Package: MsBackendSql 1.13.0

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_1.13.0.tar.gz
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manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
MsBackendSql/json (API)

# Install 'MsBackendSql' in R:

install.packages('MsBackendSql', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

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

On BioConductor:MsBackendSql-1.13.0(bioc 3.24)MsBackendSql-1.12.0(bioc 3.23)

infrastructure massspectrometry metabolomics dataimport proteomics

5.72 score 4 stars 33 scripts 30 exports 37 dependencies

Last updated from:596d363d16. Checks:1 ERROR, 9 OK. Indexed: yes.

Target	Result	Time
bioc-checks	ERROR	177
linux-devel-x86_64	OK	941
source / vignettes	OK	270
linux-release-x86_64	OK	608
macos-release-arm64	OK	412
macos-oldrel-arm64	OK	398
windows-devel	OK	913
windows-release	OK	709
windows-oldrel	OK	693
wasm-release	OK	178

Exports:backendInitialize backendMerge centroided createMsBackendSqlDatabase dataStorage extractByIndex filterDataOrigin filterMsLevel filterPrecursorMzRange filterPrecursorMzValues filterRt intensity intensity<-longForm MsBackendOfflineSql MsBackendSql mz mz<-peaksData peaksVariables precScanNum reset show smoothed spectraData spectraNames spectraNames<-supportsSetBackend tic uniqueMsLevels

Dependencies:BH BiocGenerics BiocParallel cli clue cluster codetools cpp11 crayon data.table DBI fastmatch formatR fs futile.logger futile.options generics glue hms IRanges lambda.r lifecycle MASS MetaboCoreUtils MsCoreUtils pkgconfig prettyunits progress ProtGenerics R6 Rcpp rlang S4Vectors snow Spectra stringi vctrs

Storing Mass Spectrometry Data in SQL Databases

Rendered fromMsBackendSql.Rmdusingknitr::rmarkdown

Last update: 2026-02-05
Started: 2022-11-16

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
SQL-based MS backend without active database connection	backendInitialize,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,MsBackendOfflineSql-method intensity,MsBackendSql-method intensity<-,MsBackendSql-method longForm,MsBackendOfflineSql-method longForm,MsBackendSql-method MsBackendSql MsBackendSql-class mz,MsBackendOfflineSql-method mz,MsBackendSql-method 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

Help page

Topics

SQL-based MS backend without active database connection

backendInitialize,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,MsBackendOfflineSql-method intensity,MsBackendSql-method intensity<-,MsBackendSql-method longForm,MsBackendOfflineSql-method longForm,MsBackendSql-method MsBackendSql MsBackendSql-class mz,MsBackendOfflineSql-method mz,MsBackendSql-method 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