Package: metabCombiner 1.23.0

Hani Habra

metabCombiner: Method for Combining LC-MS Metabolomics Feature Measurements

This package aligns LC-HRMS metabolomics datasets acquired from biologically similar specimens analyzed under similar, but not necessarily identical, conditions. Peak-picked and simply aligned metabolomics feature tables (consisting of m/z, rt, and per-sample abundance measurements, plus optional identifiers & adduct annotations) are accepted as input. The package outputs a combined table of feature pair alignments, organized into groups of similar m/z, and ranked by a similarity score. Input tables are assumed to be acquired using similar (but not necessarily identical) analytical methods.

Authors:Hani Habra [aut, cre], Alla Karnovsky [ths]

metabCombiner_1.23.0.tar.gz
metabCombiner_1.23.0.zip(r-4.7)metabCombiner_1.23.0.zip(r-4.6)metabCombiner_1.23.0.zip(r-4.5)
metabCombiner_1.23.0.tgz(r-4.6-x86_64)metabCombiner_1.23.0.tgz(r-4.6-arm64)metabCombiner_1.23.0.tgz(r-4.5-x86_64)metabCombiner_1.23.0.tgz(r-4.5-arm64)
metabCombiner_1.23.0.tar.gz(r-4.7-arm64)metabCombiner_1.23.0.tar.gz(r-4.7-x86_64)metabCombiner_1.23.0.tar.gz(r-4.6-arm64)metabCombiner_1.23.0.tar.gz(r-4.6-x86_64)
metabCombiner_1.23.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
metabCombiner/json (API)
NEWS

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

Bug tracker:https://github.com/hhabra/metabcombiner/issues

Datasets:
  • metabBatches - Three LC-MS Metabolomics Batch Datasets
  • plasma20 - 20 minute LC-MS Analysis of Human Plasma
  • plasma30 - 30 minute LC-MS Analysis of Human Plasma

On BioConductor:metabCombiner-1.23.0(bioc 3.24)metabCombiner-1.22.0(bioc 3.23)

softwaremassspectrometrymetabolomicsmass-spectrometry

5.71 score 13 stars 13 scripts 422 downloads 45 exports 77 dependencies

Last updated from:2467920618. Checks:1 WARNING, 11 NOTE, 2 OK. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksWARNING146
linux-devel-arm64NOTE241
linux-devel-x86_64NOTE244
source / vignettesOK299
linux-release-arm64NOTE205
linux-release-x86_64NOTE263
macos-release-arm64NOTE173
macos-release-x86_64NOTE383
macos-oldrel-arm64NOTE159
macos-oldrel-x86_64NOTE298
windows-develNOTE186
windows-releaseNOTE153
windows-oldrelNOTE180
wasm-releaseOK128

Exports:adductDatabatchCombinecalcScorescalcScoresParamcombineDatacombinedTabledatasetsevaluateParamsfeatDatafilteredfit_gamfit_loessfitgamParamfitloessParamgetAnchorsgetCoefficientsgetDatagetExtragetModelgetSamplesgetStatsidDatalabelRowslabelRowsParammetabCombinemetabCombinermetabDatamzDatamzFitmzfitParamnonmatchedopts.duplicateplotplot_fitQDatareduceTablereduceTableParamrtDataselectAnchorsselectAnchorsParamupdateTableswrite2filexxyy

Dependencies:BiocGenericscaretclasscliclockcodetoolscpp11data.tablediagramdigestdplyre1071farverforeachfuturefuture.applygenericsggplot2globalsgluegowergtablehardhatipredisobanditeratorsKernSmoothlabelinglatticelavalifecyclelistenvlubridatemagrittrMASSMatrixmatrixStatsmgcvModelMetricsnlmennetnumDerivparallellypillarpkgconfigplyrpROCprodlimprogressrproxypurrrR6RColorBrewerRcpprecipesreshape2rlangrpartS4VectorsS7scalesshapesparsevctrsSQUAREMstringistringrsurvivaltibbletidyrtidyselecttimechangetimeDatetzdbutf8vctrsviridisLitewithr

Combine LC-MS Metabolomics Datasets with metabCombiner

Hani Habra

Rendered frommetabCombiner_vignette.Rmdusingknitr::rmarkdownon May 30 2026.

Last update: 2023-04-11
Started: 2020-06-01

Readme and manuals

Help Manual

Help pageTopics
Retrieve Adduct AnnotationsadductData adductData,metabCombiner-method
Process and Filter Metabolomics Feature ListsadjustData
Stepwise Multi-batch LC-MS AlignmentbatchCombine
Compute Feature Similarity ScorescalcScores
List calcScores DefaultscalcScoresParam
Obtain All Feature DatacombineData combineData,metabCombiner-method
Obtain Feature Alignment ReportcombinedTable combinedTable,metabCombiner-method
Obtain Errors for metabCombiner Object CheckscombinerCheck
Cross Validation for Model FitscrossValFit
Obtain Dataset IDsdatasets datasets,metabCombiner-method
Detect metabData Input ColumnsdetectFields
Evaluate Similarity Score ParametersevaluateParams
Obtain Feature MetadatafeatData featData,metabCombiner-method
Filter Outlier Ordered PairsfilterAnchors
Retrieve Filtered Featuresfiltered filtered,metabData-method
Filter Features by Retention Time RangefilterRT
Fit RT Projection Model With GAMsfit_gam
Fit RT Projection Model With LOESSfit_loess
List fit_gam DefaultsfitgamParam
List fitLoess DefaultsfitloessParam
Get Ordered Retention Time PairsgetAnchors getAnchors,metabCombiner-method
Obtain Last-Used Score CoefficientsgetCoefficients getCoefficients,metabCombiner-method
Get Processed DatasetgetData getData,metabData-method
Get Extra Data Column NamesgetExtra getExtra,metabCombiner-method getExtra,metabData-method
Get Fitted RT ModelgetModel getModel,metabCombiner-method
Get Sample Names From metabCombiner or metabData ObjectgetSamples getSamples,metabCombiner-method getSamples,metabData-method
Get Object StatisticsgetStats getStats,metabCombiner-method getStats,metabData-method
Retrieve Feature IdentitiesidData idData,metabCombiner-method
Select Matching Ids as AnchorsidentityAnchorSelection
Determine 'combinedTable' ValidityisCombinedTable
Determine if object is a valid metabCombiner objectisMetabCombiner
Determine validity of input metabData objectisMetabData
Iterative Selection of Ordered PairsiterativeAnchorSelection
Annotate and Remove Report RowslabelRows reduceTable
List labelRows & reduceTable DefaultslabelRowsParam reduceTableParam
Three LC-MS Metabolomics Batch DatasetsmetabBatches
metabCombiner Wrapper FunctionmetabCombine
Form a metabCombiner object.metabCombiner
'metabCombiner' Combined Metabolomics Dataset ClassmetabCombiner-class
Constructor for the metabData object.metabData
'metabData' Single Metabolomics Dataset ClassmetabData-class
Retrieve m/z ValuesmzData mzData,metabCombiner-method
Compute m/z Shift ModelmzFit
Parameterize m/z Shift ModelmzfitParam
Binning of mass spectral features in m/z dimensionmzGroup
Get Nonmatched Featuresnonmatched nonmatched,metabCombiner-method
Weight Parameter Objective Functionobjective
Duplicate Feature Detection Parametersopts.duplicate
20 minute LC-MS Analysis of Human Plasmaplasma20
30 minute LC-MS Analysis of Human Plasmaplasma30
Plot metabCombiner Fitsplot,metabCombiner,ANY-method plot_fit
Retrieve Relative Abundance ValuesQData QData,metabCombiner-method
Resolve Conflicting Alignment SubgroupsresolveRows
Retrieve Retention Time ValuesrtData rtData,metabCombiner-method
Calculate Pairwise Alignment ScoresscorePairs
Select Anchors for Nonlinear RT ModelselectAnchors
List selectAnchors DefaultsselectAnchorsParam
Update 'metabCombiner' ObjectsupdateTables
Print metabCombiner Report to File.write2file
Obtain x & y Data Identifiersx x,metabCombiner-method xy xy,metabCombiner-method y y,metabCombiner-method