Changelog

glyread 0.8.2

Minor improvements and fixes

• glyread now depends on the CRAN version of glyparse.

glyread 0.8.1

Minor improvements and fixes

• glyread now depends on the CRAN version of glyrepr.

glyread 0.8.0

New features

• read_strucgp() now has a 0/1 expression matrix, indicating whether each glycopeptide was identified in each sample.
• read_strucgp() now performs protein inference automatically to resolve protein ambiguity.

Minor improvements and bug fixes

• Protein inference algorithm is optimized for performance.

glyread 0.7.0

Breaking changes

• read_strucgp() has been redesigned with a new API. It now returns an [glyexp::experiment()] object instead of a tibble, to be consistent with other read_xxx() functions. As StrucGP doesn’t support quantification, the expression matrix is filled with NA values.

glyread 0.6.3

Minor improvements and bug fixes

• Fix the bug in read_strucgp() that glycan compositions with “NeuGc” could not be parsed.
• Fix the bug in read_strucgp() that glycan structures with additional modifications (e.g. “+Ammonium(+17)”) could not be parsed.
• Fix the bug in read_strucgp() that sample information was not included in result tibble.

glyread 0.6.2

Minor improvements and bug fixes

• Fix bugs introduced by the breaking changes in glyexp 0.10.0.

glyread 0.6.1

Minor improvements and bug fixes

• Update dependencies to depend on release versions of glycoverse packages.

glyread 0.6.0

New features

• Add read_strucgp() to read results from StrucGP.
• Add read_glyco_decipher() to read results from Glyco-Decipher.

Minor improvements

• read_byonic_byologic() and read_byonic_pglycoquant() do not drop glycopeptides with uncertain sites anymore. Instead, they fill the “protein_site” column with NA for these glycopeptides.

glyread 0.5.0

Breaking changes

• Add a parse_structure parameter to read_pglyco3() and read_pglyco3_pglycoquant(). If FALSE (default), glycan structure strings are not parsed, and “glycan_structure” column will not be in the variable information tibble. This improves performance when structure-based analysis is not needed, and avoids implicitly implying that the structures given by pGlyco3 is accurate. Well, they are not.

Minor improvements and bug fixes

• read_pglyco3() and read_pglyco3_pglycoquant() now correctly parse “pH” and “aH” monosaccharides in glycan compositions and glycan structures.
• Messages about protein inference changes from “Performing protein inference” to “Finding leader proteins” to better illustrate what is actually happening. Relavent documentations are also updated.
• Add a “Varaible information” section to documentations of all functions. This includes the descriptions of columns in the variable information tibble.
• Fix a bug that Uniprot isomers (“O75882-2”) could not be parsed correctly.

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

• Use AnnotationDbi::mapIds() to convert protein IDs to gene symbols.
• Remove clusterProfiler from Suggests.

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”.