xsAnnotate-class: Class xsAnnotate, a class for annotated peak data

In CAMERA: Collection of annotation related methods for mass spectrometry 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, [e-mail]

See Also

xsAnnotate

CAMERA documentation built on Nov. 8, 2020, 4:59 p.m.