<-,Spectra-method combinePeaks combinePeaks,Spectra-method combineSpectra compareSpectra,Spectra,missing-method compareSpectra,Spectra,Spectra-method concatenateSpectra containsMz,Spectra-method containsNeutralLoss,Spectra-method coreSpectraVariables dataOrigin,Spectra-method dataOrigin<-,Spectra-method dataStorage,Spectra-method dataStorageBasePath,Spectra-method dataStorageBasePath<-,Spectra-method deisotopeSpectra dropNaSpectraVariables,Spectra-method entropy,ANY-method entropy,Spectra-method export,Spectra-method filterAcquisitionNum,Spectra-method filterDataOrigin,Spectra-method filterDataStorage,Spectra-method filterEmptySpectra,Spectra-method filterFourierTransformArtefacts,Spectra-method filterIntensity,Spectra-method filterIsolationWindow,Spectra-method filterMsLevel,Spectra-method filterMzRange,Spectra-method filterMzValues,Spectra-method filterPolarity,Spectra-method filterPrecursorCharge,Spectra-method filterPrecursorIsotopes filterPrecursorMaxIntensity filterPrecursorMz,Spectra-method filterPrecursorMzRange,Spectra-method filterPrecursorMzValues,Spectra-method filterPrecursorPeaks filterPrecursorScan,Spectra-method filterRanges,Spectra-method filterRt,Spectra-method filterValues,Spectra-method intensity,Spectra-method ionCount,Spectra-method isCentroided,Spectra-method isEmpty,Spectra-method isolationWindowLowerMz,Spectra-method isolationWindowLowerMz<-,Spectra-method isolationWindowTargetMz,Spectra-method isolationWindowTargetMz<-,Spectra-method isolationWindowUpperMz,Spectra-method isolationWindowUpperMz<-,Spectra-method joinSpectraData length,Spectra-method lengths,Spectra-method msLevel,Spectra-method mz,Spectra-method peaksData,Spectra-method peaksVariables,Spectra-method pickPeaks,Spectra-method polarity,Spectra-method polarity<-,Spectra-method precScanNum,Spectra-method precursorCharge,Spectra-method precursorIntensity,Spectra-method precursorMz,Spectra-method processingLog reduceSpectra replaceIntensitiesBelow,Spectra-method reset,Spectra-method rtime,Spectra-method rtime<-,Spectra-method scalePeaks scanIndex,Spectra-method selectSpectraVariables,Spectra-method setBackend,Spectra,MsBackend-method smooth,Spectra-method smoothed,Spectra-method smoothed<-,Spectra-method Spectra Spectra,ANY-method Spectra,character-method Spectra,missing-method Spectra,MsBackend-method Spectra-class spectraData,Spectra-method spectraData<-,Spectra-method spectraNames,Spectra-method spectraNames<-,Spectra-method spectrapply,Spectra-method spectraVariables,Spectra-method split,Spectra,ANY-method tic,Spectra-method uniqueMsLevels uniqueMsLevels,Spectra-method [,Spectra-method [[,Spectra-method [[<-,Spectra-method
Apply a function stepwise to chunks of datachunkapply
Combine peaks with similar m/z across spectracombinePeaksData
Count the number of identifications per scancountIdentifications
Estimate Precursor IntensitiesestimatePrecursorIntensity
Estimating precursor m/z valus for DDA dataestimatePrecursorMz
Fast fourier transform artefact filterfft_spectrum filterFourierTransformArtefacts
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 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 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 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 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 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'processingChunkFactor processingChunkSize processingChunkSize<-
Plotting SpectraplotSpectra plotSpectraMirror plotSpectraMirror,Spectra-method plotSpectraOverlay spectra-plotting
Mapping between spectra variables and data file fieldsspectraVariableMapping