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# SQL-based Mass Spectrometry Data Backend [![Project Status: Active – The project has reached a stable, usable state and is being actively developed.](]( [![R-CMD-check-bioc](]( [![codecov](]( [![license](]( [![years in bioc](]( [![Ranking by downloads](]( [![build release](]( [![build devel](]( This repository provides a *backend* for [Spectra]( objects that supports storage of mass spectrometry (MS) data in an SQL database. The package provides the functionality to create such databases from original (raw) MS data files (in mzML, mzXML or netCDF format) and allows to extract the data in an efficient way. For more information see the package [homepage]( ## Creating a database By providing the connection to an SQL database, the `createMsBackendSqlDatabase` imports raw MS data from provided file names and stores it into the dedicated database tables created during import. While `MsBackendSql` supports any type of SQL database, it is currently optimized for MySQL/MariaDB databases. ## Using a *MsBackendSql* database MS data in a *MsBackendSql* database can be accessed through the [`Spectra`]( package by using the `MsBackendSql` MS backend. Assuming the variable `dbcon` represents a (RDBI) database connection to a *MsBackendSql*, the data can be represented/used with a `Spectra` object by: ```r library(Spectra) library(MsBackendSql) sps <- Spectra(dbcon, source = MsBackendSql()) ``` For more information see the package [homepage]( # Installation The package can be installed with ```r install.packages("BiocManager") BiocManager::install("MsBackendSql") ``` # Contributions Contributions are highly welcome and should follow the [contribution guidelines]( Also, please check the coding style guidelines in the [RforMassSpectrometry vignette](