MsQuality - Quality metric calculation from Spectra and MsExperiment objects

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Documentation for package ‘MsQuality’ version 1.5.0

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

Help Pages

MsQuality-package	MsQuality - Quality metric calculation from Spectra and MsExperiment objects
.rtOrderSpectra	Order Spectra according to increasing retention time
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)
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)
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 and MsExperiment 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)
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
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)
ticQuartersRtFraction	TIC quarters RT fraction (MS:4000054)
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)