AdductQuantif-class     AdductQuantif class The AdductQuantif class
                        contains a peak integral matrix, peak ranges
                        and region of integration, the isotopic
                        distribution identified for each integrated
                        peak and the target table of peaks integrated.
AdductSpec-class        AdductSpec class
IsotopicDistributionMod
                        modified function from package OrgMassSpecR
adductQuant             Adduct quantification for adductomicsR
adductSpecGen           Constructor of AdductSpec object deconvolute
                        spectra MS2 and MS1 levels
digestMod               modified 'Digest' function (from OrgMassSpecR
                        package)
dotProdMatrix           dot product matrix calculation
dotProdSpectra          dot product calculation
dynamicNoiseFilter      Dynamic Noise filtration
filterAdductTable       filter samples with low QC and features with
                        large missing values Removes adducts that have
                        not been integrated with many missing values
                        and provides QC on samples
findPeaks               identify peaks
generateTargTable       Make a target table for adductomicsR
                        quantificaton using specSimPep results
loessWrapperMod         wrapper script for loess modeling
ms2Group                group MS/MS precursor masses
nAdjPeaks               remove lower intensity adjacent peaks
outputPeakTable         output peak table from AdductQuantif object
peakIdQuant_newMethod   Adduct Peak quant
peakIntegrate           integrate a peak from a peak table with peak
                        start and peak end retention times
peakListId              peak list Identification
peakRangeSum            raw eic signal intensity and mass summation and
                        spike removal.
probPeaks               potentially problematic peak identification
retentionCorr           loess-based retention time deviation correction
rtDevModelSave          extract and save retention time deviation
                        models from adductSpec class object
rtDevModelling          MS/MS spectrum grouping and retention time
                        deviation modelling for adductomicsR
signalGrouping          Signal grouping
specSimPepId            spectral similarity based adducted peptide
                        identification for adductomicsR
spectraCreate           Deconvolute both MS2 and MS1 levels scans
                        adductomics
truePeakTrough          true peak and trough detection
