This package, part of the R for Mass Spectrometry initiative, provides support for handling and analysing chromatographic mass spectrometry (MS) data.
It follows the API that is currenlty available in the Chromatogram class in the MSnbase package, with support for different backends to provide/represent the data, similar to the Spectra package.
General concept
A Chromatograms object is designed to contain multiple chromatographic data (i.e. chromatogram entities). The data will be stored linearly, i.e. as a long list of chromatograms. The Chromatograms object will be the main object for the end user, providing functionality to access, filter or process chromatographic data, with the actual chromatographic MS data being stored within backend classes. Different implementations of backend classes can be designed for high performance or low memory footprint.
The existing backend classes are:
ChromBackendMemory: a memory-based backend, storing the data in memory. This is the default backend and is used for testing purposes.The
ChromBackendMzRinherits all slots and methods from the baseChromBackendMemorybackend, providing additional functionality for reading chromatographic data from mzML files.ChromBackendSpectra: TheChromBackendSpectrainherits all slots and methods from the baseChromBackendMemorybackend, providing additional functionality for reading chromatographic data fromSpectraobjects.
These backend are then handled on a user level by the Chromatograms class, which provides a unified interface to access and manipulate the chromatographic data.
Installation
install.packages("BiocManager")
BiocManager::install("RforMassSpectrometry/Chromatograms")Contributions
Please the R for Mass Spectrometry code of conduct and contribution guidelines.