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-”.
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 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.
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.
Add add_glycan_descriptions(), add_struct_descriptions(), and add_comp_descriptions(). These functions are moved from glyexp to glymotif for better separation of concerns.
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.
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.
