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Enhance glycan structure

enhance_struc.Rd

Given a glycan structure vector of any resolution level (see glyrepr::get_structure_level() for details), this function gives compatible structures with more specific residue identities or linkage information.

Usage

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

Arguments

strucs

A glyrepr::glycan_structure() vector, or a character vector of glycan structure strings supported by glyparse::auto_parse(). Inputs with unresolved floating parts or substituents are excluded with a warning.

db

[Deprecated] A glydb::glydb_structures() vector, or a character vector of glycan 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

Logical. If TRUE, only return the best matching structure (highest confidence) for each input structure. 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: An unnamed glyrepr::glycan_structure() vector with the same length as strucs. Unmatched structures are returned as NA. If return_best=FALSE: A tibble with the following columns:

  • raw: The original glycan structures.

  • enhanced: The enhanced glycan structures.

  • confidence: The database confidence score for each enhanced structure, or NA when no score is available. Note that one raw glycan structure can have different enhanced structures as multiple rows in the result.

Details

Input and database vectors may mix generic, concrete, and mixed residues, as well as topological, partial, and intact structures. Each database candidate is matched against each input independently.

Examples

enhance_struc("Gal(??-?)GalNAc(??-", glycan_type = "O-GalNAc",
  species = "Homo sapiens")
#> # A tibble: 3 × 3
#>   raw                 enhanced            confidence
#>   <struct>            <glydb_st>               <dbl>
#> 1 Gal(??-?)GalNAc(??- Gal(b1-3)GalNAc(a1-       5.32
#> 2 Gal(??-?)GalNAc(??- Gal(b1-3)GalNAc(b1-       1.10
#> 3 Gal(??-?)GalNAc(??- Gal(a1-3)GalNAc(a1-       1.61