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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 all possible glycan structures of higher resolution level.

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().

db

A glydb::glydb_structures() vector, or a character vector of glycan structure strings supported by glyparse::auto_parse(). If not provided, a default structure vector is loaded from glydb::glydb_structures() at "intact" level. If db has a lower or equal resolution level than strucs, the result will be the same as strucs (no enhancement).

return_best

Logical. If TRUE, only return the best matching structure (highest confidence) for each input structure. Requires db to have a confidence attribute. Use glydb::glydb_structures() for db to enable this feature. 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. Note that one raw glycan structure can have different enhanced glycan structures as multiple rows in the result.

Details

The target resolution level is determined from db. When db is NULL, the default glydb::glydb_structures() at "intact" level is used.

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 × 2
#>   raw                 enhanced           
#>   <struct>            <struct>           
#> 1 Gal(??-?)GalNAc(??- Gal(b1-3)GalNAc(a1-
#> 2 Gal(??-?)GalNAc(??- Gal(b1-4)GalNAc(a1-

# From basic level to topological level
db_topo <- "Gal(??-?)GalNAc(??-"
enhance_struc("Hex(??-?)HexNAc(??-", db = db_topo)
#> # A tibble: 1 × 2
#>   raw                 enhanced           
#>   <struct>            <struct>           
#> 1 Hex(??-?)HexNAc(??- Gal(??-?)GalNAc(??-

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