Changelog

Source: NEWS.md

glymotif 0.12.0

We introduce the “dynamic motif” feature in this release. Instead of specifying motifs manually or using motifs from the database, you can now extract motifs existing in your set of glycans. Two functions, extract_motifs() and extract_motifs_lgl(), are added for this purpose.

New features

• Add extract_motif() to find all unique substructures (motifs) in a set of glycans. This function is suitable for motif finding in small glycans like O-GalNAc glycans.
• Add extract_branch_motif() to find all branching motifs in a set of N-glycans. This function is particular useful for N-glycan motif finding, where antennary patterns can be versatile.
• The alignment or alignments argument of all related functions now supports a new alignment type: “exact”. This type of alignment works the best with extract_branch_motif() results.

glymotif 0.11.2

Minor improvements and fixes

• glymotif now depends on the CRAN version of glyparse.

glymotif 0.11.1

Minor improvements and fixes

• glymotif now depends on the CRAN version of glyrepr.

glymotif 0.11.0

New features

• have_motif(), have_motifs(), count_motif(), and count_motifs() now support a new argument strict_sub to control the strictness of substituent matching.The argument defaults to TRUE, to be consistent with the previous behavior. When strict_sub is FALSE, the substituent is optional in the motif, so the glycan “Neu5Ac9Ac(a2-” can match the motif “Neu5Ac(a2-”.

glymotif 0.10.0

New features

• add_motifs_int() and add_motifs_lgl() now support data frames as input.

Minor improvements and bug fixes

• Fix a bug introduced by igraph v2.2.0.
• Performance optimization for the core algorithm.

glymotif 0.9.1

Minor improvements and bug fixes

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

glymotif 0.9.0

Breaking changes

• Remove quantify_motifs(). This function is reimplemented in the glydet package, with more features and better performance.

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.