MsQuality - Quality metric calculation from Spectra and MsExperiment objects

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Documentation for package ‘MsQuality’ version 1.0.0

• 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 (QC:4000077)
areaUnderTicRtQuantiles	Area under TIC RT quantiles (QC:4000078)
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
extentIdentifiedPrecursorIntensity	Extent of identified precursor intensity (QC:4000125)
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 charge in identified spectra (QC:4000177) or mean precursor charge in all MS2 (QC:4000182)
medianCharge	Median charge in identified spectra (QC:4000178) or median precursor charge in all MS2 (QC:4000183)
medianPrecursorMz	Precursor median m/z for IDs (QC:4000065)
medianTicOfRtRange	Median of TIC values in the shortest RT range in which half of the peptides are identified (QC:4000132)
medianTicRtIqr	Median of TIC values in the RT range in which the middle half of peptides are identified (QC:4000130)
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/fall (10x) count (QC:4000172/QC:4000173)
mzAcquisitionRange	m/z acquisition range (QC:4000138)
numberSpectra	Number of MS1 or MS2 spectra (QC:4000059/QC:4000060)
plotMetric	Visualize a quality metric
plotMetricTibble	Helper function for plotMetric
precursorIntensityMean	Precursor intensity distribution mean (QC:4000168), Identified precursor intensity distribution mean (QC:4000229), or Unidentified precursor intensity distribution mean (QC:4000234)
precursorIntensityQuartiles	Precursor intensity distribution Q1, Q2, Q3 (QC:4000167), Identified precursor intensity distribution Q1, Q2, Q3 (QC:4000228), or Unidentified precursor intensity distribution Q1, Q2, Q3 (QC:4000233)
precursorIntensityRange	Precursor intensity range (QC:4000144)
precursorIntensitySd	Precursor intensity distribution sigma (QC:4000169), Identified precursor intensity distribution sigma (QC:4000230), or Unidentified precursor intensity distribution sigma (QC:4000235)
qualityMetrics	Get a vector of quality metrics than can be applied to 'object'
ratioCharge1over2	Charged peptides ratio 1+ over 2+ (QC:4000174) or Charged spectra ratio 1+ over 2+ (QC:4000179)
ratioCharge3over2	Charged peptides ratio 3+ over 2+ (QC:4000175) or charged spectra ratio 3+ over 2+ (QC:4000180)
ratioCharge4over2	Charged peptides ratio 4+ over 2+ (QC:4000176) or charged spectra ratio 4+ over 2+ (QC:4000181)
rtAcquisitionRange	Retention time acquisition range (QC:4000139)
rtDuration	RT duration (QC:4000053)
rtIqr	Interquartile RT period for peptide identifications (QC:4000072)
rtIqrRate	Peptide identification rate of the interquartile RT period (QC:4000073)
rtOverMsQuarters	MS1/MS2 quantiles RT fraction (QC:4000055/QC:4000056)
rtOverTicQuantiles	RT over TIC quantile (QC:4000054)
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)
ticQuartileToQuartileLogRatio	MS1 TIC-change quartile ratios (MS:4000057) or MS1 TIC quartile ratios (MS:4000058)
vals	Example data for 'MsQuality': data set of Lee et al. (2019)