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 |