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NEWS.md

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PSMatch 1.13

PSMatch 1.13.2

  • Add CITATION to the pre-print (https://doi.org/10.31219/osf.io/62v9p_v2)
  • Add possibility to split protein groups in PSM data with makeAdjacencyMatrix (see issue #30)
  • Removed showDetails() from setMethod("show", "PSM") as discussed in issue #30
  • Add USI parameter to plotSpectraPTM.
  • Correct filterPsmFdr output message
  • Update Fragments vignette.
  • Improve labelFragments()runtime (see issue #25).
  • Add Selenocysteine and Pyrrolysine to getAminoAcids().

PSMatch 1.13.1

  • Refactor and improve plotSpectraPTM().

PSMatch 1.13.0

  • New Bioconductor devel.

PSMatch 1.11

PSMatch 1.11.5

  • Correct plotSpectraPTM annotations.

PSMatch 1.11.4

  • Added plotSpectraPTM: a plotting function to visualise post-translational modifications.

PSMatch 1.11.3

  • Deprecated addFragments. The use of labelFragments is endorsed instead. See PR #20.

PSMatch 1.11.2

  • Replace calculateFragments with calculateFragments2. See PR #19.

PSMatch 1.11.1

  • New calculateFragments2 function includes fixed and variable modifications to fragments ions. See PR #16.

PSMatch 1.11.0

  • New devel version

PSMatch 1.9

PSMatch 1.9.1

  • Fix check errors.

PSMatch 1.9.0

  • New Bioc devel.

PSMatch 1.7

PSMatch 1.7.2

  • Fix connected component dim names in show().

PSMatch 1.7.1

  • In addFragments() use ... to pass parameters to calculateFragments().

PSMatch 1.7.0

  • New Bioc devel.

PSMatch 1.5

PSMatch 1.5.0

  • New Bioc devel.

PSMatch 1.3

PSMatch 1.3.3

  • New fdr variable (default is always NA_character_ for now) that defines the spectrum FDR (or any similar/relevant metric that can be used for filtering - see next item).
  • New filterPsmFdr() function that filters based on the fdr variable.

PSMatch 1.3.2

  • Specific Matrix::rowSums() to fix error in example.

PSMatch 1.3.1

  • Fix type in vignette.

PSMatch 1.0

PSMatch 1.0.0

  • First Bioconductor release.

PSMatch 0.99

Changes in 0.99.5

  • Fix mz calculation in calculateFragments for neutral losses with a charge > 1 (ported from MSnbase - see issue 573).

Changes in 0.99.4

  • Set seed in the ConnectedComponents unit test to stop random errors after clustering.

Changes in 0.99.3

  • Fix bug in describePeptides() (close #11).

Changes in 0.99.2

  • Describe the ConnectedComponents() return value.
  • Add/update installation instructions.

Changes in 0.99.1

  • Fix typo and improve documentation.

Changes in 0.99.0

  • Prepare package for Bioconductor submission.