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Determine if a Glycan Structure has Linkages

Source: R/linkage.R
has_linkages.Rd

Unknown linkages in a glycan structure are represented by "??-?". Also, a linkage can be partially known (e.g. "a?-?"). This function checks if a glycan structure has linkages, in a strict or lenient way.

Usage

has_linkages(glycan, strict = FALSE)

Arguments

glycan

A glycan_structure() vector.

strict

A logical value.

  • If FALSE (default), a glycan is considered to have linkages if any linkage is partially known (not "??-?").

  • If TRUE, a glycan is considered to have linkages only if all linkages are fully determined (no "?" in the linkage).

Value

A logical vector indicating if each glycan structure has linkages.

See also

remove_linkages(), possible_linkages()

Examples

glycan <- o_glycan_core_1(linkage = TRUE)
has_linkages(glycan)
#> [1] TRUE
print(glycan)
#> <glycan_structure[1]>
#> [1] Gal(b1-3)GalNAc(a1-
#> # Unique structures: 1

glycan <- remove_linkages(glycan)
has_linkages(glycan)
#> [1] FALSE
print(glycan)
#> <glycan_structure[1]>
#> [1] Gal(??-?)GalNAc(??-
#> # Unique structures: 1

glycan <- as_glycan_structure("Gal(b1-?)GalNAc(a1-")
has_linkages(glycan)
#> [1] TRUE
has_linkages(glycan, strict = TRUE)
#> [1] FALSE