NEWS
glyanno 0.7.0
New features
- New
build_glyanno_cache() saves annotation databases, filter memberships, matching indexes, and mass tables in persistent user storage. library(glyanno) reminds interactive users when the cache needs building after a glydb update. Use glyanno_cache_info() to inspect it and clear_glyanno_cache() to remove it. Annotation remains available with a session-only cache. (#26)
mz_to_comp(), enhance_comp(), comp_to_struc(), and enhance_struc() now accept glycan_type, species, mono_type, and mono_range filters directly; the structure functions also accept structure_level. The db argument is deprecated but remains available for custom databases. (#25)
Minor improvements and bug fixes
comp_to_struc(), enhance_struc(), and enhance_struc_denovo() now silently exclude database candidates with unresolved floating parts or substituents from matching.
glyanno 0.6.1
comp_to_struc(), enhance_comp(), and enhance_struc() now support mixed generic and concrete residues with element-wise structure levels; structure matching excludes unresolved floating inputs and database candidates with a warning, and enhance_struc_denovo() now requires generic topological inputs. (#24)mz_to_comp(), enhance_comp(), comp_to_struc(), and enhance_struc() now include a confidence column in expanded results for customized prioritization. (#23)
glyanno 0.6.0
New features
- New
enhance_struc_denovo() reconstructs topological N-glycans and falls back to the topological database when reconstruction is not possible. (#16, #17, #18)
Breaking changes
- Remove
fill_anomer_pos() from the exported namespace. Use glyrepr::fill_anomer_pos() instead. (#15)
Minor improvements and bug fixes
enhance_struc() now accepts duplicated input structures, preserves their order and per-occurrence results, and matches each unique non-missing structure only once. (#21)calculate_mz(), comp_to_struc(), enhance_comp(), and mz_to_comp() now process vector inputs substantially faster by reusing prepared databases and direct lookups. (#20)struc_to_glytoucan() now looks up accessions from glydb::glydb_data first and only falls back to the online GlycanFormatConverter API for missing structures. (#14)
glyanno 0.5.0
New features
- Add
struc_to_glytoucan() to map glycan structures to GlyTouCan accessions (#11).
- Add
fill_anomer_pos() to fill in missing anomeric position information in glycan structures (#13).
glyanno 0.4.2
Minor improvements and bug fixes
- Fix a bug in
enhance_struc() introduced by the breaking change in glyrepr 0.11.0 (#9).
- Update vignette to mention that you can use a structure database with different structure levels.
glyanno 0.4.1
Minor improvements and bug fixes
comp_to_struc() now explicitly returns when the output is empty.
glyanno 0.4.0
Breaking changes
return_best = TRUE now returns a vector with the same length as input (with NA for unmatched glycans) instead of a tibble with potentially fewer rows. Affected functions: enhance_comp(), comp_to_struc(), mz_to_comp(), enhance_struc().
Minor improvements and bug fixes
comp_to_struc() now errors when concrete compositions are matched against a generic structure database, instead of silently returning empty results.db paramter cannot be of zero length now, in which case an error will be raised.
glyanno 0.3.0
Breaking changes
- Remove
to_level parameter from enhance_struc().
glyanno 0.2.0
New features
- Add
return_best parameter to keep the most cited match when multiple compositions or structures are possible.
glyanno 0.1.2
Minor improvements and bug fixes
- Update dependency strategy to use the r-universe repo.
glyanno 0.1.1
Minor improvements and bug fixes
glyanno 0.1.0