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MetaClean (version 1.0.0)

Detection of Low-Quality Peaks in Untargeted Metabolomics Data

Description

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 12 peak quality metrics were adapted from those defined in the following references: Zhang, W., & Zhao, P.X. (2014) Toghi Eshghi, S., Auger, P., & Mathews, W.R. (2018) .

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Version

Install

install.packages('MetaClean')

Monthly Downloads

6

Version

1.0.0

License

GPL-3

Maintainer

Kelsey Chetnik

Last Published

September 11th, 2020

Functions in MetaClean (1.0.0)

calculateEvaluationMeasures

Calculate Evaluation Measures
calculateModality

Calculate Modality (of a Chromatographic Peak)
calculateJaggedness

Calculate Jaggedness (of a Chromatographic Peak)
calculateApexMaxBoundaryRatio

Calculate Apex-Max Boundary Ratio (of a Chromatographic Peak)
calculateFWHM

Calculate FWHM2Base (of a Chromatographic Peak)
calculateSharpness

Calculate Sharpness (of a Chromatographic Peak)
calculateElutionShift

Calculate Elution Shift (of a Peak Group)
calculateGaussianSimilarity

Calculate Gaussian Similarity (of a Chromatographic Peak)
calculateRetentionTimeConsistency

Calculate Retention Time Consistency (of a Peak Group)
ex_ptsList

Example ptsList - value input to calculteElutionShift and calculateRetentionTimeConsistency
getEvalObj

Extract peak data object
runCrossValidation

Run Cross-Validation for A List of Algoirthms with Peak Quality Metric Feature Sets
rsdFilter

RSD Filteirng
evalObj-class

A custom class for storing the chromatographic peak data required by the peak metric functions for each group of samples.
getEvaluationMeasures

Calculate Evaluation Measures
pqm_development

Example Peak Quality Metrics Data Frame for Development Dataset.
calculateTPASR

Calcualte Triangle Peak Area Similarity Ratio (TPASR) (of a Chromatographic Peak)
calculateZigZagIndex

Calculate the Zig-Zag Index (of a Chromatographic Peak)
calculateSymmetry

Calculate Symmetry (of a Chromatographic Peak)
getBarPlots

Generate Bar Plots for the Seven Evaluation Measures
ex_peakDataList

Example peakDataList - value input to calculteElutionShift and calculateRetentionTimeConsistency
ex_pts

Example pts - value input to caculate... functions (except calculateElutionShift and calculateRetentionTimeConsistency)
pqm_test

Example Peak Quality Metrics Data Frame for Test Dataset.
ex_peakData

Example peakData - value input to calculate... functions (except calculateElutionShift and calculateRetentionTimeConsistency)
getPredicitons

Get MetaClean Predictions
getPeakQualityMetrics

Calculate the 12 Peak Quality Metrics
trainClassifier

Train MetaClean Classifier
summaryStats

Calculate summary statistics for evaluation measures