Package: adductomicsR 1.23.0

Josie Hayes

adductomicsR: Processing of adductomic mass spectral datasets

Processes MS2 data to identify potentially adducted peptides from spectra that has been corrected for mass drift and retention time drift and quantifies MS1 level mass spectral peaks.

Authors:Josie Hayes <[email protected]>

adductomicsR_1.23.0.tar.gz
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adductomicsR.pdf |adductomicsR.html✨
adductomicsR/json (API)

# Install 'adductomicsR' in R:
install.packages('adductomicsR', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/josielhayes/adductomicsr/issues

On BioConductor:adductomicsR-1.21.0(bioc 3.20)adductomicsR-1.20.0(bioc 3.19)

massspectrometrymetabolomicssoftwarethirdpartyclientdataimportgui

4.00 score 1 stars 5 scripts 340 downloads 10 exports 127 dependencies

Last updated 24 days agofrom:3c1217cfeb. Checks:OK: 1 WARNING: 6. Indexed: yes.

TargetResultDate
Doc / VignettesOKOct 30 2024
R-4.5-winWARNINGOct 30 2024
R-4.5-linuxWARNINGOct 30 2024
R-4.4-winWARNINGOct 30 2024
R-4.4-macWARNINGOct 30 2024
R-4.3-winWARNINGOct 30 2024
R-4.3-macWARNINGOct 30 2024

Exports:adductQuantdigestModfilterAdductTablefindPeaksgenerateTargTableIsotopicDistributionModloessWrapperModoutputPeakTablertDevModellingspecSimPepId

Dependencies:adductDataade4AnnotationDbiAnnotationHubaskpassbase64encBiobaseBiocFileCacheBiocGenericsBiocManagerBiocVersionBiostringsbitbit64blobbootbootstrapbslibcachemclasscliclustercodetoolscpp11crayoncrosstalkcurldata.tableDBIdbplyrDEoptimRdigestdiptestdoSNOWdplyrDTevaluateExperimentHubfansifastclusterfastmapfilelockflexmixfontawesomeforeachfpcfsgenericsGenomeInfoDbGenomeInfoDbDatagluehighrhtmltoolshtmlwidgetshttpuvhttrIRangesiteratorsjquerylibjsonliteKEGGRESTkernlabknitrlaterlatticelazyevallifecyclemagrittrMASSmclustmemoisemimemodeltoolsmzRncdf4nnetopensslOrgMassSpecRpastecspillarpixmappkgconfigplogrplyrpngprabcluspracmapromisesProtGenericspurrrR6rappdirsRcppRcppArmadilloRcppEigenreshape2Rhdf5librlangrmarkdownrobustbaseRSQLitervestS4VectorssassselectrsmoothersnowspstringistringrsystibbletidyrtidyselecttinytexTTRUCSC.utilsutf8vctrswithrxfunxml2xtsXVectoryamlzlibbioczoo

AdductomicsR workflow

Josie Hayes

Rendered fromadductomicsRWorkflow.Rmdusingknitr::rmarkdownon Oct 30 2024.

Last update: 2019-04-18
Started: 2018-10-18

Readme and manuals

Help Manual

Help pageTopics
Adduct quantification for adductomicsRadductQuant
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.AdductQuantif-class c,AdductQuantif-method c,file.paths,peakQuantTable,peakIdData,AdductQuantif-method peakIdData,predIsoDist,targTable,AdductQuantif,AdductQuantif-class predIsoDist,targTable,AdductQuantif-method show,c,file.paths,peakQuantTable,AdductQuantif,AdductQuantif-class
AdductSpec classAdductSpec-class c,AdductSpec-method c,Specfile.paths,adductMS2spec,metaData,Parameters,AdductSpec-method groupMS2spec,rtDevModels,sumAdductType,Parameters,AdductSpec-class groupMS2spec,rtDevModels,sumAdductType,Peptides,AdductSpec-method Peptides,specPepMatches,AdductSpec-class show,c,Specfile.paths,adductMS2spec,metaData,AdductSpec-class specPepMatches,AdductSpec-method x
Constructor of AdductSpec object deconvolute spectra MS2 and MS1 levelsadductSpecGen
modified 'Digest' function (from OrgMassSpecR package)digestMod
dot product matrix calculationdotProdMatrix
dot product calculationdotProdSpectra
Dynamic Noise filtrationdynamicNoiseFilter
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 samplesfilterAdductTable
identify peaksfindPeaks
Make a target table for adductomicsR quantificaton using specSimPep resultsgenerateTargTable
modified function from package OrgMassSpecRIsotopicDistributionMod
wrapper script for loess modelingloessWrapperMod
group MS/MS precursor massesms2Group
remove lower intensity adjacent peaksnAdjPeaks
output peak table from AdductQuantif objectoutputPeakTable
Adduct Peak quantpeakIdQuant_newMethod
integrate a peak from a peak table with peak start and peak end retention timespeakIntegrate
peak list IdentificationpeakListId
raw eic signal intensity and mass summation and spike removal.peakRangeSum
potentially problematic peak identificationprobPeaks
loess-based retention time deviation correctionretentionCorr
MS/MS spectrum grouping and retention time deviation modelling for adductomicsRrtDevModelling
extract and save retention time deviation models from adductSpec class objectrtDevModelSave
Signal groupingsignalGrouping
spectral similarity based adducted peptide identification for adductomicsRspecSimPepId
Deconvolute both MS2 and MS1 levels scans adductomicsspectraCreate
true peak and trough detectiontruePeakTrough