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Changelog

glyread 0.4.2

Minor improvements

  • Remove redundant emoji in the “Getting Started” vignette.

glyread 0.4.1

Minor improvements

  • Add a “Getting Started” vignette.

glyread 0.4.0

Major changes

This is a big update! In addition to several new workflows supported, we redesign the API to make read_xxx() functions behave more consistently. Now the read_xxx() functions will try to return experiments with similar variable information format. To ensure this, some functions perform protein inference automatically to resolve protein ambiguity, and some functions add a “gene” column by mapping protein accessions to gene symbols. Besides, all read_xxx() functions now aggregate quantification from PSM to the glycopeptide level.

Detailed list:

  • Add read_pglyco3() to read results from pGlyco3 (with built-in quantification).
  • Add read_byonic_byologic() to read results from Byonic with Byologic quantification.
  • All functions now automatically perform PSM aggregation to ensure glycopeptide-level quantification.
  • Redesign read_msfragger() to support multiple PSM files. No awkward manul post-processing is needed anymore.

Minor improvements

  • Remove protein_inference_method parameter from read_pglyco3_pglycoquant(). The function now performs the “parsimony” protein inference algorithm.
  • Optimize the logic of protein inference. For ties, alphabetical order is used.

glyread 0.3.2

Minor improvements

Bug fixes

  • Try to fix the R CMD check errors on Github Actions.

glyread 0.3.1

Minor improvements

  • read_byonic_pglycoquant() now only perform gene symbol conversion if both clusterProfiler and the specified OrgDb package (e.g., org.Hs.eg.db) are installed. If not, the gene column is omitted and a message is shown. This improves robustness in minimal or CI environments.
  • clusterProfiler and org.Hs.eg.db are now listed under Suggests, not Imports.

glyread 0.3.0

Major changes

  • Add read_byonic_pglycoquant() for reading results from Byonic identification and pGlycoQuant quantification.
  • Add read_msfragger() for reading results from MSFragger-Glyco.
  • read_pglyco3_pglycoquant() now performs protein inference automatically to resolve protein ambiguity. This means, the variable information tibble now contains “protein”, “gene”, and “protein_site” columns. The previous ambiguous “proteins”, “genes”, and “protein_sites” columns are removed.

glyread 0.2.1

Minor changes

  • The “proteins” column of read_pglyco3_pglycoquant() now contains protein uniprot accessions, e.g. “P08185”. When multiple proteins exist, separated with semicolon, e.g. “P08185;P04196”.