xcmsEIC-class {xcms} | R Documentation

## Class xcmsEIC, a class for multi-sample extracted ion chromatograms

### Description

This class is used to store and plot parallel extracted ion chromatograms from multiple sample files. It integrates with the `xcmsSet` class to display peak area integrated during peak identification or fill-in.

### Objects from the Class

Objects can be created with the `getEIC` method of the `xcmsSet` class. Objects can also be created by calls of the form `new("xcmsEIC", ...)`.

### Slots

`eic`:

  list containing named entries for every sample. for each entry, a list of two column EIC matricies with retention time and intensity

`mzrange`:

  two column matrix containing starting and ending m/z for each EIC

`rtrange`:

  two column matrix containing starting and ending time for each EIC

`rt`:

  either `"raw"` or `"corrected"` to specify retention times contained in the object

`groupnames`:

  group names from `xcmsSet` object used to generate EICs

### Methods

groupnames

  `signature(object = "xcmsEIC")`: get `groupnames` slot

mzrange

  `signature(object = "xcmsEIC")`: get `mzrange` slot

plot

  `signature(x = "xcmsEIC")`: plot the extracted ion chromatograms

rtrange

  `signature(object = "xcmsEIC")`: get `rtrange` slot

sampnames

  `signature(object = "xcmsEIC")`: get sample names

### Note

No notes yet.

### Author(s)

Colin A. Smith, csmith@scripps.edu

### See Also

`getEIC`

[Package xcms version 3.9.1 Index]