xcmspackage (version >= 3)
Version >= 3 of the
xcms package are updated and partially re-written versions
of the original
xcms package. The version number 3 was selected to avoid
confusions with the
software. While providing all of the original software's functionality,
version >= 3 aims at:
1) Better integration into the Bioconductor framework:
- Make use and extend classes defined in the
- Implement class versioning (Biobase's
BiocParallel for parallel processing.
2) Implementation of validation methods for all classes to ensure data
3) Easier and faster access to raw spectra data.
4) Cleanup of the source code:
- Remove obsolete and redundant functionality (
- 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
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
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
Discussions and suggestions are welcome: https://github.com/sneumann/xcms/issues
For more information see the package vignette.
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