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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 = NULL, return_best = FALSE)

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

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 with a warning. The default is glydb::glydb_structures() at "intact" level.

return_best

Logical. If TRUE, only return the best matching structure (highest confidence) for each input structure. db must have a confidence attribute. Default is FALSE.

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

# From topological level to intact level
db_intact <- c("Gal(b1-3)GalNAc(a1-", "Gal(b1-4)GalNAc(a1-")
enhance_struc("Gal(??-?)GalNAc(??-", db = db_intact)
#> # A tibble: 2 × 3
#>   raw                 enhanced            confidence
#>   <struct>            <struct>                 <dbl>
#> 1 Gal(??-?)GalNAc(??- Gal(b1-3)GalNAc(a1-         NA
#> 2 Gal(??-?)GalNAc(??- Gal(b1-4)GalNAc(a1-         NA

# Refine generic residues without changing the structure level
db_topo <- "Gal(??-?)GalNAc(??-"
enhance_struc("Hex(??-?)HexNAc(??-", db = db_topo)
#> # A tibble: 1 × 3
#>   raw                 enhanced            confidence
#>   <struct>            <struct>                 <dbl>
#> 1 Hex(??-?)HexNAc(??- Gal(??-?)GalNAc(??-         NA

# From partial level to intact level
enhance_struc("Gal(b1-?)GalNAc(a1-", db = db_intact)
#> # A tibble: 2 × 3
#>   raw                 enhanced            confidence
#>   <struct>            <struct>                 <dbl>
#> 1 Gal(b1-?)GalNAc(a1- Gal(b1-3)GalNAc(a1-         NA
#> 2 Gal(b1-?)GalNAc(a1- Gal(b1-4)GalNAc(a1-         NA