alignmentLC: LC alignment

Description Usage Arguments Details Value Author(s) See Also


Performs grouping and retention time correction via xcms. The settings are specified as a list with a form similar to the one discussed in the help of FEMsettings. The sequence of actions depends on the type of retention time correction, which is specified inside the Retcor list inside the Alignment slot (see details). Integration of areas of missing peaks is performed depending on the fillPeaks setting.


alignmentLC(xset, settings)



The xcmsSet object resulting from peak detection


The subset of settings contained into the "Alignment" element of the XCMSsettings list.


The sequence of actions depends on the algorithm used by xcms for retention time correction. For the density-based approach the sequence is: 1) across sample grouping, 2) retention time correction, 3) second across sample grouping, 4) optional fill-peaks. For "obiwarp", instead, the sequence of actions is: 1) retention time correction, 2) across sample grouping, 3) optional fill-peaks. For across-sample grouping in xcms, the minsamp parameter can be specified in the settings either as a minimum number of samples (min.class.size) or as the fraction of samples per class (min.class.fraction). If both are given the smallest number is used. If the retention time correction is performed by the density-based approach, the settings allow to express the xcms parameters missing and extra as fractions. When "obiwarp" is used for retention time correction, the sample with the bigger number of features is automatically selected as the "reference" sample. The xcms parameters for the retcor xcms function can be specified in the Retcor list included in the Alignment slot of FEMsettings.


A grouped and rt-aligned xcmsSet object.


Ron Wehrens and Pietro Franceschi

See Also


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