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. MsBackendSql supports any type of SQL database, with some optimizations 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:
library(Spectra)
library(MsBackendSql)
sps <- Spectra(dbcon, source = MsBackendSql())For more information see the package homepage.
Changing to a MsBackendSql using the setBackend() function
Finally, it is also possible to use the setBackend() method on a Spectra object to change to a MsBackendSql backend. This will take all the MS data of the Spectra object and store that into a new SQL database.
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.