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Enhance glycan composition

enhance_comp.Rd

Given a generic or mixed glycan composition (e.g. Hex(5)HexNAc(2)), this function gives all possible compatible concrete glycan compositions (e.g. Man(5)GlcNAc(2)).

Usage

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

Arguments

comps

A glyrepr::glycan_composition() vector, or a character vector of glycan composition strings of Byonic or simple style (e.g. "Hex(5)HexNAc(2)", "H5N4F1S1"). Generic and mixed compositions are matched to compatible concrete compositions in db. Concrete compositions are returned as is.

db

[Deprecated] A glydb::glydb_compositions() vector, or a character vector of glycan composition strings of Byonic or simple style (e.g. "Man(5)GlcNAc(2)", "H5N4F1S1"). All compositions in db must be concrete (e.g. Man(5)GlcNAc(2)). Use the filtering arguments instead. This argument cannot be combined with them.

return_best

Logical. If TRUE, only return the highest confidence match for each input composition. A custom db must have a confidence attribute. Defaults to FALSE.

glycan_type

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

species

Species to select, matched without regard to letter case.

mono_type

Monosaccharide resolution; only "concrete" is supported for enhancement.

mono_range

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

Value

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

  • raw: The original compositions.

  • enhanced: The enhanced compositions.

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

Details

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

Examples

enhance_comp("Hex(5)HexNAc(2)")
#> # A tibble: 6 × 3
#>   raw             enhanced               confidence
#>   <comp>          <glydb_cm>                  <dbl>
#> 1 Hex(5)HexNAc(2) Man(5)GlcNAc(2)             5.10 
#> 2 Hex(5)HexNAc(2) Glc(1)Gal(4)GlcNAc(2)       1.10 
#> 3 Hex(5)HexNAc(2) Man(4)GlcNAc(2)Galf(1)     -1    
#> 4 Hex(5)HexNAc(2) Man(4)Gal(1)GlcNAc(2)       0    
#> 5 Hex(5)HexNAc(2) Man(3)Gal(2)GlcNAc(2)       0.693
#> 6 Hex(5)HexNAc(2) Glc(1)Man(4)GlcNAc(2)       0.693