.rtOrderSpectra         Order Spectra according to increasing retention
                        time
Lee_2019                Example data for 'MsQuality': data set of Lee
                        et al. (2019)
Lee_2019_meta_vals      Example data for 'MsQuality': data set of Lee
                        et al. (2019)
MsQuality-package       MsQuality - Quality metric calculation from
                        Spectra, MsExperiment and Chromatograms objects
areaUnderTic            area under TIC (MS:4000155)
areaUnderTicRtQuantiles
                        area under TIC RT quantiles (MS:4000156)
baselineIntensity       Baseline Intensity per chromatogram
calculateMetrics        Calculate QC metrics from a Spectra,
                        MsExperiment, or Chromatograms object
calculateMetricsFromChromatograms
                        Calculate QC metrics from a Chromatograms
                        object
calculateMetricsFromMsExperiment
                        Calculate QC metrics from a MsExperiment object
calculateMetricsFromOneSampleChromatograms
                        Calculate QC metrics from a Chromatograms
                        object containing only chromatographic data
                        from one sample
calculateMetricsFromOneSampleSpectra
                        Calculate QC metrics from a Spectra object
                        containing only spectral data from one sample
calculateMetricsFromSpectra
                        Calculate QC metrics from a Spectra object
chromatographyDuration
                        chromatography duration (MS:4000053)
extentIdentifiedPrecursorIntensity
                        extent of identified MS2 precursor intensity
                        (MS:4000157)
gaussianSimilarity      Gaussian Similarity (Peak Shape Quality) per
                        Chromatogram
intensityMean           Intensity statistics (Mean) per chromatogram
intensityQuartiles      Intensity Quartiles per chromatogram
intensityRange          Intensity Range per chromatogram
intensitySd             Intensity statistics (Standard Deviation) per
                        chromatogram
maxIntensity            Maximum intensity per chromatogram
meanCharge              mean MS2 precursor charge in all spectra
                        (MS:4000173) or mean MS2 precursor charge in
                        identified spectra (MS:4000174)
medianCharge            median MS2 precursor charge in all spectra
                        (MS:4000175) or median MS2 precursor charge in
                        identified spectra (MS:4000176)
medianPrecursorMz       MS2 precursor median m/z of identified
                        quantification data points (MS:4000152)
medianTicOfRtRange      median of TIC values in the shortest RT range
                        in which half of the quantification data points
                        are identified (MS:4000159)
medianTicRtIqr          median of TIC values in the RT range in which
                        the middle half of quantification data points
                        are identified (MS:4000158)
msSignal10xChange       MS1 signal jump (10x) count (MS:4000097) or MS1
                        signal fall (10x) count (MS:4000098)
mzAcquisitionRange      m/z acquisition range (MS:4000069)
numberEmptyScans        number of empty MS1 scans (MS:4000099), number
                        of empty MS2 scans (MS:4000100), or number of
                        empty MS3 scans (MS:4000101)
numberSpectra           number of MS1 spectra (MS:4000059) or number of
                        MS2 spectra (MS:4000060)
peakCount               Peak Count (Number of data points) per
                        chromatogram
peakProminence          Peak Prominence (Peak-to-Baseline Ratio) per
                        Chromatogram
peakWidth               Peak Width per Chromatogram
plotMetric              Visualize a quality metric
plotMetricTibble        Helper function for plotMetric
precursorIntensityMean
                        MS2 precursor intensity distribution mean
                        (MS:4000117), identified MS2 precursor
                        intensity distribution mean (MS:4000163), or
                        unidentified MS2 precursor intensity
                        distribution mean (MS:4000164)
precursorIntensityQuartiles
                        MS2 precursor intensity distribution
                        (MS:4000116), identified MS2 precursor
                        intensity distribution (MS:4000161), or
                        unidentified MS2 precursor intensity
                        distribution (MS:4000162)
precursorIntensityRange
                        MS2 precursor intensity range (MS:4000160)
precursorIntensitySd    MS2 precursor intensity distribution sigma
                        (MS:4000118), identified MS2 precursor
                        intensity distribution sigma (MS:4000165), or
                        unidentified MS2 precursor intensity
                        distribution sigma (MS:4000166)
qualityMetrics          Get a vector of quality metrics than can be
                        applied to 'object'
ratioCharge1over2       ratio of 1+ over 2+ of all MS2 known precursor
                        charges (MS:4000167) or ratio of 1+ over 2+ of
                        identified MS2 known precursor charges
                        (MS:4000168)
ratioCharge3over2       ratio of 3+ over 2+ of all MS2 known precursor
                        charges (MS:4000169) or ratio of 3+ over 2+ of
                        identified MS2 known precursor charges
                        (MS:4000170)
ratioCharge4over2       ratio of 4+ over 2+ of all MS2 known precursor
                        charges (MS:4000171) or ratio of 4+ over 2+ of
                        identified MS2 known precursor charges
                        (MS:4000172)
rtAcquisitionRange      retention time acquisition range (MS:4000070)
rtIqr                   interquartile RT period for identified
                        quantification data points (MS:4000153)
rtIqrRate               rate of the interquartile RT period for
                        identified quantification data points
                        (MS:4000154)
rtOverMsQuarters        MS1 quarter RT fraction (MS:4000055) or MS2
                        quarter RT fraction (MS:4000056)
shinyMsQuality          Shiny application to visualize quality metrics
signalToNoiseRatio      Signal-to-Noise Ratio per chromatogram
ticQuantileRtFraction   TIC quantile RT fraction (MS:4000183)
ticQuartileToQuartileLogRatio
                        MS1 TIC-change quartile ratios (MS:4000057) or
                        MS1 TIC quartile ratios (MS:4000058)
transformIntoMzQC       Transform the metrics into a list of 'MzQCmzQC'
                        objects
xicFwhm                 Full Width at Half Maximum (FWHM) per
                        Chromatogram
