# MsQuality - Quality metric calculation from Spectra, MsExperiment and Chromatograms objects

## Documentation for package ‘MsQuality’ version 1.11.3

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package NEWS
- Package README

## Help Pages

MsQuality-package | MsQuality - Quality metric calculation from Spectra, MsExperiment and Chromatograms objects
.rtOrderSpectra | Order Spectra according to increasing retention time
areaUnderTic | area under TIC (MS:4000155)
areaUnderTic-method | area under TIC (MS:4000155)
areaUnderTicRtQuantiles | area under TIC RT quantiles (MS:4000156)
areaUnderTicRtQuantiles-method | 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
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)
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)
meta | Example data for 'MsQuality': data set of Lee et al. (2019)
msexp_hilic | Example data for 'MsQuality': data set of Lee et al. (2019)
msexp_rplc | Example data for 'MsQuality': data set of Lee et al. (2019)
MsQuality | MsQuality - Quality metric calculation from Spectra, MsExperiment and Chromatograms objects
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)
rtIqr-method | 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
sps_hilic | Example data for 'MsQuality': data set of Lee et al. (2019)
sps_rplc | Example data for 'MsQuality': data set of Lee et al. (2019)
ticQuantileRtFraction | TIC quantile RT fraction (MS:4000183)
ticQuantileRtFraction-method | 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
vals | Example data for 'MsQuality': data set of Lee et al. (2019)
xicFwhm | Full Width at Half Maximum (FWHM) per Chromatogram