Man pages for tnaake/MsQuality
MsQuality - Quality metric calculation via Spectra and MsExperiment objects

areaUnderTICArea under TIC (QC:4000077)
areaUnderTICRTquantilesArea under TIC RT quantiles (QC:4000078)
calculateMetricsCalculate QC metrics from a Spectra or MsExperiment object
calculateMetricsFromMsExperimentCalculate QC metrics from a MsExperiment object
calculateMetricsFromSpectraCalculate QC metrics from a Spectra object
dot-rtOrderSpectraOrder Spectra according to increasing retention time
extentIdentifiedPrecursorIntensityExtent of identified precursor intensity (QC:4000125)
Lee_2019Example data for 'MsQuality': data set of Lee et al. (2019)
Lee_2019_meta_valsExample data for 'MsQuality': data set of Lee et al. (2019)
meanChargeMean charge in identified spectra (QC:4000177) or mean...
medianChargeMedian charge in identified spectra (QC:4000178) or median...
medianPrecursorMZPrecursor median m/z for IDs (QC:4000065)
medianTICofRTRangeMedian of TIC values in the shortest RT range in which half...
medianTICRTIQRMedian of TIC values in the RT range in which the middle half...
MsQuality-packageMsQuality - Quality metric calculation via Spectra and...
msSignal10XChangeMS1 signal jump/fall (10x) count (QC:4000172/QC:4000173)
mzAcquisitionRangem/z acquisition range (QC:4000138)
numberSpectraNumber of MS1 or MS2 spectra (QC:4000059/QC:4000060)
plotMetricVisualize a quality metric
plotMetricTibbleHelper function for plotMetric
precursorIntensityMeanPrecursor intensity distribution mean (QC:4000168),...
precursorIntensityQuartilesPrecursor intensity distribution Q1, Q2, Q3 (QC:4000167),...
precursorIntensityRangePrecursor intensity range (QC:4000144)
precursorIntensitySDPrecursor intensity distribution sigma (QC:4000169),...
qualityMetricsGet a vector of quality metrics than can be applied to...
ratioCharge1over2Charged peptides ratio 1+ over 2+ (QC:4000174) or Charged...
ratioCharge3over2Charged peptides ratio 3+ over 2+ (QC:4000175) or charged...
ratioCharge4over2Charged peptides ratio 4+ over 2+ (QC:4000176) or charged...
rtAcquisitionRangeRetention time acquisition range (QC:4000139)
rtDurationRT duration (QC:4000053)
rtIQRInterquartile RT period for peptide identifications...
rtIQRratePeptide identification rate of the interquartile RT period...
rtOverMSQuartersMS1/MS2 quantiles RT fraction (QC:4000055/QC:4000056)
rtOverTICquantileRT over TIC quantile (QC:4000054)
shinyMsQualityShiny application to visualize quality metrics
ticQuantileToQuantileLogRatioMS1 quantile TIC change ratio to Quantile 1 (QC:4000057) or...
tnaake/MsQuality documentation built on Jan. 14, 2022, 7:34 p.m.