Branch Motifs Specification

Create a specification for branch motif extraction. This should be passed to the motifs argument of have_motifs(), count_motifs(), match_motifs(), add_motifs_lgl(), or add_motifs_int().

Usage

branch_motifs()

Value

A branch_motifs_spec object.

Details

Passing branch_motifs() to the motifs argument of supported functions will:

1. Call extract_branch_motif() with including_core = TRUE on glycans to get all branching motifs.

2. Construct a match_degree list based on the motifs.

3. Perform motif matching using the constructed match_degree list.

Specifically, setting including_core = TRUE will include an additional "Hex(??-?)Hex(??-?)HexNAc(??-?)HexNAc(??-" suffix to each branching motif. This suffix helps differentiate branching GlcNAc and bisecting GlcNAc. Then, the match_degree is constructed so that the four residues in the suffix do not have to match the node degree in the motif matching process.

Therefore, have_motifs(glycans, branch_motifs()) doesn't equal to have_motifs(glycans, extract_branch_motif(glycans)). Never use the results from extract_branch_motif() directly in these functions.

See also

dynamic_motifs(), extract_branch_motif()

Examples

glycans <- c(
  "GlcNAc(b1-2)Man(a1-3)[GlcNAc(b1-2)Man(a1-6)]Man(b1-4)GlcNAc(b1-4)GlcNAc(b1-",
  "Gal(b1-4)GlcNAc(b1-2)Man(a1-3)[Man(a1-6)]Man(b1-4)GlcNAc(b1-4)GlcNAc(b1-"
)
have_motifs(glycans, branch_motifs())
#>                                                                             GlcNAc(b1-
#> GlcNAc(b1-2)Man(a1-3)[GlcNAc(b1-2)Man(a1-6)]Man(b1-4)GlcNAc(b1-4)GlcNAc(b1-       TRUE
#> Gal(b1-4)GlcNAc(b1-2)Man(a1-3)[Man(a1-6)]Man(b1-4)GlcNAc(b1-4)GlcNAc(b1-         FALSE
#>                                                                             Gal(b1-4)GlcNAc(b1-
#> GlcNAc(b1-2)Man(a1-3)[GlcNAc(b1-2)Man(a1-6)]Man(b1-4)GlcNAc(b1-4)GlcNAc(b1-               FALSE
#> Gal(b1-4)GlcNAc(b1-2)Man(a1-3)[Man(a1-6)]Man(b1-4)GlcNAc(b1-4)GlcNAc(b1-                   TRUE