Changelog

glymotif 0.8.1

Minor improvements and bug fixes

• quantify_motifs() now returns a glyexp::experiment() object with “traitomics” type for glycomics data, and “traitproteomics” type for glycoproteomics data, instead of “traitomics” for all input.

glymotif 0.8.0

New features

• quantify_motifs() has been totally rewritten. Serious bug about column aggregation with descriptional columns about glycan structures are fixed. The function now behaves like glydet::derive_traits(), adding back columns in var_info only when they have “many-to-one” relationship with glycosites (unique combinations of protein and protein_site).
• quantify_motifs(), add_motifs_int(), and add_motifs_lgl() now support a character vector ofglycan structure strings as the “glycan_structure” column in var_info.

Minor improvements and bug fixes

• Add a section in the Get Started vignette about ambiguity handling.
• Update the “Working with glyexp” vignette to use glyexp::real_experiment.
• Update the URL of GlycoMotif in the documentation of all_motifs().
• Remove old “N-glycans” vignette from README.

glymotif 0.7.0

Breaking changes

• Remove add_comp_descriptions(), add_glycan_descriptions(), add_struct_descriptions(), describe_n_glycans(), has_bisecting(), is_n_glycan(), n_antennae(), n_arm_fuc(), n_core_fuc(), n_gal(), n_glycan_type(), n_terminal_gal(). These functions are replaced by functions in the glydet package now.

Minor improvements and bug fixes

• Update dependencies to depend on release versions of glycoverse packages.
• quantify_motifs() now returns a glyexp::experiment() object with “traitomics” type instead of “motifomics”.

glymotif 0.6.2

Minor improvements and bug fixes

• Fix bugs introduced by the breaking changes in glyrepr v0.7.0.

glymotif 0.6.1

Minor improvements and bug fixes

• Fix some incorrect structure strings in tests and vignettes.

glymotif 0.6.0

Breaking changes

• available_motifs() is renamed to all_motifs().

New features

• Add match_motif() and match_motifs() to find all occurrences of the given motif(s) in the glycans. Node-to-node mapping is returned for each match.

glymotif 0.5.0

Breaking changes

• Remove support for omitted reducing-end anomers in IUPAC-condensed strings. Strings like “Gal(b1-3)GlcNAc” are no longer valid. You must specify the anomer of the reducing-end monosaccharide, e.g. “Gal(b1-3)GlcNAc(b1-”.
• N-glycan functions now raise a warning when the input glycans are not N-glycans and return NA for those glycans, instead of throwing an error.

New features

• Add support for multiple glycan structure string formats in all functions. This includes IUPAC-condensed, IUPAC-short, IUPAC-extended, GlycoCT, WURCS, pGlyco-style, and StrucGP-style.
• All N-glycan functions now support vectorization, including is_n_glycan(), n_glycan_type(), has_bisecting(), n_antennae(), n_core_fuc(), n_arm_fuc(), n_gal(), and n_terminal_gal().

Minor improvements and bug fixes

• Update vignettes to explicitly include reducing-end anomers in IUPAC-condensed strings.
• Fix a bug that pausimannose-type glycans are not correctly recognized in describe_n_glycans().

glymotif 0.4.4

Minor improvements and bug fixes

• Update vignette “Working with glyexp” to reflect the changes in glyread v0.5.0.

glymotif 0.4.3

Minor improvements and bug fixes

• Huge (really huge) performance optimization: all motif matching functions in this package now speed up 1000x, thanks to the fix of a performance bug about monosaccharide type conversion.

glymotif 0.4.2

Minor improvements

• Better error messages for invalid input.

glymotif 0.4.1

Bug fixes

• Fix a major bug in quantify_motifs().

glymotif 0.4.0

Major changes

• Add quantify_motifs() to quantify motifs in a glyexp::experiment().

Minor improvements

• Split the “Get Started” vignette into three:
  • The new “Get Started” vignette, only covering basic motif matching functions.
  • A new “N-Glycans” vignette, covering N-glycan-specific functions.
  • A new “Working with glyexp::experiment()” vignette, covering the integration with glyexp::experiment().

glymotif 0.3.1

Minor improvements

• Update the documentation to reflect the naming rules of the return values of have_motif(), have_motifs(), count_motif(), and count_motifs().

glymotif 0.3.0

Major changes

• Add add_glycan_descriptions(), add_struct_descriptions(), and add_comp_descriptions(). These functions are moved from glyexp to glymotif for better separation of concerns.
• Add add_motifs_int() and add_motifs_lgl() for adding motif annotations to a glyexp::experiment().

Minor improvements

• Remove the parallel argument from add_glycan_descriptions(), add_struct_descriptions(), and add_comp_descriptions(). We found it not very useful on a regular basis.
• Update the vignette to reflect the new functions above.

Bug fixes

• Fix a bug in get_motif_structure(), where the order of the results was not consistent with the order of the input motifs. This caused unexpected results in a wide range of functions including have_motifs(), count_motifs(), and the new add_motifs_lgl() and add_motifs_int() functions, when using motif names as input. Alone with get_motif_structure(), similar bugs in get_motif_alignment() and get_motif_aglycon() are also fixed.

glymotif 0.2.1

Minor improvements

• have_motif(), have_motifs(), count_motif(), and count_motifs() now support multiple substituents in the motif, to align with the updates in glyrepr v0.5.0.

glymotif 0.2.0

Bug fixes

• Fixed monosaccharide type matching logic in have_motif(), have_motifs(), count_motif(), and count_motifs().
  • Generic glycans can no longer cause errors when compared with concrete motifs
  • Concrete glycans now properly match generic motifs (converted to generic first)
  • Generic glycans correctly return FALSE when compared with concrete motifs
  • This resolves incorrect results in mixed-type motif matrices

Breaking changes

• Note: While technically backward compatible in API, the behavior change in monosaccharide type matching may affect code that depended on the previous (incorrect) error-throwing or wrong-result behavior.