Detection of Low-Quality Peaks in Untargeted Metabolomics Data


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Documentation for package ‘MetaClean’ version 1.0.0

Help Pages

calculateApexMaxBoundaryRatio Calculate Apex-Max Boundary Ratio (of a Chromatographic Peak)
calculateElutionShift Calculate Elution Shift (of a Peak Group)
calculateEvaluationMeasures Calculate Evaluation Measures
calculateFWHM Calculate FWHM2Base (of a Chromatographic Peak)
calculateGaussianSimilarity Calculate Gaussian Similarity (of a Chromatographic Peak)
calculateJaggedness Calculate Jaggedness (of a Chromatographic Peak)
calculateModality Calculate Modality (of a Chromatographic Peak)
calculateRetentionTimeConsistency Calculate Retention Time Consistency (of a Peak Group)
calculateSharpness Calculate Sharpness (of a Chromatographic Peak)
calculateSymmetry Calculate Symmetry (of a Chromatographic Peak)
calculateTPASR Calcualte Triangle Peak Area Similarity Ratio (TPASR) (of a Chromatographic Peak)
calculateZigZagIndex Calculate the Zig-Zag Index (of a Chromatographic Peak)
evalObj A custom class for storing the chromatographic peak data required by the peak metric functions for each group of samples.
evalObj-class A custom class for storing the chromatographic peak data required by the peak metric functions for each group of samples.
ex_peakData Example peakData - value input to calculate... functions (except calculateElutionShift and calculateRetentionTimeConsistency)
ex_peakDataList Example peakDataList - value input to calculteElutionShift and calculateRetentionTimeConsistency
ex_pts Example pts - value input to caculate... functions (except calculateElutionShift and calculateRetentionTimeConsistency)
ex_ptsList Example ptsList - value input to calculteElutionShift and calculateRetentionTimeConsistency
getBarPlots Generate Bar Plots for the Seven Evaluation Measures
getEvalObj Extract peak data object
getEvaluationMeasures Calculate Evaluation Measures
getPeakQualityMetrics Calculate the 12 Peak Quality Metrics
getPredicitons Get MetaClean Predictions
pqm_development Example Peak Quality Metrics Data Frame for Development Dataset.
pqm_test Example Peak Quality Metrics Data Frame for Test Dataset.
rsdFilter RSD Filteirng
runCrossValidation Run Cross-Validation for A List of Algoirthms with Peak Quality Metric Feature Sets
summaryStats Calculate summary statistics for evaluation measures
trainClassifier Train MetaClean Classifier