GitHub - rformassspectrometry/MsBackendSql: MsBackend adding support to store/access mass spectrometry data in large SQL databases through the Spectra R package. (original) (raw)

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 forSpectra 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 packagehomepage.

Creating a database

By providing the connection to an SQL database, the createMsBackendSqlDatabaseimports 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 theSpectra 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:

library(Spectra) library(MsBackendSql) sps <- Spectra(dbcon, source = MsBackendSql())

For more information see the packagehomepage.

Installation

The package can be installed with

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.