Package: metabCombiner 1.17.0

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]

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metabCombiner.pdf |metabCombiner.html✨
metabCombiner/json (API)
NEWS

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

Peer review:

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-1.17.0(bioc 3.21)metabCombiner-1.16.0(bioc 3.20)

softwaremassspectrometrymetabolomicsmass-spectrometry

5.65 score 10 stars 5 scripts 202 downloads 45 exports 78 dependencies

Last updated 2 months agofrom:e8a8053b52. Checks:OK: 4 NOTE: 5. Indexed: yes.

TargetResultDate
Doc / VignettesOKDec 19 2024
R-4.5-win-x86_64NOTEDec 19 2024
R-4.5-linux-x86_64NOTEDec 19 2024
R-4.4-win-x86_64NOTEDec 19 2024
R-4.4-mac-x86_64NOTEDec 19 2024
R-4.4-mac-aarch64NOTEDec 19 2024
R-4.3-win-x86_64OKDec 19 2024
R-4.3-mac-x86_64OKDec 19 2024
R-4.3-mac-aarch64OKDec 19 2024

Exports:adductDatabatchCombinecalcScorescalcScoresParamcombineDatacombinedTabledatasetsevaluateParamsfeatDatafilteredfit_gamfit_loessfitgamParamfitloessParamgetAnchorsgetCoefficientsgetDatagetExtragetModelgetSamplesgetStatsidDatalabelRowslabelRowsParammetabCombinemetabCombinermetabDatamzDatamzFitmzfitParamnonmatchedopts.duplicateplotplot_fitQDatareduceTablereduceTableParamrtDataselectAnchorsselectAnchorsParamupdateTableswrite2filexxyy

Dependencies:BiocGenericscaretclasscliclockcodetoolscolorspacecpp11data.tablediagramdigestdplyre1071fansifarverforeachfuturefuture.applygenericsggplot2globalsgluegowergtablehardhatipredisobanditeratorsKernSmoothlabelinglatticelavalifecyclelistenvlubridatemagrittrMASSMatrixmatrixStatsmgcvModelMetricsmunsellnlmennetnumDerivparallellypillarpkgconfigplyrpROCprodlimprogressrproxypurrrR6RColorBrewerRcpprecipesreshape2rlangrpartS4VectorsscalesshapeSQUAREMstringistringrsurvivaltibbletidyrtidyselecttimechangetimeDatetzdbutf8vctrsviridisLitewithr

Combine LC-MS Metabolomics Datasets with metabCombiner

Hani Habra

Rendered frommetabCombiner_vignette.Rmdusingknitr::rmarkdownon Dec 19 2024.

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