# MsQuality - Quality metric calculation from Spectra and MsExperiment objects

## 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)