Bioconductor Code: xcms (original) (raw)

[\](https://github.com/sneumann/xcms/actions?query=workflow%3AR-CMD-check-bioc) [\](https://codecov.io/github/sneumann/xcms?branch=master) [\](http://www.bioconductor.org/packages/release/bioc/html/xcms.html) [\](http://www.bioconductor.org/packages/release/bioc/html/xcms.html) [\](http://www.bioconductor.org/checkResults/devel/bioc-LATEST/xcms.html) # The `xcms` package (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 `xcms2` (http://pubs.acs.org/doi/abs/10.1021/ac800795f) software. While providing all of the original software's functionality, `xcms` version >= 3 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 the package [vignette](vignettes/xcms.Rmd).