.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 and MsExperiment objects
areaUnderTic            area under TIC (MS:4000155)
areaUnderTicRtQuantiles
                        area under TIC RT quantiles (MS:4000156)
calculateMetrics        Calculate QC metrics from a Spectra or
                        MsExperiment object
calculateMetricsFromMsExperiment
                        Calculate QC metrics from a MsExperiment object
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)
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)
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
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
