annotate {CAMERA} | R Documentation |
Annotate isotope peaks, adducts and fragments for a (grouped) xcmsSet xs
. Returns a xsAnnotate object.
annotate(xs, sigma = 6, perfwhm = 0.6, cor_eic_th = 0.75, maxcharge = 3, maxiso = 4, ppm = 5, mzabs = 0.01, multiplier = 3, sample=1, category = NA, polarity="positive")
xs |
xcmsSet with peak group assignments |
sigma |
Isotopic peak relationship table |
perfwhm |
Adduct/Fragment peak relationship table |
cor_eic_th |
correlation threshold (0..1) |
maxcharge |
max charge of the ions |
maxiso |
max number of isotopes |
ppm |
ppm error |
mzabs |
absolut error |
multiplier |
max. number n of [nM+x] clusterions |
sample |
Index of which sample is used for the correlation |
category |
Which class label should be used |
polarity |
Which polarity mode was used for measuring of the ms sample |
Batch script for a annotation for a a (grouped) xcmsSet xs
. Generate intern a xsAnnotate object and calls the member function for the annotation step. Returns a peaklist with additonal columns for isotopes, adducts and an index for the pseudo spectra group. xsAnnotate groups Peaks into spectra groups, after there Retentiontime and EIC correlations.
Attention: For the EIC correlation only one sample can be used, so if the xcmsSet contains more than one sample, one must be chosen.
annotate
returns an xsAnnotate object. For more information about see xsAnnotate-class
Carsten Kuhl <ckuhl@ipb-halle.de>
library(CAMERA) file <- system.file('mzdata/MM14.mzdata', package = "CAMERA") xs <- xcmsSet(file, method="centWave", ppm=30, peakwidth=c(5,10)) annotated_xs<- annotate(xs)