alignmentLC {metaMS} | R Documentation

## LC alignment

### Description

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.

### Usage

    alignmentLC(xset, settings)

### Arguments

`xset` | The `xcmsSet` object resulting from peak detection
`settings` | The subset of settings contained into the "Alignment" element of the XCMSsettings list.

### Details

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`.

### Value

A grouped and rt-aligned `xcmsSet` object.

### Author(s)

Ron Wehrens and Pietro Franceschi

### See Also

`FEMsettings`

[Package metaMS version 1.16.0 Index]