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MQmetrics 0.99.2

  • Added a NEWS.md file to track changes to the package.

MQmetrics 0.99.3

  • Functions now use a general input resulting from make_MQCombined().
  • Shortened lines in the code.
  • Usage of seq_len rather than 1: ...
  • Usage of ultiples of 4 spaces for line indents.
  • Removed LazyData: TRUE.

MQmetrics 1.0.0

  • The function generateReport() now takes the parameter name_output_file to name the output pdf file.
  • Added information regarding peptides, and peptides/protein ratio in report tables.
  • Added the function PlotProteinPeptideRatio() to visualize a comparison between the proteins identified and the ratio Peptide/Proteins among Experiments.

MQmetrics 1.1.1

  • Added pagination to PlotiRT() and PlotiRTScore().
  • Updated vignette style to Bioconductor's.
  • Improved aesthethics of PlotProteinOverlap() and PlotPCA().

MQmetrics 1.1.2

  • Fixed units of time MaxQuantAnalysisInfo() when experiment lasting longer than a day.
  • Added new line to MaxQuantAnalyssInfo() showing when the experiment ended.
  • Improved aesthethics in the plots from PlotCombinedDynamicRange() and PlotAllDynamicRange().

MQmetrics 1.1.3

  • Added new function PlotPTMAcrossSamples(), it takes as input one PTM of interest and shows its intensities across the samples. This function is similar to PlotPTM() but in more detail.
  • In the function PlotPTM() a parameter combine_same_residue_ptms has been added. It combines multiple PTMs happening in the same residue such as: Dimethyl (KR), Trimethyl (KR).

MQmetrics 1.1.4

  • The function PlotProteinCoverage() now reports the coverage individually in each plot rather than the total protein coverage.

  • MQmetrics now is adapted to MaxQuant v.2.x, since the column names are different than in MaxQuant v.1.x. MQmetrics will detect the MaxQuant version used and read the columns accordingly.

  • Enhanced error message in PlotiRT() and PlotiRTScore() when irt peptides are note found. Enhanced error message for PlotProteinCoverage() when the UniprotID is not found.

MQmetrics 1.1.5, 13/09/2021

  • The plot generated by PlotPTM() will now indicate (in the legend title) whether the Post-Translational modifications have been aggregated or not as a result of the parameter aggregate_PTMs.

  • The function PlotPeptidesIdentified() and PlotProteinsIdentified() now return a plot containing Missing Values, Frequency of Identified by Match Between Runs and Frequency of identified by MS/MS. With this, the funciton PlotIdentificationType() becomes obsolete.

  • The function PlotProteinCoverage() now can take as input multiple UniprotID in a vector format.

  • The function PlotPTMAcrossSamples() now can take as input multiple PTM_of_Interest in a vector format.

  • Change in the function make_MQCombined() to read faster the tables and reducing the overall time required to generate a report.

MQmetrics 1.1.6, 06/10/2021

  • Bug fixed: If a table was missing, the report was not generated.

MQmetrics 1.1.7, 07/10/2021

  • Removed parentheses from the news that was causing issues in Bioconductor.

MQmetrics 1.1.8, 08/10/2021

  • Fixed test that was resulting in error duet to version 1.1.6 updated way to read the files.

MQmetrics 1.3.1 03/01/2022

  • Added median to the PlotAndromedaScore().
  • Remove warnings from the vignettes.
  • Now MQmetrics can read the mqpar.xml file. This one must be located on the same directory as the combined folder.
  • Reporting the number of threads used by MaxQuant if found the mqpar.xml file.

MQmetrics 1.3.2 03/01/2022

  • Reporthing the fixed Modifications if the mqpar.xml is present.

MQmetrics 1.3.3 10/01/2022

  • Removed unused dependency.