Package: MetaClean 1.0.1

Kelsey Chetnik

MetaClean: Detection of Low-Quality Peaks in Untargeted Metabolomics Data

Utilizes 11 peak quality metrics and 8 diverse machine learning algorithms to build a classifier for the automatic assessment of peak integration quality of peaks from untargeted metabolomics analyses. The 11 peak quality metrics were adapted from those defined in the following references: Zhang, W., & Zhao, P.X. (2014) <doi:10.1186/1471-2105-15-S11-S5> Toghi Eshghi, S., Auger, P., & Mathews, W.R. (2018) <doi:10.1186/s12014-018-9209-x>.

Authors:Kelsey Chetnik

MetaClean_1.0.1.tar.gz
MetaClean_1.0.1.zip(r-4.7)MetaClean_1.0.1.zip(r-4.6)MetaClean_1.0.1.zip(r-4.5)
MetaClean_1.0.1.tgz(r-4.6-any)MetaClean_1.0.1.tgz(r-4.5-any)
MetaClean_1.0.1.tar.gz(r-4.7-any)MetaClean_1.0.1.tar.gz(r-4.6-any)
MetaClean_1.0.1.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
MetaClean/json (API)

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

Bug tracker:https://github.com/kelseychetnik/metaclean/issues

Datasets:
  • ex_peakData - Example peakData - value input to calculate... functions
  • ex_peakDataList - Example peakDataList - value input to calculteElutionShift and calculateRetentionTimeConsistency
  • ex_pts - Example pts - value input to caculate... functions
  • ex_ptsList - Example ptsList - value input to calculteElutionShift and calculateRetentionTimeConsistency
  • pqm_development - Example Peak Quality Metrics Data Frame for Development Dataset.
  • pqm_test - Example Peak Quality Metrics Data Frame for Test Dataset.

On CRAN:

Conda:

s4vectorslow-quality-integrationmachine-learningmetabolomics

3.40 score 5 stars 5 scripts 7 downloads 22 exports 207 dependencies

Last updated from:d0ce1bc0b2. Checks:7 WARNING, 2 OK. Indexed: no.

TargetResultTimeFilesSyslog
linux-devel-x86_64WARNING400
source / vignettesOK302
linux-release-x86_64WARNING404
macos-release-arm64WARNING254
macos-oldrel-arm64WARNING371
windows-develWARNING328
windows-releaseWARNING322
windows-oldrelWARNING305
wasm-releaseOK196

Exports:calculateApexMaxBoundaryRatiocalculateElutionShiftcalculateEvaluationMeasurescalculateFWHMcalculateGaussianSimilaritycalculateJaggednesscalculateModalitycalculateRetentionTimeConsistencycalculateSharpnesscalculateSymmetrycalculateTPASRcalculateZigZagIndexgetBarPlotsgetCDPlotsgetEvalObjgetEvaluationMeasuresgetPeakQualityMetricsgetPredicitonsrsdFilterrunCrossValidationsummaryStatstrainClassifier

Dependencies:abindaffyaffyioAnnotationFilteraskpassbase64encBHBiobaseBiocBaseUtilsBiocGenericsbiocmakeBiocManagerBiocParallelBiocStylebitbit64bitopsbookdownbslibcachemcaretcaToolsclassclassIntclicliprclockclueclustercodetoolscombinatcommonmarkcpp11crayoncrosstalkcurldata.tableDBIDelayedArraydiagramdigestdir.expirydoParalleldplyre1071evaluatefarverfastAdaboostfastmapfilelockfontawesomeforcatsforeachformatRfsfutile.loggerfutile.optionsfuturefuture.applygenericsGenomicRangesggplot2globalsgluegowergplotsgraphgtablegtoolshardhathavenhighrhmshtmltoolshtmlwidgetshttpuvhttrigraphimputeipredIRangesisobanditeratorsjquerylibjsonlitekernlabKernSmoothklaRknitrlabelinglabelledlambda.rlaterlatticelavalazyevallifecyclelimmalistenvlubridatemagrittrMALDIquantMASSMassSpecWaveletMatrixMatrixGenericsmatrixStatsmemoiseMetaboCoreUtilsmimeminiUIMLmetricsModelMetricsMsCoreUtilsMsExperimentMsFeaturesMSnbaseMultiAssayExperimentmzIDmzRncdf4nlmennetnumDerivopensslotelparallellypcaMethodspillarpkgconfigplotlyplotrixplyrpreprocessCoreprettyunitspROCprodlimprogressprogressrpromisesProtGenericsproxyPSMatchPTModspurrrQFeaturesquestionrR.cacheR.methodsS3R.ooR.utilsR6randomForestrappdirsRColorBrewerRcppreadrrecipesreshape2RgraphvizRhdf5librlangrmarkdownROCRrpartrprojrootrstudioapiS4ArraysS4VectorsS7sassscalesSeqinfoshapeshinysnowsourcetoolsSparseArraysparsevctrsSpectraSQUAREMstatmodstringistringrstylerSummarizedExperimentsurvivalsystibbletidyrtidyselecttimechangetimeDatetinytextzdbutf8vctrsviridisLitevroomvsnwithrxcmsxfunXMLxtableXVectoryaml

MetaClean - Walkthrough

Kelsey Chetnik

Rendered fromMetaClean_WalkThrough.Rmdusingknitr::knitron May 16 2026.

Last update: 2021-05-13
Started: 2020-04-08

Readme and manuals

Help Manual

Help pageTopics
Calculate Apex-Max Boundary Ratio (of a Chromatographic Peak)calculateApexMaxBoundaryRatio
Calculate Elution Shift (of a Peak Group)calculateElutionShift
Calculate Evaluation MeasurescalculateEvaluationMeasures
Calculate FWHM2Base (of a Chromatographic Peak)calculateFWHM
Calculate Gaussian Similarity (of a Chromatographic Peak)calculateGaussianSimilarity
Calculate Jaggedness (of a Chromatographic Peak)calculateJaggedness
Calculate Modality (of a Chromatographic Peak)calculateModality
Calculate Retention Time Consistency (of a Peak Group)calculateRetentionTimeConsistency
Calculate Sharpness (of a Chromatographic Peak)calculateSharpness
Calculate Symmetry (of a Chromatographic Peak)calculateSymmetry
Calcualte Triangle Peak Area Similarity Ratio (TPASR) (of a Chromatographic Peak)calculateTPASR
Calculate the Zig-Zag Index (of a Chromatographic Peak)calculateZigZagIndex
A custom class for storing the chromatographic peak data required by the peak metric functions for each group of samples.evalObj evalObj-class
Example peakData - value input to calculate... functions (except calculateElutionShift and calculateRetentionTimeConsistency)ex_peakData
Example peakDataList - value input to calculteElutionShift and calculateRetentionTimeConsistencyex_peakDataList
Example pts - value input to caculate... functions (except calculateElutionShift and calculateRetentionTimeConsistency)ex_pts
Example ptsList - value input to calculteElutionShift and calculateRetentionTimeConsistencyex_ptsList
Generate Bar Plots for the Seven Evaluation MeasuresgetBarPlots
Generate Bar Plots for the Seven Evaluation MeasuresgetCDPlots
Extract peak data objectgetEvalObj
Calculate Evaluation MeasuresgetEvaluationMeasures
Calculate the 12 Peak Quality MetricsgetPeakQualityMetrics
Get MetaClean PredictionsgetPredicitons
Example Peak Quality Metrics Data Frame for Development Dataset.pqm_development
Example Peak Quality Metrics Data Frame for Test Dataset.pqm_test
RSD FilteirngrsdFilter
Run Cross-Validation for A List of Algoirthms with Peak Quality Metric Feature SetsrunCrossValidation
Calculate summary statistics for evaluation measuressummaryStats
Train MetaClean ClassifiertrainClassifier