Convert glycan composition to glycan structure

Given glycan compositions, this function matches them to all compatible glycan structures in the glydb database. Generic, concrete, and mixed residue identities are matched residue by residue.

Usage

comp_to_struc(
  comps,
  db = lifecycle::deprecated(),
  return_best = FALSE,
  glycan_type = NULL,
  species = NULL,
  structure_level = "intact",
  mono_type = "concrete",
  mono_range = NULL
)

Arguments

comps

Glycan compositions to match against. Can be either:

A glyrepr::glycan_composition() vector.
Byonic style composition strings (e.g. Hex(5)HexNAc(2)).
Simple style composition strings (e.g. H5N4F1S1).

db

Glycan structures to match against. Can be a glyrepr::glycan_structure() vector or any structure strings supported by glyparse::auto_parse(). Structures with unresolved floating parts or substituents are excluded silently. Use the filtering arguments instead. This argument cannot be combined with them.

return_best

If TRUE, only return the highest confidence match for each composition. A custom db must have a confidence attribute. Default is FALSE.

glycan_type

Glycan type to select from glydb::glydb_structures().

species

Species to select, matched without regard to letter case.

structure_level

Structure resolution, "intact" (default) or "topological".

mono_type

Monosaccharide resolution, "concrete" (default) or "generic".

mono_range

Named list of monosaccharide count ranges; see glydb::glydb_structures().

Value

If return_best=TRUE: A glyrepr::glycan_structure() vector with the same length as comps. Unmatched compositions are returned as NA. If return_best=FALSE: A tibble with the following columns:

composition: The glycan compositions, as glyrepr::glycan_composition() vector.
structure: The possible glycan structures, as glyrepr::glycan_structure() vector.
confidence: The database confidence score for each structure, or NA when no score is available. Note that one glycan composition can have multiple rows in the result, corresponding to different possible glycan structures.

Details

Filter the built-in database with glycan_type, species, structure_level, mono_type, and mono_range.

Examples