Get All Motifs from the Database — db

This function returns a database motif specification. We use GlycoMotif collections (https://glycomotif.glyomics.org/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.

Examples

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