xcms's Introduction

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:

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.
Implementation of validation methods for all classes to ensure data integrity.
Easier and faster access to raw spectra data.
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).
Using a more consistent naming scheme of methods that follows established naming conventions (e.g. correspondence instead of grouping).
Update, improve and extend the documentation.
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.
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.