xsAnnotate-class: 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