xsAnnotate-class {CAMERA} | R Documentation

## Class xsAnnotate, a class for annotated peak data

### Description

This class transforms a `xcmsSet` object with peaks from multiple LC/MS or GC/MS samples into a set of annotation results. It contains searching algorihms for isotopes and adducts, peak grouping algorithms to find connected peak, which originate from the same molecule.

### Objects from the Class

Objects can be created with the `xsAnnotate` constructor which include the peaktable from a provided `xcmsSet`. Objects can also be created by calls of the form `new("xsAnnotate", ...)`.

### Slots

`annoGrp`:

  Assignment of mass hypotheses to correlation groups

`annoID`:

  The assignemnt of peaks to the mass difference rule used

`derivativeIons`:

  List with annotation result for every peak

`formula`:

  Matrix containing putative sum formula (intended for future use)

`isoID`:

  Matrix containing IDs and additional of all annotated isotope peaks

`groupInfo`:

  (grouped) Peaktable with "into" values

`isotopes`:

  List with annotated isotopid results for every peak

`polarity`:

  A single string with the polarity mode of the peaks

`pspectra`:

  List contains all pseudospectra with there peak IDs

`psSamples`:

  List containing information with sample was sample was selecteted as representative (automatic selection)

`ruleset`:

  A dataframe describing the mass difference rules used for the annotion

`runParallel`:

  Flag if CAMERA runs in serial or parallel mode

`sample`:

  Number of the used xcmsSet sample (beforehand sample selection)

`xcmsSet`:

  The embedded xcmsSet

### Methods

groupFWHM

  `signature(object = "xsAnnotate")`: group the peak data after the FWHM of the retention time

groupCorr

  `signature(object = "xsAnnotate")`: group the peak data after the correlation of the EICs

findIsotopes

  `signature(object = "xsAnnotate")`: search for possible isotopes in the spectra

findAdducts

  `signature(object = "xsAnnotate")`: search for possible adducts in the spectra

plotEICs

  `signature(object = "xsAnnotate")`: plot EICs of pseudospectra

### Note

No notes yet.

### Author(s)

Carsten Kuhl, ckuhl@ipb-halle.de

### See Also

`xsAnnotate`

[Package CAMERA version 1.40.0 Index]