Changes in version 1.1 Changes in version 1.1.3 - update tests after update of OBO file / rmzqc Changes in version 1.1.2 - Fix implementation of mzAquisitionRange - add numberEmptyScans in qualityMetrics function - add unit tests for export in rmzqc format - add interpretation aid of metrics in vignette Changes in version 1.1.1 - move msdata from Suggests to Imports - rename function rtDuration to chromatographyDuration - rename function rtOverTicQuantiles to ticQuartersRtFraction - create function numberEmptyScans - add attributes (MS QC terms) to the output of the Spectra metrics functions if the output matches the described term - add rmzqc to IMPORTS - add functionality to export quality metrics as in rmzqc format - adjust documentation to newest version of PSI MS CV obo file - add to the vignette information on how the metrics are calculated - add argument filterEmptySpectra to remove entries of length 0 or that have intensity 0, implement the argument in the functions calculateMetricsFromOneSampleSpectra, calculateMetricsFromSpectra, calculateMetricsFromMsExperiment, and calculateMetrics Changes in version 0.99 Changes in version 0.99.9 (2023-04-18) - enable parallel processing in calculateMetricsFromSpectra - rename ticQuantileToQuantileLogRatio to ticQuartileToQuartileLogRatio - rename rtOverTicQuantile to rtOverTicQuantiles - return quartiles instead of quantiles in precursorIntensityQuartiles - add mzR to Suggests in DESCRIPTION Changes in version 0.99.8 (2023-09-02) - adjust behaviour of metrics function when Spectra object of length 0 is presented, return NA values instead of raising an error Changes in version 0.99.7 (2023-06-02) - adjust ticQuantileToQuantileLogRatio that it adheres to Quameter calculation Changes in version 0.99.6 (2022-11-29): - extend section Description in DESCRIPTION - add sections BugReports and URL in DESCRIPTION - update dependency to R version 4.2.0 - transfer source code in R/Lee2019-data.R to inst/sources/Lee2019-data-source.R - use partial_bundle to reduce the file size of plotly graphics Changes in version 0.99.5 (2022-10-12): - add section on alternative software in vignette - simplify the vignette with regard to dealing with the RPLC and HILIC example data set and adjust the Lee2019-data.R accordingly to keep the RPLC/HILIC information in the dataOrigin slot of the Spectra object Changes in version 0.99.4 (2022-10-11): - add missing comma in DESCRIPTION Changes in version 0.99.3 (2022-10-11): - delete Maintainer field in DESCRIPTION - add instructions to install MsQuality in vignette and README.md via remotes/BiocManager instead of devtools Changes in version 0.99.2 (2022-09-20): - create branch msexperiment to store infrastructure and functions for MsExperiment objects - remove MsExperiment objects since this is still in BioC review and solely rely on Spectra objects - adjust documentation for the implemented changes (removal of MsExperiment) Changes in version 0.99.1 (2021-11-23) - simplify calculateMetricsFromSpectra: - the function does not any longer match the arguments by the formal arguments of the metric functions - the function does not any longer combine the parameters - the additional arguments do not take longer the parameter list of arguments but comma-separated arguments given to ... - for all metric functions the ... parameter is added - adjust the vignette and help pages - rename functions to camel case Changes in version 0.99.0 (2021-09-10) - add quality metrics/functions (metrics based on HUPO-mzQC): - rtDuration (QC:4000053), - rtOverTICquantile (QC:4000054), - rtOverMsQuarters (rtOverMSQuarters), - ticQuantileToQuantileLogRatio (QC:4000057, QC:4000058), - numberSpectra (QC:4000059, QC:4000060), - medianPrecursorMz (QC:4000065), - rtIQR (QC:4000072), - rtIQRrate (QC:4000073), - areaUnderTIC (QC:4000077), - areaUnderTICRTquantiles (QC:4000078), - extentIdentifiedPrecursorIntensity (QC:4000125), - medianTICRTIQR (QC:4000130), - medianTICofRTRange (QC:4000132), - mzAcquisitionRange (QC:4000138), - rtAcquisitionRange (QC:4000139), - precursorIntensityRange (QC:4000144), - precursorIntensityQuartiles ((QC:4000167, QC:4000228, QC:4000233), - precursorIntensityMean (QC:4000168, QC:4000229, QC:4000234), - precursorIntensitySD (QC:4000169, QC:4000230, QC:4000235), - msSignal10XChange (QC:4000172, QC:4000173), - ratioCharge1over2 (QC:4000174, QC:4000179), - ratioCharge3over2 (QC:4000175, QC:4000180), - ratioCharge4over2 (QC:4000176, QC:4000181), - meanCharge (QC:4000177, QC:4000182), - medianCharge (QC:4000178, QC:4000183) - .rt_order_spectra (helper function) - add the functions calculateMetricsFromSpectra, calculateMetricsFromMsExperiment to calculate the metrics based on Spectra and MsExperiment objects - add functions plotMetric, plotMetric_tibble to visualize the metrics - add shiny application shinyMsQuality to interactively visualize the metrics