Reconstruct topological N-glycan structures de novo

Reconstructs generic topological N-glycans from their core and branches. Every non-missing input must have only generic residues and no linkage information. Inputs that cannot be reconstructed de novo are matched against a fallback database at "topological" level.

Topological de-novo enhancement preserves optional core fucose and bisecting GlcNAc residues. Complex N-glycan branches are matched against the internal branch data. For hybrid N-glycans, the all-Hex arm is assigned as mannose and the HexNAc-bearing arm uses branch matching. High-mannose candidates are constrained to core-aligned subtrees of the Glc3Man9 precursor.

Usage

enhance_struc_denovo(strucs, fallback_db = NULL)

Arguments

strucs

A glyrepr::glycan_structure() vector, or a character vector of glycan structure strings supported by glyparse::auto_parse(). Every non-missing element must be generic and topological. Missing values are allowed and preserved. Inputs with unresolved floating parts or substituents are replaced with missing values and produce a warning.

fallback_db

A glydb::glydb_structures() vector, or a character vector of glycan structure strings supported by glyparse::auto_parse(). The default is glydb::glydb_structures() at "topological" level. Every non-missing candidate must have concrete residues. Linkage information is removed before fallback matching. Candidates with unresolved floating parts or substituents are excluded with a warning. Fallback candidates require a confidence attribute.

Value

An unnamed glyrepr::glycan_structure() vector with the same length as strucs. Unmatched structures are returned as NA.

Examples

n_generic <- glyrepr::n_glycan_core(linkage = FALSE, mono_type = "generic")
enhance_struc_denovo(n_generic)
#> <glycan_structure[1]>
#> [1] Man(??-?)[Man(??-?)]Man(??-?)GlcNAc(??-?)GlcNAc(??-
#> # Unique structures: 1