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  "Package": "MetaClean",
  "Type": "Package",
  "Title": "Detection of Low-Quality Peaks in Untargeted Metabolomics Data",
  "Version": "1.0.1",
  "Author": "Kelsey Chetnik",
  "Maintainer": "Kelsey Chetnik <kelsey.chetnik@gmail.com>",
  "Description": "Utilizes 11 peak quality metrics and 8 diverse machine\nlearning algorithms to build a classifier for the automatic\nassessment of peak integration quality of peaks from untargeted\nmetabolomics analyses. The 11 peak quality metrics were adapted\nfrom those defined in the following references: Zhang, W., &\nZhao, P.X. (2014) <doi:10.1186/1471-2105-15-S11-S5> Toghi\nEshghi, S., Auger, P., & Mathews, W.R. (2018)\n<doi:10.1186/s12014-018-9209-x>.",
  "biocViews": "S4Vectors",
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  "Packaged": {
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  "Repository": "https://rickhelmus.r-universe.dev",
  "Date/Publication": "2021-05-13 15:11:48 UTC",
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    "message": "Added getCDPlots function\n\nAlso updated getBarPlots documentation to match the updated evaluation measure names and updated the vignette to include the new function.\n",
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  "_topics": [
    "s4vectors",
    "low-quality-integration",
    "machine-learning",
    "metabolomics"
  ],
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    "calculateElutionShift",
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    "calculateRetentionTimeConsistency",
    "calculateSharpness",
    "calculateSymmetry",
    "calculateTPASR",
    "calculateZigZagIndex",
    "getBarPlots",
    "getCDPlots",
    "getEvalObj",
    "getEvaluationMeasures",
    "getPeakQualityMetrics",
    "getPredicitons",
    "rsdFilter",
    "runCrossValidation",
    "summaryStats",
    "trainClassifier"
  ],
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      "name": "ex_peakData",
      "title": "Example peakData - value input to calculate... functions (except calculateElutionShift and calculateRetentionTimeConsistency)",
      "object": "ex_peakData",
      "class": [
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      ],
      "fields": [],
      "table": false,
      "tojson": true
    },
    {
      "name": "ex_peakDataList",
      "title": "Example peakDataList - value input to calculteElutionShift and calculateRetentionTimeConsistency",
      "object": "ex_peakDataList",
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      "table": true,
      "tojson": true
    },
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      "title": "Example pts - value input to caculate... functions (except calculateElutionShift and calculateRetentionTimeConsistency)",
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      "table": true,
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    },
    {
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      "title": "Example ptsList - value input to calculteElutionShift and calculateRetentionTimeConsistency",
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      "class": [
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      ],
      "fields": [],
      "table": false,
      "tojson": true
    },
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      "title": "Example Peak Quality Metrics Data Frame for Development Dataset.",
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      ],
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        "EICNo",
        "ApexBoundaryRatio_mean",
        "ElutionShift_mean",
        "FWHM2Base_mean",
        "Jaggedness_mean",
        "Modality_mean",
        "RetentionTimeCorrelation_mean",
        "Symmetry_mean",
        "GaussianSimilarity_mean",
        "Sharpness_mean",
        "TPASR_mean",
        "ZigZag_mean",
        "Class"
      ],
      "rows": 500,
      "table": true,
      "tojson": true
    },
    {
      "name": "pqm_test",
      "title": "Example Peak Quality Metrics Data Frame for Test Dataset.",
      "object": "pqm_test",
      "class": [
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      ],
      "fields": [
        "EICNo",
        "ApexBoundaryRatio_mean",
        "ElutionShift_mean",
        "FWHM2Base_mean",
        "Jaggedness_mean",
        "Modality_mean",
        "RetentionTimeCorrelation_mean",
        "Symmetry_mean",
        "GaussianSimilarity_mean",
        "Sharpness_mean",
        "TPASR_mean",
        "ZigZag_mean"
      ],
      "rows": 500,
      "table": true,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "calculateApexMaxBoundaryRatio",
      "title": "Calculate Apex-Max Boundary Ratio (of a Chromatographic Peak)",
      "topics": [
        "calculateApexMaxBoundaryRatio"
      ]
    },
    {
      "page": "calculateElutionShift",
      "title": "Calculate Elution Shift (of a Peak Group)",
      "topics": [
        "calculateElutionShift"
      ]
    },
    {
      "page": "calculateEvaluationMeasures",
      "title": "Calculate Evaluation Measures",
      "topics": [
        "calculateEvaluationMeasures"
      ]
    },
    {
      "page": "calculateFWHM",
      "title": "Calculate FWHM2Base (of a Chromatographic Peak)",
      "topics": [
        "calculateFWHM"
      ]
    },
    {
      "page": "calculateGaussianSimilarity",
      "title": "Calculate Gaussian Similarity (of a Chromatographic Peak)",
      "topics": [
        "calculateGaussianSimilarity"
      ]
    },
    {
      "page": "calculateJaggedness",
      "title": "Calculate Jaggedness (of a Chromatographic Peak)",
      "topics": [
        "calculateJaggedness"
      ]
    },
    {
      "page": "calculateModality",
      "title": "Calculate Modality (of a Chromatographic Peak)",
      "topics": [
        "calculateModality"
      ]
    },
    {
      "page": "calculateRetentionTimeConsistency",
      "title": "Calculate Retention Time Consistency (of a Peak Group)",
      "topics": [
        "calculateRetentionTimeConsistency"
      ]
    },
    {
      "page": "calculateSharpness",
      "title": "Calculate Sharpness (of a Chromatographic Peak)",
      "topics": [
        "calculateSharpness"
      ]
    },
    {
      "page": "calculateSymmetry",
      "title": "Calculate Symmetry (of a Chromatographic Peak)",
      "topics": [
        "calculateSymmetry"
      ]
    },
    {
      "page": "calculateTPASR",
      "title": "Calcualte Triangle Peak Area Similarity Ratio (TPASR) (of a Chromatographic Peak)",
      "topics": [
        "calculateTPASR"
      ]
    },
    {
      "page": "calculateZigZagIndex",
      "title": "Calculate the Zig-Zag Index (of a Chromatographic Peak)",
      "topics": [
        "calculateZigZagIndex"
      ]
    },
    {
      "page": "evalObj-class",
      "title": "A custom class for storing the chromatographic peak data required by the peak metric functions for each group of samples.",
      "topics": [
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        "evalObj-class"
      ]
    },
    {
      "page": "ex_peakData",
      "title": "Example peakData - value input to calculate... functions (except calculateElutionShift and calculateRetentionTimeConsistency)",
      "topics": [
        "ex_peakData"
      ]
    },
    {
      "page": "ex_peakDataList",
      "title": "Example peakDataList - value input to calculteElutionShift and calculateRetentionTimeConsistency",
      "topics": [
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      ]
    },
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      "page": "ex_pts",
      "title": "Example pts - value input to caculate... functions (except calculateElutionShift and calculateRetentionTimeConsistency)",
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    {
      "page": "ex_ptsList",
      "title": "Example ptsList - value input to calculteElutionShift and calculateRetentionTimeConsistency",
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      ]
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    {
      "page": "getBarPlots",
      "title": "Generate Bar Plots for the Seven Evaluation Measures",
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      ]
    },
    {
      "page": "getCDPlots",
      "title": "Generate Bar Plots for the Seven Evaluation Measures",
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        "getCDPlots"
      ]
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    {
      "page": "getEvalObj",
      "title": "Extract peak data object",
      "topics": [
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      ]
    },
    {
      "page": "getEvaluationMeasures",
      "title": "Calculate Evaluation Measures",
      "topics": [
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      ]
    },
    {
      "page": "getPeakQualityMetrics",
      "title": "Calculate the 12 Peak Quality Metrics",
      "topics": [
        "getPeakQualityMetrics"
      ]
    },
    {
      "page": "getPredicitons",
      "title": "Get MetaClean Predictions",
      "topics": [
        "getPredicitons"
      ]
    },
    {
      "page": "pqm_development",
      "title": "Example Peak Quality Metrics Data Frame for Development Dataset.",
      "topics": [
        "pqm_development"
      ]
    },
    {
      "page": "pqm_test",
      "title": "Example Peak Quality Metrics Data Frame for Test Dataset.",
      "topics": [
        "pqm_test"
      ]
    },
    {
      "page": "rsdFilter",
      "title": "RSD Filteirng",
      "topics": [
        "rsdFilter"
      ]
    },
    {
      "page": "runCrossValidation",
      "title": "Run Cross-Validation for A List of Algoirthms with Peak Quality Metric Feature Sets",
      "topics": [
        "runCrossValidation"
      ]
    },
    {
      "page": "summaryStats",
      "title": "Calculate summary statistics for evaluation measures",
      "topics": [
        "summaryStats"
      ]
    },
    {
      "page": "trainClassifier",
      "title": "Train MetaClean Classifier",
      "topics": [
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      ]
    }
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  "_vignettes": [
    {
      "source": "MetaClean_WalkThrough.Rmd",
      "filename": "MetaClean_WalkThrough.html",
      "title": "MetaClean - Walkthrough",
      "author": "Kelsey Chetnik",
      "engine": "knitr::knitr",
      "headings": [
        "Overview of MetaClean",
        "How to use MetaClean",
        "Part 1: Training a Classifier Using User Provided Data",
        "(Optional) RSD Filtering",
        "Set Up",
        "Get EvalObj",
        "Calculate Peak Quality Metrics",
        "Train Potential Classifiers",
        "Calculate Evaluation Measures",
        "Compare Classifiers and Select Best Performing",
        "Train Final Classifier",
        "Save Model",
        "Part 2: Using Existing Models to Make Predictions",
        "Load Saved Model",
        "Make Predictions"
      ],
      "created": "2020-04-08 19:47:04",
      "modified": "2021-05-13 15:11:48",
      "commits": 4
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  "_nocasepkg": "metaclean",
  "_universes": [
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