Feature compounding aims at identifying and grouping LC-MS features
representing different ions or adducts (including isotopes) of the same
The MsFeatures package
provides a general framework and functionality to group features based on
different properties. The
groupFeatures methods for XCMSnExp
objects implemented in
xcms extend these to enable the compounding of
LC-MS data. Note that these functions simply define feature groups but don't
actually aggregate or combine the features.
MsFeatures::groupFeatures() for an overview on the general feature
grouping concept as well as details on the individual settings and
The available options for
xcms preprocessing results
XCMSnExp objects after correspondence analysis with
Grouping by similar retention times:
Grouping by similar feature values across samples:
Grouping by similar peak shape of extracted ion chromatograms:
An ideal workflow grouping features should sequentially perform the above methods (in the listed order).
Compounded feature groups can be accessed with the
## S4 method for signature 'XCMSnExp' featureGroups(object) ## S4 replacement method for signature 'XCMSnExp' featureGroups(object) <- value
Johannes Rainer, Mar Garcia-Aloy, Vinicius Veri Hernandes
plotFeatureGroups() for visualization of grouped features.
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.