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Dynamic Motifs Specification

Source: R/dynamic-motifs.R
dynamic_motifs.Rd

Create a specification for dynamic 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

dynamic_motifs(max_size = 3)

Arguments

max_size

The maximum number of monosaccharides in the extracted motifs. Default is 3. Passed to extract_motif().

Value

A dynamic_motifs_spec object.

Details

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

  1. Call extract_motif() on glycans to get all dynamic motifs.

  2. Perform motif matching with alignments as "substructure".

In fact, have_motifs(glycans, dynamic_motifs()) is just a syntatic sugar of have_motifs(glycans, extract_motif(glycans)). This function exists to align with the db_motifs() and branch_motifs() API.

See also

branch_motifs(), extract_motif()

Examples

library(glyrepr)
glycans <- c(o_glycan_core_1(), o_glycan_core_2())
have_motifs(glycans, dynamic_motifs())
#>                                   Gal(b1- GalNAc(a1- Gal(b1-3)GalNAc(a1-
#> Gal(b1-3)GalNAc(a1-                  TRUE       TRUE                TRUE
#> Gal(b1-3)[GlcNAc(b1-6)]GalNAc(a1-    TRUE       TRUE                TRUE
#>                                   GlcNAc(b1- GlcNAc(b1-6)GalNAc(a1-
#> Gal(b1-3)GalNAc(a1-                    FALSE                  FALSE
#> Gal(b1-3)[GlcNAc(b1-6)]GalNAc(a1-       TRUE                   TRUE
#>                                   Gal(b1-3)[GlcNAc(b1-6)]GalNAc(a1-
#> Gal(b1-3)GalNAc(a1-                                           FALSE
#> Gal(b1-3)[GlcNAc(b1-6)]GalNAc(a1-                              TRUE