Package: MsBackendSql 1.7.1

Johannes Rainer

MsBackendSql: SQL-based Mass Spectrometry Data Backend

SQL-based mass spectrometry (MS) data backend supporting also storange and handling of very large data sets. Objects from this package are supposed to be used with the Spectra Bioconductor package. Through the MsBackendSql with its minimal memory footprint, this package thus provides an alternative MS data representation for very large or remote MS data sets.

Authors:Johannes Rainer [aut, cre], Chong Tang [ctb], Laurent Gatto [ctb]

MsBackendSql_1.7.1.tar.gz
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MsBackendSql.pdf |MsBackendSql.html✨
MsBackendSql/json (API)

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

Peer review:

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

On BioConductor:MsBackendSql-1.7.0(bioc 3.21)MsBackendSql-1.6.0(bioc 3.20)

infrastructuremassspectrometrymetabolomicsdataimportproteomics

5.43 score 4 stars 17 scripts 27 exports 36 dependencies

Last updated 3 days agofrom:1e59addc92. Checks:OK: 4 NOTE: 2 ERROR: 1. Indexed: no.

TargetResultDate
Doc / VignettesOKNov 20 2024
R-4.5-winNOTENov 20 2024
R-4.5-linuxNOTENov 20 2024
R-4.4-winOKNov 20 2024
R-4.4-macOKNov 20 2024
R-4.3-winOKNov 20 2024
R-4.3-macERRORNov 20 2024

Exports:backendInitializebackendMergecentroidedcreateMsBackendSqlDatabasedataStorageextractByIndexfilterDataOriginfilterMsLevelfilterPrecursorMzRangefilterPrecursorMzValuesfilterRtintensity<-MsBackendOfflineSqlMsBackendSqlmz<-peaksDatapeaksVariablesprecScanNumresetshowsmoothedspectraDataspectraNamesspectraNames<-supportsSetBackendticuniqueMsLevels

Dependencies:BHBiocGenericsBiocParallelcliclueclustercodetoolscpp11crayondata.tableDBIformatRfsfutile.loggerfutile.optionsgenericsgluehmsIRangeslambda.rlifecycleMASSMetaboCoreUtilsMsCoreUtilspkgconfigprettyunitsprogressProtGenericsR6RcpprlangS4VectorssnowSpectrastringivctrs

Storing Mass Spectrometry Data in SQL Databases

Rendered fromMsBackendSql.Rmdusingknitr::rmarkdownon Nov 20 2024.

Last update: 2024-03-28
Started: 2022-11-16

Readme and manuals

Help Manual

Help pageTopics
SQL-based MS backend without active database connectionbackendInitialize,MsBackendOfflineSql-method MsBackendOfflineSql MsBackendOfflineSql-class
'Spectra' MS backend storing data in a SQL database$<-,MsBackendSql-method backendBpparam,MsBackendSql-method backendInitialize,MsBackendSql-method backendMerge,MsBackendOfflineSql-method backendMerge,MsBackendSql-method centroided,MsBackendSql-method createMsBackendSqlDatabase dataStorage,MsBackendOfflineSql-method dataStorage,MsBackendSql-method dbconn,MsBackendOfflineSql-method dbconn,MsBackendSql-method extractByIndex,MsBackendSql,ANY-method filterDataOrigin,MsBackendOfflineSql-method filterDataOrigin,MsBackendSql-method filterMsLevel,MsBackendOfflineSql-method filterMsLevel,MsBackendSql-method filterPrecursorMzRange,MsBackendOfflineSql-method filterPrecursorMzRange,MsBackendSql-method filterPrecursorMzValues,MsBackendOfflineSql-method filterPrecursorMzValues,MsBackendSql-method filterRt,MsBackendOfflineSql-method filterRt,MsBackendSql-method intensity<-,MsBackendSql-method MsBackendSql MsBackendSql-class mz<-,MsBackendSql-method peaksData,MsBackendOfflineSql-method peaksData,MsBackendSql-method peaksVariables,MsBackendOfflineSql-method peaksVariables,MsBackendSql-method precScanNum,MsBackendSql-method reset,MsBackendOfflineSql-method reset,MsBackendSql-method show,MsBackendOfflineSql-method show,MsBackendSql-method smoothed,MsBackendSql-method spectraData,MsBackendOfflineSql-method spectraData,MsBackendSql-method spectraNames,MsBackendSql-method spectraNames<-,MsBackendSql-method supportsSetBackend,MsBackendOfflineSql-method supportsSetBackend,MsBackendSql-method tic,MsBackendOfflineSql-method tic,MsBackendSql-method uniqueMsLevels,MsBackendOfflineSql-method uniqueMsLevels,MsBackendSql-method [,MsBackendSql-method