| 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 |
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