Get All Motifs from the Database — db

This function returns a database motif specification. We use GlycoMotif collections (https://glycomotif.glyomics.org/glycomotif/GlycoMotif) as the source of the motifs. This function is useful to be integrated with have_motifs() and count_motifs(). For example, use have_motifs(glycans, db_motifs()) to check against the default GlyGen motif collection, or pass source_id to use another collection.

Usage

db_motifs(source_id = "GGM")

Arguments

source_id: A character vector of motif collection identifiers to use. Defaults to "GGM" for backward compatibility. Use dplyr::distinct(db_motif_info(), source_id, source) to get all available sources. You can use more than one motif collections like c("GGM", "CCRC"). To use all available motifs, use the "GM" collection directly.

Value

A db_motifs_spec object.

Details

Use db_motif_info() to inspect the motifs included in the database. You can use dplyr::distinct(db_motif_info(), source_id, source) to get all available sources.

Data source and license

The bundled annotations are derived from the GlycoMotif resource. GlyGen distributes its database sets under the Creative Commons Attribution 4.0 International license. See the package COPYRIGHTS file for attribution and snapshot details.

Examples

db_motifs()
#> <<db_motifs_spec>>
#> This object should be passed to the `motifs` argument of `have_motifs()`,
#> `count_motifs()`, or `match_motifs()`.
#> Configuration: uses GlycoMotif database source ID: "GGM"