The xcms3 package

The xcms3 package is an updated and partially re-written version of the xcms package. The version 3 was selected to avoid confusions with the xcms2 (http://pubs.acs.org/doi/abs/10.1021/ac800795f) software. While providing all of the original software’s functionality, xcms3 aims at:

1. Better integration into the Bioconductor framework:
   • Make use and extend classes defined in the MSnbase package.
   • Implement class versioning (Biobase’s Versioned class).
   • Use BiocParallel for parallel processing.
2. Implementation of validation methods for all classes to ensure data integrity.
3. Easier and faster access to raw spectra data.
4. Cleanup of the source code:
   • Remove obsolete and redundant functionality (getEIC, rawEIC etc).
   • Unify interfaces, i.e. implement a layer of base functions accessing all analysis methods (which are implemented in C, C++ or R).
5. Using a more consistent naming scheme of methods that follows established naming conventions (e.g. correspondence instead of grouping).
6. Update, improve and extend the documentation.
7. Establishing a layer of base R-functions that interface all analysis methods. These should take M/Z, retention time (or scan index) and intensity values as input along with optional arguments for the downstream functions (implemented in C, C++ or R). The input arguments should be basic R objects (numeric vectors) thus enabling easy integration of analysis methods in other R packages.
8. The user interface’s analysis methods should take the (raw) data object and a parameter class, that is used for dispatching to the corresponding analysis algorithm.

Discussions and suggestions are welcome: https://github.com/sneumann/xcms/issues

For more information see also the vignettes/new_functionality.Rmd file, for usage and description the vignettes/xcms.Rmd vignette.