Processing of adductomic mass spectral datasets

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Documentation for package ‘adductomicsR’ version 1.16.0

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

Help Pages

adductQuant	Adduct quantification for adductomicsR
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
adductSpecGen	Constructor of AdductSpec object deconvolute spectra MS2 and MS1 levels
c-method	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.
c-method	AdductSpec class
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
groupMS2spec,rtDevModels,sumAdductType,Parameters,AdductSpec-class	AdductSpec class
groupMS2spec-method	AdductSpec class
IsotopicDistributionMod	modified function from package OrgMassSpecR
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
peakIdData,predIsoDist,targTable,AdductQuantif,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.
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.
Peptides,specPepMatches,AdductSpec-class	AdductSpec class
predIsoDist-method	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.
probPeaks	potentially problematic peak identification
retentionCorr	loess-based retention time deviation correction
rtDevModelling	MS/MS spectrum grouping and retention time deviation modelling for adductomicsR
rtDevModelSave	extract and save retention time deviation models from adductSpec class object
show,c,file.paths,peakQuantTable,AdductQuantif,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.
show,c,Specfile.paths,adductMS2spec,metaData,AdductSpec-class	AdductSpec class
signalGrouping	Signal grouping
specPepMatches-method	AdductSpec class
specSimPepId	spectral similarity based adducted peptide identification for adductomicsR
spectraCreate	Deconvolute both MS2 and MS1 levels scans adductomics
truePeakTrough	true peak and trough detection
x	AdductSpec class