Man pages for tnaake/msQC
MsQuality - Quality metric calculation from Spectra and MsExperiment objects
| 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... |
| calculateMetricsFromSpectra | Calculate QC metrics from a Spectra object |
| chromatographyDuration | chromatography duration (MS:4000053) |
| dot-rtOrderSpectra | Order Spectra according to increasing retention time |
| 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... |
| medianCharge | median MS2 precursor charge in all spectra (MS:4000175) or... |
| medianPrecursorMz | MS2 precursor median m/z of identified quantification data... |
| 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 (10x) count (MS:4000097) or MS1 signal fall... |
| mzAcquisitionRange | m/z acquisition range (MS:4000069) |
| numberEmptyScans | number of empty MS1 scans (MS:4000099), number of empty MS2... |
| numberSpectra | number of MS1 spectra (MS:4000059) or number of MS2 spectra... |
| plotMetric | Visualize a quality metric |
| plotMetricTibble | Helper function for plotMetric |
| precursorIntensityMean | MS2 precursor intensity distribution mean (MS:4000117),... |
| precursorIntensityQuartiles | MS2 precursor intensity distribution (MS:4000116), identified... |
| precursorIntensityRange | MS2 precursor intensity range (MS:4000160) |
| precursorIntensitySd | MS2 precursor intensity distribution sigma (MS:4000118),... |
| qualityMetrics | Get a vector of quality metrics than can be applied to... |
| ratioCharge1over2 | ratio of 1+ over 2+ of all MS2 known precursor charges... |
| ratioCharge3over2 | ratio of 3+ over 2+ of all MS2 known precursor charges... |
| ratioCharge4over2 | ratio of 4+ over 2+ of all MS2 known precursor charges... |
| rtAcquisitionRange | retention time acquisition range (MS:4000070) |
| rtIqr | interquartile RT period for identified quantification data... |
| rtIqrRate | rate of the interquartile RT period for identified... |
| rtOverMsQuarters | MS1 quarter RT fraction (MS:4000055) or MS2 quarter RT... |
| shinyMsQuality | Shiny application to visualize quality metrics |
| ticQuantileRtFraction | TIC quantile RT fraction (MS:4000183) |
| ticQuartileToQuartileLogRatio | MS1 TIC-change quartile ratios (MS:4000057) or MS1 TIC... |
| transformIntoMzQC | Transform the metrics into a list of 'MzQCmzQC' objects |
