inst/NEWS.md

In tnaake/MsQuality: MsQuality - Quality metric calculation from Spectra and MsExperiment objects

MsQuality 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

MsQuality 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

tnaake/MsQuality documentation built on Feb. 25, 2024, 7:32 p.m.