Man pages for tnaake/msQC
MsQuality - Quality metric calculation from Spectra and MsExperiment objects
| 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... |
| calculateMetricsFromSpectra | Calculate QC metrics from a Spectra object |
| dot-rtOrderSpectra | Order Spectra according to increasing retention time |
| 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... |
| medianCharge | Median charge in identified spectra (QC:4000178) or median... |
| medianPrecursorMz | Precursor median m/z for IDs (QC:4000065) |
| medianTicOfRtRange | Median of TIC values in the shortest RT range in which half... |
| medianTicRtIqr | Median of TIC values in the RT range in which the middle half... |
| MsQuality-package | MsQuality - Quality metric calculation from Spectra and... |
| 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),... |
| precursorIntensityQuartiles | Precursor intensity distribution Q1, Q2, Q3 (QC:4000167),... |
| precursorIntensityRange | Precursor intensity range (QC:4000144) |
| precursorIntensitySd | Precursor intensity distribution sigma (QC:4000169),... |
| qualityMetrics | Get a vector of quality metrics than can be applied to... |
| ratioCharge1over2 | Charged peptides ratio 1+ over 2+ (QC:4000174) or Charged... |
| ratioCharge3over2 | Charged peptides ratio 3+ over 2+ (QC:4000175) or charged... |
| ratioCharge4over2 | Charged peptides ratio 4+ over 2+ (QC:4000176) or charged... |
| rtAcquisitionRange | Retention time acquisition range (QC:4000139) |
| rtDuration | RT duration (QC:4000053) |
| rtIqr | Interquartile RT period for peptide identifications... |
| rtIqrRate | Peptide identification rate of the interquartile RT period... |
| rtOverMsQuarters | MS1/MS2 quantiles RT fraction (QC:4000055/QC:4000056) |
| rtOverTicQuantiles | RT over TIC quantile (QC:4000054) |
| shinyMsQuality | Shiny application to visualize quality metrics |
| ticQuartileToQuartileLogRatio | MS1 TIC-change quartile ratios (MS:4000057) or MS1 TIC... |
