NEWS.md

In rformassspectrometry/PSMatch: Handling and Managing Peptide Spectrum Matches

PSMatch 1.11

PSMatch 1.11.2

• Replace calculateFragments with calculateFragments2. PR #19

PSMatch 1.11.1

• New calculateFragments2 function includes fixed and variable modifications to fragments ions. 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.

rformassspectrometry/PSMatch documentation built on Jan. 25, 2025, 10:48 a.m.