Performs grouping and retention time correction via
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
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
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
If the retention time correction is performed by the density-based approach,
the settings allow to express the
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.
xcms parameters for the
xcms function can be specified
in the Retcor list included in the Alignment slot of
A grouped and rt-aligned
Ron Wehrens and Pietro Franceschi
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