Extract All Substructures (Motifs)

Extract all unique connected subgraphs (motifs) from the input glycans up to a specified size. This function can be useful combined with count_motifs() or glydet::quantify_motifs(). If so, set alignment to "substructure" for these functions.

If you want to perform dynamic motif matching in functions like have_motifs() or glydet::quantify_motifs(), use the dynamic_motifs() helper instead, which handles additional intricacies related to how the motifs should be matched.

Usage

extract_motif(glycans, max_size = 3)

Arguments

glycans

One of:

• A glyrepr::glycan_structure() vector.

• A glycan structure string vector. All formats supported by glyparse::auto_parse() are accepted.

max_size

The maximum number of monosaccharides in the extracted motifs. Default is 3. Note that setting this value very large can be computationally expensive. Try the default value first, and increase it progressively if needed.

Value

A glyrepr::glycan_structure() vector containing the unique extracted motifs.

Examples

glycan <- "Gal(b1-3)[GlcNAc(a1-6)]GalNAc(a1-"
extract_motif(glycan, max_size = 2)
#> <glycan_structure[5]>
#> [1] Gal(b1-
#> [2] GlcNAc(a1-
#> [3] GalNAc(a1-
#> [4] Gal(b1-3)GalNAc(a1-
#> [5] GlcNAc(a1-6)GalNAc(a1-
#> # Unique structures: 5